item: #1 of 973 id: cord-000010-prsvv6l9 author: Qin, Jian title: Studying copy number variations using a nanofluidic platform date: 2008-08-18 words: 4997 flesch: 44 summary: DNA Amplification: Current Technologies and Applications Mathematical analysis of copy number variation in a DNA sample using digital PCR on a nanofluidic device Real-time reverse transcriptionpolymerase chain reaction assay for SARS-associated coronavirus Structure and transcription of a human gene for H1 RNA, the RNA component of human RNase P The effect of cytochrome P450 metabolism on drug response, interactions, and adverse effects Overview of enzymes of drug metabolism The clinical role of genetic polymorphisms in drug-metabolizing enzymes Individualized drug therapy The prevalence and clinical relevance of cytochrome P450 polymorphisms Pharmacogenetics and adverse drug reactions CYP2D6 polymorphisms and the impact on tamoxifen therapy Clinical implications of CYP2D6 genetic polymorphism during treatment with antipsychotic drugs Deletion of the entire cytochrome P450 CYP2D6 gene as a cause of impaired drug metabolism in poor metabolizers of the debrisoquine/sparteine polymorphism Ultrarapid metabolizers of debrisoquine: characterization and PCR-based detection of alleles with duplication of the CYP2D6 gene CYP2D6 genotyping strategy based on gene copy number determination by TaqMan real-time PCR Determination of cytochrome P450 2D6 (CYP2D6) gene copy number by real-time quantitative PCR Pharmacogenetic screening of the gene deletion and duplications of CYP2D6 The human debrisoquine 4-hydroxylase (CYP2D) locus: sequence and identification of the polymorphic CYP2D6 gene, a related gene, and a pseudogene Ultrarapid drug metabolism: PCR-based detection of CYP2D6 gene duplication Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene Studies of the HER-2/neu proto-oncogene in human breast and ovarian cancer Detection and quantitation of HER-2/neu gene amplification in human breast cancer archival material using fluorescence in situ hybridization Prognostic and predictive value of HER2/neu oncogene in breast cancer ERBB2 oncogene in human breast cancer and its clinical significance Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2 Ongoing adjuvant trials with trastuzumab in breast cancer Trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer ) 2-year follow-up of trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer: a randomised controlled trial Prognostic and predictive value of HER2/neu oncogene in breast cancer HER2 testing: a review of detection methodologies and their clinical performance Recent duplication, domain accretion and the dynamic mutation of the human genome Detection of large-scale variation in the human genome Large-scale copy number polymorphism in the human genome Segmental duplications and copy-number variation in the human genome Structural variation in the human genome Challenges and standards in integrating surveys of structural variation Autosomal-dominant microtia linked to five tandem copies of a copy-number-variable region at chromosome 4p16 A comprehensive analysis of common copynumber variations in the human genome New perspectives for the elucidation of genetic disorders Genomic rearrangements and sporadic disease Global variation in copy number in the human genome Methods and strategies for analyzing copy number variation using DNA microarrays Challenges and standards in integrating surveys of structural variation CYP2D6 genotyping strategy based on gene copy number determination by TaqMan real-time PCR Determination of cytochrome P450 2D6 (CYP2D6) gene copy number by real-time quantitative PCR Pharmacogenetic screening of the gene deletion and duplications of CYP2D6 HER-2/neu gene copy number quantified by real-time PCR: comparison of gene amplification, heterozygosity, and immunohistochemical status in breast cancer tissue Reliability and discriminant validity of HER2 gene quantification and chromosome 17 aneusomy analysis by real-time PCR in primary breast cancer Digital PCR for the molecular detection of fetal chromosomal aneuploidy Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene We have evaluated the digital array's performance using a model system, to show that this technology is exquisitely sensitive, capable of differentiating as little as a 15% difference in gene copy number (or between 6 and 7 copies of a target gene). keywords: array; copy; copy number; cyp2d6; digital; dna; gene; number; pcr; samples cache: cord-000010-prsvv6l9.txt plain text: cord-000010-prsvv6l9.txt item: #2 of 973 id: cord-000014-e0ou9zjb author: Dare, Ryan K. title: Screening Pneumonia Patients for Mimivirus date: 2008-03-17 words: 1438 flesch: 40 summary: Of the 496 specimens tested, no positive results were obtained for APM DNA by either assay. We developed a rapid method of screening samples for APM DNA by using 2 sensitive and specifi c realtime PCR assays designed to target conserved NCLDV class I genes. keywords: apm; assays; dna; pcr; pneumonia; time cache: cord-000014-e0ou9zjb.txt plain text: cord-000014-e0ou9zjb.txt item: #3 of 973 id: cord-000080-7s5b3lpn author: Ayodeji, Mobolanle title: A Microarray Based Approach for the Identification of Common Foodborne Viruses date: 2009-03-19 words: 6821 flesch: 42 summary: group B. Indeed, identification of coxsackieviruses at the level of serotype strain may be possible without single nucleotide polymorphism (SNP) analysis and limited only by the number of probe sequences/sets present on the array. Dendrogram showing the grouping of HAV strains based on their genetic relatedness for developing viral probe sequences to be used for oligonucleotide design. keywords: array; fig; group; hav; hybridization; identification; nucleotide; probe; sequence; strains; target; virus cache: cord-000080-7s5b3lpn.txt plain text: cord-000080-7s5b3lpn.txt item: #4 of 973 id: cord-000083-3p81yr4n author: None title: Poster Exhibition date: 2009-01-31 words: 113010 flesch: 51 summary: From this group of HBV patients 35 (98%) have had elevated urinal Dol excreation (45,8±5,2 g/ml vs . 3% and 47.4 respectively in HCC patients, 60.3% and 39.7 in LC patients, 55% and 40 in CHB patients, 55% and 40 in ACLF patients. keywords: activity; acute; adefovir; adv; afp; age; aim; aims; alt; alt levels; analysis; anti; assay; associated; b virus; background; baseline; blood; cancer; carcinoma; cases; cells; chb patients; china; chronic hcv; chronic hepatitis; clinical; combination; conclusion; control; control group; copies; correlation; data; days; development; diagnosis; difference; dna levels; dose; drug; effect; efficacy; end; etv; expression; factors; fibrosis; follow; gene; genotype; group; group b; hbeag; hbv dna; hbv genotype; hbv infection; hcc cell; hcc patients; hcv; hepatic; hepatitis b; hepatitis patients; hepatocellular; hospital; ifn; increase; infected; lamivudine; levels; liver; liver biopsy; liver cirrhosis; liver disease; load; low; male; markers; mean; median; medical; methods; model; months; mrna; mutation; nafld; negative; non; p<0.05; patients; patients chronic; pcr; positive; prevalence; protein; rate; ratio; rats; recurrence; related; resistance; respectively; response; results; rfa; risk; rna; role; samples; score; seroconversion; serum alt; serum hbv; significant; specific; study; study group; subjects; survival; svr; therapy; time; total; treatment; treatment group; tumor; university; virus; weeks; years cache: cord-000083-3p81yr4n.txt plain text: cord-000083-3p81yr4n.txt item: #5 of 973 id: cord-000113-d0eur1hq author: Fooks, Anthony R. title: Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date: 2009-09-29 words: 6946 flesch: 34 summary: Atlanta: US Department of Health and Human Services Rabies diagnosis for developing countries The primary application of direct rapid immunohistochemical test to rabies diagnosis in China Evaluation of a direct, rapid immunohistochemical test for rabies diagnosis Simple technique for the collection and shipment of brain specimens for rabies diagnosis Evaluation of a rapid immunodiagnostic test kit for rabies virus Immunochromatographic lateral flow strip tests The polymerase chain reaction (PCR) technique for diagnosis, typing and epidemiological studies Phylogenetic comparison of the genus Lyssavirus using distal coding sequences of the glycoprotein and nucleoprotein genes Identification of regional variants of the rabies virus within the Canadian province of Ontario Polymerase chain reaction protocols for rabies virus discrimination PCR technology for lyssavirus diagnosis Rabies virus detection by RT-PCR in decomposed naturally infected brains Heminested reversetranscriptase polymerase chain reaction (hnRT-PCR) as a tool for rabies virus detection in stored and decomposed samples Rabies virus in the decomposed brain of an Ethiopian wolf detected by nested reverse transcription-polymerase chain reaction An evaluation of immunofluorescence and PCR methods for detection of rabies in archival Carnoy-fixed, paraffin-embedded brain tissue Usefulness of reverse transcriptasepolymerase chain reaction for detection of rabies RNA in archival samples Molecular diagnosis of animal diseases: some experiences over the past decade PCR technique as an alternative method for diagnosis and molecular epidemiology of rabies virus Molecular methods to distinguish between classical rabies and the rabiesrelated European bat lyssaviruses Experimental infection of big brown bats (Eptesicus fuscus) with Eurasian bat lyssaviruses Aravan, Khujand, and Irkut virus A novel method for real time quantitative RT-PCR Real time quantitative PCR Development of a Real-Time, TaqMan Reverse Transcription-PCR Assay for Detection and Differentiation of Lyssavirus Genotypes 1, 5, and 6 Evaluation of a TaqMan PCR assay to detect rabies virus RNA: influence of sequence variation and application to quantification of viral loads Nucleic-acid sequence based amplification in the rapid diagnosis of rabies Integrated microfluidic tmRNA purification and real-time NASBA device for molecular diagnostics Multi-analyte single-membrane biosensor for the serotype-specific detection of Dengue virus Parallel nanoliter detection of cancer markers using polymer microchips Isothermal amplification of rabies virus gene Loop-mediated isothermal amplification of DNA Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of West Nile virus Rapid detection and quantification of Japanese Encephalitis virus by real-time reverse transcription loop-mediated isothermal amplification Novel reverse transcription loopmediated isothermal amplification for rapid detection of foot-and-mouth disease virus Rapid and real-time detection of Chikungunya virus by reverse transcription loop-mediated isothermal amplification assay Accelerated reaction by loop-mediated isothermal amplification using loop primers Host switching in Lyssavirus history from the Chiroptera to the Carnivora orders Microarray-based detection and genotyping of viral pathogens Microarrays for rapid identification of plant viruses Microassay-based detection of viruses causing vesicular or vesicular-like lesions in livestock animals An ultrasensitive and stable potentiometric immunosensor A novel hepatitis B virus surface antigen immunoassay as sensitive as hepatitis B virus nucleic acid testing in detecting early infection A novel serological assay for the detection of rabies virus neutralising antibodies Development of a TaqMan real-time RT-PCR assay for the detection of rabies virus Intravitam diagnosis of human rabies by PCR using saliva and cerebrospinal fluid Phylogenetic relationships of Irkut and West Caucasian bat viruses within the Lyssavirus genus and suggested quantitative criteria based on the N gene sequence for lyssavirus genotype definition Bat lyssaviruses (Aravan and Khujand) from Central Asia: phylogenetic relationships according to N, P and G gene sequences Primary structure of leader RNA and nucleoprotein genes of the rabies genome: segmented homology with VSV Case report: rapid ante-mortem diagnosis of a human case of rabies imported into the UK from the Philippines Expert Consultation on Rabies Longitudinally profiling neutralizing antibody response to SARS coronavirus with pseudotypes A sensitive retroviral pseudotype assay for influenza H5N1-neutralizing antibodies Retroviral pseudotypes Survival after treatment of rabies with induction of coma Applying the Milwaukee Protocol to treat canine rabies in Equatorial Guinea. In the course of the past three decades, the application of molecular biology has aided in the development of tests that result in a more rapid detection of rabies virus. keywords: amplification; countries; detection; diagnosis; pcr; rabies; rabies virus; rna; samples; techniques; tests; time; use; virus cache: cord-000113-d0eur1hq.txt plain text: cord-000113-d0eur1hq.txt item: #6 of 973 id: cord-000180-howix091 author: MacLeod, Iain J. title: Binding of Herpes Simplex Virus Type-1 Virions Leads to the Induction of Intracellular Signalling in the Absence of Virus Entry date: 2010-03-05 words: 6802 flesch: 42 summary: The patterns of accumulation of cellular RNAs in cells infected with a wild-type and a mutant herpes simplex virus 1 lacking the virion host shutoff gene Viral oncoapoptosis of human tumor cells Bcl-2, Bcl-XL and adenovirus protein E1B19kD are functionally equivalent in their ability to inhibit cell death The Bcl2 family: regulators of the cellular life-ordeath switch Innate Cellular Response to Virus Particle Entry Requires IRF3 but Not Virus Replication Identification of a Novel Pathway Essential for the Immediate-Early, Interferon-Independent Antiviral Response to Enveloped Virions Increased expression of eukaryotic translation initiation factors eIF-4E and eIF-2 alpha in response to growth induction by c-myc Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion Induction of cyclin E-cdk2 kinase activity, E2F-dependent transcription and cell growth by Myc are genetically separable events Analysis of cyclin-dependent kinase activity after herpes simplex virus type 2 infection Requirement for Cellular Cyclin-Dependent Kinases in Herpes Simplex Virus Replication and Transcription E2F Proteins Are Posttranslationally Modified Concomitantly with a Reduction in Nuclear Binding Activity in Cells Infected with Herpes Simplex Virus 1 IRFs: master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors Evidence from previous studies using soluble HSV-1 glycoprotein and UV-inactivated virus suggested that binding of HSV-1 virions to the cell surface might be sufficient to stimulate intracellular signalling pathways. keywords: binding; cell; entry; expression; herpes; hsv-1; infection; particles; signalling; virions; virus cache: cord-000180-howix091.txt plain text: cord-000180-howix091.txt item: #7 of 973 id: cord-000235-782iew86 author: Kapoor, A title: Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent enteric infections date: 2010-06-01 words: 4193 flesch: 50 summary: Duration of immunity for canine and feline vaccines: a review Review of companion animal viral diseases and immunoprophylaxis Forty years of canine vaccination New DNA viruses identified in patients with acute viral infection syndrome Cloning of a human parvovirus by molecular screening of respiratory tract samples A newly identified bocavirus species in human stool A novel bocavirus associated with acute gastroenteritis in Australian children Human bocavirus Complete nucleotide sequence and genome organization of bovine parvovirus Animal bocaviruses: a brief review The association of newly identified respiratory viruses with lower respiratory tract infections in Korean children Human bocavirus infection Human Bocavirus in children Severe pneumonia and human bocavirus in adult Detection of human bocavirus in Japanese children with lower respiratory tract infections Evidence of human coronavirus HKU1 and human bocavirus in Australian children Human bocavirus: developing evidence for pathogenicity Human bocavirus infection in young children in the United States: molecular epidemiological profile and clinical characteristics of a newly emerging respiratory virus Epidemiological profile and clinical associations of human bocavirus and other human parvoviruses Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections Human bocavirus: clinical significance and implications Serodiagnosis of human bocavirus infection Human bocavirus: passenger or pathogen in acute respiratory tract infections? Human bocavirus infection in children with gastroenteritis Human bocavirus in children hospitalized for acute gastroenteritis: a case-control study Clinical and molecular epidemiology of human bocavirus in respiratory and fecal samples from children in Hong Kong Detection of human bocavirus in children hospitalized because of acute gastroenteritis Human bocavirus, a respiratory and enteric virus Human bocavirus infection in children hospitalized with acute gastroenteritis in China Complete coding sequences and phylogenetic analysis of human bocavirus (HBoV) Genotyping of human bocavirus using a restriction length polymorphism MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences Structural constraints on RNA virus evolution Frequent detection of highly diverse variants of cardiovirus, cosavirus, bocavirus, and circovirus in sewage samples collected in the United States Virus taxonomy. keywords: bocavirus; children; figure; hbov2; human; pcr; samples; sequences; species; stool cache: cord-000235-782iew86.txt plain text: cord-000235-782iew86.txt item: #8 of 973 id: cord-000265-llilwq1u author: Gao, Rongbao title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date: 2010-10-12 words: 4904 flesch: 41 summary: Global public health concerns surrounding H5N1 viruses include not only individual transmission events between infected poultry and individual humans, but also their pandemic potential, should these viruses acquire genetic changes that result in sustained human-to-human transmission. Reactive hemophagocytosis in multiple organs, and occasional detection of viral antigen or viral RNA in extrapulmonary organs suggest a broader tissue distribution of H5N1 viruses compared with seasonal viruses in fatal human cases [21, 22] . keywords: avian; cells; gene; h5n1; human; infection; influenza; load; lung; tissues; virus; viruses cache: cord-000265-llilwq1u.txt plain text: cord-000265-llilwq1u.txt item: #9 of 973 id: cord-000322-8ctsa9sd author: Ninove, Laetitia title: RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests date: 2011-02-09 words: 2897 flesch: 36 summary: Protocols for real time PCR detection of phages TA and MS2 were elaborated in various formats and are described in Supporting Information S2. When IDP was associated with negative PCR detection results, a new assay was performed using a tenfold dilution of the nucleic acid extract. keywords: detection; dna; pcr; rna; samples; time cache: cord-000322-8ctsa9sd.txt plain text: cord-000322-8ctsa9sd.txt item: #10 of 973 id: cord-000483-zgapjjjw author: Faux, Cassandra E. title: Usefulness of Published PCR Primers in Detecting Human Rhinovirus Infection date: 2011-02-17 words: 1672 flesch: 40 summary: No speciesspecifi c bias was apparent, but generally, a specimen with a lower RNA concentration, as indicated by the cycle threshold from primer pair 5, was less likely to be detected or typed by using other primer pairs. Our selection of published primer pairs includes those from studies that have informed our current understanding of HRV epidemiology. keywords: hrv; human; pair; pcr; positive; primer cache: cord-000483-zgapjjjw.txt plain text: cord-000483-zgapjjjw.txt item: #11 of 973 id: cord-000664-085v7n6k author: Cordey, Samuel title: Pilot Evaluation of RT-PCR/Electrospray Ionization Mass Spectrometry (PLEX-ID/Flu assay) on Influenza-Positive Specimens date: 2012-05-09 words: 2028 flesch: 34 summary: Flu Assay for Rapid Identification and Differentiation of Influenza A, Influenza A 2009 H1N1, and Influenza B Evaluation of the Xpert Flu test and comparison with in-house real-time RT-PCR assays for detection of influenza virus from Rapid detection of respiratory tract viral infections and coinfections in patients with influenza-like illnesses by use of reverse transcription-PCR DNA microarray systems VereFlu: an integrated multiplex RT-PCR and microarray assay for rapid detection and identification of human influenza A and B viruses using lab-on-chip technology Rapid identification viruses from nasal pharyngeal aspirates in acute viral respiratory infections by RT-PCR and electrospray ionization mass spectrometry Reverse transcription polymerase chain reaction and electrospray ionization mass spectrometry for identifying acute viral upper respiratory tract infections Genomic signature-based identification of influenza A viruses using RT-PCR/electro-spray ionization mass spectrometry (ESI-MS) technology RT-PCR/electrospray ionization mass spectrometry approach in detection and characterization of influenza viruses Global surveillance of emerging Influenza virus genotypes by mass spectrometry Rapid identification of emerging infectious agents using PCR and electrospray ionization mass spectrometry Identification of Acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry Analysis of nucleic acids by FTICR MS Rapid identification of emerging pathogens: coronavirus Ibis T5000: a universal biosensor approach for microbiology Universal primer set for the full-length amplification of all influenza A viruses Evolutionary pattern of the hemagglutinin gene of influenza B viruses isolated in Japan: cocirculating lineages in the same epidemic season Open Virol J DOI: 10.2174/1874357901206010064 sha: doc_id: 664 cord_uid: 085v7n6k The PLEX-ID/Flu assay has been recently developed to enable the detection and typing of influenza viruses based on the RT-PCR/electrospray ionization mass spectrometry technology. keywords: assay; influenza; pcr; plex cache: cord-000664-085v7n6k.txt plain text: cord-000664-085v7n6k.txt item: #12 of 973 id: cord-000715-zl1s82yi author: Shulman, Lester M. title: Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition date: 2012-07-16 words: 4791 flesch: 42 summary: The number of stool suspension RNA extracts with inhibitors of MS2 rRT-PCR varied between RNA extraction protocols for randomly chosen stool suspensions. Potential inhibitors that might be incompletely removed from stool suspensions during RNA extraction include hemoglobin, immunoglobulins, bilirubin, triglycerides, complex polysaccharides, organic and phenolic compounds, glycogen, fats, and metabolic products especially those from pathological conditions, bacteria, vegetables, medications, anticoagulants, and drugs or alcohol keywords: extraction; inhibition; inhibitors; ms2; pcr; rna; rrt; samples; stool cache: cord-000715-zl1s82yi.txt plain text: cord-000715-zl1s82yi.txt item: #13 of 973 id: cord-000718-7whai7nr author: None title: ESP Abstracts 2012 date: 2012-08-22 words: 166798 flesch: 44 summary: Of those, 11 were also positive for tumor cells on cytological smears. At the papillary thyroid cancer progression matrix metalloprotease and specific tissue inhibitors of metalloprotease (TIMP-2) increased in the cytoplasm of tumor cells, but the concentration of TIMP-1 decreased. keywords: activity; acute; adenocarcinoma; age; aim; alk; amplification; analysis; antibodies; antibody; areas; associated; association; benign; biopsies; biopsy; bladder; blood; bone; braf; breast; breast cancer; breast carcinoma; cadherin; cancer; cancer cases; cancer cell; cancer patients; carcinoma; carcinoma cases; cases; cell carcinoma; cell lung; cell lymphoma; changes; chemotherapy; chronic; clinical; colon; colorectal; conclusion; control; correlation; cystic; cytoplasmic; data; dept; detection; development; diagnosis; diameter; differentiation; diffuse; disease; dna; egfr; epithelial; evaluation; examination; expression; expression levels; factor; features; female; fibrosis; findings; fish; follow; gastric; gene; gene expression; grade; group; growth; her2; high; histological; history; hospital; human; ihc; immunohistochemistry; index; infiltration; inflammation; inflammatory; invasion; invasive; involvement; ki67; kidney; left; lesions; levels; like; literature; liver; loss; lung; lung cancer; lymph; lymphoma; male; malignant; markers; mass; material; mean; median; medical; melanoma; metastases; metastatic; method; molecular; months; morphology; mutation; necrosis; negative; neoplasm; neoplastic; new; node; non; normal; nuclear; nuclei; number; objective; outcome; overexpression; p53; paraffin; parameters; pathology; patients; pattern; pcr; positive; positivity; potential; presence; present; primary; prognostic; progression; proliferation; prostate; protein expression; pulmonary; range; receptor; recurrence; renal; report; resection; respectively; response; results; right; risk; role; samples; sarcoma; score; sections; series; serum; significance; situ; size; skin; specific; specimens; spindle; stage; staining; status; stromal; studies; study; surgery; survival; system; therapy; thyroid; time; tissue; total; treatment; tumor cells; tumor grade; tumor size; tumor tissue; tumors; tumour; turkey objective; type; university; value; vascular; vimentin; women; years cache: cord-000718-7whai7nr.txt plain text: cord-000718-7whai7nr.txt item: #14 of 973 id: cord-000736-6f8vyziv author: Pripuzova, Natalia title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date: 2012-08-17 words: 6827 flesch: 47 summary: The results of sensitivity testing of the real-time PCR array primer sets specific for HIV-1, HIV-2, HBV, HCV, and WNV the with FDA/CBER analytical plasma panels. Example of the experimental testing of HIV-1 specific primer set targeting gag gene (NP3/4) for its sensitivity with DNA analytical standards is shown in Figure S1 . keywords: array; copies; dna; hiv-1; human; pcr; plasma; primer; samples; sets; specific; virus cache: cord-000736-6f8vyziv.txt plain text: cord-000736-6f8vyziv.txt item: #15 of 973 id: cord-000750-l9ozvlae author: Betts, Corinne title: Pip6-PMO, A New Generation of Peptide-oligonucleotide Conjugates With Improved Cardiac Exon Skipping Activity for DMD Treatment date: 2012-08-14 words: 6565 flesch: 39 summary: To this end, Pip peptides containing partial deletions of the hydrophobic core by 1 aa (removal of tyrosine; Pip6c) and by 2 aa (removal of isoleucine and tyrosine; Pip6d) were synthesised as PMO conjugates (Figure 1a) . Our data indicate that the hydrophobic core of the Pip sequences is critical for PMO delivery to the heart and that specific modifications to this region can enhance activity further. keywords: arginine; core; dystrophin; exon; figure; heart; hydrophobic; mdx; mice; muscle; peptide; pip6; pmo; protein; skipping cache: cord-000750-l9ozvlae.txt plain text: cord-000750-l9ozvlae.txt item: #16 of 973 id: cord-000830-jiy4cp4n author: Cobo, Fernando title: Application of Molecular Diagnostic Techniques for Viral Testing date: 2012-11-30 words: 7970 flesch: 35 summary: An international collaborative study to establish a World Health Organization international standard for hepatitis B virus DNA nucleic acid amplification techniques The clinical implications of hepatitis B virus genotype: recent advances Hepatitis C virus RNA assays: current and emerging technologies and their clinical applications Identifying women with cervical neoplasia: Using human papillomavirus DNA testing for equivocal Papanicolaou results Declared none. Both ligated products can then serve as templates for the next reaction cycle, leading to an exponential amplification process similar to PCR amplification. keywords: acid; amplification; assays; detection; diagnosis; dna; laboratory; methods; nucleic; pcr; reaction; rna; target; techniques; time; virus; viruses cache: cord-000830-jiy4cp4n.txt plain text: cord-000830-jiy4cp4n.txt item: #17 of 973 id: cord-000979-cav9n18w author: Hoppe, Sebastian title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni date: 2013-05-29 words: 10065 flesch: 45 summary: NCBI gene expression and hybridization array data repository Primer3 on the WWW for general users and for biologist programmers Geneious v5 Basic local alignment search tool Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes A hidden Markov model for predicting transmembrane helices in protein sequences A semi-empirical method for prediction of antigenic determinants on protein antigens New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and x-ray derived accessible sites The SWISS-MODEL Workspace: A web-based environment for protein structure homology modeling The SWISS-MODEL Repository and associated resources SWISS-MODEL: an automated protein homology-modeling server SWISS-MODEL and the Swiss-PdbViewer: A case-control study in FoodNet sites Typing of Campylobacter jejuni and Campylobacter coli isolated from live broilers and retail broiler meat by flaA-RFLP, MLST, PFGE and REP-PCR Rapid pulsed-field gel electrophoresis protocol for subtyping of Campylobacter jejuni Evaluation of three commercial latex agglutination tests for identification of Campylobacter spp Molecular Cloning: A Laboratory Manual, Third Edition Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray Immunogenic cross-reaction among outer membrane proteins of Gram-negative bacteria Microarray-based method for screening of immunogenic proteins from bacteria Proteinprotein interactions: analysis of a false positive GST pulldown result HaloTag: a novel protein labeling technology for cell imaging and protein analysis Validation of two ribosomal RNA removal methods for microbial metatranscriptomics Polyadenylic acid sequences in E. coli messenger RNA Identification of the gene for an Escherichia coli poly(A) polymerase A simple method to enrich mRNA from prokaryotic RNA Magnetic capturehybridization method for purification and probing of mRNA for neutral protease of Bacillus cereus Direct detection of recombinant gene expression by two genetically engineered yeasts in soil on the transcriptional and translational level Normalization of full-length-enriched cDNA Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq Ligation-independent cloning of PCR products (LIC-PCR) High efficiency transformation of E. coli by high voltage electroporation The Campylobacter jejuni/coli CjaA (cj0982c) gene encodes an N-glycosylated lipoprotein localized in the inner membrane Genetic diversity of the Campylobacter genes coding immunodominant proteins Immunogenicity and immunoprotection of recombinant PEB1 in Campylobacter-jejuni-infected mice The National Center for Biotechnology Information's Protein Clusters Database Characterization of Genetically Matched Isolates of Campylobacter jejuni Reveals that Mutations in Genes Involved in Flagellar Biosynthesis Alter the Organism's Virulence Potential Nutrient Acquisition and Metabolism by Campylobacter jejuni Identification of Campylobacter jejuni Genes Contributing to Acid Adaptation by Transcriptional Profiling and Genome-Wide Mutagenesis Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures The 2.0 Crystal Structure of ABC Transporter from Thermatoga maritima Toward the estimation of the absolute quality of individual protein structure models Construction and Evaluation of Normalized cDNA keywords: antibodies; antibody; antigenic; binding; campylobacter; cdna; epitope; immunodominant; incubation; jejuni; linear; min; pcr; proteins; reaction; rna; screening; sequence; specific cache: cord-000979-cav9n18w.txt plain text: cord-000979-cav9n18w.txt item: #18 of 973 id: cord-000988-79fp75u3 author: Al-Siyabi, Turkiya title: A cost effective real-time PCR for the detection of adenovirus from viral swabs date: 2013-06-07 words: 6262 flesch: 38 summary: Secondly, the performance characteristics of homogenization may vary between PCR assays and should not be implemented without proper validation [27] . As expected, virus culture-positive specimens had positive PCR results with low Cp values, whereas the virus culture-negative specimens had PCR-positive results with Cp values greater than 30 keywords: acid; adenovirus; culture; detection; dna; extraction; hadv; heat; homogenization; pcr; time; treatment; type; virus cache: cord-000988-79fp75u3.txt plain text: cord-000988-79fp75u3.txt item: #19 of 973 id: cord-001134-8ljgxnhf author: Lin, Chao-Nan title: Comparison of viremia of type II porcine reproductive and respiratory syndrome virus in naturally infected pigs by zip nucleic acid probe-based real-time PCR date: 2013-09-12 words: 2984 flesch: 48 summary: Moreover, based on the present results, it can be concluded that when pigs are infected with PRRSV, the amount of PRRSV in serum samples is significantly higher in PRDC pigs. The presence of this marker in a sample of animals with high PRRSV loads (>10(4.2) keywords: pcr; pigs; porcine; prrsv; syndrome; time; virus cache: cord-001134-8ljgxnhf.txt plain text: cord-001134-8ljgxnhf.txt item: #20 of 973 id: cord-001371-wf0vonkn author: Xiao, Shuqi title: Simultaneous Detection and Differentiation of Highly Virulent and Classical Chinese-Type Isolation of PRRSV by Real-Time RT-PCR date: 2014-06-12 words: 2787 flesch: 53 summary: [12] , Pb-N (only detecting PRRSV strain), and Pb-all (simultaneously detecting both HP-PRRSV and PRRSV strains) When Pb-N (HEX) and Pb-all (FAM) were combined in a duplex real-time PCR system, the Pb-N (HEX signal) probe could only detect PRRSV strain (c), whereas Pb-all (FAM signal) probe could detect both HP-PRRSV and PRRSV strains (d). keywords: detection; pcr; prrsv; time cache: cord-001371-wf0vonkn.txt plain text: cord-001371-wf0vonkn.txt item: #21 of 973 id: cord-001435-ebl8yc92 author: Hoppe, Sebastian title: Identification of Antigenic Proteins of the Nosocomial Pathogen Klebsiella pneumoniae date: 2014-10-21 words: 9628 flesch: 46 summary: The structure of bacterial outer membrane proteins Identification and characterization of ompl as a potential vaccine candidate for immune-protection against salmonellosis in mice The unique structure of Haemophilus influenzae protein E reveals multiple binding sites for host factors Directed evaluation of enterotoxigenic Escherichia coli autotransporter proteins as putative vaccine candidates Structure of the c-terminal domain of Neisseria heparin binding antigen (nhba), one of the main antigens of a novel vaccine against Neisseria meningitidis In vivo versus in vitro protein abundance analysis of Shigella dysenteriae type 1 reveals changes in the expression of proteins involved in virulence, stress and energy metabolism Surface expression, singlechannel analysis and membrane topology of recombinant Chlamydia trachomatis major outer membrane protein Predicting transmembrane protein topology with a hidden markov model: application to complete genomes A hidden markov model for predicting transmembrane helices in protein sequences A semi-empirical method for prediction of antigenic determinants on protein antigens New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and x-ray-derived accessible sites Toward the estimation of the absolute quality of individual protein structure models The rin: an rna integrity number for assigning integrity values to rna measurements Gene expression omnibus: Protein expression, lysis, and spotting of fulllength proteins were performed as described above. keywords: a.u; alanine; antibodies; antibody; cdna; epitope; linear; min; model; pcr; peptides; pneumoniae; position; proteins; reaction; sequence; specificity cache: cord-001435-ebl8yc92.txt plain text: cord-001435-ebl8yc92.txt item: #22 of 973 id: cord-001455-n7quwr4s author: Rapin, Noreen title: Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans date: 2014-11-12 words: 3724 flesch: 45 summary: Although damage caused by the fungus is restricted to the superficial skin, infected bats clearly show signs of systemic physiological perturbation such as dehydration, hypovolemia and metabolic acidosis [24] . Infected bats arouse from torpor more frequently than uninfected bats [25, 26] possibly leading to emaciation. keywords: bats; destructans; fungal; genes; infection; levels; lucifugus; pcr; response; transcripts cache: cord-001455-n7quwr4s.txt plain text: cord-001455-n7quwr4s.txt item: #23 of 973 id: cord-001521-l36f1gp7 author: None title: Oral and Poster Manuscripts date: 2011-04-08 words: 183853 flesch: 46 summary: The concept that swine are a mixing-vessel for the reassortment of influenza viruses and for the emergence of pandemic influenza viruses has been re-enforced by the emergence of the recent pandemic. This study was supported by Contract HHSN266200700005C from the National Institute of Allergy and Infectious Diseases, National Institutes of Pigs have been considered as hypothetical 'mixing vessels' facilitating the genesis of pandemic influenza viruses. keywords: age; analysis; animals; antibodies; antibody; antiviral; assay; associated; avian; b viruses; b ⁄; balb ⁄; binding; c virus; c ⁄; cases; cells; challenge; children; control; cross; culture; data; days; detection; disease; dk ⁄; dose; effect; ferrets; figure; following; gene; group; h1n1 influenza; h1n1 pandemic; h1n1 virus; h5n1 infection; h5n1 viruses; h9n2; health; high; hong; hours; human h1n1; human influenza; humans; immunity; infected; infections; influenza antigenic; influenza c; influenza epidemic; influenza infection; influenza influenza; influenza neuraminidase; influenza outbreaks; influenza pandemic; influenza patients; influenza research; influenza samples; influenza season; influenza strains; influenza surveillance; influenza transmission; influenza vaccination; influenza vaccine; influenza virus; isolates; kong ⁄; laboratory; laiv; lg ⁄; like; low; lung; mallard ⁄; mdck; method; mg ⁄; mice; model; mutation; nasal; new; non; novel; number; observed; origin influenza; oseltamivir; patients; pcr; period; pigs; population; positive; post; potential; potsdam ⁄; protection; protein; public; rate; research; resistance; respiratory; response; results; risk; rna; samples; school; seasonal; sensitivity; sequence; serum; severe; specific; specimens; studies; study; subjects; subtype influenza; sw ⁄; swine influenza; swine viruses; system; t ⁄; table; test; time; treatment; type virus; vaccines; values; virus gene; virus infection; virus isolation; virus ns1; virus replication; virus strains; virus titers; virus transmission; virus vaccine; virus ⁄; viruses; wave; years; ⁄ brisbane; ⁄ california; ⁄ genoa; ⁄ h1n1; ⁄ h3n2; ⁄ h5n1; ⁄ hk; ⁄ hok; ⁄ lee; ⁄ leningrad; ⁄ ml; ⁄ netherlands; ⁄ ns1; ⁄ panama; ⁄ pr8; ⁄ vietnam cache: cord-001521-l36f1gp7.txt plain text: cord-001521-l36f1gp7.txt item: #24 of 973 id: cord-001655-uqw74ra0 author: Stenglein, Mark D. title: Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections date: 2015-05-20 words: 8113 flesch: 45 summary: In this case, snake arenavirus genotypes could be grouped into one or possibly more species. In all cases there were more L than S segment genotypes (Fig 4and S4 Fig). keywords: animals; arenavirus; fig; genome; genotypes; pcr; reads; recombination; rna; samples; segment; sequences; sequencing; snake; virus; viruses cache: cord-001655-uqw74ra0.txt plain text: cord-001655-uqw74ra0.txt item: #25 of 973 id: cord-001762-dtvzwin8 author: Jeong, Joojin title: Development of a Rapid Detection Method for Potato virus X by Reverse Transcription Loop-Mediated Isothermal Amplification date: 2015-09-30 words: 2859 flesch: 45 summary: RT-LAMP PCR, one of the variants of LAMP PCR, has been used for the diagnosis of plant RNA viruses (Ju, 2011; Nie, 2005) . Diagnosis and control of cereal viruses in the Middle East A sensitive and reliable RT-nested PCR assay for detection of Citrus tristeza Virus from naturally infected Citrus plants Simultaneous detection of potato viruses, PLRV, PVA, PVX and PVY from dormant potato tubers by TaqMan real-time RT-PCR Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnological drivers Sensitive and rapid detection of peach latent mosaic viroid by the reverse transcription loop-mediated isothermal amplification Visual detection of turkey coronavirus RNA in tissues and feces by reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with hydroxynaphthol blue dye Characteristics of the microplate method of enzyme linked immunosorbent assay for the detection of plant viruses Biological, Serological and molecular diagnosis of three major potato viruses in Egypt Requirement of sense transcription for homology-dependent virus resistance and trans-inactivation Development of immunocapture reverse transcription loop-mediated isothermal amplification for the detection of Tomato spotted wilt virus from chrysanthemum Climate change effects on plant disease: genomes and ecosystems Immunocapture reverse transcription-polymerase chain reaction combined with nested PCR greatly increases the detection of Prunus necrotic ring spot virus in the peach Enhanced detection of Prune dwarf virus in peach leaves by immunocapture-reverse transcription-polymerase chain reaction with nested polymerase chain Reaction (IC-RT-PCR Nested PCR) Simple and rapid detection of Potato leafroll virus (PLRV) by reverse transcription loop-mediated isothermal amplification (RT-LAMP) Further studies on resistance -breaking strains of Potato virus X Detection of important plant viruses in In vitro regenerated potato plants by Double antibody sandwich method of ELISA Rapid detection of squash leaf curl virus by loop-mediated isothermal amplification Molecular diagnosis of plant viruses Estimation of vector propensity for Lettuce mosaic virus based on viral detection in single aphids A single tube, quantitative real-time RT-PCR assay that detects four potato viruses simultaneously Accelerated reaction by loop-mediated isothermal amplification using loop primers Reverse transcription loop-mediated isothermal amplification of DNA for detection of Potato virus Y Loop-mediated isothermal amplification of DNA New device and method for capture, reverse transcription, and nested PCR in a single closed-tube Rapid detection and differentiation of Dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay a new generation of innovative gene amplification technique perspectives in clinical diagnosis of infectious diseases Agroinfiltration-based Potato virus X replicons to dissect the requirements of viral infection Primerdirected enzymatic amplification of DNA with a thermostable DNA polymerase Reverse transcription loo-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of product Development of loop-mediated isothermal amplification assay for specific and rapid detection of camelpox virus in clinical samples Development of a Rapid Detection Method for PVX by RT Potato viruses in China Detection of Roundup ready soybean by loop-mediated isothermal amplification combined with a lateral-flow dipstick Detection of mix-infected potato viruses with multiplex RT-PCR Diagnosis of plant viral pathogens One-step detection of Bean pod mottle virus in soybean seed by the reverse-transcription loop-mediated isothermal amplification keywords: detection; lamp; pcr; pvx cache: cord-001762-dtvzwin8.txt plain text: cord-001762-dtvzwin8.txt item: #26 of 973 id: cord-001787-lj1nd922 author: Liu, Ying title: Enhancing production of ergosterol in Pichia pastoris GS115 by over-expression of 3-hydroxy-3-methylglutaryl CoA reductase from Glycyrrhiza uralensis date: 2014-04-02 words: 3130 flesch: 48 summary: The level of ergosterol in all recombinant P. pastoris strains was 1.07-2.51 times higher than in the negative control but with increase in the copy number of GuHMGR gene; the content of ergosterol showed an increasing-decreasingincreasing pattern. Arg 3-hydroxyl-3-methylglutary coenzyme A reductase 1 in tobacco results in sterolover production Cloning and characterization of a novel 3-hydroxy-3-methylglutaryl-coenzyme a reductase gene from Salvia miltiorrhiza involved in diterpenoid tanshinone accumulation Short protocols in molecular biology Researches on the influences of CNVs of functional genes HMGR, SQS and β-AS on their expression in Glycyrrhiza uralensis Isolation of the Pichia Pastoris glyceradehyde-3-phosphate dehydrogenase gene and regulation and use of its promoter Mechanism of genuineness of liquorice Glycyrrhiza uralensis based on CNVs of HMGR, SQS1 and β-AS gene Researches on the influence of 3-hydroxy-3-methylglutary-coenzyme A reductase gene polymorphism on catalytic efficiency of its encode enzyme in Glycyrrhiza uralensis Analysis on correlation between 3-hydroxy-3-methylglutary-coenzyme A reductase gene polymorphism of Glycyrrhiza uralensis and content of glycyrrhizic acid Copy number variations (CNVs) identified in Korean individuals Global variation in copy number in the human genome Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability Relative impact of nucleotide and copy number variation on gene expression phenotypes Mechanisms of change in gene copy number Increasing morphinan alkaloid production by over-expressing codeinone reductase in transgenic Papaver somniferum The regulation of K þ influx into roots of rye (secale cereale L.) seedlings by negative feedback via the K þ flux from shoot to root in the phloem This work was supported by the National Natural Science foundation of China (81072988). keywords: copy; ergosterol; gene; guhmgr; number; pastoris cache: cord-001787-lj1nd922.txt plain text: cord-001787-lj1nd922.txt item: #27 of 973 id: cord-001843-ceatyj3o author: Huang, Yong title: Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay date: 2015-11-06 words: 5196 flesch: 45 summary: The sensitivity, specificity, and reproducibility of the UNDP-PCR assay for TGEV TGEV genomic RNA was extracted using RNA Kit and reverse transcribed to synthesize cDNA. Therefore, a UNDP-PCR method for RNA virus TGEV needs to be established first. keywords: assay; dna; duplex; pcr; pcv2; rna; samples; tgev; undp; virus cache: cord-001843-ceatyj3o.txt plain text: cord-001843-ceatyj3o.txt item: #28 of 973 id: cord-001858-nmi39n6h author: Petriccione, Milena title: Reference gene selection for normalization of RT-qPCR gene expression data from Actinidia deliciosa leaves infected with Pseudomonas syringae pv. actinidiae date: 2015-11-19 words: 5577 flesch: 42 summary: Reference genes selection and normalization of oxidative stress responsive genes upon different temperature stress conditions in Hypericum perforatum L Reference gene selection for quantitative real-time PCR analysis in virus infected cells: SARS corona virus,Yellow fever virus, Human Herpesvirus-6, Camelpox virus and Cytomegalovirus infections Biphasic haustorial differentiation of coffee rust (Hemileia vastatrix race II) associated with defence responses in resistant and susceptible coffee cultivars Validation of reference genes for RT-qPCR normalization in common bean during biotic and abiotic stresses Reference gene selection for qPCR gene expression analysis of rust-infected wheat Validation of reference genes for gene expression studies in virus-infected Nicotiana benthamiana using quantitative real-time PCR Assessment of reference gene stability influenced by extremely divergent disease symptoms in Solanum lycopersicum L Reactive oxygen and oxidative stress tolerance in plant pathogenic Pseudomonas The antioxidant systems vis à vis reactive oxygen species during plant-pathogen interaction Selected reactive oxygen species and antioxidant enzymes in common bean after Pseudomonas syringae pv. phaseolicola and Botrytis cinerea infection Identification of Pseudomonas syringae pv. actinidiae as causal agent of bacterial canker of yellow kiwifruit (Actinidia chinensis Planchon) in Central Italy Molecular and phenotypic features of Pseudomonas syringae pv. actinidiae isolated during recent epidemics of bacterial canker of yellow kiwifruit (Actinidia chinensis) in central Italy Isolation of total RNA from tissues rich in polyphenols and polysaccharides of mangrove plants Guideline to reference gene selection for quantitative real-time PCR Analysis of relative gene expression data using real-time quantitative PCR and the 2 −ΔΔCt method This work was financed by the Regione Campania Programme under the grant agreement UR.CO. seedlings using serial analysis of gene expression (SAGE) Selection and validation of reference genes for quantitative gene expression studies by real-time PCR in eggplant (Solanum melongena L) Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera Selection of reference genes for expression studies in Cicer arietinum L.: analysis of cyp81E3 gene expression against Ascochyta rabiei Normalisation of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations Analysis of qPCR reference gene stability determination methods and a practical approach for efficiency calculation on a turbot (Scophthalmus maximus) gonad dataset Identification and validation of reference genes for normalization of transcripts from virus-infected Arabidopsis thaliana Reference gene selection for quantitative real-time PCR normalization in Caragana intermedia under different abiotic stress conditions The choice of reference genes for assessing gene expression in sugarcane under salinity and drought stresses Identification of a novel reference gene for apple transcriptional profiling under postharvest conditions keywords: analysis; deliciosa; dose; expression; gapdh; genes; leaves; normalization; pcr; reference; rgs; time cache: cord-001858-nmi39n6h.txt plain text: cord-001858-nmi39n6h.txt item: #29 of 973 id: cord-001891-5op0yss9 author: Gordon, Julian title: A simple novel device for air sampling by electrokinetic capture date: 2015-12-27 words: 4159 flesch: 45 summary: In addition, a variety of air sampling methods have been applied to the airborne transmission of disease [19] [20] [21] 1 sample capture with a random sample of air (bathroom of Table 1 ) and examined the size distribution of captured particles by atomic force microscopy. keywords: air; analysis; capture; device; filter; methods; particles; pcr; range; reference; sampler; sampling; size cache: cord-001891-5op0yss9.txt plain text: cord-001891-5op0yss9.txt item: #30 of 973 id: cord-001932-sklwt76a author: Cunningham, Scott A. title: Rapid PCR Detection of Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum date: 2013-03-11 words: 2775 flesch: 43 summary: Ureaplasma PCR detected 139/144 Ureaplasma culture-positive specimens, as well as 9 that were culture negative (sensitivity, 96.5%; specificity, 93.6%). 283 genitourinary specimens received in the clinical bacteriology laboratory for M. hominis and Ureaplasma species culture were evaluated. keywords: culture; hominis; pcr; positive; urealyticum; ureaplasma cache: cord-001932-sklwt76a.txt plain text: cord-001932-sklwt76a.txt item: #31 of 973 id: cord-002178-ggtxuulg author: Mauk, Michael G. title: Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification date: 2015-10-20 words: 5757 flesch: 32 summary: Figure 2 shows the results for plasma samples spiked with three different concentrations of HIV virons plus a negative control, indicating a LOD (limit of detection) of 350 copies per mL of plasma sample. These instruments cost over $100,000 and their use is restricted to modern clinical laboratory facilities. Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection Monitoring systems and quantitative measurement of biomolecules for the management of trauma Microfluidic technology for molecular diagnostics Advances in microfluidic PCR for point-of-care infectious disease diagnostics Antibody production, design and use for biosensor-based applications Point-of-care diagnostics: An advancing sector with nontechnical issues Present technology and future trends in point-of-care microfluidic diagnostics Point-of-care technologies for molecular diagnostics using a drop of blood A handheld flow genetic analysis system (FGAS): Towards rapid, sensitive, quantitative and multiplex molecular diagnosis at the point-of-care level Smartphones for cell and biomolecular detection Microfluidic chip for molecular amplification of influenza A RNA in human respiratory specimens Miniaturized nucleic acid amplification systems for rapid and point-of-care diagnostics: A review Anal Chim Advances in developing HIV-1 viral load assays for resource-limited settings Elevating sampling Rapid development of nucleic acid diagnostics Point of care technologies for HIV Isothermal nucleic acid amplification technologies for point-of-care diagnostics: A critical review An isothermal amplification reactor with an integrated isolation membrane for point-of-care detection of infectious diseases Simultaneous quantification of multiple food-and waterborne pathogens by use of microfluidic quantitative PCR Lab-on-a-chip pathogen sensors for food safety A handheld point-of-care genomic diagnostic system Application of microfluidics in waterborne pathogen monitoring: A review Point-of-care diagnostics for ricin exposure A lab-on-a-chip for detection of nerve agent sarin in blood Capturing cancer: Emerging microfluidic technologies for the capture and characterization of circulating tumor cells Point-of-care rare cell cancer diagnostics Microfluidics for research and applications in oncology Nucleic-acid testing, new platforms and nanotechnology for point-of-decision diagnosis of animal pathogens A microfluidic technique for quantification of steroids in core needle biopsies Microfluidic biosensor for β-Hydroxybutyrate (βHBA) determination of subclinical ketosis diagnosis Microfluidics for food, agriculture and biosystems industries A low-cost microfluidic chip for rapid genotyping of malaria-transmitting mosquitoes A microfluidic platform to isolate avian erythrocytes infected with Plasmodium gallinaceum malaria parasites based on surface morphological changes Simultaneous detection of C-reactive protein and other cardiac markers in human plasma using micromosaic immunoassays and self-regulating microfluidic networks Microfluidic chips for immunoassays Rapid development of real-time RT-PCR assays and positive controls in response to emerging coronavirus 2012 A novel thermostable polymerase for RNA and DNA loop-mediated isothermal amplification (LAMP) keywords: amplification; blood; care; chip; detection; diagnostics; membrane; nucleic; plasma; point; reaction; sample; target; time cache: cord-002178-ggtxuulg.txt plain text: cord-002178-ggtxuulg.txt item: #32 of 973 id: cord-002376-970934vm author: Mikel, Pavel title: Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices date: 2016-12-01 words: 6588 flesch: 39 summary: The present article describes the process of preparation and use of such PCV– MS2 phage-like particles (MS2 PLP) – in RT-qPCR detection and quantification of enteric RNA viruses. To evaluate the usefulness of MS2 PLP in routine diagnostics different matrices known to harbor enteric RNA viruses (swab samples, liver tissue, serum, feces, and vegetables) were artificially contaminated with specific amounts of MS2 PLP. keywords: control; detection; extraction; ms2; ms2 plp; pcv; plp; qpcr; quantification; rna; samples; viruses cache: cord-002376-970934vm.txt plain text: cord-002376-970934vm.txt item: #33 of 973 id: cord-002399-z3in6bi2 author: FAZ, Mirna title: Reliability of clinical diagnosis and laboratory testing techniques currently used for identification of canine parvovirus enteritis in clinical settings date: 2016-11-06 words: 2594 flesch: 46 summary: A comparative study of a new rapid and one-step test for the detection of parvovirus in faeces from dogs, cats and mink Canine parvovirus Sensitive detection of canine parvovirus DNA by the nested polymerase chain reaction Evaluación de las pruebas diagnósticas Diagnostic performance of a rapid in-clinic test for the detection of Canine Parvovirus under different storage conditions and vaccination status A sensitive method to detect canine parvoviral DNA in faecal samples by nested polymerase chain reaction Parvovirus infection in domestic companion animals Genotyping of Canine parvovirus in western Mexico Molecular characterization of canine parvovirus in Brazil by polymerase chain reaction assay Canine parvoviral enteritis: a review of diagnosis, management, and prevention Influence of clinical and laboratory variables on faecal antigen ELISA results in dogs with canine parvovirus infection Uso de cuestionarios de investigación Biomarkers in canine parvovirus enteritis Although clinical signs of canine parvovirus infection may vary, the most common signs reported were: anorexia, depression, lethargy, fever keywords: canine; diagnosis; dogs; npcr; parvovirus; pcr; test cache: cord-002399-z3in6bi2.txt plain text: cord-002399-z3in6bi2.txt item: #34 of 973 id: cord-002560-pue5q5wp author: Moreno, Paloma S. title: Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics date: 2017-06-01 words: 5140 flesch: 47 summary: Our shotgun metagenomic sequence data indicated that the most frequent RNA viral family in dog samples with acute diarrhoea was Astroviridae, being identified in more than half of the diarrheal samples. Other dog sample had contigs/singletons similar to a canine kobuvirus (JN387133.1), covering 2.2% of complete genome. keywords: acute; astrovirus; canine; contigs; diarrhoea; dogs; faecal; genome; samples; sequences; singletons; viruses cache: cord-002560-pue5q5wp.txt plain text: cord-002560-pue5q5wp.txt item: #35 of 973 id: cord-002757-upwe0cpj author: Sullivan, Kathleen E. title: Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies date: 2017-08-07 words: 24227 flesch: 37 summary: Importantly, after a novel PIDD has been described, subsequent reports often reveal a wider variation in associated infections and cellular findings, often without clear genotype-phenotype correlations [320] [321] Human infection, called Cat Scratch Disease, is assumed to involve inoculation of Bartonella-infected flea feces into the skin during a cat scratch. keywords: associated; azole; bartonella; cases; cause; cell; children; chronic; clinical; cns; countries; days; deficiency; dengue; diagnosis; disease; epidemiology; fever; hiv; human; immune; immunodeficiency; immunoglobulin; individuals; infection; influenza; mandrillaris; patients; pcr; pidd; primary; resistance; review; risk; skin; species; susceptibility; symptoms; syndrome; therapy; tick; transmission; treatment; vaccination; vaccine; virus cache: cord-002757-upwe0cpj.txt plain text: cord-002757-upwe0cpj.txt item: #36 of 973 id: cord-002795-i1qcanti author: Yang, Jing title: Development of a Quantitative Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Novel Goose Parvovirus date: 2017-12-12 words: 3143 flesch: 46 summary: In addition, LAMP has been considered as a time-saving, lowcost, highly specific and sensitive method (Chotiwan et al., 2017) , which can be completed within 60 min under condition of constant temperature, and it has been established to detect GPV, Muscovy duck parvovirus (MDPV), porcine parvovirus (PPV), canine parvovirus (CPV), and others targeting at VP gene (Cho et al., 2006; Chen et al., 2009; Ji et al., 2010; JinLong et al., 2010) . Specificity of this method was determined by GPV and other duckorigin viruses, such as duck plague virus, duck tembusu virus, duck hepatitis virus, duck reovirus, Muscovy duck parvovirus, and H9N2-AIV. keywords: amplification; assay; duck; gpv; method; parvovirus; pcr; qlamp cache: cord-002795-i1qcanti.txt plain text: cord-002795-i1qcanti.txt item: #37 of 973 id: cord-002852-m4l2l2r1 author: Munyua, Peninah M. title: Detection of influenza A virus in live bird markets in Kenya, 2009–2011 date: 2012-04-19 words: 3993 flesch: 55 summary: Background Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating avian influenza viruses (AIVs). In Sub‐Saharan Africa, limited data exist on AIVs in animal hosts, and in Kenya the presence of influenza virus in animal hosts has not been described. keywords: birds; detection; influenza; markets; poultry; specimens; virus; viruses cache: cord-002852-m4l2l2r1.txt plain text: cord-002852-m4l2l2r1.txt item: #38 of 973 id: cord-003047-3ejfxj6r author: Bai, Jianfa title: Comparison data of a two-target real-time PCR assay with and without an internal control in detecting Salmonella enterica from cattle lymph nodes date: 2018-04-22 words: 1095 flesch: 49 summary: A multiplex real-time PCR assay, based on invA and pagC genes, for the detection and quantification of Salmonella enterica from cattle lymph nodes Detection of Helicobacter pylori in stool samples of young children using realtime polymerase chain reaction A one step quantitative RT-PCR for detection of SARS coronavirus with an internal control for PCR inhibitors Interlaboratory validation for a real-time PCR Salmonella detection method using the ABI 7500 FAST real-time PCR system A multiplexed droplet digital PCR assay performs better than qPCR on inhibition prone samples Efficacy of a salmonella siderophore receptor protein vaccine on fecal shedding and lymph node carriage of Salmonella in commercial feedlot cattle Microbiological analysis of bovine lymph nodes for the detection of Salmonella enterica Data was generated by the duplex qPCR assay on 138 enriched cattle lymph node samples without the internal control, and compared with data on the same samples tested by the triplex qPCR assay that has the 18S rRNA gene as internal control. keywords: control; gene; pcr cache: cord-003047-3ejfxj6r.txt plain text: cord-003047-3ejfxj6r.txt item: #39 of 973 id: cord-003505-qr6ukfti author: Tabraue-Chávez, Mavys title: A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species date: 2019-03-06 words: 5671 flesch: 45 summary: Briefly, abasic PNA probes, PNA 1 and PNA 2 were designed in order to hybridize efficiently with the amplified single strand sense DNA, with the important particularity that the abasic positions in the PNA probes are opposing the nucleobases under interrogation. 3B , the Spin-Tube consists of: (i) a centrifuge collection tube; (ii) an internal column for the assay; (iii) a nylon membrane (pre-spotted with abasic PNA probes) immobilized onto the bottom of the column via a plastic pressure ring (iv). keywords: assay; biotin; detection; dna; fig; gdna; pcr; pna; probes; rna; smart; spin; tube cache: cord-003505-qr6ukfti.txt plain text: cord-003505-qr6ukfti.txt item: #40 of 973 id: cord-003850-in7he5o4 author: Xiu, Leshan title: Simultaneous detection of eleven sexually transmitted agents using multiplexed PCR coupled with MALDI-TOF analysis date: 2019-08-28 words: 5481 flesch: 36 summary: Sexually transmitted diseases treatment guidelines Serological investigation of the role of selected sexually transmitted infections in the aetiology of ectopic pregnancy Opportunities and pitfalls of molecular testing for detecting sexually transmitted pathogens Detection of Chlamydia trachomatis and Neisseria gonorrhoeae by enzyme immunoassay, culture, and three nucleic acid amplification tests Evaluation of laboratory testing methods for Chlamydia trachomatis infection in the era of nucleic acid amplification Polymerase chain reaction for detection of herpes simplex virus (HSV) DNA on mucosal surfaces: comparison with HSV isolation in cell culture Laboratory diagnosis and interpretation of tests for syphilis Multiplex PCR testing for nine different sexually transmitted infections Evaluation of conventional and real-time PCR assays using two targets for confirmation of results of the COBAS AMPLICOR Chlamydia trachomatis/Neisseria gonorrhoeae test for detection of Neisseria gonorrhoeae in clinical samples Analytical evaluation of GeneXpert CT/NG, the first genetic point-of-care assay for simultaneous detection of Neisseria gonorrhoeae and Chlamydia trachomatis Multicenter evaluation of the BDProbeTec ET system for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in urine specimens, female endocervical swabs, and male urethral swabs Epidemiological investigation and antimicrobial susceptibility analysis of ureaplasma species and Mycoplasma hominis in outpatients with genital manifestations Prevalence of 10 human polyomaviruses in fecal samples from children with acute gastroenteritis: a case-control study Type-specific detection of 30 oncogenic human papillomaviruses by genotyping both E6 and L1 genes Human papillomavirus and polyomavirus coinfections among Chinese men who have sex with men MW polyomavirus and STL polyomavirus present in tonsillar tissues from children with chronic tonsillar disease Sensitive and rapid detection of viruses associated with hand foot and mouth disease using multiplexed MALDI-TOF analysis Establishment and application of a universal coronavirus screening method using MALDI-TOF mass spectrometry Application of multiplex PCR coupled with matrix-assisted laser desorption ionization-time of flight analysis for simultaneous detection of 21 common respiratory viruses Simultaneous detection of key bacterial pathogens related to pneumonia and meningitis using multiplex PCR coupled with mass spectrometry Anal HPV infection in HIV-positive men who have sex with men from China Detection of Herpes simplex virus DNA by real-time PCR Detection of herpes viruses in clinical samples using real-time PCR Detection of Mycoplasma genitalium by PCR amplification of the 16S rRNA gene Simultaneous detection and identification of STI pathogens by multiplex Real-Time PCR in genital tract specimens in a selected area of Apulia, a region of Southern Italy Bead-based multiplex sexually transmitted infection profiling Use of nucleic acid amplification testing for diagnosis of extragenital sexually transmitted infections Assessment of coinfection of sexually transmitted pathogen microbes by use of the anyplex II STI-7 molecular kit Performance of the APTIMA Combo 2 assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in female urine and endocervical swab specimens Performance of the Abbott RealTime CT/NG for detection of Chlamydia trachomatis and Neisseria gonorrhoeae Evaluation of Seeplex (R) STD6 ACE detection kit for the diagnosis of six bacterial sexually transmitted infections Profile of the triplex assay for detection of chlamydia, gonorrhea and trichomonas using the BD MAX System Combined testing for chlamydia, gonorrhea, and trichomonas by use of the BD max CT/GC/TV assay with genitourinary specimen types Evaluation of six commercial nucleic acid amplification tests for detection of Neisseria gonorrhoeae and other Neisseria species Development and validation of a rotor-gene real-time PCR assay for detection, identification, and quantification of Chlamydia trachomatis in a single reaction Evaluation of Chlamydia trachomatis and Neisseria gonorrhoeae detection in urine, endocervical, and vaginal specimens by a multiplexed isothermal thermophilic helicase-dependent amplification (tHDA) assay Blind evaluation of the microwave-accelerated metal-enhanced fluorescence ultrarapid and sensitive Chlamydia trachomatis test by use of clinical samples A variant of Chlamydia trachomatis with deletion in cryptic plasmid: implications for use of PCR diagnostic tests A Chlamydia trachomatis strain with a 377-bp deletion in the cryptic plasmid causing false-negative nucleic acid amplification tests Chlamydia trachomatis prevalence, genotype distribution and identification of the new Swedish variant in Southern Germany Whole-genome sequencing of bacterial sexually transmitted infections: implications for clinicians Droplet digital PCR diagnosis of human schistosomiasis: parasite cell-free DNA detection in diverse clinical samples Molecular methods (digital PCR and real-time PCR) for the quantification of low copy DNA of Phytophthora nicotianae in environmental samples Digital PCR methods improve detection sensitivity and measurement precision of low abundance mtDNA deletions Sexually transmitted infections associated with alcohol use and HIV infection among men who have sex with men in Kampala Performance of Anyplex II multiplex real-time PCR for the diagnosis of seven sexually transmitted infections: comparison with currently available methods Prevalence and antimicrobial susceptibility of Ureaplasma urealyticum and Mycoplasma hominis in Chinese women with genital infectious diseases We give special thanks to Junhua Guo for technical assistance, and to Lei Gao and Zhujun Shao for kindly providing us clinical samples and clinical isolates, respectively. Positive clinical samples and isolates of H. ducreyi were not obtained, and positive plasmids with target genes were used to validate the specificity in this study. keywords: assay; detection; infections; pathogens; pcr; results; samples; specimens; sti; stis; time cache: cord-003850-in7he5o4.txt plain text: cord-003850-in7he5o4.txt item: #41 of 973 id: cord-004003-rlgzgyzn author: Lee, Jeewon title: Applying a Linear Amplification Strategy to Recombinase Polymerase Amplification for Uniform DNA Library Amplification date: 2019-11-12 words: 3388 flesch: 46 summary: At first, we hypothesized that RPA can be a replacement of PCR for DNA library amplification. Taken together, we show that single-primer linear RPA can be one of the alternative methods to PCR for DNA library amplification. keywords: amplification; dna; library; pcr; polymerase; primer; rpa cache: cord-004003-rlgzgyzn.txt plain text: cord-004003-rlgzgyzn.txt item: #42 of 973 id: cord-004133-32w6g7qk author: Walker, Faye M. title: Advances in Directly Amplifying Nucleic Acids from Complex Samples date: 2019-09-30 words: 13589 flesch: 39 summary: A Useful Tool for the Surveillance of blaOXA-23-Positive Carbapenem-Resistant Acinetobacter baumannii Flinders technology associates (FTA) filter paper-based DNA extraction with polymerase chain reaction (PCR) for detection of Pneumocystis jirovecii from respiratory specimens of immunocompromised patients Operational feasibility of using loop-mediated isothermal amplification for diagnosis of pulmonary tuberculosis in microscopy centers of developing countries Successful use of saliva without DNA extraction for detection of macrolide-resistant Mycoplasma pneumoniae DNA in children using LNA probe-based real-time PCR Rapid typing of STRs in the human genome by HyBeacon melting Ultra-rapid DNA analysis using HyBeacon probes and direct PCR amplification from saliva Comparison of boiling and robotics automation method in DNA extraction for metagenomic sequencing of human oral microbes Comparison of DNA Extraction Methods in Analysis of Salivary Bacterial Communities Study of inter-and intra-individual variations in the salivary microbiota Microbiological diversity of generalized aggressive periodontitis by 16S rRNA clonal analysis A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Diagnosis of mycobacterial infections by nucleic acid amplification: 18-month prospective study Pilot study of a rapid and minimally instrumented sputum sample preparation method for molecular diagnosis of tuberculosis Efficacy of loop mediated isothermal amplification (LAMP) assay for the laboratory identification of Mycobacterium tuberculosis isolates in a resource limited setting A novel and more sensitive loop-mediated isothermal amplification assay targeting IS6110 for detection of Mycobacterium tuberculosis complex Development of an in-house loop-mediated isothermal amplification (LAMP) assay for detection of Mycobacterium tuberculosis and evaluation in sputum samples of Nepalese patients Rapid detection of Mycobacterium tuberculosis by recombinase polymerase amplification Polymerase chain reaction for diagnosis of M. tuberculosis: Comparison of simple boiling and a conventional method for DNA extraction Detection of Mycobacterium tuberculosis in sputum samples by polymerase chain reaction using a simplified procedure Detection of Mycobacterium tuberculosis in clinical samples by two-step polymerase chain reaction and nonisotopic hybridization methods Rapid, simple method for treating clinical specimens containing Mycobacterium tuberculosis to remove DNA for polymerase chain reaction An extremely rapid and simple DNA-release method for detection of M. tuberculosis from clinical specimens Evaluation of a simple loop-mediated isothermal amplification test kit for the diagnosis of tuberculosis Evaluation of the efficacy of five DNA extraction methods for the detection of Mycobacterium tuberculosis DNA in direct and processed sputum by an in-house PCR method Clinical usefulness of multiplex PCR lateral flow in MRSA detection: A novel, rapid genetic testing method Development and evaluation of a rapid multiplex-PCR based system for Mycobacterium tuberculosis diagnosis using sputum samples Polymerase chain reaction for detection of Mycobacterium tuberculosis A simple method for diagnosing M. tuberculosis infection in clinical samples using PCR Self-Collected versus Clinician-Collected Sampling for Chlamydia and Gonorrhea Screening: A Systemic Review and Meta-Analysis Validation of real-time PCR for laboratory diagnosis of Acanthamoeba keratitis Effects of topical anaesthetics and fluorescein on the real-time PCR used for the diagnosis of Herpesviruses and Acanthamoeba keratitis Inhibition of PCR by Aqueous and Vitreous Fluids Use of the polymerase chain reaction to detect Bordetella pertussis in patients with mild or atypical symptoms of infection Diagnostic accuracy of a prototype point-of-care test for ocular chlamydia trachomatis under field conditions in the Gambia and Senegal High-throughput STR analysis for DNA database using direct PCR Multicenter clinical evaluation of the novel Amongst the collection of approaches for direct PCR amplification on saliva samples, those that begin with dried saliva swabs fully circumvent DNA extraction, purification, and quantification [93] . keywords: acid; amplification; assay; blood; clinical; detection; diagnostics; dna; extraction; isothermal; lamp; loop; method; nucleic; pcr; polymerase; reaction; samples; sensitivity; serum; sputum; testing; tests cache: cord-004133-32w6g7qk.txt plain text: cord-004133-32w6g7qk.txt item: #43 of 973 id: cord-004356-r83g3n0m author: Zheng, Zaiyu title: Development and characterization of a continuous cell line (EL) from the liver of European eel Anguilla anguilla date: 2019-12-19 words: 6422 flesch: 49 summary: These data suggested the application of EL cell line for viral identification, as well as for immunodiagnosis and pharmacological targeting. However, a limited number of cell lines have been developed from A. anguilla. keywords: anguilla; cell; culture; eel; et al; expression; figure; fish; levels; line; pcr; ° c cache: cord-004356-r83g3n0m.txt plain text: cord-004356-r83g3n0m.txt item: #44 of 973 id: cord-004675-n8mlxe7p author: None title: 2019 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference date: 2019-02-26 words: 86609 flesch: 43 summary: Background: Patients with primary immune deficiencies characterized by severe T lymphopenia and/or poor T cell function and patients posthematopoietic cell transplantation are at high risk of severe viral infections. In this study, we investigated effect of IL12R1 mutation in IL-12/IFNaxis by evaluation of patients whole blood cell response to IL-12 and IFN-, IL-12R1 expression in PBMCs and T cell blasts. keywords: age; age patients; analysis; anti; antibody; assay; autoimmune; autoimmunity; b cells; background; biopsy; blood; bone; case; cd3; cd4; cgd; chronic; cohort; conclusions; cvid patients; data; defects; development; diagnosis; disease; disorders; dose; ebv; elevated; evaluation; expression; failure; family; female; fever; flow; function; gene; group; heterozygous; history; hsct; human; hypogammaglobulinemia; iga; igg; igm; immune; immunodeficiency; immunoglobulin; infants; infections; inflammatory; introduction; laboratory; levels; life; liver; loss; low; lung; lymphocyte; lymphopenia; male; marrow; medical; methods; months; mutations; negative; nk cells; non; normal; novel; number; patients; phenotype; pid; post; presentation; proliferation; protein; range; recurrent; report; respiratory; response; results; risk; scid; sequencing; severe; specific; stem; studies; study; symptoms; syndrome; t cells; testing; therapy; time; transplant; transplantation; treatment; variant; weeks; years cache: cord-004675-n8mlxe7p.txt plain text: cord-004675-n8mlxe7p.txt item: #45 of 973 id: cord-004717-41ui4lqc author: Laurin, Marc-André title: Detection and genetic characterization of a novel pig astrovirus: relationship to other astroviruses date: 2011-09-08 words: 2226 flesch: 44 summary: The data reported in this study extend the number of porcine astrovirus lineages to a total of five, all of which most likely represent distinct species of different origins. The general strategy employed for obtaining PoAstV sequences is summarized in Fig. 1 . keywords: astrovirus; characterization; novel; poastv; species; strains cache: cord-004717-41ui4lqc.txt plain text: cord-004717-41ui4lqc.txt item: #46 of 973 id: cord-004808-6w9n03fy author: Sekiguchi, K. title: Detection of equine arteritis virus (EAV) by polymerase chain reaction (PCR) and differentiation of EAV strains by restriction enzyme analysis of PCR products date: 1995 words: 2069 flesch: 50 summary: Molecular cloning and nucleotide sequencing ofthe 3'-terminal genomic RNA of the porcine reproductive and respiratory syndrome virus Lelystad virus, the causative agent of porcine epidemic abortion and respiratory syndrome (PEARS), is related to LDV and EAV Preparing for equine arteritis Detection and differentiation of EAV strains by PCR 149t Analysis ofgenetic variation among strains of equine arteritis virus Genomic variability among globally distributed isolates of equine arteritis virus Lactate dehydrogenase-elevating virns, equine arteritis virus, and simian hemorrhagic fever virus: a new group of positive-strand RNA viruses Molecular evolution of equine arteritis virus Sequence analysis of modified Bucyrus strain of equine arteritis virus Each of the PCR products amplified using the M 1-M 14 primer was digested with each of the four restriction enzymes; Xba I, Mva I, Mbo II, and Alu I. Digestion of PCR products from the Bucyrus, modified Bucyrus, live vaccine, and Wroclaw-2 strains with Xba I gave rise to fragments of about 174 bp and 57 bp (Fig. 4a) . keywords: eav; pcr; strains; virus cache: cord-004808-6w9n03fy.txt plain text: cord-004808-6w9n03fy.txt item: #47 of 973 id: cord-004810-g0y7ied0 author: Lee, S. K. title: S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea date: 2003-11-13 words: 3753 flesch: 55 summary: Korean IBV isolates showed amino acid sequence similarity between 61.8% (K446-01 and K161-02) and 96.1% (K281-01 and K210-02) with each other and they showed amino acid sequence similarity between 42.9% (K161-02 and GA980470) and 96.5% (K203-02 and KB8523) compared to non-Korean IBV strains. The whole S 1 gene of representative 9 of Korean IBV isolates was sequenced to further characterize the isolates. keywords: ibv; isolates; korean; pcr; rflp; strains; virus cache: cord-004810-g0y7ied0.txt plain text: cord-004810-g0y7ied0.txt item: #48 of 973 id: cord-004840-4rbrzv5o author: Choudhary, Manohar Lal title: Development of real-time RT-PCR for detection of human metapneumovirus and genetic analysis of circulating strains (2009-2011) in Pune, India date: 2013-08-09 words: 3382 flesch: 47 summary: A newly discovered human pneumovirus isolated from young children with respiratory tract disease Children with respiratory disease associated with metapneumovirus in Hong Kong Human metapneumovirus infection in Japanese children First detection of human metapneumovirus in children with acute respiratory infection in India: a preliminary report Human metapneumovirus genetic variability Genetic diversity of human Real-time RT-PCR for human metapneumovirus 223 metapneumovirus over 4 consecutive years in Australia Genetic variability and circulation pattern of human metapneumovirus isolated in Italy over five epidemic seasons Detection and genetic diversity of human metapneumovirus in hospitalized children with acute respiratory infections in Southwest China Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups Ruuskanen O (2002) Metapneumovirus and acute wheezing in children Human metapneumovirus infections in young and elderly adults Human metapneumovirus in severe respiratory syncytial virus bronchiolitis Human metapneumovirus among children hospitalized for acute respiratory illness Seasonality and clinical features of human metapneumovirus infection in children in Northern Alberta Epidemiology of human metapneumovirus The role of human metapneumovirus in upper respiratory tract infections in children: a 20-year experience Study of human metapneumovirus-associated lower respiratory tract infections in Egyptian adults An outbreak of severe respiratory tract infection due to human metapneumovirus in a long-term care facility for the elderly in Oregon Rates of hospitalizations for respiratory syncytial virus, human metapneumovirus, and influenza virus in older adults Severe metapneumovirus infections among immunocompetent and immunocompromised patients admitted to hospital with respiratory infection Humane metapneumovirus (HMPV) associated pulmonary infections in immunocompromised adults-initial CT findings, disease course and comparison to respiratory-syncytialvirus (RSV) induced pulmonary infections Comparative evaluation of realtime PCR assays for detection of the human metapneumovirus Molecular assays for detection of human metapneumovirus Real-time reverse transcriptase PCR assay for detection of human metapneumoviruses from all known genetic lineages Detection of human metapneumovirus RNA sequences in nasopharyngeal aspirates of young French children with acute bronchiolitis by real-time reverse transcriptase PCR and phylogenetic analysis Detection and quantification of human metapneumovirus in pediatric specimens by real-time RT-PCR Diagnosis and epidemiological studies of human metapneumovirus using real-time PCR Detection and characterisation of human metapneumovirus from children with acute respiratory symptoms in northwest England Real-time reverse transcriptase PCR assay for improved detection of human metapneumovirus Analysis of the genomic sequence of a human metapneumovirus Antigenic and genetic variability of human metapneumoviruses Global genetic diversity of human metapneumovirus fusion gene Novel human metapneumovirus sublineage Genetic variability of attachment (G) and Fusion (F) protein genes of human metapneumovirus strains circulating during Detection and genetic diversity of human metapneumovirus in hospitalized children with acute respiratory infections in India Genomic analysis of four human metap-neumovirus prototypes Development of a multiplex one step RT-PCR that detects eighteen respiratory viruses in clinical specimens and comparison with real time RT-PCR Molecular epidemiology of human metapneumovirus from Phylogenetic analysis of human metapneumovirus from New York State patients during February through Genotype variability and clinical features of human metapneumovirus isolated from Korean children Human metapneumovirus strains circulating in Latin America Human metapneumovirus-associated hospital admissions over five consecutive epidemic seasons: evidence for alternating circulation of different genotypes Evolutionary Dynamics Analysis of Human Metapneumovirus Subtype A2: Genetic Evidence for Its Dominant Epidemic Real-time RT-PCR for human metapneumovirus Human metapneumovirus (HMPV), first isolated from children with acute lower-respiratory-tract infections (ALRTI) in the Netherlands in 2001, is an enveloped, non-segmented RNA virus that belongs to the family Paramyxoviridae and the genus Metapneumovirus keywords: assay; hmpv; human; metapneumovirus; pcr; time cache: cord-004840-4rbrzv5o.txt plain text: cord-004840-4rbrzv5o.txt item: #49 of 973 id: cord-004879-pgyzluwp author: None title: Programmed cell death date: 1994 words: 81833 flesch: 47 summary: 8cl-2(z is a mitochondrial or perinuclear-associated oncoprotein that prolongs the life span of a variety of cell types by interfering with programmed cell death. Single and repetitive uptake and release of CPZ were measured in each cell type after individual exposure or exposure in any combination of cell types: In 2 hour competitive uptake studies fibreblasts reached 1.7 and 2.6 times the concentrations of C6-and ROC-cells, :respectively. keywords: acid; activation; activity; addition; adult; amino; analysis; animals; antibodies; binding; brain; calcium; cdna; cell lines; cells; changes; cloned; complex; concentrations; conditions; contrast; control; cultures; current; data; days; decrease; development; different; differentiation; dna; domain; early; effects; end; enzyme; epithelial; experiments; expression; extracts; factor; family; fold; form; formation; function; fusion; gene; gene expression; growth; homology; hormone; human; increase; induction; infected; inhibition; institut; interaction; intracellular; kda; kinase; levels; major; mammalian; mechanisms; medium; membrane; mice; molecular; mouse; mrna; muscle; mutant; nerve; neuronal; neurons; new; non; nuclear; nucleus; number; order; pathway; phosphorylation; play; positive; potential; presence; present; process; production; promoter; properties; protein; protein expression; rat; rate; rats; reaction; receptor; recombinant; recombination; region; regulation; release; replication; response; results; rna; role; sequence; signal; sites; species; specific; stage; stimulation; structure; studies; study; subunit; surface; synthesis; system; t cells; target; terminal; time; tissue; tnf; transcription; treatment; tumor; type; university; virus; vitro; vivo; yeast cache: cord-004879-pgyzluwp.txt plain text: cord-004879-pgyzluwp.txt item: #50 of 973 id: cord-005048-9fs1ienf author: Retief, E. title: Potential Inoculum Sources of Phaeomoniellachlamydospora in South African Grapevine Nurseries date: 2006-06-07 words: 5058 flesch: 52 summary: Several putative P. chlamydospora PCR products (360 bp amplicons) were obtained with the onetube nested-PCR ( Figure 2 ): 25% of rootstock cane sections collected from mother blocks, 42% of rootstock cuttings collected during grafting, 16% of scion cuttings, 40% of water samples collected after the pre-storage hydration, 76% of water samples collected during grafting, 50% of the callusing medium samples and 17% of the soil samples collected from mother blocks. (2003) also found a very high percentage of positive P. chlamydospora samples from both pre-storage and pre-grafting hydration and fungicide tanks in New Zealand commercial nurseries. keywords: callusing; chlamydospora; cuttings; dna; pcr; samples; soil; water cache: cord-005048-9fs1ienf.txt plain text: cord-005048-9fs1ienf.txt item: #51 of 973 id: cord-005147-mvoq9vln author: None title: Autorenregister date: 2017-02-23 words: 86765 flesch: 41 summary: While a long list of gene mutations have so far been described to be responsible for the disease phenotype, little is known about the underlying neuronal mechanisms. WD pathogenesis, however, can not only be explained by gene coding mutations since phenotypes exhibit strong variations despite the same exonic DNA makeup in the gene. keywords: activity; addition; age; allele; analysis; approach; array; association; autosomal; blood; brain; breast; cancer; candidate; carriers; cases; cause; cell; children; chromosome; clones; coding; cohort; complex; conclusion; controls; data; delay; deletion; development; diagnosis; different; disability; disease; disease genes; disorders; dna; dominant; effect; exome; exome sequencing; exon; expression; factors; families; family; features; female; findings; function; gene; gene expression; generation; genetic; genome; genomic; germany; germline; growth; heterozygous; homozygous; human; identification; individuals; institute; levels; loci; loss; low; methods; methylation; mice; missense; model; molecular; mouse; mrna; mutations; negative; new; ngs; non; normal; novel; novo; number; onset; p =; panel; parents; pathways; patients; pcr; phenotype; potential; present; protein; receptor; recessive; regions; report; results; risk; rna; role; samples; sequence; sequencing; sites; skin; specific; spectrum; splice; splicing; studies; study; syndrome; system; target; testing; time; tissue; transcription; treatment; tumor; variants; wes; years cache: cord-005147-mvoq9vln.txt plain text: cord-005147-mvoq9vln.txt item: #52 of 973 id: cord-005309-147erliy author: Senanayake, Savithra D. title: Precise large deletions by the PCR-based overlap extension method date: 1995 words: 859 flesch: 47 summary: The phenol-chloroform extracted and ethanol precipitated recombinant 1319 nt DNA fragment from the third PCR was cut with BgllI and the resulting 846 nt fragment, resolved by agarose gel electrophoresis an electroeluted, was ligated into the BgllI-cut sites of pDrepl from which the homologous 1043 nt BgllI fragment had been removed, and JM109 cells were transformed. GT3', the universal primer for pGEM vectors, and primer B, 5'CTTACCAGGAGTAAAAGA CATTGTGACCTATGGGTGGGCC3', which anneals to bases 192-213 and 502-519 in the genome-sense (plus) strand of pDrepl and forms the deletion, were used in the first round of PCR. keywords: fragment; min cache: cord-005309-147erliy.txt plain text: cord-005309-147erliy.txt item: #53 of 973 id: cord-005453-4057qib7 author: None title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date: 2019-07-03 words: 276280 flesch: 51 summary: Goals: In the present study, we describe the frequencies of CRE colonization and analyzed its relationship with development of CRE bacteremia and mortality in two different scenarios: stem cell transplant patients (HSCT) and Leukemia patients. The aim of this study was to analyse a single centre experience with HSCT patients requiring ICU admission and the factors affecting outcome. keywords: /kg; acute gvhd; administration; adult patients; age; agvhd; aim; allogeneic hsct; allosct; aml; analysis; anti; asct; associated; atg; autologous; b cells; based; blood; blood cells; blood stem; bone; busulfan; car; cases; cause; cd19; cd34; cd4; cell count; cell depletion; cell disease; cell dose; cell graft; cell lymphoma; cell source; cell therapy; cell transplantation; cells; center; chemotherapy; children; chimerism; chronic gvhd; clinical; cmv; cmv disease; cohort; combination; common; complications; conclusions; conditioning; conditioning regimen; control; count; criteria; csa; csf; cyclophosphamide; data; days; days post; death; declare; development; diagnosis; difference; disclosure; disease; disease patients; disease relapse; dli; donor; donor age; donor chimerism; donor t; donor transplant; dose; early; ebv; ecp; effect; efficacy; engraftment; experience; expression; factors; failure; female; figure; flow; fludarabine; follow; following; free; function; grade; graft; group; group patients; gvhd grade; gvhd patients; gvhd prophylaxis; haploidentical; haploidentical hsct; hct; hematopoietic; high; hla; hospital; host disease; hsct group; hsct patients; hsct recipients; iii; immune; impact; incidence; increase; induction; infection; infusion; intensity; leukemia patients; levels; lymphocyte; lymphoma patients; major; male; marrow; marrow transplantation; matched; mds; mean; median; median os; medical; methods; mm patients; mobilization; months; mortality; mrd; msd; mud; multiple; myeloid; myeloma patients; n=1; negative; neutrophil; nhl patients; nk cells; non; nrm; number; option; outcome; overall; patients; patients age; patients background; patients characteristics; pbsc; pcr; pediatric; period; pfs; pgf patients; phase; platelet; population; positive; post; post transplant; potential; pre; present; previous; primary; prior; procedure; progression; protocol; ptcy; pts; range; rate; ratio; reactivation; received; reconstitution; recovery; reduced; refractory; regimen; relapse; remission; response; results; retrospectively; risk patients; safety; samples; sc patients; second; secondary; serum; severe; sibling; specific; standard; status; stem cell; steroid; studies; study; study patients; survival; syndrome; system; t cells; table; term; test; therapy; time; total; toxicity; transplant patients; transplantation background; transplanted; treatment; tumor; type; underwent; unrelated; use; versus; vod; years cache: cord-005453-4057qib7.txt plain text: cord-005453-4057qib7.txt item: #54 of 973 id: cord-005460-ezrn8cva author: None title: Physicians – Poster Session date: 2017-07-28 words: 287532 flesch: 53 summary: After three months of treatment patient showed an increase in T cells count (CD3, 411/mmc), and a decrease of toxic metabolites: AXP, 1.652 micromol/ml RBC; dAXP, 0.011 micromol/ml RBC; %dAXP, 0.7 maternal T-cell engraftment persists, despite a good response to the PEG-ADA therapy. Moreover, caspases pathway was significantly activated in thawing CD3+, CD56+ and CD14 + cells: FLICA+ cells % in thawing cells were, respectively, 16.8%, 31.1% and 6.2% vs 3%, 9.7% and o1% in fresh cells. keywords: acute gvhd; adult patients; age; aim; allogeneic; allogeneic hsct; aml patients; analysis; anti; asct; associated; atg; autologous; based; beam; blood; blood cell; blood stem; bone; busulfan; cases; cause; cd34; cell count; cell disease; cell dose; cell lymphoma; cell source; cell therapy; cell transplantation; cells; center; chemotherapy; children; chimerism; chronic gvhd; clinical; cmv; cohort; collection; complete; complications; conditioning; conditioning regimen; conflict; consecutive; control; cord; count; cr patients; criteria; csf; cyclophosphamide; data; days; death; development; diagnosis; difference; disclosure; disease; disease relapse; disease risk; dli; donor; donor cell; donor hsct; dose; early; ebv; ecp; effect; efficacy; engraftment; experience; factors; failure; female; figure; fludarabine; follow; following; free; function; grade; graft; group; group patients; gvhd; gvhd grade; gvhd patients; gvhd prophylaxis; haploidentical; hct; hematology; hematopoietic; high; hla; hospital; host disease; hr =; hsct patients; hsct recipients; iii; immune; impact; incidence; increase; induction; infection; infusion; intensity; interest; leukemia patients; levels; line; lymphoma patients; major; male; malignancies; marrow; marrow transplantation; matched; mds patients; mean; median; median follow; median os; melphalan; mobilization; months; mortality; mrd; mud; myeloablative; myeloid; myeloma patients; n =; negative; neutrophil; nk cell; non; nrm; number; outcome; overall; p =; patients; patients characteristics; patients relapse; pbsc; pediatric; period; pfs; platelet; population; positive; post; post hsct; post transplant; potential; pre; primary; prior; procedure; progression; pts; range; rate; reactivation; receiving; recipients; recovery; refractory; regimen; relapse; related; remission; report; respectively; response; results; ric; risk group; risk patients; score; second; secondary; setting; severe; sibling; significant; specific; standard; status; stem cell; steroid; studies; study; survival; syndrome; t cell; table; tbi; term; therapy; time; tma patients; total; toxicity; transplant patients; transplanted; treatment; trm; type; underwent; university; unrelated; use; versus; vod; years cache: cord-005460-ezrn8cva.txt plain text: cord-005460-ezrn8cva.txt item: #55 of 973 id: cord-005687-gj6q0ft0 author: Paiva, José-Artur title: Real -time PCR for early microbiological diagnosis: is it time? date: 2017-05-23 words: 1490 flesch: 25 summary: Given higher diagnostic sensitivity and turnaround, do the results of the EVAMICA study indicate that rapid diagnostic tests be integrated into standard diagnostic laboratory practice? This multicentre cluster-randomised crossover trial included 1416 patients and confirms that adding direct molecular detection of pathogens in the blood of patients hospitalized with severe sepsis to standard blood cultures results in an overall higher microbial diagnosis rate (increase from 28.1 to 42.6%) and shorter time to results (22.9 vs. 49.5 h). keywords: blood; patients; study; time cache: cord-005687-gj6q0ft0.txt plain text: cord-005687-gj6q0ft0.txt item: #56 of 973 id: cord-005752-tur57xd9 author: Linden, Saara title: Parechovirus infection preceding Guillain–Barré syndrome date: 2012-05-12 words: 1314 flesch: 44 summary: Examination of stool samples is recommended when suspecting picornavirus, such as HPeV infection (Kupila et al. 2005) , since Picornaviruses are secreted into stool for many days, even weeks, after symptom onset. The criteria for a C. jejuni infection preceding GBS include serological evidence of C. jejuni infection (C. jejuni IgG antibody titer≥1:2,000 by ELISA test) and a definite history of diarrhea within the previous 3 weeks of GBS onset (Kuwabara et al. 2004) . keywords: gbs; infection; parechovirus cache: cord-005752-tur57xd9.txt plain text: cord-005752-tur57xd9.txt item: #57 of 973 id: cord-005865-7lohh5ty author: Pipper, Juergen title: Catching bird flu in a droplet date: 2007-09-23 words: 4176 flesch: 45 summary: At present, we are working on the implementation of a second optical channel for an internal control that allows the user to check on the SPE of the RNA as well as for possible PCR inhibition. QuantiTect SYBR Green RT-PCR Kit (Qiagen) (8.7, 50, 480), SuperScript III Platinum SYBR Green One-Step qRT-PCR Kit (Invitrogen) (8.4, 60, 180) and LightCycler RNA Master SYBR Green I Kit (Roche) (8.5, 61, 240). keywords: droplet; h5n1; influenza; particles; pcr; rna; sample; time cache: cord-005865-7lohh5ty.txt plain text: cord-005865-7lohh5ty.txt item: #58 of 973 id: cord-006230-xta38e7j author: None title: Deutsche Gesellschaft für Experimentelle und Klinische Pharmakologie und Toxikologie e.V. date: 2012-02-22 words: 136000 flesch: 40 summary: In in-vitro studies on rat and canine mast cells and human mast cell leukemia cells HMC1.2 BZ at micromolar concentrations inhibited mediator release which appeared to be related to an inhibition of the intracellular cAMP pathway. Previous work showed that mouse cells lacking the immediate-early gene c-fos are hypersensitive to ultraviolet (UVC) light. keywords: acid; activation; activity; acute; addition; adducts; agonist; aim; analysis; animals; anti; apoptosis; approach; assay; assessment; binding; blood; brain; calcium; camp; cancer; cancer cells; cardiac; cell line; cells; cellular; cgmp; changes; channels; chronic; clinical; complex; compounds; concentration; conclusion; conditions; contrast; control; current; damage; data; days; death; decrease; deficient; development; differences; differentiation; disease; dna; dose; drug; e.g.; effects; endothelial; enzyme; evidence; experiments; exposure; expression; factor; failure; family; fibroblasts; findings; fold; food; formation; function; für; g protein; gene; gene expression; germany; glucose; growth; health; heart; human; hypertrophy; increase; induction; inflammation; inhibition; inhibitors; institut; insulin; interaction; intracellular; kidney; kinase; leads; levels; like; line; liver; loss; low; lung; macrophages; mechanisms; membrane; methods; mice; model; mouse; mrna; muscle cells; mutations; nanoparticles; ndpk; non; novel; number; pain; pathway; patients; pcr; pharmakologie; phosphorylation; plasma; potential; presence; present; pressure; primary; processes; production; products; proliferation; promoter; properties; protein; protein expression; pulmonary; rats; receptor; reduced; regulation; release; response; results; risk; rkip; role; ros; samples; selective; signaling; site; skin; smooth; specific; stimulation; stress; studies; study; substances; subunits; synthesis; system; t cells; target; test; tested; therapy; time; tissue; toxicity; toxikologie; toxin; transcription; transport; treatment; tumor; tumor cells; type; universität; uptake; values; vascular; vitro; vivo; water cache: cord-006230-xta38e7j.txt plain text: cord-006230-xta38e7j.txt item: #59 of 973 id: cord-006450-si5168pb author: Jouneau, S. title: Which patients should be tested for viruses on bronchoalveolar lavage fluid? date: 2012-12-14 words: 3121 flesch: 32 summary: To better inform the use of viral tests in patients with respiratory diseases, we performed an observational, retrospective study in our institution, with three aims: (i) to assess the diagnostic value of viral tests on BALF in routine practice; (ii) to analyze the characteristics of patients with virus-positive BALF; and (iii) to identify the factors predictive of positive viral tests in BALF. The variables associated with positive viral tests on univariate analysis were immunosuppression [human immunodeficiency virus (HIV), corticosteroids >10 mg/day for ≥3 weeks, or other immunosuppressive therapy], ground-glass attenuations on computed tomography (CT) scanning, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) intensive care unit (ICU) stay, and (iii) mechanical ventilation before BAL (p < 0.01 for each comparison). keywords: balf; cmv; patients; pcr; study; tests; virus; viruses cache: cord-006450-si5168pb.txt plain text: cord-006450-si5168pb.txt item: #60 of 973 id: cord-006860-a3b8hyyr author: None title: 40th Annual Meeting of the GTH (Gesellschaft für Thrombose- und Hämostaseforschung) date: 1996 words: 90772 flesch: 46 summary: The data show that children with low risk did in part receive higher doses of heparin and/or AT III concentrate than did high risk patients, whereas plasma therapy was adjusted to severity of eoagnlopathy. Inhibitor testing was done on patients plasma samples using the Bethesda method. keywords: activation; activity; acute; addition; age; agents; aggregation; analysis; antibodies; anticoagulant; anticoagulation; antigen; antithrombin; apc; aptt; assay; binding; bleeding; blood; blood coagulation; blood samples; cases; cells; children; clinical; clotting; coagulation; coagulation factor; complex; complications; concentrations; conclusion; contrast; control; coronary; correlation; count; data; day; days; deficiency; diagnosis; disease; dose; effect; elevated; endothelial; events; expression; factor; factor v; factor viii; family; fibrin; fibrinogen; formation; group; heparin; hirudin; hours; human; incidence; increase; influence; infusion; inhibitor; inr; laboratory; levels; low; mean; median; method; months; mutation; normal; order; parameters; patients; period; phase; plasma; plasma samples; plasminogen; platelet; platelet activation; platelet factor; present; products; protein; protein c; prothrombin; pts; range; reagent; receptor; reduced; release; resistance; response; results; risk; risk factor; role; samples; specific; studies; study; surface; surgery; system; test; therapy; thrombin; thrombosis; time; tissue; total; treatment; type; use; values; vascular; vein; venous; viii; vwf; weight; years cache: cord-006860-a3b8hyyr.txt plain text: cord-006860-a3b8hyyr.txt item: #61 of 973 id: cord-006960-9pho3hk6 author: Prakash, R. title: Droplet Microfluidic Chip Based Nucleic Acid Amplification and Real-Time Detection of Influenza Viruses date: 2013-12-27 words: 6281 flesch: 46 summary: Single surface droplet actuation methodologies for transport, mixing and cycling of PCR samples and reagents.-Dispensing, mixing and subsequent manipulations of PCR sample and reagent droplets were achieved using two popular electro-actuation methods, namely Droplet dielectrophoresis (D-DEP) 16, 17 and/or, Electrowetting (EW). In this investigation, we have leveraged electro-actuation based Droplet microfluidics (DMF), where electric field effects are utilized for dispensing and subsequent handling of droplets, as the method of choice for handling PCR samples and reagents. keywords: amplification; chip; detection; droplet; electrode; figure; influenza; micro; pcr; reaction; rna; sample; temperature cache: cord-006960-9pho3hk6.txt plain text: cord-006960-9pho3hk6.txt item: #62 of 973 id: cord-007047-7ty9mxa9 author: Reller, L. Barth title: Implications of New Technology for Infectious Diseases Practice date: 2006-11-15 words: 4096 flesch: 32 summary: The use of laboratory tests for diagnosis of enteroviral CNS disease was shown to be cost effective long ago [8] , but the availability of rapid molecular tests for this purpose has been long coming. The clinical relevance of 'CSF viral culture': a two-year experience with aseptic meningitis in A rapid and highly accurate assay for the detection of enterovirus infections in cerebrospinal fluid samples using the GeneXpert Dx system Impact of human immunodeficiency virus type 1 (HIV-1) genetic diversity on performance of four commercial viral load assays: LCx HIV RNA Quantitative, AM-PLICOR HIV-1 MONITOR v1.5, VERSANT HIV-1 RNA 3.0, and NucliSens HIV-1 QT Comparing first-void urine specimens, self-collected vaginal swabs, and endocervical specimens to detect Chlamydia trachomatis and Neisseria gonorrhoeae by a nucleic acid amplification test Comparison of methods for detection of Chlamydia trachomatis and Neisseria gonorrhoeae using commercially available nucleic acid amplification tests and a liquid pap smear medium Validation of molecular-diagnostic techniques in the parasitological laboratory Diagnostic PCR: validation and sample preparation are two sides of the same coin Failure of commercial ligase chain reaction to detect Mycobacterium tuberculosis DNA in sputum samples from a patient with smear-positive pulmonary tuberculosis due to a deletion of the target region Reproducibility of positive test results in the BDProbeTec ET system for detection of Chlamydia trachomatis and Neisseria gonorrhoeae False-positive Gen-Probe direct Mycobacterium tuberculosis amplification test results for patients with pulmonary M. kansasii and M. avium infections The current status and potential role of laboratory testing to prevent transfusion-transmitted malaria Characteristics of apparently false-negative digene hybrid capture 2 high-risk HPV DNA testing Occurrence and documentation of low-level bacteremia in a community hospital's patient population Comparison of 9 different PCR primers for the rapid detection of severe acute respiratory syndrome coronavirus using 2 RNA extraction methods Comparison of six DNA extraction methods for recovery of fungal DNA as assessed by quantitative PCR Rapid diagnosis of tuberculous meningitis: what is the optimal method? Comparison of conventional bacteriology with nucleic acid amplification (amplified mycobacterium direct test) for diagnosis of tuberculous meningitis before and after inception of antituberculosis chemotherapy The bacteriological diagnosis of tuberculous meningitis Diagnostic accuracy of nucleic acid amplification tests for tuberculous meningitis: a systematic review and meta-analysis Rapid identification of the species of the Bacteroides fragilis group by multiplex PCR assays using group-and species-specific primers Sequence analysis of four Shigella boydii O-antigen loci: implication for Escherichia coli and Shigella relationships Rhinosporidium seeberi: a human pathogen from a novel group of aquatic protistan parasites Lack of serological evidence for Mycoplasma fermentans infection in army Gulf War veterans: a large scale case-control study Mycoplasma fermentans in individuals seropositive and seronegative for HIV-1 Serological responses to mycoplasmas in HIV-infected and non-infected individuals Monitoring of Chlamydia trachomatis infections after antibiotic treatment using RNA detection by nucleic acid sequence based amplification Multicenter study of a rapid molecular-based assay for the diagnosis of group B Streptococcus colonization in pregnant women Comparison of rapid intrapartum screening methods for group B streptococcal vaginal colonization Perinatal screening for group B streptococci: cost-benefit analysis of rapid polymerase chain reaction Risk factors for early-onset group B streptococcal sepsis: estimation of odds ratios by critical literature review Prevention of perinatal group B streptococcal disease: revised guidelines from CDC Centers for Disease Control and Prevention. keywords: acid; diseases; dna; group; laboratory; methods; nucleic; pcr; results; sample; technology; tests cache: cord-007047-7ty9mxa9.txt plain text: cord-007047-7ty9mxa9.txt item: #63 of 973 id: cord-007066-zn10rnrm author: Park, Noh Jin title: Characterization of RNA in Saliva date: 2006-06-01 words: 4651 flesch: 55 summary: In this study, we analyzed the integrity, sources, and stability of salivary RNA. Methods: We measured the integrity of salivary RNA with reverse transcription followed by PCR (RT-PCR) or RT-quantitative PCR (RT-qPCR). keywords: -actin; fig; human; mrna; pcr; rna; saliva; salivary cache: cord-007066-zn10rnrm.txt plain text: cord-007066-zn10rnrm.txt item: #64 of 973 id: cord-007068-vcfs41eb author: Moradi, Tony title: Use of Procalcitonin and a Respiratory Polymerase Chain Reaction Panel to Reduce Antibiotic Use via an Electronic Medical Record Alert date: 2019-10-22 words: 3670 flesch: 34 summary: While the electronic medical record (EMR) has been used in various manners for antibiotic stewardship [22, 23] , we are unaware of its use to automate stewardship recommendations for viral respiratory infections. A study by Timbrook and colleagues found low rates of antibiotic discontinuation in patients with positive viral respiratory PCR, negative PCT, or both, which were suggestive of viral etiology. keywords: alert; antibiotic; bpa; days; patients; pcr; pct; therapy cache: cord-007068-vcfs41eb.txt plain text: cord-007068-vcfs41eb.txt item: #65 of 973 id: cord-007234-hcpa8ej5 author: Renwick, Neil title: A Recently Identified Rhinovirus Genotype Is Associated with Severe Respiratory-Tract Infection in Children in Germany date: 2007-12-15 words: 2515 flesch: 31 summary: Frequency and natural history of rhinovirus infections in adults during autumn Viruses and bacteria in the etiology of the common cold The seasonality of rhinovirus infections and its implications for clinical recognition Characterization and classification of ECHO 28-rhinovirus-coryzavirus agents Detection of rhinovirus RNA in lower airway cells during experimentally induced infection Rhinoviruses infect the lower airways Quantitative and qualitative analysis of rhinovirus infection in bronchial tissues Rhinovirus and the lower respiratory tract Interleukin-10 gene expression in acute virus-induced asthma Rhinovirus viremia in children with respiratory infections Viral infections of human Association of rhinovirus infection with increased disease severity in acute bronchiolitis International Committee on Taxonomy of Viruses. Universal Database of the International Committee on Taxonomy of Viruses Virus taxonomy: eighth report of the International Committee on Taxonomy of Viruses Antigenic groupings of 90 rhinovirus serotypes A collaborative report: rhinoviruses-extension of the numbering system from 89 to 100 Two groups of rhinoviruses revealed by a panel of antiviral compounds present sequence divergence and differential pathogenicity Alignment of capsid protein VP1 sequences of all human rhinovirus prototype strains: conserved motifs and functional domains Molecular relationships between 21 human rhinovirus serotypes Genetic clustering of all 102 human rhinovirus prototype strains: serotype 87 is close to human enterovirus 70 Many rhinovirus serotypes share the same cellular receptor The major and minor group receptor families contain all but one human rhinovirus serotype Human rhinovirus 87 and enterovirus 68 represent a unique serotype with rhinovirus and enterovirus features VP1 sequencing of all human rhinovirus serotypes: insights into genus phylogeny and susceptibility to antiviral capsid-binding compounds Rapid simultaneous diagnosis of infections with respiratory syncytial viruses A and B, influenza viruses A and B, and human parainfluenza virus types 1, 2, and 3 by multiplex quantitative reverse transcription-polymerase chain reaction-enzyme hybridization assay (Hexaplex) GeneScan reverse transcription-PCR assay for detection of six common respiratory viruses in young children hospitalized with acute respiratory illness Diagnostic system for rapid and sensitive differential detection of pathogens Microarray-based detection and genotyping of viral pathogens Panmicrobial oligonucleotide array for diagnosis of infectious diseases MassTag polymerase-chainreaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influeza-like illness in New York State during Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult Improved detection of rhinoviruses in nasal and throat swabs by seminested RT-PCR Molecular diagnosis of human rhinovirus infections: comparison with virus isolation Detection of rhinoviruses by tissue culture and two independent amplification techniques, nucleic acid sequence-based amplification and reverse transcription-PCR, in children with acute respiratory infections during a winter season Picornavirus infections in children diagnosed by RT-PCR during longitudinal surveillance with weekly sampling: association with symptomatic illness and effect of season Application of a fluorogenic PCR assay for typing and subtyping of influenza viruses in respiratory samples Simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested-PCR assays MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment Use of polymerase chain reaction for diagnosis of picornavirus infection in subjects with and without respiratory symptoms Human picornavirus and coronavirus RNA in nasopharynx of children without concurrent respiratory symptoms Novel Rhinovirus Genotype in LRTI • JID Respiratory picornaviruses and respiratory syncytial virus as causative agents of acute expiratory wheezing in children Rhinovirus and respiratory syncytial virus in wheezing children requiring emergency care: IgE and eosinophil analyses Rhinovirus-associated hospitalizations in young children Persistence of rhinovirus and enterovirus RNA after acute respiratory illness in children Lower airways inflammation during rhinovirus colds in normal and in asthmatic subjects Low grade rhinovirus infection induces a prolonged release of IL-8 in pulmonary epithelium Rhinovirus replication causes RANTES production in primary bronchial epithelial cells Rhinovirus infection increases 5-lipoxygenase and cyclooxygenase-2 in bronchial biopsy specimens from nonatopic subjects Rhinovirus infections in an industrial population. keywords: children; hrv; human; infections; pcr; rhinovirus; viruses cache: cord-007234-hcpa8ej5.txt plain text: cord-007234-hcpa8ej5.txt item: #66 of 973 id: cord-007427-iqwojhq2 author: Dedkov, Vladimir G. title: Development and Evaluation of a One-Step Quantitative RT-PCR Assay for Detection of Lassa Virus date: 2019-06-03 words: 4056 flesch: 42 summary: One-step RT-PCR assay targeting GP, with primers OWS-1-fwd ( GCGCACCGGGGATCCTAGGC) and OWS-1000-rev (AGCATGTCACAA-AAYTCYTCATCATG) was used for LASV detection (Ehichioya et al., 2011) . In this paradigm, a number of RT-PCR assays for LASV detection were developed and evaluated. keywords: assay; detection; fever; lassa; lasv; pcr; rna; virus cache: cord-007427-iqwojhq2.txt plain text: cord-007427-iqwojhq2.txt item: #67 of 973 id: cord-007564-ljqrxjvv author: Leroy, O. title: 04 – Apport des explorations microbiologiques au diagnostic des infections des voies respiratoires basses date: 2006-11-13 words: 13544 flesch: 44 summary: Le rôle de la quantification bactérienne dans la prise en compte du résultat de la culture doit être également discuté. [17] , portant sur 209 patients, retrouve une augmentation de la fréquence de positivité de l'hémoculture avec celle du risque de décès apprécié par la classe de risque établie selon le PSI initial. keywords: bien; cas; ces; cette; chez; comme; community; culture; d'une; dans; des; detection; deux; diagnostic; données; est; infections; les; microbiologiques; même; ont; pac; par; pas; patients; pcr; peut; plus; pneumonia; pour; que; résultats; selon; sensibilité; sont; spécificité; sur; technique; test; toutefois; traitement; une; virus; étiologique; été; être cache: cord-007564-ljqrxjvv.txt plain text: cord-007564-ljqrxjvv.txt item: #68 of 973 id: cord-007874-oq8gpl91 author: Bao, Jian R. title: Reverse-transcription polymerase chain reaction/pyrosequencing to characterize neuraminidase H275 residue of influenza A 2009 H1N1 virus for rapid and specific detection of the viral oseltamivir resistance marker in a clinical laboratory date: 2011-10-13 words: 3312 flesch: 39 summary: Fact sheet for health care providers Characteristics of patients with oseltamivir-resistant pandemic (H1N1) 2009, United States Detection of influenza virus resistance to neuraminidase inhibitors by an enzyme inhibition assay Rapid genotypic assay for detection of oseltamivir-resistant influenza A (H1N1) viruses Oseltamivir-resistant influenza viruses circulating during the first year of the influenza The presence of 2 types of viruses -2009 H1N1 and other seasonal influenza A H1N1in each patient specimen was determined using the Influenza A H1N1 (2009) Real Time RT-PCR kit (Focus Diagnostics, Cypress, CA, USA) on an ABI 7500 real-time PCR system (ABI, Foster, CA, USA) according to the manufacturer's instructions. keywords: detection; h1n1; influenza; oseltamivir; pcr; resistance cache: cord-007874-oq8gpl91.txt plain text: cord-007874-oq8gpl91.txt item: #69 of 973 id: cord-007890-bie1veti author: None title: ECC-4 Abstracts date: 2002-04-16 words: 86133 flesch: 45 summary: On the whole, E. coli showed an elevated sensitivity rate ( !/90% of tested strains) to nitrofurantoin, gentamicin, amikacin, and 2nd-and 3rd-generation cephalosporins, while only amoxicillin and piperacillin had a mean resistance rate !/30 % for M41L, D67N, K103N, M184V, L210W, T215YF, and for L10I, M36I, L63P, A71VT, L90M for P Inhibitors (PI). keywords: acid; activity; acute; administration; aeruginosa; agar; agents; aim; amoxicillin; analysis; antibiotic; antimicrobial; associated; aureus; b b; bacteria; beta; blood; candida; care; cases; cells; children; chronic; ciprofloxacin; clinical; coli; combination; concentrations; conclusion; control; cultures; data; days; department; diagnosis; disease; dna; dose; drug; effect; efficacy; erythromycin; esbl; fever; following; france; general; gentamicin; gram; group; haart; hcv; health; hepatitis; high; hiv; hospital; human; ifn; imipenem; incidence; infected; infection; influenza; institute; isolates; l b; laboratory; level; linezolid; mean; medical; medicine; methods; microbiology; mics; months; mrsa; nccls; negative; new; non; nosocomial; number; oral; patients; pcr; penicillin; period; plasma; pneumoniae; positive; presence; present; prevalence; pts; purpose; rate; resistance; results; risk; rna; samples; school; sensitivity; serum; spain; species; specific; spp; staphylococcus; strains; streptococcus; study; susceptibility; system; teicoplanin; tested; therapy; time; tissue; total; tract; treatment; university; urinary; urine; use; vancomycin; virus; vitro; years cache: cord-007890-bie1veti.txt plain text: cord-007890-bie1veti.txt item: #70 of 973 id: cord-008678-zi3aunqz author: Piñana, José Luis title: Clinical significance of Pneumocystis jirovecii DNA detection by real-time PCR in hematological patient respiratory specimens date: 2020-01-10 words: 2053 flesch: 40 summary: Detection or recovery of other microbial agents (one or more) was documented in 17 of the 27 specimens testing positive by PJ PCR ( Table 2 ). In our view, however, the variability in the performance of different PCR assays and sampling conditions, heterogeneity of patient populations, and in particular the lack of a PJ international standard material for PCR result normalization precludes defining a consensus universal threshold nowadays. keywords: diagnosis; patients; pcr; pjp; pneumonia; specimens cache: cord-008678-zi3aunqz.txt plain text: cord-008678-zi3aunqz.txt item: #71 of 973 id: cord-008777-i2reanan author: None title: ECB12: 12th European Congess on Biotechnology date: 2005-07-19 words: 151661 flesch: 40 summary: During the process development for protein production, short time to market and the demand for cheap processes dominate today's process development. Interdependence of the impact of methanol and oxygen supply on protein production with recombinant Pichia pastoris N.K. Khatri, F. Hoffmann Martin-Luther-University Halle-Wittenberg, Institute for Biotechnology, Halle D-06120, Germany. keywords: acid; acid production; activities; activity; addition; adsorption; affinity; aim; alternative; amino; analysis; animal; ankara; antibody; application; applied; approach; assay; bacillus; bacteria; batch; bed; binding; biology; biomass; bioreactor; biosynthesis; biotechnology; capacity; carbon; case; cell; cell growth; cerevisiae; changes; chemical; chitosan; chromatography; coli; column; complex; composition; compounds; concentration; conditions; control; conversion; cost; cultivation; culture; data; days; degradation; denmark; department; design; development; differences; different; disease; dna; e.g.; effect; efficiency; energy; engineering; environmental; enzymatic; enzyme; enzyme activity; enzyme production; ethanol; ethanol production; experiments; expression; extract; factors; fed; fermentation; fermentation process; flow; flux; food; formation; function; gel; gene; gene expression; genome; glucose; group; growth; health; high; host; human; hydrolysis; identification; increase; induction; industrial; industry; influence; institute; interest; intracellular; knowledge; laboratory; level; limited; line; lipase; liquid; mail; mass; maximum; media; medium; metabolic; metabolites; method; microbial; microorganisms; milk; model; molecular; molecules; natural; network; new; niger; nitrogen; non; novel; number; oil; operation; optimization; order; oxygen; parameters; pathway; pcr; peptide; performance; phase; phosphate; plant; plasmid; potential; presence; present; procedure; process; processes; produce; production; production process; productivity; products; project; properties; protein; protein expression; protein production; purification; quality; range; rate; reaction; recombinant; regulation; removal; research; response; resulting; results; role; samples; scale; science; screening; separation; sequence; signal; source; species; specific; stability; state; step; strains; stress; structure; studies; study; substrate; sucrose; sugar; surface; synthesis; system; target; technical; technique; temperature; therapy; time; total; transfer; treatment; turkey; type; university; use; value; vitro; water; weight; work; yeast; yield cache: cord-008777-i2reanan.txt plain text: cord-008777-i2reanan.txt item: #72 of 973 id: cord-009376-a35a92gh author: Lovatt, Archie title: Applications of quantitative PCR in the biosafety and genetic stability assessment of biotechnology products date: 2002-01-07 words: 9218 flesch: 45 summary: The development and validation of PCR assays to meet the requirements of regulatory authorities is a key element in the production and marketing of final products. Further studies Quantitation of DNArRNA using real time PCR detection Inverted Alu repeats unstable in yeast are excluded from the human genome High throughput detection of retrovirus-associated reverse transcriptase using an improved Fluorescent Product Enhanced Reverse Ž Transcriptase Assay F-PERT and its comparison to conventional detection methods Pharmaceutical perspectives of nonviral gene therapy Zoonoses and haemorrhagic fever Elimination of background signals in a modified polymerase chain reaction-based reverse transcriptase assay The role of deer as a possible reservoir host of Potosi virus recognised arbovirus in the United States Simultaneous screening for HBV DNA and HCV RNA genomes in blood donations using a novel TaqMan PCR Rapid reverse transcription-PCR detection of hepatitis C virus RNA in serum using TaqMan fluorogenic detection system Development of a real-time PCR procedure including an internal control for the measurement of HCMV viral load Different real-time PCR formats compared for the quantitative detection of human cytomegalovirus DNA Human exposure to bovine polyomavirus: a zoonosis? Target selection and optimisation of amplification reactions Ultra-sensitive retro-v irus detection by a reverse transcriptase assay based on product enhancement Critical factors for successful PCR. keywords: acid; assay; cell; control; copy; detection; dna; extraction; nucleic; number; pcr; rna; sample; target; test; time; virus; viruses cache: cord-009376-a35a92gh.txt plain text: cord-009376-a35a92gh.txt item: #73 of 973 id: cord-009664-kb9fnbgy author: None title: Oral presentations date: 2014-12-24 words: 71226 flesch: 44 summary: Resistance to penicillin, clindamycin and tetracycline fluctuated over time at~75%, 4−8% and 2−10% respectively. The median expected power was 10.0% (IQR, 7.2−13.6%) for a risk ratio for mortality of 0.85 between the compared groups; 14.7% (IQR, 10.6−21.8%) for a risk ratio of 0.80; and 7.9% (IQR, 6.3−10.2%) for a reduction in mortality from 30% to 25%. keywords: age; analysis; antibiotic; assay; associated; aureus; bacterial; blood; cases; cause; cdi; cells; clinical; common; community; conclusion; control; countries; culture; data; days; detection; diagnosis; different; difficile; disease; dna; drug; efflux; europe; expression; factors; gene; group; high; hospital; human; identification; incidence; increase; infections; influenza; isolates; laboratory; levels; like; methods; microbiology; model; mortality; mrsa; n =; negative; new; non; number; objectives; pathogens; patients; pcr; period; plasmid; pneumoniae; population; positive; potential; presence; present; prevalence; pvl; range; rate; resistance; resistance genes; response; results; risk; role; samples; screening; sensitivity; sequence; species; specimens; spread; strains; studies; study; susceptibility; system; testing; therapy; time; total; treatment; type; use; virus; years cache: cord-009664-kb9fnbgy.txt plain text: cord-009664-kb9fnbgy.txt item: #74 of 973 id: cord-010027-r0tl01kq author: None title: Dublin Pathology 2015. 8th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland date: 2015-09-15 words: 36337 flesch: 44 summary: Tumoral melanosis refers to complete regression of a melanoma, a diagnosis that it is often missed because of the absence of tumour cells within the regressed area. Background: During the metastatic cascade, circulating tumour cells rapidly and efficiently adopt a platelet cloak. keywords: analysis; benign; biopsies; biopsy; breast; cancer; carcinoma; cases; cell; changes; data; diagnosis; digital; disease; dna; expression; features; findings; genes; grade; hospital; immunohistochemistry; lesions; lines; lung; lymphoma; melanoma; methods; molecular; mutations; negative; non; number; ovarian; pathology; patients; potential; practice; primary; protein; quality; report; resection; results; review; risk; role; samples; sequencing; specific; specimens; staining; status; study; survival; testing; time; tissue; treatment; tumour; use; years cache: cord-010027-r0tl01kq.txt plain text: cord-010027-r0tl01kq.txt item: #75 of 973 id: cord-010092-uftc8inx author: None title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 words: 233543 flesch: 50 summary: One central question is the need of individual NAT screening (ID) versus minipool NAT screening (MP) approaches to identify all relevant viremias in blood donors. 3A-S02-03 Background: The screening of blood donors and returning travelers from active transmission areas have highlighted the importance of diagnosis of acute arboviral infections. keywords: abo blood; addition; aims; allele; alloimmunization; analysis; anemia; anti; antibodies; antibody; antigen; apheresis; approach; assay; available; average; background; bacterial; bleeding; blood bank; blood cells; blood center; blood chimerism; blood collection; blood components; blood count; blood culture; blood demand; blood donation; blood donors; blood establishments; blood flow; blood group; blood grouping; blood loss; blood management; blood plasma; blood platelet; blood pressure; blood processing; blood products; blood results; blood safety; blood samples; blood services; blood supply; blood system; blood test; blood transfusion; blood type; blood units; blood volume; care; cases; cause; cell donors; cell transfusion; clinical; concentrates; concentration; conclusions; confirmed; content; control; cord blood; countries; criteria; cross; current; data; day; days; deferral; detection; difference; disease; dna; donations; donor samples; effect; events; evidence; exon; expression; factors; female; ferritin; flow; following; frequency; gel; gene; genotyping; group system; groups; hbv; hcv; health; hemoglobin; hev; history; hiv; hla; hospital; hospital blood; human; identification; igg; impact; incidence; increase; individuals; infection; information; international; iron; laboratory; levels; life; low; major; mean; median; medical; methods; min; ml blood; model; molecular; months; n =; national; need; negative; new; non; number; order; overall; p =; patients; pcr; pcs; period; phenotype; plasma; plasma donors; plasma transfusion; platelet; platelet donors; platelet transfusion; population; positive; post; potential; practice; presence; present; prevalence; procedure; process; production; quality; quality blood; range; rate; rbc blood; rbc transfusion; rbcs; reactive; red; reduced; repeat donors; research; results; rhd; rhd blood; risk; routine; screening; selection; sequencing; serum; significant; specific; staff; standard; status; storage; studies; study; summary; surgery; systems; tested; testing; tests; therapy; time donors; total; transfusion medicine; transfusion reactions; transfusion safety; transfusion service; transfusion therapy; transfusions; treated; treatment; typing; use; value; variant; versus; weak; women; years cache: cord-010092-uftc8inx.txt plain text: cord-010092-uftc8inx.txt item: #76 of 973 id: cord-010119-t1x9gknd author: None title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 words: 230433 flesch: 50 summary: Probability of occurrence of cannabis metabolites in blood donor samples is likely to be highly variable across donor centers and is largely dependent on blood donor demographics. OBRR, CBER, FDA Background/Case Studies: Extended molecular typing of a large number of blood donors can increase the likelihood of identifying donor red blood cells (RBCs) that match those of the recipient. keywords: abo; abo blood; acute; addition; alleles; alloimmunization; analysis; anemia; anti; antibodies; antibody; antigen; apheresis; approach; assay; average; background; bacterial; blood; blood bank; blood cells; blood center; blood collection; blood components; blood count; blood donation; blood donors; blood group; blood loss; blood management; blood order; blood ordering; blood products; blood safety; blood samples; blood screening; blood services; blood specimens; blood supplier; blood supply; blood system; blood testing; blood transfusion; blood type; blood units; blood volume; care; case studies; case study; cases; cd36; cell transfusion; center background; centers; change; clinical; collections; concentration; conclusion; control; cord blood; cost; count; cross; culture; current; data; days; decreased; detection; difference; disease; dna; donations; donor samples; dose; dtt; effect; emergency blood; evaluation; events; evidence; expression; factors; fda; female; ffp; finding; flow; following; frequency; fresh; gel; gene; genotyping; given; groups; hbv; hcv; health; hemoglobin; hemolysis; high; history; hiv; hla; hospital; hospital blood; hospital transfusion; hours; human; identification; igg; immucor; impact; implementation; improvement; incidence; increase; infection; information; initial; institution; inventory; iron; laboratory; levels; low; manual; mean; median; medical; method; mice; minutes; model; molecular; months; mtp; need; negative; new; non; normal; number; order; partial; pathogen; patients; pcr; performance; period; phase; phenotype; plasma; plasma samples; plasma transfusion; plasma units; platelet; platelet blood; platelet transfusion; platelet units; plt; plts; population; positive; post; post transfusion; potential; practice; pre; presence; present; prevalence; procedure; process; processing; program; protocol; quality; r blood; range; rate; rbc; rbc blood; rbc transfusion; rbc units; rbcs; reactive; reactivity; reagent; recipients; recovery; red; reduced; reduction; reference; report; response; results; review; rhd; risk; routine; screening; second; sensitivity; sequencing; serum; set; small; solution; specific; specificity; staff; standard; storage; study design; study period; survey; systems; table; technology; test results; testing; tests; therapy; time; titer; total; tpe; training; transfused; transfusion medicine; transfusion practice; transfusion protocol; transfusion reactions; transfusion results; transfusion service; transfusions; trauma; treatment; tube; typing; units; university; use; values; virus; wastage; wbc; weak; weeks; women; year; zika; zikv cache: cord-010119-t1x9gknd.txt plain text: cord-010119-t1x9gknd.txt item: #77 of 973 id: cord-010235-hu6o1ggc author: Atmar, Robert L. title: Nonculturable agents of viral gastroenteritis date: 1997-12-01 words: 3995 flesch: 36 summary: Sixth report of the International Committee on Taxonomy of Viruses Use of solidphase immune electron microscopy for classification of Norwalk-like viruses into six antigenic groups from 10 outbreaks of gastroenteritis in the United States Sequence and genomic organization of Norwalk virus Comparison of the polymerase region of small round structured virus strains previously classified in three antigenic types by solid-phase immune electron microscopy Application of PCR to detect Norwalk virus in fecal specimens from outbreaks of gastroenteritis Genomic diversity of small round structured viruses in the United Kingdom Characterization of SRSVs using RT-PCR and a new antigen ELISA: a short communication Detection and differentiation of antigenically distinct small round-structured viruses (Norwalk-like viruses) by reverse transcription-PCR and Southern hybridization Molecular characterization of a human calicivirus with sequence relationships closer to animal caliciviruses than other known human caliciviruses 25-to 30-nm virus particle associated with a hospital outbreak of acute gastroenteritis with evidence for airborne transmission Airborne transmission of small round structured virus Epidemiology of Norwalk virus during an outbreak of acute gastroenteritis aboard a US aircraft carrier Nosocomial infantile gastroenteritis associate with minirotavirus and calicivirus Epidemiology of Norwalk gastroenteritis and the role of Norwalk virus in outbreaks of acute nonbacterial gastroenteritis Expression, self-assembly, and antigenicity of the Norwalk virus capsid protein Pattern of shedding of the Norwalk particle in stools during experimentally induced gastroenteritis in volunteers as determined by immune electron microscopy Solid-phase microtiter radioimmunoassay for detection of the Norwalk strain of acute nonbacterial, epidemic gastroenteritis virus and its antibodies Detection of Norwalk virus antibodies and antigen with a biotin-avidin immunoassay Detection of Norwalk virus in stools by enzyme immunoassay Norwalk virus infection of volunteers: new insights based on improved assays Development of an enzyme immunoassay to detect MX virus, a human calicivirus in the Snow Mountain agent genogroup Evaluation of an antigen capture ELISA based on recombinant Mexico virus capsid protein Molecular characterization of morphologically typical human calicivirus Sapporo Antigenic mapping of the recombinant Norwalk virus capsid protein using monoclonal antibodies Evaluation of the immunogenicity and antigenicity of Norwalk virus capsid employing synthetic peptides and peptide-specific antibodies Comparison of the reactivities of baculovirus-expressed recombinant Norwalk virus capsid antigen with those of the native Norwalk virus antigen in serologic assays and some epidemiologic observations Sub-class specific serum antibody responses to recombinant Norwalk virus capsid anti gen (rNV) in adults infected with Detection of immunoglobulin M (IgM), IgA, and IgG Norwalk virus-specific antibodies by indirect enzyme-linked immunosorbent assay with baculovirus-expressed Norwalk virus capsid antigen in adult volunteers challenged with Norwalk virus Antibody prevalence and immunoglobulin IgG subclass pattern to Norwalk virus in Sweden Detection of Norwalk virus in stool by polymerase chain reaction Polymerase chain reaction detection of small roundstructured viruses from two related hospital outbreaks of gastroenteritis using inosine-containing primers Broadly reactive reverse transcriptase polymerase chain reaction for the diagnosis of SRSVassociated gastroenteritis Evaluation of a degenerate primer for the detection of human caliciviruses Detection of Norwalk virus in stool specimens by reverse transcriptase-polymerase chain reaction and nonradioactive oligoprobes An altemative method for direct sequencing of PCR products, for epidemiological studies performed by nucleic sequence comparison. (3) provided the first clear demonstration of the causal relationship between a virus (Norwalk virus [NV] ) and gastroenteritis by using immune electron microscopy (IEM) to detect the presence of viral particles in the stools of individuals from an epidemic outbreak of gastroenteritis. keywords: antigen; assays; detection; gastroenteritis; hucvs; human; norwalk; pcr; virus; viruses cache: cord-010235-hu6o1ggc.txt plain text: cord-010235-hu6o1ggc.txt item: #78 of 973 id: cord-010608-eaa2znom author: Butt, Salman L. title: Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples date: 2020-03-05 words: 6858 flesch: 45 summary: Therefore, our aim was to create a single, amplicon-based protocol to sequence the IBV S1 gene and develop a sequence analysis workflow to identify IBV types from clinical swab samples. A universal S1 primer set, 27 tailed with the MinION universal adapter sequence of 22 nucleotides (underlined, Table 2 ) to allow barcoding of amplicons, was used for targeted amplification of the IBV S1 gene for IBV. keywords: ampseq; bronchitis; ibv; lineage; minion; pcr; reads; samples; sequence; sequencing; virus cache: cord-010608-eaa2znom.txt plain text: cord-010608-eaa2znom.txt item: #79 of 973 id: cord-011073-uiabpbxd author: Gebrekidan, Hagos title: An appraisal of oriental theileriosis and the Theileria orientalis complex, with an emphasis on diagnosis and genetic characterisation date: 2019-12-06 words: 7019 flesch: 32 summary: (2012) Nested PCR for ITS-1-5.8S-ITS-2 region Aktas et al. (2007) Loop-mediated isothermal amplification (LAMP) for p33 and ITS1-5.8S-ITS2 region Wang et al. (2010b) , Liu et al. However, only two studies have reported the use of LAMP for the diagnosis of T. orientalis infection in China (Wang et al. 2010; Liu et al. 2013 ). keywords: assay; blood; cattle; complex; detection; dna; et al; genotypes; orientalis; pcr; perera; theileria; theileriosis; tick; time cache: cord-011073-uiabpbxd.txt plain text: cord-011073-uiabpbxd.txt item: #80 of 973 id: cord-011322-olvqgs85 author: El-Senousy, Waled M. title: Clinical and Environmental Surveillance of Rotavirus Common Genotypes Showed High Prevalence of Common P Genotypes in Egypt date: 2020-04-11 words: 9528 flesch: 40 summary: Standard methods for the examination of water and wastewater Efficacy of pentavalent rotavirus vaccine against severe rotavirus gastroenteritis in infants in developing countries in sub-Saharan Africa: A randomised, double-blind, placebo-controlled trial Family Reoviridae Systematic review of regional and temporal trends in global rotavirus strain diversity in the pre rotavirus vaccine era: Insights for understanding the impact of rotavirus vaccination programs Rotavirus seasonality in urban sewage from Argentina: effect of meteorological variables on the viral load and the genetic diversity Effectiveness of a monovalent rotavirus vaccine in infants in Malawi after programmatic rol-out: An observational and case-control study Intussusception risk and disease prevention associated with rotavirus vaccines in Australia's national immunization program Characterization of genotype P[9]G12 rotavirus strains from Argentina: High similarity with Japanese and Korean G12 strains Rotavirus infection and the current status of rotavirus vaccines Biotechnologies applied in biomedical vaccines Trends in intussusceptions associated deaths among US infants from 1979-2007 Molecular epidemiology of rotavirus causing diarrhea among children less than five years of age visiting national level children hospitals The prevalence and genotype distribution of rotavirus A infection among children with acute gastroenteritis in Kunming Prevalence of rotavirus genotypes in children younger than 5 years of age before the introduction of a universal rotavirus vaccination program: Report of rotavirus surveillance in Turkey Epidemiology of rotavirus in Greater Cairo Assessment and evaluation of an integrated hybrid anaerobic-aerobic sewage treatment system for the removal of enteric viruses Molecular epidemiology of human adenoviruses and rotaviruses as candidate viral indicators in the Egyptian sewage and water samples Method validation for norovirus detection in naturally contaminated irrigation water and fresh produce Prevalence of human and animal rotaviruses and HEV in Egyptian Nile water resources Prevalence of noroviruses among detected enteric viruses in Egyptian aquatic environment Effect of chlorine on noroviruses, rotaviruses, and Hepatitis E virus in drinking water Detection and genotyping of rotaviruses in water treatment plants of El-Dakahlia Governorate Survival of adenovirus, rotavirus, hepatitis A virus, pathogenic bacteria and bacterial indicators in ground water Epidemiology of human enteric viruses in the Cairo water environment Rotaviruses group A and C in clinical samples. Correlation of genogroups with subgroups and evidence of independent segregation Rotavirus A strains obtained from children with acute gastroenteritis in Mozambique, 2012-2013: G and P genotypes and phylogenetic analysis of VP7 and partial VP4 genes Incidence of rotavirus infection in children with gastroenteritis attending Jos university teaching hospital To serotype or not to serotype: that is still the question The need for rotavirus vaccine introduction in the national immunization program of more than 100 countries around the world Sequence analysis of VP7 and VP4 genes of G1P[8] rotaviruses circulating among diarrhoeic children in Pune, India: A comparison with Rotarix and RotaTeq vaccine strains Protection against live rotavirus challenge in mice induced by parenteral and mucosal delivery of VP6 subunit rotavirus vaccine Rotavirus strain distribution in Ghana pre-and post-rotavirus vaccine introduction Monitoring and evaluation of infectious rotaviruses in various wastewater effluents and receiving waters revealed correlation and seasonal pattern of occurrences Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans Efficacy and safety of an oral live attenuated human rotavirus vaccine against rotavirus gastroenteritis during the first 2 years of life in Latin American infants: A randomised, double-blind, placebo-controlled phase III study Rotavirus genotypes circulating in Brazil Effect of human rotavirus vaccine on severe diarrhea in African infants Reduced price on rotavirus vaccines: Enough to facilitate access where most needed? keywords: children; common; egyptian; et al; genotypes; human; p[8; pcr; rotavirus; samples; sewage; sewage samples; specimens; vaccine; vp8 cache: cord-011322-olvqgs85.txt plain text: cord-011322-olvqgs85.txt item: #81 of 973 id: cord-011436-ud35mf5l author: Li, Yingying title: Interferon-λ Attenuates Rabies Virus Infection by Inducing Interferon-Stimulated Genes and Alleviating Neurological Inflammation date: 2020-04-06 words: 7463 flesch: 47 summary: Twenty fluorescent foci were examined to calculate the number of infected cells per fluorescent focus by using Image J software [31] . Taken together, these results suggest that expression of IFN-λ2 or IFN-λ3 inhibits RABV replication and spread in infected cells. keywords: astrocytes; brain; cells; expression; figure; ifn; ifnλ2; infection; mice; rabies; rabv; rb2c; virus cache: cord-011436-ud35mf5l.txt plain text: cord-011436-ud35mf5l.txt item: #82 of 973 id: cord-011966-7k2cxy8a author: Jang, Seong Sik title: The Epidemiological Characteristics of the Korean Bat Paramyxovirus between 2016 and 2019 date: 2020-06-04 words: 2999 flesch: 54 summary: Additionally, the phylogenetic analysis based on partial F and HN nucleotide sequences showed that Korean bat paramyxoviruses are closely related to the single clade (Figures 3 and 4) . B16-154, B19-151, and B19-152 are bat paramyxoviruses detected in the same cave. In conclusion, this study revealed that bat paramyxoviruses in Korea belonged to a single genus and circulated sporadically in several provinces, including Chungbuk, Gangwon, Jeju, and Jeonnam. keywords: b19; bat; korea; paramyxoviruses; pcr; samples cache: cord-011966-7k2cxy8a.txt plain text: cord-011966-7k2cxy8a.txt item: #83 of 973 id: cord-012085-ubdzhkfq author: Jin, Tao title: Diversity and quantity of ammonia-oxidizing Archaea and Bacteria in sediment of the Pearl River Estuary, China date: 2011-02-01 words: 4375 flesch: 50 summary: AluI was selected to digest PCR products of AOB amoA gene. Similarly, AOB amoA gene resulted in 67 to 333 copies per nanogram DNA and 9.5×10 4 to 6.2×10 5 copies per gram of sediment. keywords: abundance; ammonia; amoa; aoa; aob; clone; gene; oxidizing; pcr; primer; sediment cache: cord-012085-ubdzhkfq.txt plain text: cord-012085-ubdzhkfq.txt item: #84 of 973 id: cord-012430-3uvhoca9 author: Sanchis, Joaquin title: Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates date: 2008-11-01 words: 5541 flesch: 39 summary: The ideal methodology for performing site saturation mutagenesis is the one yielding (1) a uniform statistical distribution of the desired mutations (quality criteria) and (2) a number of colonies sufficient to get 95% coverage of the given library in one step (quantity criteria). key: cord-012430-3uvhoca9 authors: Sanchis, Joaquin; Fernández, Layla; Carballeira, J. Daniel; Drone, Jullien; Gumulya, Yosephine; Höbenreich, Horst; Kahakeaw, Daniel; Kille, Sabrina; Lohmer, Renate; Peyralans, Jérôme J.-P.; Podtetenieff, John; Prasad, Shreenath; Soni, Pankaj; Taglieber, Andreas; Wu, Sheng; Zilly, Felipe E.; Reetz, Manfred T. title: Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates date: 2008-11-01 journal: keywords: evolution; megaprimer; method; mutagenesis; pcr; quikchange; saturation cache: cord-012430-3uvhoca9.txt plain text: cord-012430-3uvhoca9.txt item: #85 of 973 id: cord-012461-v8d91fdo author: Marnissi, Boutheina title: Generation of ssDNA aptamers as diagnostic tool for Newcastle avian virus date: 2020-08-13 words: 6116 flesch: 47 summary: DNA polymerase Aptasensors as the future of antibiotics test kits-a case study of the aptamer application in the chloramphenicol detection New Prostate Cancer Targets for Diagnosis, Imaging, and Therapy: Focus on Prostate-Specific Membrane Antigen Screening of nucleic acid aptamer of lung cancer cells based on cell exponential enrichment ligand system evolution and its application in tumor diagnosis and treatment Rapid and highly sensitive method for influenza A (H1N1) virus detection Exploiting enzyme catalysis in ultra-low ion strength media for impedance biosensing of avian influenza virus using a bare interdigitated electrode A novel method for detection of H9N2 influenza viruses by an aptamer-real time-PCR Advancements in Nucleic Acid Based Therapeutics against Respiratory Viral Infections One round of SELEX for the generation of DNA aptamers directed against KLK6 A combined enrichment and aptamer pulldown assay for Francisella tularensis detection in food and environmental matrices FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections Development of a real-time reverse-transcription PCR for detection of newcastle disease virus RNA in clinical samples Limit of blank, limit of detection and limit of quantitation Investigations on the interface of nucleic acid aptamers and binding targets Increased inhibitory ability of conjugated RNA aptamers against the HCV IRES Evolution of a T7 RNA polymerase variant that transcribes 2'-Omethyl RNA New NTP analogs: the synthesis of 4'-thioUTP and 4'-thioCTP and their utility for SELEX Magnetic Separation-Based Multiple SELEX for Effectively Selecting Aptamers against Saxitoxin, Domoic Acid, and Tetrodotoxin Selection of aptamers by systematic evolution of ligands by exponential enrichment: addressing the polymerase chain reaction issue Emulsion PCR: a high efficient way of PCR amplification of random DNA libraries in aptamer selection Development and validation of a new PCR optimization method by combining experimental design and artificial neural network Optimization and troubleshooting in PCR Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing Selection, Characterization and Interaction Studies of a DNA Aptamer for the Detection of Bifidobacterium bifidum Identification and application of ssDNA aptamers against H(3)(7)Rv in the detection of Mycobacterium tuberculosis A self-assemble aptamer fragment/target complex based high-throughput colorimetric aptasensor using enzyme linked aptamer assay A colorimetric sandwich-type assay for sensitive thrombin detection based on enzymelinked aptamer assay Aptamers as a replacement for antibodies in enzyme-linked immunosorbent assay. The first step was the elution of high affinity aptamers using high concentration of NaCl. keywords: affinity; aptamers; detection; dna; elaa; ndv; pbs; pcr; samples; sandwich; selex; vaccine; virus cache: cord-012461-v8d91fdo.txt plain text: cord-012461-v8d91fdo.txt item: #86 of 973 id: cord-013416-ooq1q5gy author: El-Tholoth, Mohamed title: Molecular Characterization and Developing a Point-of-Need Molecular Test for Diagnosis of Bovine Papillomavirus (BPV) Type 1 in Cattle from Egypt date: 2020-10-21 words: 5498 flesch: 45 summary: The samples were collected in bottles containing sterile saline for the molecular identification of BPV types 1, 2, 4, 5, and 10 by PCR. The samples were collected in bottles containing sterile saline for the molecular identification of BPV types 1, 2, 4, 5, and 10 by PCR. keywords: amplification; bovine; bpv; cattle; detection; egypt; infection; papillomavirus; pcr; rpa; samples; test; virus cache: cord-013416-ooq1q5gy.txt plain text: cord-013416-ooq1q5gy.txt item: #87 of 973 id: cord-013589-3l8kar3k author: Doummar, Diane title: Biallelic PDE2A variants: a new cause of syndromic paroxysmal dyskinesia date: 2020-05-28 words: 4149 flesch: 39 summary: Interestingly, analysis of the fibroblasts with the biallelic variants in PDE2A variants revealed mitochondria network morphology changes. After exome analysis, PDE2A variants were confirmed by Sanger sequencing using patient's, and parents' DNA. keywords: camp; disorders; dyskinesia; eeg; epilepsy; fig; interictal; mitochondria; movement; patient; pde2a; variants cache: cord-013589-3l8kar3k.txt plain text: cord-013589-3l8kar3k.txt item: #88 of 973 id: cord-014462-11ggaqf1 author: None title: Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date: 2011-04-21 words: 35463 flesch: 47 summary: The following virus isolates have been used in the analysis: GTPV-Uttarkashi, P60, vaccine virus; GTPV Mukteswar, P10, Challenge virus; GTPV (Akola), GTPV Bareilly/00, GTPV Ladakh/01 and GTPV Sambalpur/82, field isolates and SPPV Srinagar, P40; SPPV Ranipet, P50; SPPV-RF, P50, vaccine viruses and SPPV Makdhoom/07, SPPV CIRG/08, SPPV Pune/08, SPPV Bareilly, SPPV 183/03 and SPPV 125/02, field isolates. Present paper discusses about virus disease of quarantine importance affecting ornamental and fruit plants such as Chrysanthimum, Dahlia, Dianthus, Rosabengalensis, Cattleya, Cymbidium, Dendrobium, Lilium, Citrus, Vitis etc. keywords: acid; analysis; animals; antibodies; antigen; assay; cases; cells; cloned; control; crop; curl; dengue; detection; development; disease; dna; elisa; expression; field; food; gene; host; india; infection; isolates; leaf; management; methods; molecular; mosaic; mosaic virus; nucleotide; pathogens; patients; pcr; plant; positive; present; primers; production; protein; region; resistance; response; results; rna; samples; sequence; specific; study; symptoms; time; tomato; total; vaccine; vector; viral; virus; virus infection; viruses; world; yellow cache: cord-014462-11ggaqf1.txt plain text: cord-014462-11ggaqf1.txt item: #89 of 973 id: cord-014516-r59usk02 author: None title: Research Communications of the 24th ECVIM‐CA Congress date: 2015-01-10 words: 55086 flesch: 49 summary: Method specificity was confirmed by the absence of matrix effect in six serum specimen obtained from clinical dogs. Stage C dogs had lower SRs (p = 0.0005), higher SRe (p = 0.0029) and SRa (p = 0.0004) than other dogs. keywords: age; aim; analysis; animal; associated; blood; body; breed; canine; cardiac; cases; cats; cell; chronic; common; concentrations; conflicts; control; data; days; diagnosis; disease; dogs; fcv; fecal; feline; following; function; group; healthy; heart; human; interest; loss; ltd; mean; measurements; median; months; non; normal; patients; pcr; positive; prevalence; range; rate; reference; renal; results; risk; samples; serum; severity; signs; studies; study; test; time; total; treatment; values; veterinary; weeks; weight; years cache: cord-014516-r59usk02.txt plain text: cord-014516-r59usk02.txt item: #90 of 973 id: cord-014527-nvzfpntu author: None title: Research Communications of the 25th ECVIM‐CA Congress date: 2015-11-09 words: 89290 flesch: 49 summary: Dogs in the prolonged OS group were more likely to be anaemic on presentation (PCV<37%, P = 0.041), experienced a greater FRD (P = 0.012) and were more likely to be treated with a rescue protocol (P = 0.036) than other dogs. Dogs that did not respond to treatment had significantly higher S100A12 levels than dogs with partial (P = 0.005) or complete (P = 0.003) remission, but response to treatment was associated with disease classification (P = 0.020). keywords: 0.001; age; aim; analysis; animals; bcs; blood; body; breed dogs; breeds; canine; cardiac; cases; cats; cells; chronic; clinical; concentrations; control; control dogs; correlation; crp; data; days; diagnosis; difference; disclosures; disease; dogs; echocardiography; examination; feline; function; group; heart; humans; infection; levels; mean; measurements; median; method; mmhg; months; n =; non; outcome; owners; p =; patients; pcr; population; positive; presence; present; prevalence; range; rate; renal; report; results; right; samples; serum; signs; small; specific; studies; study; survival; systolic; test; time; total; treatment; use; values; veterinary; weight; years cache: cord-014527-nvzfpntu.txt plain text: cord-014527-nvzfpntu.txt item: #91 of 973 id: cord-014794-yppi30a0 author: None title: 19th European Congress of Pathology, Ljubljana, Slovenia, September 6-11, 2003 date: 2003-07-31 words: 158305 flesch: 41 summary: The comparison in paired tumor and normal tissue samples showed that phosphorylated ERK-1/ERK-2 expression was higher in tumor cells as compared to surrounding normal salivary parenchyma. IRF-1 derepression by invading tumor cells was associated with poor prognosis. keywords: actin; activity; adenocarcinoma; aim; alpha; analysis; antibodies; antibody; antigen; apoptosis; apoptotic; areas; associated; association; bcl-2; benign; biopsies; biopsy; bladder; blood; bone; breast; breast cancer; breast carcinoma; cancer; cancer cells; cancer patients; carcinoma; cases; cases introduction; cd10; cell carcinoma; cell lymphoma; cell proliferation; cells; changes; chronic; classification; clinical; colorectal; conclusion; control; correlation; cyclin; data; department; detection; development; diagnosis; differences; differentiation; diffuse; disease; dna; electron; epithelial; evaluation; examination; expression; factor; features; female; fibrosis; findings; follow; gastric; gene expression; genes; gland; grade; group; growth; hospital; hpv; human; immunohistochemistry; immunoreactivity; index; infection; inflammatory; introduction; invasion; involvement; ki-67; kit; left; lesions; levels; like; liver; lung; lymph; lymphocytes; lymphoma; malignant; markers; mass; material; mean; metastases; metastatic; methods; microscopy; monoclonal; months; mucosa; muscle; negative; neoplasms; node; non; normal; nuclear; nuclei; number; ovarian; overexpression; p53; p53 expression; papillary; paraffin; parameters; pathology; patients; pattern; pcr; positive; positivity; presence; present; primary; prognostic; progression; proliferation; prostate; protein expression; proteins; receptor; renal; report; results; right; risk; role; samples; sections; series; significance; size; skin; smooth; specific; specimens; stage; staining; status; stromal; studies; study; surgery; survival; system; thyroid; time; tissue; total; treatment; tumor cells; tumors; tumour; type; university; value; vascular; vegf; vessels; women; years cache: cord-014794-yppi30a0.txt plain text: cord-014794-yppi30a0.txt item: #92 of 973 id: cord-014942-4hk0veck author: Boone, Stephanie A. title: The Prevalence of Human Parainfluenza Virus 1 on Indoor Office Fomites date: 2010-02-09 words: 3439 flesch: 43 summary: The offices sampled in Arizona indicated a greater variation in the total percentage of HPIV1 positive surfaces per building (Fig. 3) . In addition to surfaces usage, variations in HPIV1 positive surfaces may also be a reflection of office cleaning practices (frequency of wiping surfaces to remove matter) and surface disinfection (use of a product that kills or inactivates microorganisms). keywords: fomites; hpiv1; office; parainfluenza; pcr; surfaces; virus cache: cord-014942-4hk0veck.txt plain text: cord-014942-4hk0veck.txt item: #93 of 973 id: cord-014965-efmozngq author: None title: Infectious diseases other than CMV (1st Section) date: 2001-06-11 words: 8012 flesch: 47 summary: First signs of LPD appeared 64, 64 and 67 days after last dose of ATG (16mg/kg) in transplant patients, 30 days after last dose of ATG (30mg/kg) in patient treated with ATG+CsA for relapsing SAA. In transplant patients, cure rate was 41 % and an overall mortality was 58 %. keywords: cell; days; dose; fungal; infection; median; patients; pcr; positive; prophylaxis; pts; results; therapy; treatment cache: cord-014965-efmozngq.txt plain text: cord-014965-efmozngq.txt item: #94 of 973 id: cord-014976-546zaoxn author: None title: Publication only date: 2006-03-08 words: 51973 flesch: 49 summary: On admission before transplantation patient was presented with massive lymphadenopathy, anemia (Hb 76 g/L), WBC 24.8 x 109/L with absolute lymphocytosis (lymphocytes 98%) and thrombocytopenia 23 x 109/L. Pre-transplant conditioning consisted of high-dose cyclophosphamide and total body irradiation. There are publications about hyperkalemia in patients after renal transplantation but only few reports devote this phenomen in bone marrow transplantation patients. keywords: acute; age; allogeneic; aml; analysis; asct; autologous; blood; blood stem; bone; bone marrow; case; cd34; cell dose; cell transplantation; cells; chemotherapy; children; chimerism; chronic; clinical; complete; conclusion; conditioning; count; csf; cyclophosphamide; day; days; diagnosis; disease; donor; dose; engraftment; follow; grade; graft; group; gvhd; high; hla; host; hsct; levels; lymphoma; marrow; marrow transplantation; median; methods; months; non; number; patients; pbsc; post; prophylaxis; pts; range; recovery; regimen; relapse; remission; results; risk; sct; second; severe; skin; stem cell; study; therapy; time; total; transplanted; treatment; years cache: cord-014976-546zaoxn.txt plain text: cord-014976-546zaoxn.txt item: #95 of 973 id: cord-015147-h0o0yqv8 author: None title: Oral Communications and Posters date: 2014-09-12 words: 73903 flesch: 39 summary: After 3 months of exposures, inflammatory cells in bronchoalveolar lavage fluid were increased in both the HCR-and LCR-smokeexposed(SE) animals compared to air-exposed controls (p<0.001); however there was a 2-3-fold increase in the number of neutrophils and lymphocytes in the LCR-over the HCR-SE group (p<0.001).Histopathology revealed there was greater inflammation and lung damage present in the LCR-versus HCR-SE group (p<0.05). This causes the symptoms of the early phase of AI and the onset of the late phase characterized by the penetration in the inflamed tissue of inflammatory cells, notably the eosinophils. keywords: activation; activity; acute; addition; adhesion; administration; aim; alpha; analysis; animals; anti; antibodies; antibody; arthritis; associated; beta; binding; blood; bone; cancer; cartilage; cells; chronic; complex; conditions; control; cox-2; cytokines; data; day; days; development; disease; dose; effect; expression; factor; function; gene; group; hours; human; il-1b; il-6; immune; increase; induction; inflammation; inflammatory; inhibited; inhibition; inhibitors; injection; injury; joint; kinase; leukocyte; levels; lps; lung; macrophages; mechanisms; mediators; methods; mice; mif; model; molecular; molecules; monocytes; mouse; mrna; neutrophils; new; novel; number; p38; pathways; patients; pcr; plasma; potential; presence; present; production; protein; rats; receptor; reduced; regulation; release; research; response; results; rheumatoid; role; selective; serum; signaling; skin; specific; stimulation; studies; study; synthesis; system; t cells; therapeutic; time; tissue; tnf; tnfa; treatment; tumor; type; university; vitro; vivo cache: cord-015147-h0o0yqv8.txt plain text: cord-015147-h0o0yqv8.txt item: #96 of 973 id: cord-015324-y44sfr0c author: None title: Scientific Programme date: 2007-09-01 words: 197844 flesch: 49 summary: In the group I, consisted of 63 infants (35 males and 28 females) PCD increased during the time in 3,2% infants, remained unchanged in 11,1%, decreased in 14,3%, and disappeared in 71,4% patients. There was no significant difference between renal transplant patients and healthy controls in genotype distribution of allelic frequencies of IL-6, FAS and MCP-1 polymorphisms. keywords: abnormalities; according; acid; activity; acute; adult patients; adults; age; aim; analysis; anti; associated; background; baseline; biopsy; blood; body; bone; boys; calcium; cases; cause; cells; changes; childhood; children; chronic; ckd; clinical; complete; conclusion; control; control group; correlation; course; creatinine; crf patients; csa; damage; data; day; days; development; diagnosis; dialysis; dialysis patients; difference; disease; dose; duration; dysfunction; effect; elevated; end; esrd; examination; excretion; expression; factor; failure; family; findings; follow; fsgs; function; gene; gfr; girls; glomerular; glomerulonephritis; grade; graft; group; growth; hd patients; hematuria; history; hospital; human; hus; hypertension; iga; incidence; increase; infants; infection; initial; injury; kidney; kidney disease; levels; male; mean; median; mesangial; metabolic; methods; mice; min/1.73; mmf; months; mrna; mutations; negative; nephritis; nephrology; nephropathy; nephrotic; non; normal; number; objective; onset; outcome; p<0.001; p<0.05; parameters; patients; pcr; pediatric; period; peritoneal; plasma; population; positive; post; prednisone; presence; present; pressure; primary; progression; proteinuria; pth; range; rare; rate; ratio; rats; reflux; rejection; relapse; remission; renal; renal biopsy; renal transplantation; report; response; results; risk; role; second; serum; severe; specific; srns; stage; steroid; studies; study; study group; survival; symptoms; syndrome; system; tacrolimus; term; test; therapy; time; total; tract; transplant patients; transplantation; treated; treatment; tubular; type; ultrasound; urinary; urine; uti; values; vs.; vur; vur patients; weeks; weight; years; yrs cache: cord-015324-y44sfr0c.txt plain text: cord-015324-y44sfr0c.txt item: #97 of 973 id: cord-015348-qt0worsl author: None title: Abstract date: 2010-07-30 words: 74228 flesch: 40 summary: The role of autophagy in cancer seems to be dual: On one hand, there is a growing body of evidence supporting the idea that autophagy may represent a tumor suppressor mechanism by reducing intratumoral necrosis, restricting oxidative stress and limiting chromosomal instability; on the other hand, autophagy may be an important process used by tumor cells to escape various types of stress and even therapeutic agents. At a higher magnification, tumor cells are grouped in small nests formed by large cells, with an abundant, pale, mucus-laden cytoplasm and an eccentric nucleus. keywords: adenocarcinoma; age; aim; analysis; antibodies; antibody; benign; biopsies; biopsy; brain; breast; breast cancer; cancer; carcinoma; cases; cells; changes; chronic; clinical; colorectal; conclusion; control; correlation; cystic; data; dept; development; diagnosis; disease; egfr; epithelial; evaluated; evaluation; examination; expression; factors; features; findings; gastrointestinal; gene; grade; group; growth; high; hyperplasia; ihc; immunohistochemistry; inflammatory; information; kit; lesions; like; lung; lymph; lymphoma; malignant; markers; mass; melanoma; metastatic; method; microscopy; molecular; mutations; new; node; non; nuclear; number; objective; p53; parameters; pathologists; pathology; patients; presence; present; primary; prognostic; proliferation; protein; report; results; risk; role; samples; slides; specimens; stage; staining; stromal; studies; study; system; therapy; time; tissue; treatment; tumor; tumor cells; tumours; type; use; vascular; vegf; years cache: cord-015348-qt0worsl.txt plain text: cord-015348-qt0worsl.txt item: #98 of 973 id: cord-015372-76xvzvdg author: None title: National scientific medical meeting 1996 abstracts date: 1996 words: 36628 flesch: 50 summary: Control patients were enrolled who had no clinical evidence of rheumatological disease, A salivary sample was collected and examined by light microscopy. Drug induced photosensitivity may look identical clinically, have a similar history and patients with CAD may be treated with potentially photosensitising drugs. keywords: acid; activity; age; aim; analysis; antibodies; blood; bone; care; cases; cells; children; controls; data; day; difference; disease; drug; expression; females; findings; following; group; hiv; hospital; incidence; increase; infection; irish; levels; males; mean; months; negative; number; pain; patients; pcr; period; population; positive; present; range; rate; response; results; risk; samples; serum; skin; studies; study; subjects; test; therapy; time; total; treatment; type; use; virus; years cache: cord-015372-76xvzvdg.txt plain text: cord-015372-76xvzvdg.txt item: #99 of 973 id: cord-015394-uj7fe5y6 author: None title: Scientific Abstracts date: 2008-12-23 words: 242809 flesch: 48 summary: The highest level of -tubulin acetylation (2.5-fold) was observed with Vinblastine at 10-fold IC 50 after 48 h. Exposure to Microtubule interacting agents and TSA resulted in increased cell surface expression of Ep-CAM in a time and dose dependent manner. Finally, we elucidated a link between the RA and TGF-pathways by assessing the impact of RA treatment of TGF-3 expression, demonstrating that TGF-3 template decreased to levels comparable to myometrial cell expression (0.84±0.12 fold). keywords: acid; activation; activity; addition; administration; adult; aea; age; aim; analysis; animals; anova; anti; antibodies; antibody; apoptosis; arteries; artery; assay; associated; association; background; baseline; binding; birth; blood; blood cells; blot; bmi; body; brain; cancer; cancer cells; cases; cells; center; cervix; cesarean; changes; clinical; collagen; concentrations; conclusions; conditions; contractions; contrast; contribute; control; control cells; control group; correlation; cortisol; crf; culture; cycle; cytokines; data; day; days; decidua; decrease; delivery; design; development; differences; differentiation; disease; dna; dose; effect; elisa; endometriosis; endometrium; endothelial; eoc cells; epithelial; estradiol; estrogen; evidence; explants; exposure; expression; expression levels; factor; fat; female; fetal; fetuses; findings; flow; fluid; fold; following; free; function; gene; gestation; glucose; gnrh; group; growth; gynecology; hcg; high; hormone; hospital; hours; human; hypertension; hypothesis; hypoxia; il-6; il-8; immune; immunohistochemistry; implantation; increase; induction; infection; inflammation; inhibitor; insulin; introduction; invasion; iugr; ivf; kinase; labor; leptin; levels; lps; male; maternal; mean; mechanisms; media; medical; medicine; medium; membranes; menstrual; methods; mice; min; model; mouse; mrna expression; mrna levels; muscle cells; myometrial; n=6; neonatal; new; non; normal; novel; nuclear; number; obesity; objective; obstetrics; offspring; onset; oocytes; outcome; ovarian; oxygen; p<0.001; p<0.05; pathway; patients; pattern; pcos; pcr; period; phase; phosphorylation; placental; placental cells; plasma; play; population; positive; post; potential; preeclampsia; pregnancies; pregnancy; pregnant; presence; present; pressure; preterm; primary; production; progesterone; proliferation; protein expression; protein levels; proteins; range; rate; rats; receptor; receptor expression; reduced; regulation; relative; release; reproductive; response; restriction; results; risk; role; samples; secretion; sections; serum; sheep; signaling; smooth; specific; staining; stress; studies; study; study group; subjects; syndrome; system; t cells; term; test; time; tissue; tnf; total; treatment; trimester; trophoblast cells; tumor; type; university; usa; uterine; uterus; vascular; vegf; vehicle; vitro; vivo; weeks; weight; western; women; years cache: cord-015394-uj7fe5y6.txt plain text: cord-015394-uj7fe5y6.txt item: #100 of 973 id: cord-015683-a9a82of4 author: Gupta, Varsha title: Molecular Diagnostics date: 2016-10-23 words: 4776 flesch: 49 summary: This is an alternative strategy where samples containing several proteins are arrayed on slide and probed with labeled antibodies. Traditional PCR procedure includes amplification of specifi c genes ( Fig. 9.4 ) of the microorganisms and running the product on a gel. keywords: antibodies; antibody; antigen; detection; diagnosis; diseases; dna; elisa; pcr; protein; specifi; tests cache: cord-015683-a9a82of4.txt plain text: cord-015683-a9a82of4.txt item: #101 of 973 id: cord-015763-5lx179pa author: Thellier, D. title: Quels prélèvements aux urgences pour le diagnostic microbiologique d’une infection pulmonaire communautaire grave du sujet immunocompétent ? date: 2014-09-23 words: 5181 flesch: 41 summary: La réduction possible du spectre antibiotique permet la diminution de la pression de sélection, des effets secondaires et du coût du traitement. Au moins deux études retrouvent une augmentation de la fréquence de positivité de l'hémoculture avec celle de la classe du score PSI keywords: bactérienne; charge; community; dans; des; diagnostic; est; les; ont; par; patients; pcg; pcr; pneumonia; pour; que; test; une; virus cache: cord-015763-5lx179pa.txt plain text: cord-015763-5lx179pa.txt item: #102 of 973 id: cord-015941-4fz79wzf author: Hu, Yuan title: Molecular Techniques for Blood and Blood Product Screening date: 2018-11-10 words: 7210 flesch: 47 summary: Detection of early HBV infection of blood donors is still a major problem of blood transfusion. Section two: Specific virus families Evaluation of a prototype Trypanosoma cruzi antibody assay with recombinant antigens on a fully automated chemiluminescence analyzer for blood donor screening Transfusion-transmitted malaria in countries where malaria is endemic: a review of the literature from sub-Saharan Africa Detection and species identification of malaria parasites by isothermal tHDA amplification directly from human blood without sample preparation 18 years of research and surveillance Prions: beyond a single protein Crerutzfeldt-Jakob disease and blood transfusion: updated results of the UK transfusion medicine epidemiology review study Detection of prion infection in variant Creutzfeldt-Jakob disease: a blood-based assay Preclinical detection of variant CJD and BSE prions in blood Quantitative assessment of prion infectivity in tissues and body fluids by real-time quaking-induced conversion Analytical and clinical performance of the CDC real time RT-PCR assay for detection and typing of dengue virus Threat of dengue to blood safety in dengueendemic countries Comparison of a commercial IgM capture ELISA with dengue antigen focus reduction microneutralization test and the centers for disease control dengue IgM capture-ELISA PCR detection of nearly any dengue virus strain using a highly sensitive primer cocktail Do babesiosis and malaria share a common disease process? Babesia: a world emerging Babesia infection through blood transfusions: reports received by the US Food and Drug Administration Transfusion-transmitted Babesia spp.: keywords: acid; assay; blood; detection; disease; dna; hcv; hepatitis; infection; nucleic; pcr; screening; testing; tests; transfusion; virus cache: cord-015941-4fz79wzf.txt plain text: cord-015941-4fz79wzf.txt item: #103 of 973 id: cord-016000-le22pknc author: Saikumar, G. title: Porcine Circovirus date: 2019-06-06 words: 9694 flesch: 34 summary: The efficacy of nimodipine drug delivery using mPEG-PLA micelles and mPEG-PLA/TPGS mixed micelles Retrospective study on the occurrence of porcine circovirus 2 infection and associated entities in northern Germany Distinction between porcine circovirus type 2 enteritis and porcine proliferative enteropathy caused by Lawsonia intracellularis Experimental in utero inoculation of late-term swine fetuses with porcine circovirus type 2 Emergence of porcine circovirus 2 associated reproductive failure in Southern India Effects of dexamethasone on the pathogenesis of porcine circovirus type 2 infection in piglets Absence of evidence of porcine circovirus infection in piglets with congenital tremors Differentiation of porcine circovirus 1 and 2 in formalin-fixed, paraffinwax-embedded tissues from pigs with postweaning multisystemic wasting syndrome by in-situ hybridisation Simultaneous detection of porcine circovirus 2 and porcine parvovirus in naturally and experimentally coinfected pigs by double in situ hybridization Multiplex nested PCR compared with in situ hybridization for the differentiation of porcine circoviruses and porcine parvovirus from pigs with postweaning multisystemic wasting syndrome Necrotising lymphadenitis associated with porcine circovirus type 2 in pigs Association of porcine circovirus 2 with porcine respiratory disease complex Simultaneous detection and differentiation between porcine circovirus and porcine parvovirus in boar semen by multiplex seminested polymerase chain reaction Enteritis associated with porcine circovirus 2 in pigs Immunologic features of porcine circovirus type 2 infection Mycoplasma hyopneumoniae bacterins and porcine circovirus type 2 (PCV2) infection: induction of postweaning multisystemic wasting syndrome (PMWS) in the gnotobiotic swine model of PCV2-associated disease Identification and genetic characterization of porcine circovirus type 3 in China Porcine Circovirus-2 an emerging disease of crossbred pigs in Tamil Nadu, India Prevalence of novel porcine circovirus 3 in Korean pig populations Typing of porcine circovirus in clinical specimens by multiplex PCR PCR detection and evidence of shedding of porcine circovirus type 2 in boar semen Possible cross-species transmission of circoviruses and cycloviruses among farm animals Seroprevalence of porcine circovirus type 2 in swine populations in Canada and Costa Rica The ORF3 protein of porcine circovirus type 2 is involved in viral pathogenesis in vivo The ORF3 protein of porcine circovirus type 2 interacts with porcine ubiquitin E3 ligase Pirh2 and facilitates p53 expression in viral infection Hsp70 positively regulates porcine circovirus type 2 replication in vitro Heat shock protein 27 is involved in PCV2 infection in PK-15 cells Post-weaning multisystemic wasting syndrome (PMWS) clinical expression under field conditions is modulated by the pig genetic background Characterization of shedding patterns of porcine circovirus types 2a and 2b in experimentally inoculated mature boars Apoptosis and proliferative activity in lymph node reaction in postweaning multisystemic wasting syndrome (PMWS) Global status of porcine circovirus type 2 and its associated diseases in Sub-Saharan Africa Cost of post-weaning multi-systemic wasting syndrome and porcine circovirus type-2 subclinical infection in England -an economic disease model Porcine circoviruses: a review Experimental reproduction of severe wasting disease by co-infection of pigs with porcine circovirus and porcine parvovirus Experimental infection of colostrum deprived piglets with porcine circovirus 2 (PCV2) and porcine reproductive and respiratory syndrome virus (PRRSV) potentiates PCV2 replication Porcine circovirus 2 replication in colostrum-deprived piglets following experimental infection and immune stimulation using A modified live vaccine against porcine respiratory and reproductive syndrome virus Discovery and evolving history of two genetically related but phenotypically different viruses, porcine circoviruses 1 and 2 Influence of husbandry and control measures on porcine circovirus type 2 (PCV-2) dynamics within a farrow-to-finish pig farm: a modelling approach Isolation and identification of porcine circovirus 2 from cases of respiratory disease and postweaning multisystemic wasting syndrome in pigs Genetic characterisation and phylogenetic analysis of PCV2 isolates from India: indications for emergence of natural inter-genotypic recombinants Porcine circovirus type 2 DNA influences cytoskeleton rearrangements in plasmacytoid and monocyte-derived dendritic cells Retrospective study of porcine circovirus type 2 infection reveals a novel genotype PCV2f Efficacy and future prospects of commercially available and experimental vaccines against porcine circovirus type 2 (PCV2) Complete genome sequence of emerging porcine circovirus types 2a and 2b from India House fly vector for porcine circovirus 2b on commercial pig farms Quantitation of porcine circovirus type 2 isolated from serum/plasma and tissue samples of healthy pigs and pigs with postweaning multisystemic wasting syndrome using a TaqMan-based real-time PCR The emergence of a new strain of porcine circovirus-2 in Ontario and Quebec swine and its association with severe porcine circovirus associated disease Immunopathological effects of porcine circovirus type 2 (PCV2) on swine alveolar macrophages by in vitro inoculation The involvement of Fas/FasL interaction in porcine circovirus type 2 and porcine reproductive and respiratory syndrome virus co-inoculation-associated lymphocyte apoptosis in vitro Fast diagnosis and quantification for porcine circovirus type 2 (PCV-2) using real-time polymerase chain reaction Interaction of porcine circovirus type 2 replication with intracellular redox status in vitro The ubiquitin-proteasome system is required for the early stages of porcine circovirus type 2 replication The ORF3 protein of porcine circovirus type 2 promotes secretion of IL-6 and IL-8 in porcine epithelial cells by facilitating proteasomal degradation of regulator of G protein signalling 16 through physical interaction Post-weaning multisystemic wasting syndrome Characterization of a new disease syndrome associated with porcine circovirus type 2 in previously vaccinated herds Porcine circovirus type 3 in the UK Brain lesions in pigs affected with postweaning multisystemic wasting syndrome Low levels of diversity among genomes of porcine circovirus type 1 (PCV1) points to differential adaptive selection between porcine circoviruses Immunology of porcine circovirus type 2 (PCV2) Cytokine profiles of peripheral blood mononuclear cells from pigs with postweaning multisystemic wasting syndrome in response to mitogen, superantigen or recall viral antigens Cytokine mRNA expression profiles in lymphoid tissues of pigs naturally affected by postweaning multisystemic wasting syndrome Molecular characterization of porcine circovirus type 2 isolates from post-weaning multisystemic wasting syndrome-affected and non-affected pigs Distribution and characterization of IL-10-secreting cells in lymphoid tissues of PCV2-infected pigs Porcine dermatitis and nephropathy syndrome (PDNS): an overview of the disease Genomic analysis of PCV2 isolates from Danish archives and a current PMWS case-control study supports a shift in genotypes with time Porcine circovirus: an old virus in a new guise causes an emerging disease through a novel pathogenesis Co-infection by porcine circovirus and porcine parvovirus in pigs with multisystemic wasting syndrome Prevalence of infection and genetic diversity of porcine circovirus type 2 (PCV2) in wild boar (Sus scrofa) in Poland Detection and genetic characterization of porcine circovirus type 3 in Italy Genetic characterization of type 2 porcine circovirus (PCV-2) from pigs with postweaning multisystemic wasting syndrome in different geographic regions of North America and development of a differential PCR-restriction fragment length polymorphism assay to detect and differentiate between infections with PCV-1 and PCV-2 Two aminoacid mutations in the capsid protein of type 2 porcine circovirus (PCV2) enhanced PCV2 replication in vitro and attenuated the virus in vivo Porcine circovirus type 2 (PCV2) vaccination of conventional pigs prevents viremia against PCV2 isolates of different genotypes and geographic origins strain variation: what does it mean? Development and use of a multiplex real-time quantitative polymerase chain reaction assay for detection and differentiation of porcine circovirus-2 genotypes 2a and 2b in an epidemiological survey Emergence of a new type of porcine circovirus in swine (PCV): a type 1 and type 2 PCV recombinant Characterization of necrotizing lymphadenitis associated with porcine circovirus type 2 infection Ochratoxin A promotes porcine circovirus type 2 replication in vitro and in vivo Recent advances in the epidemiology, diagnosis and control of diseases caused by porcine circovirus type 2 Genomesequence analysis of 10 Dutch porcine circovirus type 2 (PCV-2) isolates from a PMWS case-control study Reproduction of postweaning multisystemic wasting syndrome in pigs by prenatal porcine circovirus 2 infection and postnatal porcine parvovirus infection or immunostimulation Evidence of shedding of porcine circovirus type 2 in milk from experimentally infected sows Nucleotide sequence of porcine circovirus associated with postweaning multisystemic wasting syndrome in pigs PCR detection and characterization of type-2 porcine circovirus Post-weaning multisystemic wasting syndrome: preliminary epidemiology and clinical findings Recognizing and diagnosing postweaning multisystemic wasting syndrome (PMWS) Identification and functional analysis of the novel ORF4 protein encoded by porcine circovirus type 2 keywords: cells; circovirus; circovirus type; detection; disease; et al; infection; pcr; pcv1; pcv2; pcv3; pigs; porcine; porcine circovirus; protein; replication; samples; swine; syndrome; type; vaccination cache: cord-016000-le22pknc.txt plain text: cord-016000-le22pknc.txt item: #104 of 973 id: cord-016020-awanrm9u author: Fox, Julie D. title: Respiratory Pathogens date: 2007 words: 4604 flesch: 22 summary: Future directions will incorporate the use of microarray systems for respiratory pathogen detection and analysis to allow crossing of the barriers between conventional virology and bacteriology (and mycology/parasitology). For respiratory viruses, other methods have been used for typing, including heteroduplex mobility assay (HMA), single-strand conformation polymorphism (SSCP), and RFLP analysis of amplified PCR products. keywords: amplification; analysis; detection; diagnosis; infections; influenza; methods; pathogens; pcr; viruses cache: cord-016020-awanrm9u.txt plain text: cord-016020-awanrm9u.txt item: #105 of 973 id: cord-016073-uhei3bvr author: Belák, Sándor title: Recent Advances in Veterinary Diagnostic Virology: Report from a Collaborating Centre of the World Organization for Animal Health (OIE) date: 2012-04-05 words: 6134 flesch: 38 summary: Of fi ce International desEpizooties (OIE), manual of diagnostic tests and vaccines for terrestrial animals (mammals Advances in viral disease diagnostic and molecular epidemiological techniques DNA enrichment by functionalized magnetic nanoparticles for onsite and fast detection of virus in biomedical application Evaluation of automated nucleic acid extraction methods for virus detection in a multiCentre comparative trial Real time quantitative PCR Molecular diagnosis of viral diseases, present trends and future aspects: a view from the OIE Collaborating Centre for the application of polymerase chain reaction methods for diagnosis of viral diseases in veterinary medicine Pan-serotypic detection of foot and mouth disease virus using a minor-groove binder probe reverse transcription polymerase chain reaction assay Validation of a loop-mediated isothermal ampli fi cation assay for visualised detection of wild-type classical swine fever virus Development of a loop-mediated isothermal ampli fi cation for visual detection of the HCLV vaccine against classical swine fever in China A one-step reverse transcriptase loop-mediated isothermal ampli fi cation assay for simple and rapid detection of swine vesicular disease virus An avirulent chimeric pestivirus with altered cell tropism protects pigs against lethal infection with classical swine fever virus CP7_E2alf: a safe and ef fi cient marker vaccine strain for oral immunisation of wild boar against classical swine fever virus (CSFV) The research activities at our Collaborating Centre aimed to develop real-time PCR assays for diagnostics to differentiate infected from vaccinated animals (DIVA), for speci fi c detection of emerging viruses, and for detection of zoonotic agents, in particular water-and food borne pathogens. keywords: assay; cation; detection; disease; novel; pathogens; pcr; samples; speci; time; veterinary; virus cache: cord-016073-uhei3bvr.txt plain text: cord-016073-uhei3bvr.txt item: #106 of 973 id: cord-016144-280kwlev author: Maan, Sushila title: Novel Molecular Diagnostics and Therapeutic Tools for Livestock Diseases date: 2018-04-26 words: 6527 flesch: 39 summary: In multiplex PCR the design of various primer pairs is crucial so that they complementarily anneal to specific DNA sequences at more or less similar temperatures, i.e. annealing temperature should be the same for different primer pairs used in combination. This is to avoid false positive results from contaminating DNA from previous PCR reactions (Raoult et al. 2000) . keywords: amplification; detection; diagnosis; disease; dna; et al; method; nucleic; pathogens; pcr; primer; rna; sequencing; target; virus cache: cord-016144-280kwlev.txt plain text: cord-016144-280kwlev.txt item: #107 of 973 id: cord-016179-4i1n9j4x author: Chen, Yi-Ning title: Real-Time Reverse Transcription-Polymerase Chain Reaction for Detection and Quantitation of Turkey Coronavirus RNA in Feces and Intestine Tissues date: 2015-09-10 words: 2085 flesch: 54 summary: In step 2, TCoV RNA was extracted from feces using QIAamp viral RNA mini kit or intestine tissues using RNAeasy mini kit. In this chapter, the protocol for one-step real-time RT-PCR to detect, differentiate, and quantitative TCoV RNA in the feces and intestinal tissue is presented. keywords: pcr; rna; tcov; time; turkey cache: cord-016179-4i1n9j4x.txt plain text: cord-016179-4i1n9j4x.txt item: #108 of 973 id: cord-016417-3cwwmyv9 author: Sluijter, J. P. G. title: Quantitative Real-Time PCR date: 2006 words: 3111 flesch: 49 summary: PCR amplification of your target DNA will increase the number of probes that hybridize with the complementary template. It is characterized by the point during amplification when the accumulation of PCR product is first detected rather than the amount of PCR product accumulated after a fixed number of cycles. keywords: amplification; dna; fluorescent; pcr; signal; target; time cache: cord-016417-3cwwmyv9.txt plain text: cord-016417-3cwwmyv9.txt item: #109 of 973 id: cord-016499-5iqpl23p author: Mackay, Ian M. title: Rhinoviruses date: 2014-02-27 words: 23417 flesch: 34 summary: ARIs linked to HRV infections are associated with excessive and perhaps inappropriate antibiotic prescribing and with significant direct and indirect healthcare expenditure. ARIs linked to HRV infections are associated with excessive and perhaps inappropriate antibiotic prescribing [ 4 ] and with signifi cant direct and indirect healthcare expenditure [ 5 , 6 ] . keywords: acute; adults; airway; antiviral; ari; asthma; cells; children; cold; culture; defi; detection; disease; exacerbations; host; hrsv; hrv; hrv infection; hrvs; human; identifi; ifn; illness; infection; infl; nasal; pcr; receptor; response; rhinovirus; rna; role; species; studies; study; symptoms; time; tract; type; viruses cache: cord-016499-5iqpl23p.txt plain text: cord-016499-5iqpl23p.txt item: #110 of 973 id: cord-016640-pvlg3nkp author: Baron, Ellen Jo title: Technical and Clinical Niches for Point of Care Molecular Devices date: 2012-04-05 words: 2869 flesch: 37 summary: No molecular test has yet achieved CLIA waived status (although some are being developed for FDA submission), so POC molecular tests are still physician's of fi ce lab or satellite lab tests rather than true bedside methods. Several pathogens can be detected in patient samples using molecular tests within 4 h. However, there are formidable obstacles to moving molecular diagnostics into the POC setting. keywords: assay; detection; fda; methods; patients; pcr; poc; test cache: cord-016640-pvlg3nkp.txt plain text: cord-016640-pvlg3nkp.txt item: #111 of 973 id: cord-016796-g4kqqpy1 author: Bramhachari, Pallaval Veera title: Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges date: 2019-11-05 words: 5647 flesch: 24 summary: Immunofluorescence assay is extensively used for rapid identification of virus infections through detection of virus antigen or virus-specific antibodies in clinical specimens. AuNP-based detection techniques were reported by various groups of clinically relevant viruses with a unique focus on applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats were recently developed (Draz and Shafiee 2018). keywords: antibodies; assay; detection; diagnosis; human; infections; influenza; pcr; rna; sensitivity; time; virus; viruses; zikv cache: cord-016796-g4kqqpy1.txt plain text: cord-016796-g4kqqpy1.txt item: #112 of 973 id: cord-016882-c9ts2g7w author: Ribeiro, Edna title: Viruses Present Indoors and Analyses Approaches date: 2017-06-12 words: 10252 flesch: 32 summary: Presently, numerous valuable cell monolayers are commercially available, and are regularly utilized in clinical laboratories for the diagnosis of virus infections. Respiratory viruses can be transported over considerable distances by air currents and be inhaled, penetrating deep into the respiratory system (Prussin II et al., 2015) . keywords: aerosol; air; cause; children; contact; contamination; disease; droplets; environments; et al; health; human; indoor; infections; influenza; patients; pcr; samples; spread; surfaces; transmission; viruses cache: cord-016882-c9ts2g7w.txt plain text: cord-016882-c9ts2g7w.txt item: #113 of 973 id: cord-017072-qwe1ne3q author: Poritz, Mark A. title: Multiplex PCR for Detection and Identification of Microbial Pathogens date: 2018-11-10 words: 7208 flesch: 36 summary: This has enabled IVD manufacturers to develop broad test panels that include organisms which have not been a part of standard testing protocols because of the technical limitations of existing methods. There are currently three vendors with multiplex blood culture panels that are both FDA-cleared and CE-marked (BioFire Diagnostics; Luminex and Accelerate Diagnostics, Tucson, Arizona), while GenMark (San Diego, California, USA) and Curetis (Holzgerlingen, Germany) have panels that are CE-marked. keywords: blood; culture; filmarray; multiplex; panel; pathogen; patients; pcr; pouch; respiratory; result; test; testing; time; use cache: cord-017072-qwe1ne3q.txt plain text: cord-017072-qwe1ne3q.txt item: #114 of 973 id: cord-017199-dn413uud author: Heineman, M.J. title: 21 Infecties, ziekte en zwangerschap date: 2016 words: 36475 flesch: 54 summary: zijn van de conditie van de foetus. Derhalve is het van belang tijdens een ingreep in de tweede helft van de zwangerschap de foetus door middel van een CTG continu te bewaken en te letten op de positie op de operatietafel. keywords: aan; aan de; aan het; aandoening; aantal; acute; afwijkingen; alleen; als; als een; andere; anemie; antistoffen; behandeling; bekend; besmetting; bestaat; bevalling; bij de; bij deze; bij een; bij het; bij vrouwen; binnen; borstvoeding; buiten de; chronische; dagen; dan; dat; dat de; dat het; de diagnose; de eerste; de foetus; de geboorte; de gevallen; de kans; de laatste; de medicatie; de meeste; de partus; de placenta; de ziekte; de zwangerschap; deze; diabetes; diagnose; diagnostiek; die; dient; dit; door; door een; door het; dosering; drie; echter; een infectie; eerste; en een; en het; ernstige; foetale; foetus; gbs; gebruik; gebruik van; gedurende; geen; gevallen; gevolg; gevolg van; gezien; geïnfecteerd; goed; hebben; heeft; het; het eerste; het kind; het kraambed; hiv; infectie; infectie van; intra; jaar; kan; kan ook; kan worden; kans; kans op; kind; kinderen; klachten; klinische; komen; komt; koorts; kraambed; kunnen; laatste; leiden; leidt; maar; maternale; medicatie; meer; meestal; minder; moeder; moet; mogelijk; na de; naar; nederland; neonatale; niet; nog; omdat; onder; onderzoek; ongeveer; ontstaan; ook; ook bij; ook de; ook een; op de; op een; op het; op te; op van; optreden; optreden van; partus; patiënten; plaats; placenta; post; pregnancy; risico; soms; sprake; sprake van; te worden; tegen; tijdens de; tijdens zwangerschap; toe; tot; tot de; tot een; trimester; trombose; tussen; tussen de; twee; type; uit; uit een; uit het; uteriene; uur; vaak; vaker; van de; van deze; van een; van het; vanwege; veel; verder; verhoogde; veroorzaakt; vindt; virus; voor bij; voor de; voor een; voor het; vooral; voorkeur; voorkomen; vorm; vroeggeboorte; vrouwen; waarbij; waardoor; wanneer; weer; weken; wel; worden; worden door; wordt; wordt bij; wordt de; wordt een; zal; zeer; zich; ziekte; ziekte van; zijn; zijn een; zijn van; zoals; zwangeren; zwangerschap wordt cache: cord-017199-dn413uud.txt plain text: cord-017199-dn413uud.txt item: #115 of 973 id: cord-017331-ru7mvfc0 author: Samanta, Indranil title: Infectious Diseases date: 2017-02-25 words: 37743 flesch: 42 summary: Among different species under the genus Mycoplasma, M. gallisepticum, M. iowae, and M. sturni are associated with pet bird infection. Among the members of family Reoviridae, Orbivirus mostly causes pet bird infection. keywords: acid; amazon; avian; avium; birds; blood; blue; body; borrelia; budgerigars; burgdorferi; cases; cells; chlamydia; crop; days; death; detection; disease; faeces; family; feather; fig; finches; form; growth; host; human; infected; infection; influenza; intestine; isolation; lesions; liver; major; mycobacterium; non; oocysts; oral; organs; parakeets; parrots; passerine birds; pcr; period; pet; pigeons; presence; protein; psittacine; psittacine birds; red; salmonella; samples; signs; species; specific; spleen; spp; symptoms; ticks; tissue; transmission; treatment; tuberculosis; virus; virus infection; water; weight; wild; wnv cache: cord-017331-ru7mvfc0.txt plain text: cord-017331-ru7mvfc0.txt item: #116 of 973 id: cord-017363-dmb42kna author: Vemulapalli, Ramesh title: Real-Time Reverse Transcription Polymerase Chain Reaction for Rapid Detection of Transmissible Gastroenteritis Virus date: 2015-09-10 words: 1071 flesch: 55 summary: Time DNase/RNase-free distilled water Feces samples from suspected pigs RNasin Ribonuclease Inhibitor (Promega) or equivalent mM MgCl 2 solution for PCR (Sigma-Aldrich) or equivalent DNase/RNase-free distilled water μM Forward primer CCA(BHQ1)-3′(FAM, 6-carboxyfl uorescein; BHQ1, black hole quencher 1; Eurofi ns MWG Operon) Real-time PCR machine, such as Smart Cycler II (Cepheid), 7300 Real-Time PCR System (Applied Biosystems), or equivalent PCR reaction tubes suitable for the real-time PCR machine platform Transmissible gastroenteritis Immunity to transmissible gastroenteritis virus and porcine respiratory coronavirus infections in swine Porcine respiratory coronavirus differs from transmissible gastroenteritis virus by a few genomic deletions Respiratory and fecal shedding of porcine respiratory coronavirus (PRCV) in sentinel weaned pigs and sequence of the partial S-gene of the PRCV isolates A real-time TaqMan ® RT-PCR assay with an internal amplifi cation control for rapid detection of transmissible gastroenteritis virus in swine fecal samples Attempted experimental reproduction of porcine periweaning-failure-to-thrive syndrome using tissue homogenates The fi rst case of porcine epidemic diarrhea in Canada A novel watery diarrhea caused by the co-infection of neonatal piglets with Clostridium perfringens type A The presence of PCR inhibitors in the extracted can be monitored by using an internal control ( see Note 2 ). keywords: pcr; tgev; time; tube cache: cord-017363-dmb42kna.txt plain text: cord-017363-dmb42kna.txt item: #117 of 973 id: cord-017543-60q9iecq author: Tian, Wei-Chang title: Microfluidic Applications in Biodefense date: 2008-08-23 words: 16571 flesch: 33 summary: DNA samples were forced onto the surface of the glass capillary using chaotrophic agents, the DNA-coated capillary was then evacuated, and 500 nL of PCR reagents re-filled the tube by capillary action. [37] as a stand-alone, autonomous aerosol detection device. keywords: agents; amplification; analysis; anthracis; applications; array; assays; bacillus; beads; biodefense; capillary; detection; device; dna; electrophoresis; field; identification; immunoassays; methods; microchip; microfluidics; nucleic; pcr; polymerase; preparation; reaction; sample; separations; sequencing; system; target; time; use cache: cord-017543-60q9iecq.txt plain text: cord-017543-60q9iecq.txt item: #118 of 973 id: cord-017600-4e7mw041 author: Pfister, H. -W. title: Infektionen date: 2008 words: 12958 flesch: 35 summary: Die akute Schmerzsymptomatik der klassischen Trias der Neuroborreliose bildet sich sehr rasch zurück, bestehende Paresen brauchen sehr viel länger zur Rückbildung. Stereotaktische oder off ene Biopsien einerseits, die Implantation eines ventrikuloatrialen oder ventrikuloperitonealen Shunts bei Hydrozephalus andererseits sowie die Implantation eines Rickham-oder Ommaya-Reservoirs zur intraventrikulären Medikamentenapplikation sind im keywords: aber; aids; akuten; als; auch; auf; auft; aus; bakteriellen; bei; bereits; besteht; bis; bzw; cerebral; das; dass; defi; dem; der; des; diagnose; die; diff; durch; eine; entzündungen; enzephalitis; erapie; erkrankungen; erreger; fälle; für; hiv; hydrozephalus; häufi; infektion; insbesondere; intrakraniellen; ist; kann; klinischen; kommt; komplikationen; können; liquor; läsionen; malaria; meist; meningitis; mit; mittels; mrt; muss; myelitis; nach; nachweis; neben; neurologische; nicht; nur; oder; patienten; patients; pcr; pleozytose; pml; prognose; sche; sehr; selten; sich; sie; sind; sollte; sowie; spezifi; spinalen; tab; treatment; und; unter; verdacht; verlauf; virus; von; vor; wenn; werden; wird; wochen; während; zeigen; zeigt; zns; zum; zur; über cache: cord-017600-4e7mw041.txt plain text: cord-017600-4e7mw041.txt item: #119 of 973 id: cord-017767-zj1h5ixf author: Shieh, Wun-Ju title: Advanced Pathology Techniques for Detecting Emerging Infectious Disease Pathogens date: 2012-04-05 words: 5250 flesch: 28 summary: Additionally, IHC performed on fi xed tissues can minimize laboratory worker's potential risk of exposure to infectious agents because of the deactivation of pathogens by formalin fi xation. PCR ampli fi cation undoubtedly is the most sensitive method available to detect microbial organisms in tissue specimens and has become a common practice in many pathology laboratories. keywords: diagnosis; ihc; methods; pathogens; pathology; pcr; samples; speci; techniques; tissue; virus cache: cord-017767-zj1h5ixf.txt plain text: cord-017767-zj1h5ixf.txt item: #120 of 973 id: cord-017867-8cn4c6cu author: Collántes-Fernández, Esther title: Trichomonas date: 2017-11-08 words: 24073 flesch: 40 summary: Correlation with time of exposure and with subsequent estrual cycles Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites Trichomonas gallinae in columbiform birds from the Galapagos Islands Trichomoniasis of turkeys Identification of trichomonadid protozoa from the bovine preputial cavity by polymerase chain reaction and restriction fragment length polymorphism typing A reduction in the duration of infection with Tritrichomonas foetus following vaccination in heifers and the failure to demonstrate a curative effect in infected bulls The morphology and incidence of the trichomonads of swine Detection of bovine trichomoniasis with a specific DNA probe and PCR amplification system Characterization of Tritrichomonas foetus antigens by use of monoclonal antibodies Trichomoniasis in Bonelli's eagle nestlings in south-west Portugal Tritrichomonas foetus infection in cats with diarrhoea in a rescue colony in Italy Diagnostic PCR: validation and sample preparation are two sides of the same coin Isolation of Tritrichomonas foetus from cats sampled at a cat clinic, cat shows and a humane society in southern Ontario Detection and identification of Tetratrichomonas in a preputial wash from a bull by PCR and SSCP Development and testing of a bovine trichomoniasis vaccine Bovine vaginal antibody responses to immunoaffinitypurified surface antigen of Tritrichomonas foetus Risk factors associated with bovine trichomoniasis in beef cattle identified by a questionnaire Pentatrichomonas hominis in empyema thoracis The intradermal test in bovine trichomoniasis Bovine trichomoniasis-diagnosis and treatment Comparison of diagnostic methods for detection of active infection with Tritrichomonas foetus in beef heifers Molecular phylogeny of Trichomonadidae family inferred from ITS-1, 5.8S rRNA and ITS-2 sequences Production of ammonia by Tritrichomonas foetus and Trichomonas vaginalis Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, alpha-tubulin and HSP90 genes: implications for the evolutionary history of the double karyomastigont of diplomonads Prevalence of Trichomonas gallinae in northern goshawks from the Berlin area of northeastern Germany Tritrichomonas foetus infection in purebred cats in Germany: prevalence of clinical signs and the role of co-infection with other enteroparasites Investigations of the incidence of bovine trichomoniasis in Nevada and of the efficacy of immunizing cattle with vaccines containing Tritrichomonas foetus Clinical evaluation of the efficacy of inoculating cattle with a vaccine containing Tritrichomonas foetus Evidence of spread of the emerging infectious disease, finch trichomonosis, by migrating birds A pathogenic trichomonas from the upper digestive tract of chickens Tritrichomonas foetus and not Pentatrichomonas hominis is the etiologic agent of feline trichomonal diarrhea In-situ hybridization for the detection and identification of Histomonas meleagridis in tissues Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions A simple and rapid method for staining Tritrichomonas foetus and Trichomonas vaginalis Comparison of growth rates of Tritrichomonas foetus isolates from various geographic regions using three different culture media Are Tritrichomonas foetus and Tritrichomonas suis synonyms? Prevalence of Campylobacter foetus and Trichomonas foetus among cattle from Southern Africa Persistence of Tritrichomonas foetus in naturally infected cows and heifers in Argentina Update on the diagnosis and management of Tritrichomonas foetus infections in cats Risk factors associated with Tritrichomonas foetus infection in beef herds in the Province of Prevalence of bovine venereal disease in the Victoria River District of the Northern Territory: likely economic effects and practicable control measures Improved detection of Tritrichomonas foetus in bovine diagnostic specimens using a novel probe-based real time PCR assay Fine structure of the bird parasites Trichomonas gallinae and Tetratrichomonas gallinarum from cultures High prevalence of Tritrichomonas foetus infection in Asturiana de la Montana beef cattle kept in extensive conditions in northern Spain Differences in the prevalence of Tritrichomonas foetus infection in beef cattle farmed under extensive conditions in northern Spain A review of sexually transmitted bovine trichomoniasis and campylobacteriosis affecting cattle reproductive health Spatial and temporal epidemiology of bovine trichomoniasis and bovine genital campylobacteriosis in La Pampa province (Argentina) Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification Host origin determines pH tolerance of Tritrichomonas foetus isolates from the feline gastrointestinal and bovine urogenital tracts Comparative RNA-seq analysis of the Tritrichomonas foetus PIG30/1 isolate from pigs reveals close association with Tritrichomonas foetus BP-4 isolate 'bovine genotype Investigations on the prevalence and potential pathogenicity of intestinal trichomonads in pigs using in situ hybridization Detection of Tritrichomonas foetus and Pentatrichomonas hominis in intestinal tissue specimens of cats by chromogenic in situ hybridization High prevalence of Tritrichomonas foetus 'bovine genotype' in faecal samples from domestic pigs at a farm where bovine trichomonosis has not been reported for over 30 years Evaluation of a PCR test for the diagnosis of Tritrichomonas foetus infection in bulls: effects of sample collection method, storage and transport medium on the test In vivo and in vitro sensitivity of Trichomonas gallinae to some nitroimidazole drugs Field and laboratory observations on trichomoniasis of dairy cattle in Victoria Pathologic changes in pigeons infected with a virulent Trichomonas gallinae strain (Eiberg) First report of epizootic trichomoniasis in wild finches (family Fringillidae) in southern Fennoscandia Tritrichomonas foetus prevention and control in cattle Obtención de muestras prepuciales para el diagnóstico de Tritrichomonas foetus porraspado de mucosas The prevalence of intestinal protozoa in wild and domestic pigs Enteropathogen co-infection in UK cats with diarrhoea Comparison of two sampling tools for diagnosis of Tritrichomonas foetus in bulls and clinical interpretation of culture results Application of a PCR assay to enhance the detection and identification of Tritrichomonas foetus in cultured preputial samples Comparison of the diagnostic sensitivity of a commercially available culture kit and a diagnostic culture test using Diamond's media for diagnosing Tritrichomonas foetus in bulls Sample collection factors affect the sensitivity of the diagnostic test for Tritrichomonas foetus in bulls The pathogenesis of Tritrichomonas foetus infection in the bull Early pathogenesis and pathology of Tritrichomonas foetus infection in virgin heifers Tritrichomonas foetus: budding from multinucleated pseudocysts Prevalence and risk-factors for Trichomonas-fetus infection in cattle in northeastern Costa-Rica Bayesian estimation of Tritrichomonas foetus diagnostic test sensitivity and specificity in range beef bulls Clinical and microbiological aspects of Trichomonas vaginalis The demonstration of an agglutinin to Trichomonas foetus in the vaginal discharge of infected heifers The mucus agglutination test for the diagnosis of bovine trichomoniasis Prevalence of Tritrichomonas foetus infections in French catteries Prevalence of selected bacterial and parasitic agents in feces from diarrheic and healthy control cats from northern California Impact of trichomoniasis on the cow-calf producer's profitability Tritrichomonas foetus Prevalence of Tritrichomonas fetus in a bull population and effect on production in a large cow-calf enterprise Epidemiology of Tritrichomonas foetus in beef bull populations in Florida Some observations on cultural and transport conditions for Tritrichomonas foetus var. keywords: amin et; birds; bondurant; bondurant et; bovine; bulls; cats; cattle; cows; culture; detection; diagnostic; disease; et al; feline; foetus; foetus infection; gallinae; gookin et; herds; infection; medium; number; parasite; pcr; positive; risk; samples; sensitivity; skirrow; studies; t. foetus; test; transmission; trichomonads; trichomonosis; tritrichomonas; tritrichomonas foetus cache: cord-017867-8cn4c6cu.txt plain text: cord-017867-8cn4c6cu.txt item: #121 of 973 id: cord-017894-8iahlshj author: Loa, Chien Chang title: A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus date: 2015-09-10 words: 1309 flesch: 46 summary: On the other hand, IBV-positive result is able to exclude the presence of TCoV. Coronaviral enteritis of turkeys (blue comb disease) Coronavirus immunogens Antigenic characterization of a turkey coronavirus identifi ed in poult enteritis and mortality syndrome-affected turkeys Phylogenetic analysis of a highly conserved region of the polymerase gene from 11 coronaviruses and development of a consensus polymerase chain reaction assay Sequence analysis of the matrix/nucleocapsid gene region of turkey coronavirus Sequence analysis of the turkey coronavirus nucleocapsid protein gene and 3′ untranslated region identifi es the virus as a close relative of infectious bronchitis virus Detection of antibody to turkey coronavirus by antibodycapture enzyme-linked immunosorbent assay utilizing infectious bronchitis virus antigen Nucleocapsid protein gene sequence analysis reveals close genomic relationship between turkey coronavirus and avian infectious bronchitis virus Experimental bovine coronavirus in turkey poults and young chickens Antigenic and genomic relationships among turkey and bovine enteric coronaviruses Sequence analysis of the turkey enteric coronavirus nucleocapsid and membrane protein genes: a close genomic relationship with bovine coronavirus Complete sequences of 3′end coding region for structural protein genes of turkey coronavirus Comparison of 3′ end encoding regions of turkey coronavirus isolates from Indiana, North Carolina, and Minnesota Complete nucleotide sequence of polyprotein gene 1 and genome organization of turkey coronavirus Differential detection of turkey coronavirus, infectious bronchitis virus, and bovine coronavirus by a multiplex polymerase chain reaction Redesign of primers and application of the reverse transcriptase-polymerase chain reaction and restriction fragment length polymorphism test to the DE072 strain of infectious bronchitis virus The protocol A multiplex polymerase chain reaction for differential detection of turkey coronavirus from chicken infectious bronchitis virus and bovine coronavirus outlined in this chapter had been successfully carried out in the authors' studies on molecular diagnostics and molecular virology of turkey coronavirus infection in turkeys. key: cord-017894-8iahlshj authors: Loa, Chien Chang; Wu, Ching Ching; Lin, Tsang Long title: A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus date: 2015-09-10 journal: Animal Coronaviruses DOI: 10.1007/978-1-4939-3414-0_12 sha: doc_id: 17894 cord_uid: 8iahlshj A multiplex polymerase chain reaction (PCR) method for differential detection of turkey coronavirus (TCoV), infectious bronchitis virus (IBV), and bovine coronavirus (BCoV) is presented in this chapter. keywords: coronavirus; pcr; tcov; turkey cache: cord-017894-8iahlshj.txt plain text: cord-017894-8iahlshj.txt item: #122 of 973 id: cord-017948-fqhl1qb4 author: Hu, Yuan title: Molecular Techniques for Blood and Blood Product Screening date: 2012-04-05 words: 7305 flesch: 51 summary: Diagnosis depends upon fi nding parasites on blood fi lm examination which can be detected 2-4 weeks after a tick bite. Detection of early HBV infection of blood donors is still a major problem of blood transfusion. keywords: blood; cation; detection; disease; dna; hcv; hepatitis; infection; pcr; safety; screening; tests; transfusion; virus cache: cord-017948-fqhl1qb4.txt plain text: cord-017948-fqhl1qb4.txt item: #123 of 973 id: cord-017959-g0nf1iwm author: Lipkin, W. Ian title: Diagnosis, Discovery and Dissection of Viral Diseases date: 2014-02-27 words: 5018 flesch: 27 summary: The pause on Avian H5N1 infl uenza virus transmission research should be ended The changing face of pathogen discovery and surveillance Rethinking biosafety in research on potential pandemic pathogens Diagnosis of herpes simplex encephalitis with PCR Evaluation of immunoglobulin M (IgM) and IgG enzyme immunoassays in serologic diagnosis of West Nile Virus infection NS1 protein secretion during the acute phase of West Nile virus infection Asymptomatic circulation of HEV71 in Norway Loop-mediated isothermal amplification of DNA Loop-mediated isothermal amplifi cation method for detection of human papillomavirus type 6, 11, 16, and 18 Diagnosis of human respiratory syncytial virus infection using reverse transcription loopmediated isothermal amplifi cation Loop-mediated isothermal amplifi cation for infl uenza A (H5N1) virus. In current array platforms, virus detection is achieved via fl uorescent reporter systems-either through direct incorporation of fl uorescent nucleotides into the PCR product that is bound to the array or with a sandwich approach whereby fl uorescent-branched chains of DNA are added to the product after it is bound to the array [ 75 , 76 ] . keywords: assays; cation; detection; diagnosis; disease; human; infection; infl; pathogens; pcr; rhinovirus; uenza; virus; viruses cache: cord-017959-g0nf1iwm.txt plain text: cord-017959-g0nf1iwm.txt item: #124 of 973 id: cord-017984-w19kd6yp author: Chen, Yi-Ning title: PCR Amplification and Sequencing Analysis of Full-Length Turkey Coronavirus Spike Gene date: 2015-09-10 words: 1711 flesch: 50 summary: A protocol for PCR amplifi cation, sequencing , and sequence analysis of TCoV S gene for genotyping of TCoV isolates based on TCoV S gene sequences is highlighted in this chapter. 1. Assemble 12 nucleotide sequences from 12 sequencing primers (Table 1 ) to obtain the full length of TCoV S gene by using DNAstar Lasergene ® software. keywords: alignment; coronavirus; gene; tcov; turkey cache: cord-017984-w19kd6yp.txt plain text: cord-017984-w19kd6yp.txt item: #125 of 973 id: cord-018721-othar2uv author: Schwab, Stefan title: Infektionen date: 2012-03-17 words: 13437 flesch: 30 summary: Die Letalität einer manifesten Erkrankung beträgt beim westlichen Erregersubtyp 1−2 % (bei der myelitischen Neben einem entzündlich veränderten Liquor mit lymphozytärer Pleozytose von einigen 100 Zellen, Eiweißvermehrung und Glucosereduktion fi nden sich bei der Diagnostik chronischer Meningitiden häufi g Allgemeinveränderungen in der EEG-Untersuchung. keywords: abscess; acute; adults; aids; als; auch; auf; aus; bacterial; bakteriellen; bei; bis; brain; bzw; case; cerebral; children; clinical; complications; das; dass; dem; der; des; diagnosis; die; diff; disease; durch; eine; encephalitis; erapie; erkrankung; erreger; fungal; fälle; für; herpes; hiv; human; häufi; infektion; ist; kann; klinische; komplikationen; können; liquor; läsionen; malaria; management; meist; meningitis; mit; mittels; mrt; muss; myelitis; nach; nachweis; nden; neben; nicht; nipah; nur; oder; patienten; patients; pcr; regel; report; review; sein; sich; sie; sind; sollte; sowie; spezifi; study; system; therapie; therapy; treatment; und; verlauf; virus; von; vor; werden; wird; wochen; wurde; zns; zum; zur; über cache: cord-018721-othar2uv.txt plain text: cord-018721-othar2uv.txt item: #126 of 973 id: cord-018848-6kemhsyu author: Stürenburg, Enno title: Mikrobiologische Schnelltests und molekularbiologische Analytik date: 2011-12-17 words: 1268 flesch: 26 summary: Bei Fragestellungen, die weniger zeitkritisch sind, dürfte ein kultureller Nachweis in einem mikrobiologischen Labor vor allem angesichts der mit der PCR-Technik verbundenen höheren Kosten (derzeit 30-40 € pro Test) weiterhin Standard bleiben. Ein weiteres Beispiel für einen Multiplex-Test ist der Clostridium difficile-Nachweis, der nicht nur das Bakterium selbst erkennt, sondern außerdem den »hypervirulenten« Stamm NAP1/O27 identifizieren kann. keywords: auf; den; der; die; einem; für; ist; mit; pcr; sind; tests; und; von; werden cache: cord-018848-6kemhsyu.txt plain text: cord-018848-6kemhsyu.txt item: #127 of 973 id: cord-018865-melttpiq author: Yu, Tian-fei title: Express Transmissible Gastroenteritis Virus Spike Gene B and C Antigen Sites in Multiple Expression Systems date: 2012 words: 2194 flesch: 46 summary: Although site B is conformation dependent, MAbs specific for this site can bind TGEV spike protein by immunoblotting providing that the samples were not treated with 2-mercaptoethanol. It is recognized by MAbs in Western blot analysis after treatment of the virus with 2.5% SDS and 5% 2-mercaptoethanol; It is represented by synthetic nonapeptides derived from TGEV spike protein [9] ; It is present in recombinant products expressed in bacteria, which do not reconstitute the native spike protein [10] ; and it is formed in the absence of glycosylation [8] . keywords: gastroenteritis; protein; recombinant; sites; tgev; transmissible; virus cache: cord-018865-melttpiq.txt plain text: cord-018865-melttpiq.txt item: #128 of 973 id: cord-018944-du42ho11 author: Shin, Jeong Hwan title: Nucleic Acid Extraction and Enrichment date: 2018-11-10 words: 6858 flesch: 38 summary: Philadelphia: F.A. Davis Molecular cloning: A laboratory manual Comparison of different methods of isolation of DNA of commonly encountered Candida species and its quantitation by using a real-time PCR-based assay Correlates of quantitative measurement of BK polyomavirus (BKV) DNA with clinical course of BKV infection in renal transplant patients A solid-phase extraction procedure for DNA purification Detection of microorganisms in vessel wall specimens of the abdominal aorta: development of a PCR assay in the absence of a gold standard Current nucleic acid extraction methods and their implications to point-of-care diagnostics RNA purification and analysis; Sample preparation, extraction, chromatography The effect of metal ions on the activity and thermostability of the extracellular proteinase from a thermophilic Bacillus, strain EA.1 Comparison of commercial DNA extraction kits for extraction of bacterial genomic DNA from whole-blood samples Evaluation of LightCycler PCR for implementation of laboratory diagnosis of herpes simplex virus infections Diagnosis of herpes simplex virus infections in the clinical laboratory by LightCycler PCR Comparison of the Roche LightCycler vanA/vanB detection assay and culture for detection of vancomycin-resistant enterococci from perianal swabs Automated extraction of viral-pathogen RNA and DNA for high-throughput quantitative real-time PCR Comparison of automated nucleic acid extraction methods with manual extraction Monitoring transplant patients for human cytomegalovirus: diagnostic update Comparison of methods for extraction of viral DNA from cellular specimens Comparison of the NucliSENS easyMAG and Qiagen BioRobot 9604 nucleic acid extraction systems for detection of RNA and DNA respiratory viruses in nasopharyngeal aspirate samples Evaluation of NucliSENS easyMAG for automated nucleic acid extraction from various clinical specimens Comparison of two highly automated DNA extraction systems for quantifying Epstein-Barr virus in whole blood Severe acute respiratory syndrome (SARS) Laboratory diagnosis of SARS Multicenter comparison of nucleic acid extraction methods for detection of severe acute respiratory syndrome coronavirus RNA in stool specimens Improved amplification of microbial DNA from blood cultures by removal of the PCR inhibitor sodium polyanetholesulfonate A simple and sensitive method to extract bacterial, yeast and fungal DNA from blood culture material Hydrogen peroxide improves the efficiency of a peripheral blood PCR assay for diagnosis of human brucellosis Serum is the preferred clinical specimen for diagnosis of human brucellosis by PCR Comparison of seven commercial DNA extraction kits for the recovery of Brucella DNA from spiked human serum samples using real-time PCR Real-time PCR of the 16S-rRNA gene in the diagnosis of neonatal bacteraemia Molecular detection and identification of Candida and Aspergillus spp. The method for the nucleic acid extraction can be divided into manual or automated, and this is an important point in the classification of nucleic acid extraction methods. keywords: acid; blood; detection; dna; extraction; kits; method; nucleic; pcr; rna; specimens; time cache: cord-018944-du42ho11.txt plain text: cord-018944-du42ho11.txt item: #129 of 973 id: cord-019490-m1cuuehi author: None title: Abstracts cont. date: 2015-12-28 words: 93719 flesch: 45 summary: Mean age (78 vs 77), Charlson score (2.5 vs. 2.6), neoplasm (22% vs. 21%), HIV (0.7% vs. 0.8%), chronic liver disease (9% vs.7%), diabetes mellitus ( 19% vs.22%), ICU admission (4% vs. 4%), monotherapy (63% vs. 66%), and aetiology (S. pneumoniae 34% vs. 36%; L. pneumophila 3% vs.2%; others 8% vs.11%; unknown 54% vs.51%) were similar. The same was found for mecillinam, i.e. no correlation for AUC/MIC vs. CFÚ s in urine or organs, while Time > MIC % significantly (P < 0.05) correlated with CFÚ s in urine (R 2 = 0.48), and kidney tissue (R 2 = 0.82), respectively. keywords: activity; aeruginosa; agar; agents; aim; analysis; anthrax; antibiotics; antimicrobial; assay; associated; aureus; bacteria; blood; broth; cases; ciprofloxacin; clinical; coli; concentrations; conclusions; control; data; days; detection; diagnosis; disease; dose; drug; effect; erythromycin; gene; gram; grn; group; hospital; hours; human; imipenem; infections; isolates; laboratory; levofloxacin; linezolid; low; mcg; mean; methicillin; methods; mic; mic90; mics; moxifloxacin; mrsa; mrsa strains; nccls; negative; new; non; objectives; oral; pathogens; patients; pcr; penicillin; period; pfge; phenotype; plasma; pneumoniae; population; positive; presence; prevalence; pylori; rates; resistance; results; risk; s. aureus; samples; serum; single; skin; species; spectrum; spp; staphylococcus; strains; studies; study; subjects; susceptibility; susceptible; tested; testing; therapy; tigecycline; time; tissue; total; tract; treatment; type; use; values; vancomycin; vitro; water; years cache: cord-019490-m1cuuehi.txt plain text: cord-019490-m1cuuehi.txt item: #130 of 973 id: cord-020568-c5425959 author: Blatny, Janet Martha title: Detecting and Responding to Bioterrorism date: 2007 words: 3482 flesch: 37 summary: Many experts believe that biological threat agents may be more useful for obtaining panic and anxiety causing serious psychological impact instead of resulting in high preserved tissue samples Few companies check and compare the ordered sequences against sequences from biological threat agents and there are no national regulations requiring these firms to do so. keywords: agents; air; anthracis; bioterrorism; detection; identification; methods; pcr; threat; use cache: cord-020568-c5425959.txt plain text: cord-020568-c5425959.txt item: #131 of 973 id: cord-020954-mt8mm7y4 author: Relich, Ryan F. title: Syndromic and Point-of-Care Molecular Testing date: 2018-10-10 words: 5347 flesch: 29 summary: 1 1 1 À 1 1 1 1 1 1 1 1 À 1 1 1 1 1 1 1 1 1 1 1 À 1 BioThreat Panel a À 1 1 1 À 1 1 À À 1 1 1 À À À 1 1 À 1 1 À À 1 1 1 À 1 À À À c À À À À À À À À 1 À À À À À À À À À À À À À À À À À À À FilmArray Global Fever ePlex RP 1 1 À À À À/À 1 1 1 1 1 1 À 1 À 1 1 1 1 1 1 1 À 1 1 1 eSensor RVP 1 1 1 À À À À À À À À 1 c À 1 À 1 1 1 À 1 1 1 À À 1 1 FilmArray RP Panel 1 1 À À À 1/À 1 1 1 1 1 1 À 1 À 1 1 1 1 1 1 1 À 1 1 À FilmArray RP2 Panel 1 1 À À À 1/1 1 1 1 1 1 1 À 1 À 1 1 1 1 1 1 1 À 1 1 À FilmArray RP EZ a 1 1 À À À 1/À 1 1 1 1 1 1/1 À 1 À 1 1 1 1 1 1 1 À 1 1 À NxTAG RPP b 1 1 À À À À/À 1 1 1 1 1 1 1 1 À 1 1 1 1 1 1 1 À À 1 1 VERIGENE RP Flex b 1 1 À 1 1 1/1 À À À À À 1 c À 1 À 1 1 1 1 1 1 1 À À 1 1 keywords: assays; culture; detection; filmarray; methods; multiplex; panel; pathogens; pcr; performance; respiratory; system; testing; time cache: cord-020954-mt8mm7y4.txt plain text: cord-020954-mt8mm7y4.txt item: #132 of 973 id: cord-021052-qydc404w author: Fernandez-Flores, Angel title: Aportaciones de la anatomía patológica en el diagnóstico de las infecciones cutáneas: una perspectiva histórica date: 2015-11-02 words: 4485 flesch: 41 summary: Por el contrario, el nuevo avance en el diagnó stico de enfermedades infecciosas llegó de la mano de la reacció n en cadena de la polimerasa (PCR), que permitía diagnó sticos certeros del germen causante, incluso con estudios sobre susceptibilidades a antibió ticos. En 1893 Guarneri describió los cuerpos de inclusió n de la viruela y de la viruela de vaca 12 y en 1904, Mallory describió los de la fiebre escarlata en autopsias 13 , mientras que tan solo un añ o má s tarde, Field W. Cyrus los aislaría directamente de ampollas, ilustrando su artículo con bellos dibujos a color 14 . keywords: carcinoma; cell; cnicas; como; con; del; diagnó; era; este; fue; herpesvirus; inmunohistoquímica; kaposi; las; los; merkel; microorganismos; para; pcr; polyomavirus; por; que; sarcoma; sin; stico; una; virus cache: cord-021052-qydc404w.txt plain text: cord-021052-qydc404w.txt item: #133 of 973 id: cord-021402-wq770ik9 author: Relford, Roberta L. title: New Diagnostic Tools for Infectious Disease date: 2009-05-15 words: 3167 flesch: 32 summary: The main limitation of using antibody detection for diagnosis is that, in most diseases, the presence of antibody against an infectious agent cannot differentiate among patients with previous exposure having lingering antibodies, patients with current active infection, or patients with antibodies generated by previous vaccination. This severely limits the utility of FIV antibody detection in FIV-vaccinated cats. keywords: antibodies; antibody; antigen; assays; detection; organism; pcr; serum cache: cord-021402-wq770ik9.txt plain text: cord-021402-wq770ik9.txt item: #134 of 973 id: cord-021596-5s8lksxp author: Colegrove, Kathleen M. title: Pinnipediae date: 2018-10-26 words: 10419 flesch: 34 summary: Hormone induced morphologic changes are noted in the reproductive tract during different periods of the reproductive cycle and have been reviewed in CSLs by Colegrove et al. (2009c) . Alterations in p53, the heparanase 2 (HPSE2) gene, endogenous hormones, and contaminants that interact with steroid hormone receptor have all been postulated as other potential factors involved in UGC (Browning et al., 2015; Colegrove et al., 2009b) . keywords: acid; animals; california; california sea; californianus; csls; disease; et al; exposure; fig; fur; harbor; infection; lesions; lions; mammals; marine; pcr; phoca; pinnipeds; ranging; seals; species; virus; vitulina; zalophus cache: cord-021596-5s8lksxp.txt plain text: cord-021596-5s8lksxp.txt item: #135 of 973 id: cord-021772-5v4gor2v author: Levine, Gwendolyn J. title: Cerebrospinal Fluid and Central Nervous System Cytology date: 2019-05-31 words: 12659 flesch: 41 summary: 10, 20 Approximately 80% to 95% of CSF protein is albumin, and 5% to 12% of CSF total protein comprises gammaglobulins. 20 Increased bilirubin leakage into the SAS or high concentrations of CSF protein (>100-150 mg/dL) may cause xanthrochromia. keywords: analysis; canine; cases; cats; cells; cns; concentration; csf; diagnosis; disease; dogs; fluid; neutrophilic; pleocytosis; protein; samples; spinal; study cache: cord-021772-5v4gor2v.txt plain text: cord-021772-5v4gor2v.txt item: #136 of 973 id: cord-022034-o27mh4wz author: OLANO, JUAN P. title: Distinguishing Tropical Infectious Diseases from Bioterrorism date: 2009-05-15 words: 10732 flesch: 36 summary: Shigella is a highly infectious organism that requires very low numbers (10 2 -10 3 organisms) to provoke clinical disease. They include presence of disease outbreaks of the same illness in noncontiguous areas, disease outbreaks with zoonotic impact, different attack rates in different environments (indoor versus outdoor), presence of large epidemics in small populations, increased number of unexplained deaths, unusually high severity of a disease for a particular pathogen, unusual clinical manifestations owing to route of transmission for a given pathogen, presence of a disease (vector-borne or not) in an area not endemic for that particular disease, multiple epidemics with different diseases in the same population, a case of a disease by an uncommon agent (smallpox, viral hemorrhagic fevers, inhalational anthrax), unusual strains of microorganisms when compared to conventional strains circulating in the same affected areas, and genetically homogenous organisms isolated from different locations. keywords: agents; anthrax; attack; cases; detection; diagnosis; disease; fever; hemorrhagic; human; infections; isolation; laboratory; manifestations; outbreak; patients; pcr; smallpox; techniques; time; toxin; virus cache: cord-022034-o27mh4wz.txt plain text: cord-022034-o27mh4wz.txt item: #137 of 973 id: cord-022053-idft1p6d author: Pecora, Nicole title: New Technologies for the Diagnosis of Infection date: 2017-07-21 words: 11502 flesch: 32 summary: RVP fast multiplex assays for detection of respiratory viruses Phylogenetic structure of the prokaryotic domain: the primary kingdoms Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology Interpretive Criteria for Identification of Bacteria and Fungi by DNA Target Sequencing; Approved Guideline Broad-range 16S rRNA gene polymerase chain reaction for diagnosis of culturenegative bacterial infections Utility of 16S rDNA sequencing for identification of rare pathogenic bacteria Identification of bacteria in formalin-fixed, paraffin-embedded heart valve tissue via 16S rRNA gene nucleotide sequencing 16S rRNA sequencing in routine bacterial identification: a 30-month experiment Improved diagnosis of mycobacterial infections in formalin-fixed and paraffin-embedded sections with nested polymerase chain reaction Rapid real-time PCR for detection of Mycobacterium tuberculosis complex DNA in formalin-fixed paraffin embedded tissues: 16% of histological 'sarcoid' may contain such DNA Broad-range PCR and sequencing in routine diagnosis of infective endocarditis Duration of hypotension before initiation of effective antimicrobial therapy is the critical determinant of survival in human septic shock Emerging technologies for rapid identification of bloodstream pathogens ID learning unit-diagnostics update: current laboratory methods for rapid pathogen identification in patients with bloodstream infections Nonculture techniques for the detection of bacteremia and fungemia an automated nested multiplex PCR system for multi-pathogen detection: development and application to respiratory tract infection Multicenter evaluation of the BioFire FilmArray gastrointestinal panel for etiologic diagnosis of infectious gastroenteritis Comparative evaluation of two commercial multiplex panels for detection of gastrointestinal pathogens by use of clinical stool specimens Spectrum of enteropathogens detected by the FilmArray GI panel in a multicentre study of community-acquired gastroenteritis Multi-center clinical evaluation of a multiplex meningitis/encephalitis PCR panel for simultaneous detection of bacteria, yeasts and viruses in cerebrospinal fluid specimens General Meeting Enhancing pathogen identification in patients with meningitis and a negative Gram stain using the BioFire FilmArray((R)) Species identification of clinical isolates of Bacteroides by matrixassisted laser-desorption/ionization time-of-flight mass spectrometry Performance of MALDI-TOF MS platforms for fungal identification MALDI-TOF mass spectrometry proteomic phenotyping of clinically relevant fungi Improved clinical laboratory identification of human pathogenic yeasts by matrix-assisted laser desorption ionization time-offlight mass spectrometry Comparison of the accuracy of two conventional phenotypic methods and two MALDI-TOF MS systems with that of DNA sequencing analysis for correctly identifying clinically encountered yeasts Comparative evaluation of the Bruker Biotyper and Vitek MS matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry systems for identification of yeasts of medical importance Interlaboratory comparison of sample preparation methods, database expansions, and cutoff values for identification of yeasts by matrix-assisted laser desorption ionization-time of flight mass spectrometry using a yeast test panel Clinical performance evaluation of the Sofia RSV FIA rapid antigen test for diagnosis of respiratory syncytial virus infection Serological markers in early stages of human immunodeficiency virus infection in haemophiliacs Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology Matrix-assisted laser desorption ionization-time of flight mass spectrometry in clinical microbiology MS for the diagnosis of infectious diseases A side by side comparison of Bruker Biotyper and VITEK MS: utility of screening methods and matrix-assisted laser desorption ionizationtime of flight mass spectrometry Direct identification of urinary tract pathogens from urine samples using the Vitek MS system based on matrix-assisted laser desorption ionization-time of flight mass spectrometry Mass spectrometry: pneumococcal meningitis verified and Brucella species identified in less than half an hour Direct application of MALDI-TOF mass spectrometry to cerebrospinal fluid for rapid pathogen identification in a patient with bacterial meningitis Sample preparation for mass spectrometry analysis of formalin-fixed paraffin-embedded tissue: proteomic analysis of formalin-fixed tissue Urinary pellet sample preparation for shotgun proteomic analysis of microbial infection and host-pathogen interactions PNA for rapid microbiology Peptide nucleic acid fluorescence in situ hybridization for rapid detection of Klebsiella pneumoniae from positive blood cultures Direct identification of major blood culture pathogens, including Pseudomonas aeruginosa and Escherichia coli, by a panel of fluorescence in situ hybridization assays using peptide nucleic acid probes Rapid identification of Staphylococcus aureus directly from blood cultures by fluorescence in situ hybridization with peptide nucleic acid probes Rapid detection of Enterococcus spp. keywords: analysis; assays; bacterial; biotyper; detection; evaluation; identification; ionization; isolates; laser; maldi; mass; organisms; panel; pathogens; pcr; performance; rapid; sequencing; species; spectrometry; system; time; vitek cache: cord-022053-idft1p6d.txt plain text: cord-022053-idft1p6d.txt item: #138 of 973 id: cord-022084-hap7flng author: ARRUDA, EURICO title: Respiratory Tract Viral Infections date: 2009-05-15 words: 19198 flesch: 38 summary: Although a HMPV vaccine is not available at this time, the demonstration that hamsters, ferrets, and African green monkeys are susceptible to infection by HMPV, and that hamsters vaccinated with serotype A The epidemiology of acute respiratory tract infection in young children: Comparison of findings from several developing countries Report of a workshop on respiratory viral infections: Epidemiology, diagnosis, treatment and prevention Acute respiratory viral infections in ambulatory children of urban northeast Brazil Longitudinal studies of infectious diseases and physical growth of infants in Huascar, an underprivileged peri-urban community in At the edge of Development: Health Crises in a Transitional Society Epidemiology of acute respiratory infections in children of developing countries Pan American Health Organization: Acute respiratory infections in the Americas The magnitude of mortality from acute respiratory infections in children under 5 years in developing countries Acute lower respiratory tract infections in hospitalized patients with diarrhea in Dhaka Day-care center attendance and hospitalization for lower respiratory tract illness Viral respiratory infections in young children attending day care in urban Northeast Brazil Epidemiology and seasonality of respiratory tract virus infections in the tropics The cultural context of breastfeeding: Perspectives on the recent decline in breast-feeding in Northeast and Northcentral Brazil Reduced mortality among children in Southern India receiving a small weekly dose of vitamin A Search for a solution: Blending oral rehydration therapy (ORT) and popular medicine Pathogenesis of respiratory infections due to influenza virus: Implications for developing countries Respiratory viruses predisposing to bacterial infections: Role of neuraminidase Influenza: Emergence and control Orthomyxoviridae: The viruses and their replication Influenza virus Viral vaccines for the prevention of childhood pneumonia in developing nations: Priorities and prospects The effect of influenza on hospitalizations, outpatient visits, and courses of antibiotics in children Etiology of acute respiratory infections in children in tropical southern India A community-based study of acute respiratory tract infection in Thai children Etiology of acute lower respiratory tract infection in children from Alabang, Metro Manilla Outbreak of influenza type A (H1N1) in Iporanga Antigenic and genomic relation between human influenza viruses that circulated in Argentina in the period 1995-1999 and the corresponding vaccine components Regional perspectives on influenza surveillance in Africa H5N1 influenza: A protean pandemic threat Influenza type A and B infections in hospitalized pediatric patients Influenza viruses, cell enzymes, and pathogenicity Detection of influenza virus by centrifugal inoculation of MDCK cells and staining with monoclonal antibodies Rapid detection and simultaneous subtype differentiation of influenza A viruses by real time PCR Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 Rational design of potent sialidase-based inhibitors of influenza virus replication Efficacy and safety of the neuraminidase inhibitor zanamivir in the treatment of influenzavirus infections Resistant influenza 31 Up to 50% of influenza virus infections in adults are subclinical. keywords: acute; adults; age; cause; cell; children; clinical; cov; days; detection; disease; hcov; hmpv; hrv; human; illness; infants; infections; influenza; patients; pcr; rna; rsv; sars; studies; tract; tropical; vaccine; virus; viruses; years cache: cord-022084-hap7flng.txt plain text: cord-022084-hap7flng.txt item: #139 of 973 id: cord-022310-yc6xtw0s author: Lappin, Michael R. title: Microbiology and Infectious Disease date: 2011-12-15 words: 14122 flesch: 35 summary: In cats, the combination of serum antigen test results with serum antibody test results is more sensitive than performing either test alone (see Heartworm Antibody Titer, next). In addition, positive serum antibody tests do not document infection by R. rickettsii because infection with nonpathogenic spotted fever group agents induce cross-reacting antibodies. keywords: analysis; antibodies; antibody; assay; blood; cats; culture; diagnosis; disease; dogs; elisa; feline; infection; interpretation; negative; organism; pcr; results; serum; spp; test; titers cache: cord-022310-yc6xtw0s.txt plain text: cord-022310-yc6xtw0s.txt item: #140 of 973 id: cord-022501-9wnmdvg5 author: None title: P1460 – P1884 date: 2015-12-28 words: 128422 flesch: 46 summary: In the first half-year of 2005 family doctors most often prescribed penicyllins -(44.8%), makrolids -(27.1%), cephalosporins -(12.5%), tetracyclins -(9.4%) and lincozamidsbased (3.1%) treatments Specialist doctors, on the other hand, prescribed penicllins (41.7%), makrolids (17.9%), cephalosporins (17.7%), tetracyclins (12.1%), lincozamids (5.2%) and chinolons (3%). State-wide antibiotic consumption in the AC setting during the same time was 12 DID (~85% of total consumption). keywords: acid; activity; acute; aeruginosa; agar; age; agents; aim; analysis; antibiotic; antimicrobial; assay; aureus; bacteria; beta; blood; care; cases; cause; cfu; children; ciprofloxacin; clinical; coli; common; community; concentrations; conclusion; consumption; control; cost; culture; daily; data; days; detection; diagnosis; diarrhoea; differences; different; difficile; disease; distribution; dna; dose; drug; duration; effect; efficacy; erythromycin; factors; faecium; following; frequency; gene; gram; group; guidelines; health; hospital; hours; human; identification; imipenem; incidence; increase; infections; information; isolates; laboratory; level; levofloxacin; linezolid; mean; medical; meningitis; methicillin; methods; mic; mics; model; months; mortality; moxifloxacin; mrsa; n =; negative; new; non; number; objectives; pathogens; patients; pcr; penicillin; period; phenotype; pneumoniae; population; positive; presence; prevalence; protein; range; rates; resistance; respiratory; results; risk; s. aureus; samples; sequence; sequencing; serum; skin; species; specific; specimens; spectrum; spp; standard; staphylococcus; strains; streptococcus; studies; study; subjects; susceptibility; susceptible; test; tetracycline; therapy; tigecycline; time; tissue; total; toxin; tract; treatment; type; use; values; vancomycin; vitro; years cache: cord-022501-9wnmdvg5.txt plain text: cord-022501-9wnmdvg5.txt item: #141 of 973 id: cord-022888-dnsdg04n author: None title: Poster Sessions date: 2009-08-19 words: 189173 flesch: 41 summary: Our aim is to describe how B cell lymphoma cells respond to TGF-b compared to normal peripheral B cells, to create an overview of the different signaling pathways involved, and to characterize the mechanisms behind the loss of sensitivity to TGF-b. Methods: Proliferation assays were performed on 11 different B-cell lymphoma cell lines and normal peripheral B cells to screen for TGF-b-induced effects. Using a CD3 and CD28 activation model system -TLR4 presence on CD4+ cells is found in mouse T cells, human T cells and Jurkat cell lines. keywords: + cells; ability; absence; activity; addition; analysis; antibodies; antibody; antigen; apoptosis; apoptotic; assay; associated; autoimmune; b cells; b t; binding; blood; bone; c mice; cancer cells; capacity; cd4; cd8 +; cd8 cells; cd8 t; cell activation; cell activity; cell culture; cell cycle; cell death; cell development; cell differentiation; cell epitopes; cell function; cell level; cell lines; cell membrane; cell population; cell proliferation; cell receptor; cell responses; cell subsets; cell surface; cell tolerance; cell types; cells cells; changes; chronic; class; clinical; colitis; complex; conclusion; contrast; control; control cells; cross; ctl; cytokine; cytokine production; cytometry; cytotoxic t; data; day; days; dcs; deficient; delta t; dendritic; disease; dna; early; effector cells; effector t; effects; elisa; expansion; experiments; expression; expression levels; factor; family; findings; flow; following; formation; function; gamma; gd cells; gd t; gene; gene expression; group; high; hiv; hla; host; human; ifn; ifng; igg; il-10; il-2; il-4; il-6; immune; immunity; increase; independent; induction; infected; infection; inflammation; inflammatory; inhibition; inkt; interaction; intracellular; levels; lps; macrophages; major; marrow cells; mast cells; mechanisms; membrane; memory t; methods; mhc; mice; model; molecules; monocytes; mouse; mouse t; mrna; murine; negative; neutrophils; new; nkt cells; non; normal; novel; number; objectives; pathway; patients; pcr; peptide; peripheral; plasma cells; play; positive; potential; presence; presentation; primary; production; promoter; protein; protein expression; receptors; regulation; regulatory; release; results; role; secretion; serum; signaling; skin; sle; specific; spleen; stem cells; stimulation; studies; study; surface expression; system; t cells; t em; t h; t helper; t lymphocytes; target cells; tcr; test; th1 cells; time; tissue; tlr; tnf; tolerance; transcription; treatment; tumor cells; type; university; vaccination; vaccine; vg9vd2 t; virus; vitro; vivo; work cache: cord-022888-dnsdg04n.txt plain text: cord-022888-dnsdg04n.txt item: #142 of 973 id: cord-022889-lv6fy6e6 author: Dávalos, Alberto title: Literature review of baseline information on non‐coding RNA (ncRNA) to support the risk assessment of ncRNA‐based genetically modified plants for food and feed date: 2019-08-07 words: 96106 flesch: 44 summary: In a later observational study, Lukasik et al. evaluated plant miRNAs miR-166a, miR-156a, miR-157a, miR-172a and miR-168a and reported the presence of plant miRNAs in human (n=6) breast milk, both in whole milk and exosomes . This HEN1-dependent 2'-Omethylation on the 3' terminal ribose is a Mg2+ dependent methylation mechanism that will ultimately stabilize miRNAs (Abe et al., 2010; Molnar et al., 2007; Yu et al., 2005; Yang et al., 2006) .The keywords: activity; administration; animals; authors; barriers; biological; blood; bodies; breast; cells; cellular; conclusions; conditions; context; contract; degradation; delivery; dietary; document; dsrna; effects; efsa; et al; european food; exogenous; exosomes; expression; food safety; function; gene; human; immune; information; issues; juliano et; key; levels; literature; mammalian; mice; milk; molecules; mouse; mrna; naked; ncrnas; non; oligonucleotides; oral; output; pathway; plant mirnas; plant ncrna; plant rna; plants; plasma; position; prejudice; presence; present; principle; procedure; proteins; publication; review; rice; rights; rnai; role; safety authority; samples; search; section; serum; silencing; sirna; small; specific; srnas; stability; studies; study; subject; synthetic; system; target; task; tender; tender procedure; tissue; total; transparency; transparency principle; uptake; view; vivo; words; zhang et cache: cord-022889-lv6fy6e6.txt plain text: cord-022889-lv6fy6e6.txt item: #143 of 973 id: cord-022940-atbjwpo5 author: None title: Poster Sessions date: 2016-09-07 words: 241687 flesch: 44 summary: Among used cancer cell lines, ERICD was highly expressed and ARID3A had lower expression in U-2OS (osteosarcoma), A-172 (glioblastoma) and A549 (lung cancer). Clear cell renal cell cancer (ccRCC) with metastases has pour prognosis: 5-year survival is about 9%. keywords: a549 cells; acid; activation; activities; activity; activity levels; acute; addition; administration; affinity; agents; aim; albumin; allele; alterations; alternative; amino; analysis; analysis results; animals; ankara; anti; antibodies; antibody; anticancer; antioxidant; apoptosis; applications; approach; assay; association; bacteria; beta; binding; biology; blood; body; bone; brain; breast cancer; cancer cells; cancer group; cancer patients; cancer stem; cancer treatment; cancers; cause; cell cycle; cell death; cell growth; cell lines; cell proliferation; cell survival; cell viability; changes; characterization; chemical; cholesterol; chronic; clinical; coli; colorectal; combination; comparison; complex; complexes; compounds; concentrations; conclusion; conditions; content; control cells; control group; control study; controls; correlation; culture; curcumin; current; cytotoxic; damage; data; day; days; decrease; department; detection; determination; development; diabetes; differences; differentiation; discussion; disease; dna; domain; dose; drug; effects; elevated; elisa; energy; enzyme; enzyme activity; ethanol; experimental; expression analysis; expression levels; expressions; extract; factor; faculty; family; fat; findings; flow; fluorescence; fold; food; formation; free; function; gene expression; genes; genetic; genome; genotype; glucose; glutathione; group; growth; gsh; health; hours; human; immune; increase; inflammation; inflammatory; inhibition; inhibitors; injury; institute; insulin; interaction; intracellular; introduction; invasion; investigation; ischemia; kinase; laboratory; lead; levels; light; like; lipid; liver; low; lung; male; manner; markers; mass; materials; matrix; mcf-7; mda; mda levels; mean; mechanisms; medical; medicine; medium; membrane; metabolism; methods; methylation; mice; microscopy; migration; mirnas; mitochondrial; model; modified; molecular; molecules; mrna; muscle; mutant; mutations; n =; nanoparticles; negative; non; normal; novel; number; obese; obesity; oil; order; oxidative; oxygen; p =; p-02.08.5; parameters; pathway; patients; pcr; peptide; phase; plant; plasma; play; point; polymorphisms; population; potential; presence; present; process; processes; production; products; profile; progression; promoter; properties; prostate; prostate cancer; protective; protein; protein expression; protein levels; purpose; radical; range; rate; rats; reaction; receptor; recombinant; region; regulation; related; relationship; research; resistance; response; results; risk; role; samples; science; scientific; screening; sequence; serum; serum levels; signaling; site; size; sod; species; specific; stability; stage; status; stem cells; strain; stress; structure; studies; study; study group; subjects; surface; survival; synthesis; system; target; technique; temperature; test; tested; therapeutic; therapy; time; tissue; tnf; total; transcription; treatment; treatment group; tumor; tumor cells; turkey; type; university; use; values; vitamin; vitro; water; weight; western; wild; women; work; years cache: cord-022940-atbjwpo5.txt plain text: cord-022940-atbjwpo5.txt item: #144 of 973 id: cord-023017-k6edtg58 author: None title: AASLD Abstracts (pp. 282A–382A) date: 2006-02-10 words: 65964 flesch: 47 summary: The aim of the present study was to investigate if the same inhibition takes place in livers cells of patients with chronic hepatitis C. From February 2001 to April 2002, all patients with chronic hepatitis C referred to the outpatient liver clinic of the University Hospital Basel were asked for their permission to use part of the liver biopsy for this study. Increased T cell activation with Eta may also suggest that TNFA suppress T cell function and may contribute to refractoriness to INF therapy in HCV patients. keywords: -no; activation; activity; addition; age; alpha; alt; analysis; anti; biopsies; biopsy; blood; cases; cd8; cells; chronic; chronic hcv; chronic hepatitis; cirrhosis; combination; conclusions; control; core; culture; data; days; dcs; different; disease; dose; effect; expression; factors; fibrosis; gene; genotype; group; hcc; hcv; hcv genotype; hcv infection; hcv patients; hcv rna; hepatic; hepatitis; hepatocytes; hsc; human; ifn; infection; interferon; levels; liver; mean; meld; methods; mice; months; negative; non; ns3; patients; pcr; population; positive; protein; rats; rejection; relationships; response; results; ribavirin; risk; role; serum; specific; steatosis; stem; studies; study; subjects; survival; system; t cells; therapy; time; total; transplantation; treated; treatment; virus; weeks; years cache: cord-023017-k6edtg58.txt plain text: cord-023017-k6edtg58.txt item: #145 of 973 id: cord-023026-2r84ndzv author: None title: Posters date: 2013-06-14 words: 138804 flesch: 38 summary: Levels of expression of NG2 mRNA and protein in mouse glial cells are regulated by the neurotransmitter glutamate and overexpression of cleaved fragments modulates protein expression in murine glial cells. Interestingly, when we analyzed the in vitro expression pattern of rCD300f in brain cells by Q-PCR and immunohistochemistry, in addition to the expected expression in microglial cells, we detected expression of CD300f in oligodendrocytes and neurons. keywords: activation; activity; acute; addition; adult; analysis; animals; anti; astrocytes; astroglial; axons; blood; brain; brain cells; brain injury; cells; cerebral; changes; chronic; cns; conditions; contrast; control; cord; cortex; cortical; cultures; cytokines; damage; data; days; death; decrease; derived; development; differentiation; disease; eae; effect; evidence; experiments; expression; expression levels; extracellular; factors; findings; formation; function; gene; gene expression; gfap; glial; glucose; glutamate; hippocampal; human; imaging; immune; increase; inflammation; inflammatory; inhibition; injection; injury; ischemic; ko mice; lactate; lesions; levels; loss; lps; macrophages; markers; mechanisms; membrane; metabolic; methods; mice; microglia; microglia activation; microglia cells; migration; model; molecules; morphology; mouse; mrna; myelin; nerve; neural; neurons; new; ng2 cells; non; number; oligodendrocytes; opcs; order; pathway; patients; pcr; phenotype; play; post; potential; precursor cells; presence; present; primary; processes; production; progenitor cells; progression; proliferation; properties; protein; protein expression; rats; receptors; reduced; regulation; release; remyelination; response; results; role; schwann cells; signaling; slices; spinal; stem cells; stress; studies; study; surface; survival; synaptic; system; test; therapeutic; time; tissue; transgenic; treatment; type; uptake; vitro; vivo; weeks cache: cord-023026-2r84ndzv.txt plain text: cord-023026-2r84ndzv.txt item: #146 of 973 id: cord-023095-4dannjjm author: None title: Research Abstract Program of the 2011 ACVIM Forum Denver, Colorado, June 15–18, 2011 date: 2011-05-03 words: 134382 flesch: 49 summary: Mminimum HR, mean HR and the HRV variables (7 and 10) differing between dog groups, also consistently decreased with increasing MR, LA/Ao and the proximal isovelocity surface area in CKCS. The apparently normal levels of hexosaminidase A activity in affected dog samples may be a result of b subunit overexpression. keywords: abnormalities; acid; acth; activity; administration; adult; age; aim; analysis; animals; assay; association; available; baseline; blood; blood samples; body; breed dogs; breeds; canine; cardiac; cases; cats; cell; changes; chf; chronic; clinical; cobalamin; compare; concentrations; control dogs; controls; correlation; cortisol; creatinine; data; days; decrease; detection; diagnosis; diet; difference; disease; dna; dogs; dose; drug; duration; effects; elisa; equine; evidence; examination; expression; failure; fecal; feline; findings; foals; following; food; function; gastrointestinal; gene; glucose; group; heart; horses; hours; human; increase; infection; insulin; isolates; levels; mean; median; medical; minutes; model; months; negative; non; number; observed; outcome; p o; parameters; patients; pcr; period; plasma; platelet; post; potential; presence; present; prevalence; protein; pulmonary; purpose; range; rate; reference; resistance; response; results; risk; role; samples; serum; serum concentrations; serum samples; severity; significance; signs; species; specific; spinal; spp; standard; studies; study; survival; test; therapy; time; tissue; total; treatment; type; urinary; urine; uroliths; use; values; veterinary; weeks; weight; years cache: cord-023095-4dannjjm.txt plain text: cord-023095-4dannjjm.txt item: #147 of 973 id: cord-023134-y665agnh author: None title: Oral Research Communications of the 22(nd) ECVIM‐CA Congress date: 2012-11-20 words: 29627 flesch: 47 summary: Concerning gross pathology findings in hearts with clinical DCM diagnosis, LV chambers were dilated in 3/4 cases of group 4, while in groups 3 and 5, the papillary muscles appeared grossly prominent and not flattened as in group 4.Histopathologically, in control dogs LV and RV myocardium showed no (3/4) or mild (1/4) interstitial collagen deposits, no or single adipocytes, and normal vessels. Histopathologically, RAA in control dogs showed small amounts of interstitialcollagen and single adipocytes. keywords: acth; analysis; animals; baseline; bem; blood; canine; cases; cats; concentrations; control; cortisol; dcm; diagnosis; disease; dogs; expression; feline; function; gene; group; heart; high; human; ibd; insulin; mean; median; parameters; plasma; post; pressure; range; results; samples; serum; studies; study; test; time; treatment; values; ventricular cache: cord-023134-y665agnh.txt plain text: cord-023134-y665agnh.txt item: #148 of 973 id: cord-023211-kt5gt26t author: None title: Poster Session Abstracts date: 2007-08-29 words: 221712 flesch: 48 summary: Understanding how its modulation modifies transepithelial transport and inflammation in CF versus non CF cells should give new therapeutic clues to reduce exaggerated inflammation and improve fluid secretion in CF patients. This finding indicates that CFTR potentiators have a wide efficacy on many class III mutants and therefore may represent a promising therapeutic strategy for a significant number of CF patients. keywords: acid; addition; adult cf; adult patients; adults; aeruginosa; age; aim; airway; airway cells; amiloride; analysis; antibiotic; asl; assay; atp; background; bacterial; baseline; binding; biofilm; blood; bmi; cells; cf airways; cf care; cf center; cf clinic; cf foundation; cf gene; cf group; cf lung; cf mouse; cf nbs; cf patients; cf research; cf sputum; cff; cfrd; cftr; cftr activation; cftr activity; cftr cells; cftr channel; cftr chloride; cftr expression; cftr function; cftr gene; cftr inhibitor; cftr mice; cftr mutations; cftr promoter; cftr protein; cftr trafficking; changes; channel; children; chronic; clearance; clinical; concentrations; conclusion; conditions; contrast; control; cultures; current; cystic; daily; data; day; days; decline; decreased; dependent; diabetes; differences; disease; dna; domain; dose; drug; effect; enac; epithelial; exacerbation; experiments; exposure; expressing; f508del; factors; family; fev1; fibrosis patients; findings; fold; forskolin; functional; genes; glands; group; growth; health; hospital; hours; human; human cf; il-8; improvement; increase; individuals; infants; infection; inflammation; inflammatory; information; inhibited; inhibition; isolates; levels; life; low; lung cells; lung disease; lung function; lungs; mean; measure; mechanism; median; medical; membrane; methods; mice; model; months; mrsa; mucus; mutant; nasal; nbd1; neutrophil; new; non; normal; novel; number; observed; order; pancreatic; parents; pathway; patients age; pcr; pediatric; period; plasma; population; positive; post; potential; presence; present; production; proteins; pseudomonas; pulmonary; quality; range; rate; regulation; research; respiratory; response; results; risk; role; samples; scores; screening; secretion; sensitive; serum; specific; status; stimulation; strains; studies; study; study patients; subjects; support; surface; symptoms; system; test; testing; therapeutic; therapies; therapy; time; tobramycin; total; transport; treatment; type cftr; university; usa; use; values; vitamin; vitro; vivo; volume; weight; wt cells; wt cftr; years; ∆f508 cftr cache: cord-023211-kt5gt26t.txt plain text: cord-023211-kt5gt26t.txt item: #149 of 973 id: cord-023288-sqr33y72 author: None title: Paediatric SIG: Poster Session date: 2008-03-12 words: 30188 flesch: 50 summary: Conclusions This is the first Australian study to identify alexithymia among asthma patients and investigate relationship to control as well as management and communication. Methods Cross sectional study of 25 moderate to severe asthma patients recruited from Royal Adelaide Hospital Outpatients. keywords: age; aim; airway; analysis; asm; asthma; asthmatics; blood; cancer; cells; children; conclusions; control; copd; data; days; disease; effect; expression; fev1; flow; function; group; health; il-6; increase; infection; inflammatory; levels; lung; mean; methods; mice; n =; non; p =; participants; patients; pulmonary; response; results; risk; smokers; study; subjects; therapy; treatment; use; years cache: cord-023288-sqr33y72.txt plain text: cord-023288-sqr33y72.txt item: #150 of 973 id: cord-023303-fxus38mp author: None title: Lung Cancer/Bronchology SIGs: Combined Poster Session date: 2008-03-12 words: 30191 flesch: 50 summary: Conclusions This is the first Australian study to identify alexithymia among asthma patients and investigate relationship to control as well as management and communication. Methods Cross sectional study of 25 moderate to severe asthma patients recruited from Royal Adelaide Hospital Outpatients. keywords: age; aim; airway; analysis; asm; asthma; asthmatics; blood; cancer; cells; children; conclusions; control; copd; data; days; disease; effect; expression; fev1; flow; function; group; health; il-6; increase; infection; inflammatory; levels; lung; mean; methods; mice; n =; non; p =; participants; patients; pulmonary; response; results; risk; smokers; study; subjects; therapy; treatment; use; years cache: cord-023303-fxus38mp.txt plain text: cord-023303-fxus38mp.txt item: #151 of 973 id: cord-023308-af5nihyi author: None title: COPD SIG: Poster Session 2 date: 2008-03-12 words: 30189 flesch: 50 summary: Conclusions This is the first Australian study to identify alexithymia among asthma patients and investigate relationship to control as well as management and communication. Methods Cross sectional study of 25 moderate to severe asthma patients recruited from Royal Adelaide Hospital Outpatients. keywords: age; aim; airway; analysis; asm; asthma; asthmatics; blood; cancer; cells; children; conclusions; control; copd; data; days; disease; effect; expression; fev1; flow; function; group; health; il-6; increase; infection; inflammatory; levels; lung; mean; methods; mice; n =; non; p =; participants; patients; pulmonary; response; results; risk; smokers; study; subjects; therapy; treatment; use; years cache: cord-023308-af5nihyi.txt plain text: cord-023308-af5nihyi.txt item: #152 of 973 id: cord-023331-jrvmgnu3 author: None title: Asthma & Allergy SIG: Poster Session 3. Physiology, Environment, Investigation and Management date: 2008-03-12 words: 30195 flesch: 50 summary: Conclusions This is the first Australian study to identify alexithymia among asthma patients and investigate relationship to control as well as management and communication. Methods Cross sectional study of 25 moderate to severe asthma patients recruited from Royal Adelaide Hospital Outpatients. keywords: age; aim; airway; analysis; asm; asthma; asthmatics; blood; cancer; cells; children; conclusions; control; copd; data; days; disease; effect; expression; fev1; flow; function; group; health; il-6; increase; infection; inflammatory; levels; lung; mean; methods; mice; n =; non; p =; participants; patients; pulmonary; response; results; risk; smokers; study; subjects; therapy; treatment; use; years cache: cord-023331-jrvmgnu3.txt plain text: cord-023331-jrvmgnu3.txt item: #153 of 973 id: cord-023346-8sqbqjm1 author: None title: MONDAY: POSTERS date: 2005-06-08 words: 130150 flesch: 50 summary: The Polish Blood Transfusion Act of 22nd August 1997, in force since January 1st 1999, has been supplemented by 8 Decrees: 1. procedures for external BTS audits; 2. requirements for donor selection; 3. requirements and procedures for organization and safe management of blood transfusion in hospitals; 4. requirements for implementing of national and regional donor registers; 5. employment criteria for BTS personnel; 6. training requirements for hospital personnel involved in blood and blood product administration; 7. national, uniform price list for blood and blood products; 8. organization requirements for setting up of a National Committee for Blood and Blood Transfusion. Introduction: TRALI is a life threatening adverse reaction of blood transfusion. keywords: aim; analysis; anti; antibodies; antibody; antigens; apheresis; assay; associated; background; blood banking; blood banks; blood cells; blood center; blood collection; blood components; blood donation; blood donors; blood establishments; blood group; blood loss; blood plasma; blood pressure; blood products; blood safety; blood samples; blood service; blood supply; blood system; blood transfusion; blood units; blood volume; cases; clinical; complications; concentrates; conclusion; control; cord blood; count; data; day; days; detection; disease; dna; donations; effect; events; factor; ffp; following; frequency; general; groups; hbsag; hbv; hcv; health; high; hla; hospital; hospital blood; identification; important; increase; infections; information; introduction; iron; laboratory; level; low; major; management; mean; medical; methods; national; negative; new; non; number; order; patients; pcr; period; plasma; platelet; platelet transfusion; population; positive; post; practice; presence; present; procedure; process; quality; range; rbc; rbc transfusion; rbcs; red; results; rhd; risk; routine; screening; serum; specific; standard; storage; studies; study; surgery; system; table; test; tested; testing; therapy; time blood; total; transfusion medicine; transfusion reactions; transfusion service; transfusion therapy; transfusions; treatment; type; use; weak; women; years cache: cord-023346-8sqbqjm1.txt plain text: cord-023346-8sqbqjm1.txt item: #154 of 973 id: cord-023354-f2ciho6o author: None title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 words: 130154 flesch: 50 summary: The Polish Blood Transfusion Act of 22nd August 1997, in force since January 1st 1999, has been supplemented by 8 Decrees: 1. procedures for external BTS audits; 2. requirements for donor selection; 3. requirements and procedures for organization and safe management of blood transfusion in hospitals; 4. requirements for implementing of national and regional donor registers; 5. employment criteria for BTS personnel; 6. training requirements for hospital personnel involved in blood and blood product administration; 7. national, uniform price list for blood and blood products; 8. organization requirements for setting up of a National Committee for Blood and Blood Transfusion. Introduction: TRALI is a life threatening adverse reaction of blood transfusion. keywords: aim; analysis; anti; antibodies; antibody; antigens; apheresis; assay; associated; background; blood banking; blood banks; blood cells; blood center; blood collection; blood components; blood donation; blood donors; blood establishments; blood group; blood loss; blood plasma; blood pressure; blood products; blood safety; blood samples; blood service; blood supply; blood system; blood transfusion; blood units; blood volume; cases; clinical; complications; concentrates; conclusion; control; cord blood; count; data; day; days; detection; disease; dna; donations; effect; events; factor; ffp; following; frequency; general; groups; hbsag; hbv; hcv; health; high; hla; hospital; hospital blood; identification; important; increase; infections; information; introduction; iron; laboratory; level; low; major; management; mean; medical; methods; national; negative; new; non; number; order; patients; pcr; period; plasma; platelet; platelet transfusion; population; positive; post; practice; presence; present; procedure; process; quality; range; rbc; rbc transfusion; rbcs; red; results; rhd; risk; routine; screening; serum; specific; standard; storage; studies; study; surgery; system; table; test; tested; testing; therapy; time blood; total; transfusion medicine; transfusion reactions; transfusion service; transfusion therapy; transfusions; treatment; type; use; weak; women; years cache: cord-023354-f2ciho6o.txt plain text: cord-023354-f2ciho6o.txt item: #155 of 973 id: cord-023364-ut56gczm author: None title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date: 2005-06-08 words: 130157 flesch: 50 summary: The Polish Blood Transfusion Act of 22nd August 1997, in force since January 1st 1999, has been supplemented by 8 Decrees: 1. procedures for external BTS audits; 2. requirements for donor selection; 3. requirements and procedures for organization and safe management of blood transfusion in hospitals; 4. requirements for implementing of national and regional donor registers; 5. employment criteria for BTS personnel; 6. training requirements for hospital personnel involved in blood and blood product administration; 7. national, uniform price list for blood and blood products; 8. organization requirements for setting up of a National Committee for Blood and Blood Transfusion. Introduction: TRALI is a life threatening adverse reaction of blood transfusion. keywords: aim; analysis; anti; antibodies; antibody; antigens; apheresis; assay; associated; background; blood banking; blood banks; blood cells; blood center; blood collection; blood components; blood donation; blood donors; blood establishments; blood group; blood loss; blood plasma; blood pressure; blood products; blood safety; blood samples; blood service; blood supply; blood system; blood transfusion; blood units; blood volume; cases; clinical; complications; concentrates; conclusion; control; cord blood; count; data; day; days; detection; disease; dna; donations; effect; events; factor; ffp; following; frequency; general; groups; hbsag; hbv; hcv; health; high; hla; hospital; hospital blood; identification; important; increase; infections; information; introduction; iron; laboratory; level; low; major; management; mean; medical; methods; national; negative; new; non; number; order; patients; pcr; period; plasma; platelet; platelet transfusion; population; positive; post; practice; presence; present; procedure; process; quality; range; rbc; rbc transfusion; rbcs; red; results; rhd; risk; routine; screening; serum; specific; standard; storage; studies; study; surgery; system; table; test; tested; testing; therapy; time blood; total; transfusion medicine; transfusion reactions; transfusion service; transfusion therapy; transfusions; treatment; type; use; weak; women; years cache: cord-023364-ut56gczm.txt plain text: cord-023364-ut56gczm.txt item: #156 of 973 id: cord-023592-w96h4rir author: None title: Abstracts cont. date: 2015-12-28 words: 67976 flesch: 48 summary: The maximum amino acid identities of genes among different non-antibiotic-producing bacterial isolates were close to 100% for most genes, but those between antibiotic-producing and human or animal bacteria ranged from <28 to <77%. Results: Seven or eight participants provided qualifying results in the two separate QC studies, and the calculated (proposed) ranges were (range; % results in range): E. faecalis ATCC 29212 (2-8 mg/ L; 95.6), S. aureus ATCC 29213 (0.5-2 mg/L; 99.4), S. pneumoniae ATCC 49619 (0.25-1 mg/L; 97.5 and 30-37 mm; 97.6), H. influenzae ATCC 49247 (1-4 mg/L; 97.5 and 24-32 mm; 99.8), and S. aureus ATCC 25923 keywords: activity; aeruginosa; agar; agents; aim; analysis; antibiotic; antimicrobial; aureus; bacterial; beta; blood; candida; cases; catheter; cfu; ciprofloxacin; clinical; coli; conclusions; control; culture; data; days; detection; dna; esbl; faecium; genes; gram; group; hospital; human; identification; infection; isolates; lactamase; methods; mic; mice; mics; mortality; mrsa; nccls; negative; new; non; number; objectives; pathogens; patients; pcr; period; pfge; pneumoniae; positive; presence; prevalence; producing; production; pylori; range; resistance; results; salmonella; samples; sequence; species; specific; specimens; spp; strains; study; susceptibility; system; tested; tests; therapy; time; total; toxin; treatment; type; vancomycin; years cache: cord-023592-w96h4rir.txt plain text: cord-023592-w96h4rir.txt item: #157 of 973 id: cord-023698-wvk200j0 author: Hammerschlag, Margaret R. title: Chlamydia pneumoniae date: 2014-10-31 words: 10021 flesch: 30 summary: Determination of whether C. pneumoniae infection is an acute primary infection or reinfection, a chronic persistent stage, or a past infection is also very difficult. In clinical settings, routine diagnosis of C. pneumoniae infection has been based on results of serologic testing to identify anti-C. pneumoniae immunoglobulin G (IgG), IgA, and IgM antibodies. keywords: assays; asthma; cell; chlamydia; chlamydia pneumoniae; culture; detection; disease; dna; infection; patients; pcr; pneumoniae; pneumoniae infection; results; specimens; studies; treatment cache: cord-023698-wvk200j0.txt plain text: cord-023698-wvk200j0.txt item: #158 of 973 id: cord-023830-w218ogsk author: Perlin, David title: Rapid Detection of Bioterrorism Pathogens date: 2008-09-10 words: 6051 flesch: 35 summary: The problem is not limited to a bioterrorism outbreak as hospital and public health laboratories, confounded by inadequate and slow methodology for pathogen detection, often have difficulty identifying pathogens. This technique allows for continuous, automated operation over an extended time with an assay time is less than 30 min for pathogen detection. keywords: acid; agents; antibody; assays; detection; disease; dna; identification; nucleic; pathogens; pcr; probes; system; target; time cache: cord-023830-w218ogsk.txt plain text: cord-023830-w218ogsk.txt item: #159 of 973 id: cord-024080-eh3ztsv5 author: Dheda, Keertan title: Diagnosis of COVID-19: Considerations, Controversies and Challenges in South Africa date: 2020-04-17 words: 3958 flesch: 35 summary: (6, 7) In early disease, procalcitonin may distinguish COVID-19 from bacterial infections but not from other viral diseases (data are awaited to confirm this supposition). Clinical and laboratory parameters that may suggest viral infection may include pyrexia, acute malaise and myalgia, and lymphopenia. keywords: coronavirus; covid-19; disease; infection; patients; pcr; sars; symptoms; testing cache: cord-024080-eh3ztsv5.txt plain text: cord-024080-eh3ztsv5.txt item: #160 of 973 id: cord-025232-5itrsfmk author: Yan, Yuqian title: Construction and Characterization of a Novel Recombinant Attenuated and Replication-Deficient Candidate Human Adenovirus Type 3 Vaccine: “Adenovirus Vaccine Within an Adenovirus Vector” date: 2020-05-26 words: 5684 flesch: 36 summary: A community-derived outbreak of adenovirus type 3 in children in Taiwan between Molecular identification and epidemiological features of human adenoviruses associated with acute respiratory infections in hospitalized children in Southern China Comparative genomic analysis of re-emergent human adenovirus type 55 pathogens associated with adult severe communityacquired pneumonia reveals conserved genomes and capsid proteins Adenoviral infections in Singapore: should new antiviral therapies and vaccines be adopted? Analysis of 15 adenovirus hexon proteins reveals the location and structure of seven hypervariable regions containing serotype-specific residues Generation and characterization of a novel candidate gene therapy and vaccination vector based on human species D adenovirus type 56 Mortime P (eds) Principles and practice of clinical virology, 6th edn Hexon and fiber of adenovirus type 14 and 55 are major targets of neutralizing antibody but only fiber-specific antibody contributes to cross-neutralizing activity Molecular epidemiology of adenovirus type 3 detected from 1994 to 2006 in Hyogo Prefecture Immune response to recombinant capsid proteins of adenovirus in humans: antifiber and anti-penton base antibodies have a synergistic effect on neutralizing activity Gene therapy clinical trials worldwide to 2017: an update A recombinant adenovirusbased vector elicits a specific humoral immune response against the V3 loop of HIV-1 gp120 in mice through the 'Antigen Capsid-Incorporation' strategy Identification and typing of respiratory adenoviruses in Guangzhou, Southern China using a rapid and simple method A primary school outbreak of pharyngoconjunctival fever caused by adenovirus type 3 Novel replicationincompetent vector derived from adenovirus type 11 (Ad11) for vaccination and gene therapy: low seroprevalence and non-crossreactivity with Ad5 Household transmission of human adenovirus type 55 in case of fatal acute respiratory disease Emergent US adenovirus 3 strains associated with an epidemic and serious disease Comprehensive serotyping and epidemiology of human adenovirus isolated from the respiratory tract of Korean children over 17 consecutive years Epidemiology, clinical presentation and respiratory sequelae of adenovirus pneumonia in children in Kuala Lumpur Molecular epidemiology and clinical features of adenovirus infection in Taiwanese children Adenovirus infections in immunocompetent and immunocompromised patients Gene therapy progress and prospects cancer: oncolytic viruses Detection and molecular characterization of human adenovirus infections among hospitalized children with acute diarrhea in Safety and immunogenicity of novel adenovirus type 26-and modified vaccinia ankara-vectored Ebola vaccines: a randomized clinical trial Rapid construction of a replication-competent infectious clone of human adenovirus type 14 by gibson assembly Delivery of a foot-and-mouth disease virus empty capsid subunit antigen with nonstructural protein 2B improves protection of swine Adenoviruses and acute respiratory infections in children living in an equatorial area of Brazil Oral administration of an adenovirus vector encoding both an avian influenza A hemagglutinin and a TLR3 ligand induces antigen specific granzyme B and IFN-gamma T cell responses in humans Adenovirus assay by the fluorescent cell-counting procedure Structure-based identification of a major neutralizing site in an adenovirus hexon Dramatic decline of respiratory illness among US military recruits after the renewed use of adenovirus vaccines Gene therapy: the first approved gene-based medicines, molecular mechanisms and clinical indications Vaccine-preventable adenoviral respiratory illness in US military recruits Type-specific epitope locations revealed by X-ray crystallographic study of adenovirus type 5 hexon Structural and phylogenetic analysis of adenovirus hexons by use of high-resolution X-ray crystallographic, molecular modeling, and sequence-based methods An adenovirus-based vaccine with a double-stranded RNA adjuvant protects mice and ferrets against H5N1 avian influenza in oral delivery models a placebo-controlled trial of immunization of HIV-1-infected persons with a replication-deficient adenovirus type 5 vaccine expressing the HIV-1 core protein Using the whole-genome sequence to characterize and name human adenoviruses A two-dose heterologous prime-boost vaccine regimen eliciting sustained immune responses to Ebola Zaire could support a preventive strategy for future outbreaks Recombination of the epsilon determinant and corneal tropism: human adenovirus species D types 15 A human type 5 adenovirus-based tuberculosis vaccine induces robust T cell responses in humans despite preexisting anti-adenovirus immunity Generation of adenovirus vectors devoid of all viral genes by recombination between inverted repeats Development and assessment of human adenovirus type 11 as a gene transfer vector Mapping the epitope of neutralizing monoclonal antibodies against human adenovirus type 3 Increasing the efficacy of oncolytic adenovirus vectors Community outbreak of adenovirus Epidemical features of HAdV-3 and HAdV-7 in pediatric pneumonia in Adenovirus vectors for gene therapy, vaccination and cancer gene therapy Characterization of culture-positive adenovirus serotypes from respiratory specimens in Fatal community-acquired pneumonia in children caused by re-emergent human adenovirus 7d associated with higher severity of illness and fatality rate Comparative genomic analysis of two strains of human adenovirus type 3 isolated from children with acute respiratory infection in southern China Construction and characterization of a replication-competent human adenovirus type 3-based vector as a livevaccine candidate and a viral delivery vector Comparative genomic analysis of two emergent human adenovirus type 14 respiratory pathogen isolates in China reveals similar yet divergent genomes A survey of recent adenoviral respiratory pathogens in Hong Kong reveals emergent and recombinant human adenovirus type 4 (HAdV-E4) circulating in civilian populations Molecular typing of human respiratory adenoviruses with universal PCR and sequencing primers for three major capsid genes: penton base, hexon, and fiber Re-emergent human adenovirus genome type 7d caused an acute respiratory disease outbreak in Southern China after a twenty-one year absence Comparison of viral and epidemiological profiles of hospitalized children with severe acute respiratory infection in Beijing and Construction and Characterization of a Novel HAdV-3 Vaccine Author Contributions QZ designed the experiments. A PCRderived product comprising the complete hexon gene (epsilon epitope) of adenovirus type 3 was directly cloned into the multiple cloning site of pShuttle using the EcoR V and Xho I restriction sites. keywords: adenovirus; cells; et al; gene; hadv-3; hexon; pcr; rad3h; recombinant; strain; type; vaccine cache: cord-025232-5itrsfmk.txt plain text: cord-025232-5itrsfmk.txt item: #161 of 973 id: cord-025634-31n5fvex author: Zhuge, Shurui title: The prevalence of occult HBV infection in immunized children with HBsAg-positive parents: a hospital-based analysis date: 2020-05-29 words: 3987 flesch: 46 summary: Considering the significant reservoir of HBV infections, the status of HBV infection in many countries is still not optimistic. For HBV DNA detectable children, 20 (13.6%, 95% CI 8.0-19.2%), 24 (14.0%, 95% CI 8.7-19.2%) were found with HBV father-carriers, mother-carriers. keywords: anti; children; dna; hbsag; hbv; hepatitis; infection; obi; positive cache: cord-025634-31n5fvex.txt plain text: cord-025634-31n5fvex.txt item: #162 of 973 id: cord-027498-cfzfgzqi author: Hattori, Takeshi title: Older age is associated with sustained detection of SARS-CoV-2 in nasopharyngeal swab samples date: 2020-06-21 words: 844 flesch: 48 summary: In our analysis, older age is significantly associated with prolonged duration of positive PCR tests from nasopharyngeal swab samples, irrespective of the disease severity and the used of medication ( Figure 1 ). We speculate that in older individuals, cell turnover is less robust and as such, clearance of virus from the nasopharynx is prolonged; these factors may lead to positive PCR tests that persist after acute disease has resolved. keywords: nasopharyngeal; pcr; samples cache: cord-027498-cfzfgzqi.txt plain text: cord-027498-cfzfgzqi.txt item: #163 of 973 id: cord-029183-3aotgq6m author: Monard, Céline title: Multicenter evaluation of a syndromic rapid multiplex PCR test for early adaptation of antimicrobial therapy in adult patients with pneumonia date: 2020-07-14 words: 5860 flesch: 30 summary: Therefore, in pneumonia patients, international guidelines state that an attempt should be made to obtain respiratory samples and recommend to start early empirical treatment while awaiting for the results of culture and antimicrobial susceptibility testing (AST) Second, although we included a large panel of pneumonia patients (severe ICU patients with VAP or HAP and non-severe CAP patients from the emergency room), it remains unclear what group of patients will benefit most from the syndromic rm-PCR diagnosis. keywords: antibiotic; committee; culture; episodes; pathogens; patients; pcr; pneumonia; results; therapy cache: cord-029183-3aotgq6m.txt plain text: cord-029183-3aotgq6m.txt item: #164 of 973 id: cord-029710-ythz9ax0 author: Homayounieh, Fatemeh title: CT Radiomics, Radiologists and Clinical Information in Predicting Outcome of Patients with COVID-19 Pneumonia date: 2020-07-23 words: 3096 flesch: 37 summary: Pneumonia Feasibility of CT radiomics to predict treatment response of individual liver metastases in esophagogastric cancer patients Unsupervised machine learning of radiomic features for predicting treatment response and overall survival of early stage non-small cell lung cancer patients treated with stereotactic body radiation therapy Novel Quantitative Imaging for Predicting Response to Therapy: Techniques and Clinical Applications Radiomics predicts survival of patients with advanced non-small cell lung cancer undergoing PD-1 blockade using Nivolumab Diagnostic performance between CT and initial real-time RT-PCR for clinically Radiomics differentiated chest CT in outpatient vs inpatient with an AUC of 0.84 (p<0.005), while radiologists’ interpretations of disease extent and opacity type had an AUC of 0.69 (p<0.0001). keywords: chest; covid-19; lung; patients; pneumonia; radiomics; study cache: cord-029710-ythz9ax0.txt plain text: cord-029710-ythz9ax0.txt item: #165 of 973 id: cord-029775-mntcor5d author: Oka, Tomoichiro title: Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses date: 2020-07-27 words: 1844 flesch: 47 summary: 62nt-CTGCTATCCTGCCACCAGGTG CACAGGGGCAGTCACGAGTAA-75nt-TTTCCTTGGGGCTATCCACC-35nt-AGCGCA ATGTTTGCTGGGTGGGG -62nt-CTGCCATCTTGCCACCCGGAG TACAGGGGCCGTCAGCAACAA-75nt-CTTTCTTGGTGCCATCCATC-35nt-AGTGCC ATGTTTGCTGGCTGGGG -62nt-TCGCAGTGCTGCCTCCAGGTG AACTGGGGCAGTCACCAGCAA-75nt-GTTCCTGGGCGCAATCCACC Comprehensive review of human sapoviruses Children attending day care centers are a year-round reservoir of gastrointestinal viruses A foodborne outbreak of sapovirus linked to catered box lunches in Japan Characterization of sapoviruses detected in gastroenteritis outbreaks and identification of asymptomatic adults with high viral load Detection of human sapovirus by real-time reverse transcription-polymerase chain reaction Human sapovirus classification based on complete capsid nucleotide sequences Genetic diversity of human sapovirus across the Americas Viral metagenomics reveals sapoviruses of different genogroups in stool samples from children with acute gastroenteritis in Jiangsu Investigation of a food-borne outbreak of gastroenteritis in a school canteen revealed a variant of sapovirus genogroup V not detected by standard PCR Complete genome sequence of a novel GV.2 sapovirus strain, NGY-1, detected from a suspected foodborne gastroenteritis outbreak Broadly reactive real-time reverse transcription-polymerase chain reaction assay for the detection of human sapovirus genotypes Molecular epidemiology and phylogenetic analysis of Sapporo-like viruses The detection of human sapoviruses with universal and genogroup-specific primers Detection of norovirus (GI, GII), Sapovirus and astrovirus in fecal samples using reverse transcription single-round multiplex PCR Detection and genetic analysis of human sapoviruses in river water in Japan Surveillance of pathogens in outpatients with gastroenteritis and characterization of sapovirus strains between Epidemiology and genotype analysis of sapovirus associated with gastroenteritis outbreaks in A confirmation of sapovirus re-infection gastroenteritis cases with different genogroups and genetic shifts in the evolving sapovirus genotypes Quantification and genotyping of human sapoviruses in the Llobregat river catchment Near-Complete Human Sapovirus Genome Sequences from Kenya PCR assays were performed using 20 µL of a reaction mixture containing 1 µL of synthetic double-stranded DNA or 2 µL of cDNA or DNA from clinical specimens, 10 µL of KAPA2G Fast HotStart ReadyMix with dye (KAPA Biosystems, Wilmington, MA), and 10 pmol of each primer. keywords: fig; human; m13r; pcr; sapovirus cache: cord-029775-mntcor5d.txt plain text: cord-029775-mntcor5d.txt item: #166 of 973 id: cord-030026-4jew57ce author: Vasala, Antti title: Modern Tools for Rapid Diagnostics of Antimicrobial Resistance date: 2020-07-15 words: 14198 flesch: 30 summary: LCR can be easily integrated into detection systems such as electrochemical and magnetic biosensors, quantum dots, quartz crystal and leaky surface acoustic surface biosensors, Surface Enhanced Raman Scattering (SERS), chemiluminescence and fluorescence resonance energy transfer (Oblath et al., 2013) . The IRIDICA PCR/electrospray ionization-mass spectrometry assay on bronchoalveolar lavage for bacterial etiology in mechanically ventilated patients with suspected pneumonia Cell-on-hydrogel platform made of agar and alginate for rapid, low-cost, multidimensional test of antimicrobial susceptibility Antimicrobial susceptibility test with plasmonic imaging and tracking of single bacterial motions on nanometer scale Current and emerging techniques for antibiotic susceptibility tests Antibiotic Susceptibility Testing via Plasmonic Imaging and Tracking Evaluation and use of a rapid Staphylococcus aureus assay by an antimicrobial stewardship program United nations meeting on antimicrobial resistance Detection of group a streptococcus from pharyngeal swab samples by bacterial culture is challenged by a novel mariPOC point-of-care test Developmental roadmap for antimicrobial susceptibility testing systems Developmental roadmap for antimicrobial susceptibility testing systems Laboratory-based and point-of-care testing for MSSA/MRSA detection in the age of whole genome sequencing ELISA-Based Identification and Detection of Microbes Rapid phenotypic antibiotic susceptibility testing of uropathogens using optical signal analysis on the nanowell slide Isothermal micro calorimetry-a new method for MIC determinations: results for 12 antibiotics and reference strains of E. coli and S. aureus MALDI-TOF mass spectrometry technology for detecting biomarkers of antimicrobial resistance: current achievements and future perspectives Strand displacement amplification-an isothermal, in vitro DNA amplification technique Analytical validation of an ultra low-cost mobile phone microplate reader for infectious disease testing Bacterial nanoscale cultures for phenotypic multiplexed antibiotic susceptibility testing MALDI-TOF MS in microbiological diagnostics-identification of microorganisms and beyond (mini review) Detection of methicillin-resistant staphylococcus aureus using a specific Anti-PBP2a chicken IgY antibody A multiplex loopmediated isothermal amplification assay for rapid screening of Acinetobacter baumannii and D carbapenemase OXA-23 gene Direct antimicrobial susceptibility testing of bloodstream infection on SlipChip Recent developments in antibody-based assays for the detection of bacterial toxins keywords: amplification; analysis; antibiotic; ast; bacteria; blood; cell; clinical; cultures; detection; diagnostics; et al; growth; identification; isothermal; methods; monitoring; naat; pathogen; pcr; resistance; samples; susceptibility; system; technologies; technology; testing; tests; time; use cache: cord-030026-4jew57ce.txt plain text: cord-030026-4jew57ce.txt item: #167 of 973 id: cord-030028-s6sxi8uj author: Rubio, Luis title: Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution date: 2020-07-17 words: 14694 flesch: 22 summary: IF acknowledges financial support from the Spanish Ministerio de Economia y Competitividad, through the Severo Ochoa Programme for Centers of Excellence in R&D 2016-2019 (SEV-2015-0533). Detection and quantitation of two cucurbit criniviruses in mixed infection by real-time RT-PCR Mutations associated with resistancebreaking isolates of Beet necrotic yellow vein virus and their allelic discrimination using TaqMan technology Advances in plant virus evolution: translating evolutionary insights into better disease management Codon usage bias amongst plant viruses Virus adaptation by manipulation of host's gene expression Ecogenomic survey of plant viruses infecting tobacco by next generation sequencing Simultaneous detection and identification of Pepino mosaic virus (PepMV) isolates by multiplex one-step RT-PCR Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants Analysis of genetic bottlenecks during horizontal transmission of Cucumber mosaic virus Multiplex RT-PCR detection of three common viruses infecting orchids Rapid generation of genetic heterogeneity in progenies from individual cDNA clones of peach latent mosaic viroid in its natural host Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers Control methods of virus diseases in the Mediterranean basin Simultaneous detection of six RNA plant viruses affecting tomato crops using a single digoxigenin-labelled polyprobe Development of a molecular assay for the detection of Cucumber mosaic virus and the discrimination of its subgroups I and II Detection of five seedborne legume viruses in one sensitive multiplex polymerase chain reaction test Single-step multiplex RT-PCR for simultaneous and colourimetric detection of six RNA viruses in olive trees Real-time RT-PCR high-resolution melting curve analysis and multiplex RT-PCR to detect and differentiate grapevine leafroll-associated virus 3 variant groups I, II, III and VI Estimation of the effective number of founders that initiate an infection after aphid transmission of a multipartite plant virus Localizing viruses in their insect vectors Third generation sequencing: technology and its potential impact on evolutionary biodiversity research Microarrays for rapid identification of plant viruses Methods in virus diagnostics: from ELISA to next generation sequencing Real time portable genome sequencing for global food security Epidemiology and control of tomato mosaic virus Nanopore sequencing as a surveillance tool for plant pathogens in plant and insect tissues Multiple virus resistance at a high frequency using a single transgene construct DNA microarray: parallel detection of potato viruses Design, synthesis, and functional analysis of highly specific artificial small RNAs with antiviral activity in plants Fast-forward generation of effective artificial small RNAs for enhanced antiviral defense in plants Multi-targeting of viral RNAs with synthetic trans-acting small interfering RNAs enhances plant antiviral resistance A real-time RT-PCR assay for quantifying the fitness of Tobacco etch virus in competition experiments Diagnosis of plant diseases using the Nanopore sequencing platform Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission A phylogenetic survey of recombination frequency in plant RNA viruses Antibody array in a multiwell plate format for the sensitive and multiplexed detection of important plant pathogens Multiple virus resistance using artificial trans-acting siRNAs Next-generation diagnostics with CRISPR Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses The promiscuous evolutionary history of the family Bromoviridae NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian vineyards Lethal mutagenesis of an RNA plant virus via lethal defection Contribution of uneven distribution of genomic RNA variants of citrus tristeza virus (CTV) within the plant to changes in the viral population following aphid transmission A multiplex reverse transcription PCR assay for simultaneous detection of five tobacco viruses in tobacco plants Induction of silencing in plants by high-pressure spraying of in vitro-synthesized small RNAs Recombination profiles between Tomato yellow leaf curl virus and Tomato yellow leaf curl Sardinia virus in laboratory and field conditions: evolutionary and taxonomic implications Emergence and Phylodynamics of Citrus tristeza virus in Sicily, Italy Molecular detection of papaya meleira virus in the latex of carica papaya by RT-PCR Characterization of RNA-mediated resistance to tomato spotted wilt virus in transgenic tobacco plants Dominant resistance against plant viruses Detection, discrimination and absolute quantitation of Tomato spotted wilt virus isolates using real time RT-PCR with TaqMan ® MGB probes Transmission of Tomato spotted wilt virus isolates able and unable to overcome tomato or pepper resistance by its vector Frankliniella occidentalis Increase in Zucchini yellow mosaic virus symptom severity in tolerant zucchini cultivars is related to a point mutation in P3 protein and is associated with a loss of relative fitness on susceptible plants Differentiation of Cucumber mosaic virus isolates by hybridization to Rubio et al. genome move systemically and protect cucurbits against ZYMV Entomopathogenic viruses and bacteria for insect-pest control, in Integrated Pest Management: Current concepts and ecological perspective Nonparametric estimation from incomplete observations Plant virology and next generation sequencing: experiences with a potyvirus Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control Polycistronic artificial miRNA-mediated resistance to Wheat dwarf virus in barley is highly efficient at low temperature Current trends in diagnostics of viral infections of unknown etiology Lateral flow assays Population structure and genetic diversity within California Citrus tristeza virus (CTV) isolates The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses MEGA X: molecular evolutionary genetics analysis across computing platforms Multiple artificial microRNAs targeting conserved motifs of the replicase gene confer robust transgenic resistance to negative-sense singlestranded RNA plant virus Tempo and mode of plant RNA virus escape from RNA interferencemediated resistance Improving the effectiveness of artificial microRNA (amiR)-mediated resistance against Turnip mosaic virus by combining two amiRs or by targeting highly conserved viral genomic regions Viruses of cucurbit crops in the Mediterranean region: an ever-changing picture Phylogenetic and recombination analysis of tomato spotted wilt virus Simultaneous detection of three lilyinfecting viruses using a multiplex Luminex bead array Genetic diversity and biological variation among California isolates of Cucumber mosaic virus Molecular evolution of a viral non-coding sequence under the selective Virus Variability: Diagnosis and Control pressure of amiRNA-mediated silencing Development of a one-step immunocapture real-time TaqMan RT-PCR assay for the broad spectrum detection of Pepino mosaic virus Effectiveness of chemo-and thermotherapeutic treatments on Pepino mosaic virus in tomato seed MicroRNA-mediated gene silencing in plant defense and viral counter-defense Development of real-time and conventional RT-PCR assays for the detection of potato yellow vein virus (PYVV) keywords: analysis; citrus; control; detection; disease; dna; et al; hybridization; isolates; mosaic; multiplex; new; nucleotide; pcr; plant; plant viruses; primers; probes; recombination; resistance; rna; sequence; sequencing; species; techniques; time; tomato; variants; virus; viruses cache: cord-030028-s6sxi8uj.txt plain text: cord-030028-s6sxi8uj.txt item: #168 of 973 id: cord-030191-tekgcthp author: Suchá, Dominika title: Suboptimal Quality and High Risk of Bias in Diagnostic Test Accuracy Studies on Chest Radiography and Computed Tomography in the Acute Setting of the COVID-19 Pandemic: A Systematic Review date: 2020-07-30 words: 5038 flesch: 35 summary: Mean number of reported STARD items was 12/34 (35%) for all studies (Figure- Based on the GRADE framework the certainty of evidence for the totality of CT test accuracy studies for COVID-19 diagnosis was rated very low for both sensitivity and specificity estimates ( Table 7) . Study design, risk of bias, and indirectness in rating the certainty across a body of evidence for test accuracy Sources of variation and bias in studies of diagnostic accuracy: a systematic review A systematic review classifies sources of bias and variation in diagnostic test accuracy studies STARD 2015 guidelines for reporting diagnostic accuracy studies: explanation and elaboration GRADE guidelines: 21 part 2. keywords: accuracy; bias; coronavirus; covid-19; disease; patients; risk; studies; study; test cache: cord-030191-tekgcthp.txt plain text: cord-030191-tekgcthp.txt item: #169 of 973 id: cord-031565-mos619wp author: Troedsson, Christofer title: Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR) date: 2009-02-01 words: 4221 flesch: 39 summary: In order to evaluate whether the dla-qPCR could be used to correct for prey DNA digestion, additional experiments were conducted with C. finmarchicus fed R. marina for different time periods. A possible explanation for the underestimation of ingested prey cells by qPCR is the digestion of prey genomic DNA in copepod gut. keywords: copepod; digestion; dla; dna; et al; feeding; gut; pcr; prey cache: cord-031565-mos619wp.txt plain text: cord-031565-mos619wp.txt item: #170 of 973 id: cord-031907-ilhr3iu5 author: None title: ISEV2020 Abstract Book date: 2020-07-15 words: 201435 flesch: 40 summary: Normal pancreas cells (hTERT-HPNE and HPDE-H6c7) were co-cultured with cancer cell EVs for 24-48 hours. Before EV isolation cells were kept for 24 h either under normoxia or hypoxia (1% oxygen). keywords: ability; activation; activity; ad evs; addition; aim; analysis; analysis methods; anti; approach; assay; associated; bacterial evs; biological; biomarkers; blood; blood cells; blood evs; blot; bone; brain; breast; breast cancer; cancer cells; cancer evs; cancer introduction; cancer patients; cd63; cd81; cd9; cell communication; cell culture; cell evs; cell exosomes; cell function; cell lines; cell proliferation; cell surface; cell types; cells; cells introduction; changes; characterization; chromatography; composition; concentration; conclusion; conditions; content; control; control evs; cultured; current; cytometry; data; delivery; density; detection; development; diagnosis; differential; disease; distribution; dna; drug; effect; electron; endothelial; enrichment; epithelial; ev analysis; ev cargo; ev evs; ev isolation; ev markers; ev numbers; ev preparations; ev production; ev protein; ev release; ev research; ev rna; ev samples; ev subpopulations; ev surface; ev treatment; ev uptake; evs; exclusion; exosomal; exosomes; experiments; expression; expression analysis; extracellular; factors; findings; flow; fluorescent; fluorescent evs; fold; formation; fractions; free; function; funding; gene; group; growth; host cells; human; human evs; imaging; immune; increase; inflammation; inflammatory; introduction; isolated; isolation methods; key; large; levels; lipid; lung; macrophages; mass; mechanisms; media; medium; membrane; membrane vesicles; mesenchymal; metastasis; methods; mice; microscopy; migration; milk evs; mirna; model; molecular; molecules; mouse; msc evs; mscs; nanoparticle; national; neuronal; neurons; new; non; normal; novel; nta; number; particles; pathway; patients; plasma evs; plasma samples; platelet; platform; play; positive; positive evs; post; potential; presence; present; primary; process; production; profile; profiling; progression; proliferation; properties; prostate; prostate cancer; protein; protein cargo; protein expression; protein markers; proteomic; purification; purity; range; recipient cells; research; resistance; response; results; rna; rnas; role; samples; sec; secretion; sequencing; serum; sevs; signalling; single; size; small evs; specific; specific evs; spectrometry; stem cells; stromal cells; studies; study; summary; surface; system; target cells; targets; tau; techniques; tested; therapeutic; therapy; time; tissue; total; total evs; tracking; transfer; transmission; treatment; tumour cells; ultracentrifugation; university; uptake; urinary evs; urine; usa; usa introduction; use; vesicles; vesicles introduction; vitro; vivo; work cache: cord-031907-ilhr3iu5.txt plain text: cord-031907-ilhr3iu5.txt item: #171 of 973 id: cord-032134-mvj7i1er author: Ballauff, Antje title: Funktions- und Laboruntersuchungen date: 2013 words: 9323 flesch: 40 summary: Bei der Interpretation der Testergebnisse sind mögliche Fehlerquellen zu beachten. Zum Nachweis importierter Parasitosen wie der Schistosomiasis, bei der die adulten Würmer extraintestinal liegen, die Eier aber über den Darm ausgeschieden werden, setzt man die Immundiagnostik zum Nachweis spezifischer keywords: aber; allerdings; als; anderen; antikörper; auch; auf; aufgrund; aus; bakterien; bei; beim; bestimmung; bis; bzw; children; coli; daher; dann; das; dass; dem; der; des; diagnostik; diarrhö; die; diese; dna; durch; ehec; eine; elisa; enzym; erfolgt; erkrankungen; etwa; für; gör; insbesondere; ist; jedoch; kann; können; lassen; liver; malabsorption; messung; mit; mittels; nach; nachweis; nicht; noch; nur; oder; pcr; reflux; sensitivität; serum; sich; sie; sind; sowie; spezifität; stuhl; test; und; verfahren; von; vor; werden; wie; wird; während; zum; zur; über; üblicherweise cache: cord-032134-mvj7i1er.txt plain text: cord-032134-mvj7i1er.txt item: #172 of 973 id: cord-034689-se1hdn61 author: Smith, David L. title: A Characteristic Chest Radiographic Pattern in the Setting of COVID-19 Pandemic date: 2020-09-03 words: 2920 flesch: 43 summary: Rather, these societies recommend CT use be reserved for management of COVID-19 patients with worsening and/or severe respiratory symptoms, in particular for those in a hospital setting or those having special indications for CT Characteristic CXR of a 63-year-old female presenting with dyspnea and fever. keywords: chest; covid-19; cxr; patients; pcr cache: cord-034689-se1hdn61.txt plain text: cord-034689-se1hdn61.txt item: #173 of 973 id: cord-034746-uxhpufnv author: Nusshag, Christian title: Glomerular filtration barrier dysfunction in a self-limiting, RNA virus-induced glomerulopathy resembles findings in idiopathic nephrotic syndromes date: 2020-11-05 words: 3655 flesch: 29 summary: Interestingly, the start of normalization of urinary nephrin and PCR levels preceded the first decline of SCr by 48-72 h. Furthermore, in patients with an available urine sample at the time of PCR normalization, the normalization of urinary nephrin levels tended to precede the normalization of PCR levels. In contrast to INS, proteinuria recovered autonomously in hantavirus patients. keywords: hantavirus; igg; infection; levels; nephrin; patients; pcr; proteinuria; urinary cache: cord-034746-uxhpufnv.txt plain text: cord-034746-uxhpufnv.txt item: #174 of 973 id: cord-035280-z0bbz19b author: Lee, Seung Hun title: First identification of Anaplasma phagocytophilum in both a biting tick Ixodes nipponensis and a patient in Korea: a case report date: 2020-11-11 words: 3948 flesch: 43 summary: infection rates in ticks collected from migratory birds on Hongdo Island, Korea, A. phagocytophilum was detected in only 1 I. nipponensis nymph, among a total of 212 ticks (40 Haemaphysalis flava, 12 H. longicornis, 146 I. turdus, 13 I. nipponensis, and 1 I. ornithophilia) A. phagocytophilum has previously been identified in three tick species (H. longicornis, I. persulcatus, and I. nipponensis) in Korea, but no direct transmission from ticks to humans has been confirmed. keywords: anaplasma; blood; fig; korea; patient; pcr; phagocytophilum; spp; tick cache: cord-035280-z0bbz19b.txt plain text: cord-035280-z0bbz19b.txt item: #175 of 973 id: cord-048359-lz37rh82 author: Li, Jin title: s-RT-MELT for rapid mutation scanning using enzymatic selection and real time DNA-melting: new potential for multiplex genetic analysis date: 2007-06-01 words: 6264 flesch: 39 summary: s-RT-MELT was subsequently applied in the same manner to screen for p53 mutations in exons 5-7 from cell lines and surgical colon samples harboring sequencing-identified mutations including a single-base frameshift mutation in exon 7 (listed in Supplementary Table 2 ). Since 480% of p53 mutations in human tumors are encountered in exons 5-9 (45), the multiplex single-tube s-RT-MELT reaction could be used to identify most p53 mutations encountered in clinical tumor samples. keywords: dna; exon; figure; melt; melting; mutation; p53; pcr; samples; time cache: cord-048359-lz37rh82.txt plain text: cord-048359-lz37rh82.txt item: #176 of 973 id: cord-048470-33mqfj2t author: Takano, T title: Quantitative measurement of thyroglobulin mRNA in peripheral blood of patients after total thyroidectomy date: 2001-07-17 words: 3043 flesch: 48 summary: Further, there was no statistical difference in expression levels of TG mRNA in the patients with or without metastasis, and no significant correlation was found between serum TG concentrations and the expression levels of TG mRNA. For example, TG mRNA in peripheral blood became detectable earlier than serum TG in a case of recurrent thyroid papillary carcinoma. keywords: blood; mrna; patients; pcr; thyroid cache: cord-048470-33mqfj2t.txt plain text: cord-048470-33mqfj2t.txt item: #177 of 973 id: cord-102411-0mo1198e author: Moreno Borraz, LA title: PREVALENCIA DE INFECCIÓN POR CORONAVIRUS SARS-CoV-2 EN PACIENTES Y PROFESIONALES DE UN HOSPITAL DE MEDIA Y LARGA ESTANCIA EN ESPAÑA date: 2020-11-13 words: 3432 flesch: 39 summary: De acuerdo con el procedimiento emitido el 24 de enero de 2020 por la Dirección General de Salud Pública del Ministerio de Sanidad de España para solicitar una PCR confirmatoria, se consideró caso en investigación por COVID-19 los pacientes que hubieran viajado a Wuham o hubieran tenido un contacto estrecho con un caso confirmado en los 14 días previos al comienzo de los síntomas sumado al criterio clínico (neumonía o fiebre con infección respiratoria aguda). Presentamos un estudio de prevalencia de la infección por SARS-CoV-2 en pacientes y profesionales de un hospital de Media y Larga Estancia realizado en los meses del pico de la pandemia en España. keywords: con; cov-2; del; estudio; hospital; infección; los; pacientes; para; patients; pcr; por; prevalencia; profesionales; que; sars; staff; una cache: cord-102411-0mo1198e.txt plain text: cord-102411-0mo1198e.txt item: #178 of 973 id: cord-102511-7zgd45fl author: Khodakov, Dmitriy title: Donut PCR: a rapid, portable, multiplexed, and quantitative DNA detection platform with single-nucleotide specificity date: 2020-05-05 words: 4292 flesch: 39 summary: There are patents pending on the Donut PCR chip and Donut PCR instrument presented in this work. key: cord-102511-7zgd45fl authors: Khodakov, Dmitriy; Li, Jiaming; Zhang, Jinny X.; Zhang, David Yu title: Donut PCR: a rapid, portable, multiplexed, and quantitative DNA detection platform with single-nucleotide specificity date: 2020-05-05 journal: bioRxiv DOI: 10.1101/2020.04.24.058453 sha: doc_id: 102511 cord_uid: 7zgd45fl Current platforms for molecular analysis of DNA markers are either limited in multiplexing (qPCR, isothermal amplification), turnaround time (microarrays, NGS), quantitation accuracy (isothermal amplification, microarray, nanopore sequencing), or specificity against single-nucleotide differences (microarrays, nanopore sequencing). keywords: amplification; chamber; chip; dna; donut; fig; human; instrument; pcr; platform; reaction; snp cache: cord-102511-7zgd45fl.txt plain text: cord-102511-7zgd45fl.txt item: #179 of 973 id: cord-103163-0rreoh4o author: Smith, Sydni Caet title: Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage date: 2020-10-22 words: 8989 flesch: 40 summary: The rsT3D I S4 RNA profiles were more consistent among lineages than those of the M1 and L1 segments and were similar to those of rsT1L S4, with non-canonical RNA segments just slightly larger than the full-length segment and at ~0.15 kb detected in several passages (Fig. 4) . Non-canonical reovirus segments feature large deletions. keywords: cells; dvgs; fig; length; passage; products; recombination; reovirus; rna; rotavirus; rst1l; rst3d; segments; sequence; sites; viruses cache: cord-103163-0rreoh4o.txt plain text: cord-103163-0rreoh4o.txt item: #180 of 973 id: cord-103417-2uinislh author: Doi, Hideyuki title: On-site eDNA detection of species using ultra-rapid mobile PCR date: 2020-10-01 words: 1507 flesch: 43 summary: Our ultra-rapid on-site eDNA extraction and measurement method using mobile PCR successfully detected the eDNA of H. molitrix, and analysis took only 30 min. The Ct of mobile PCR was larger than that of qPCR, because the DNA concentration in the field-extracted samples was lower. keywords: detection; edna; method; pcr; site cache: cord-103417-2uinislh.txt plain text: cord-103417-2uinislh.txt item: #181 of 973 id: cord-103563-7a3wdduq author: Nunez-Bajo, Estefania title: Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens date: 2020-03-25 words: 4541 flesch: 35 summary: As shown in Figure 4C , the peak current intensity (measured from the recorded SWVs) increased two to four times in comparison to room temperature when operated at higher temperatures; this is due to enhanced transport of the analyte to the surface of the electrode. We speculate that this could be related to thermal and electrical crosstalk between the heater and the electrochemical sensing structures which introduce additional noise to the electroanalytical measurements at higher temperatures. keywords: amplification; chip; cost; detection; dna; figure; pcr; silicon; temperature; time; trisilix cache: cord-103563-7a3wdduq.txt plain text: cord-103563-7a3wdduq.txt item: #182 of 973 id: cord-103735-nil1vv6h author: Alfano, Niccolo title: Non-invasive surveys of mammalian viruses using environmental DNA date: 2020-03-29 words: 5837 flesch: 49 summary: Viral contigs were confirmed by PCR and Sanger sequencing for samples L7, L17, L25 and L37 (Suppl. Of the 11 water filtrate samples tested, two samples from Mongolia (WM3 and WM20) (18.2%) had viral contigs with 100% identity to the Equid herpesvirus 1 and 3 (EHV-1 and EHV-3). keywords: capture; contigs; dna; fig; identity; leeches; pcr; reads; rna; samples; sediment; sequences; suppl; viruses; water; wildlife cache: cord-103735-nil1vv6h.txt plain text: cord-103735-nil1vv6h.txt item: #183 of 973 id: cord-103787-qhftb6d7 author: Garcia, Elizabeth P. title: Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics date: 2005-10-31 words: 7379 flesch: 42 summary: PCR primers are designed for each target so that the amplicon length serves as a unique identifier for each particular target. Second, because detection does not require probe hydrolysis, all restrictions related to the probe design (probe length and composition, distance to PCR primers) do not influence primer selection. keywords: amplification; analysis; expression; gene; multiplex; pcr; primers; reaction; rna; samples; sars; sequence; star; time cache: cord-103787-qhftb6d7.txt plain text: cord-103787-qhftb6d7.txt item: #184 of 973 id: cord-140318-xtx8hl14 author: Martin, Alexandra title: High-sensitivity COVID-19 group testing by digital PCR date: 2020-06-03 words: 4254 flesch: 49 summary: This can prevent weakly positive specimen from being detected in group samples (3, 8) . Group testing has been proposed as a solution to expand testing capabilities but sensitivity concerns have limited its impact on the management of the pandemic. keywords: dpcr; groups; individual; pcr; samples; sars; testing cache: cord-140318-xtx8hl14.txt plain text: cord-140318-xtx8hl14.txt item: #185 of 973 id: cord-158252-l43ztxsl author: Pawlowski, Colin title: Longitudinal laboratory testing tied to PCR diagnostics in COVID-19 patients reveals temporal evolution of distinctive coagulopathy signatures date: 2020-05-21 words: 6131 flesch: 30 summary: During each time window, we then compared the distribution of results from COVIDpos versus COVIDneg patients, allowing us to identify any lab tests which were significantly altered in COVIDpos patients during any time of disease acquisition, onset, and/or progression. With respect to erythrocytes, we found that both COVIDpos and COVIDneg patients developed a worsening mild anemia after PCR testing, but the trajectory was actually slower for COVIDpos patients (Figures 1B, 1H, Table 1 ). keywords: cohort; covid-19; covidneg; covidpos; diagnosis; lab; patients; platelet; test; testing; time cache: cord-158252-l43ztxsl.txt plain text: cord-158252-l43ztxsl.txt item: #186 of 973 id: cord-245161-xbw72k4m author: Castano, Nicolas title: Fomite transmission and disinfection strategies for SARS-CoV-2 and related viruses date: 2020-05-23 words: 11563 flesch: 37 summary: 67 Plaque assays involve culturing cells that are susceptible to virus infection in a titration of the collected virus samples, monitoring the cytopathic effects, and counting plaque forming units (PFU). The long persistence of viruses (hours to days) on surfaces calls for an urgent need for surface disinfection strategies to intercept virus transmission and the spread of the disease. keywords: adsorption; contact; contamination; coronavirus; cov-2; disinfectant; disinfection; dose; effectiveness; fomites; inactivation; interactions; methods; model; particles; risk; sars; study; surfaces; transfer; transmission; virus; viruses cache: cord-245161-xbw72k4m.txt plain text: cord-245161-xbw72k4m.txt item: #187 of 973 id: cord-252198-gs52k4lq author: Onions, David title: Validation of the safety of MDCK cells as a substrate for the production of a cell-derived influenza vaccine date: 2010-09-30 words: 6601 flesch: 38 summary: The use of cell based vaccines has the potential to transform the strategies for prophylaxis of seasonal and pandemic influenza, but demonstrating the safety of these vaccines is an essential prerequisite. Since these experiments were conducted, Khan and colleagues have formulated a specific algorithmic approach for the exclusion of retroviruses in vaccine cell substrates keywords: bpl; cells; control; dna; influenza; manufacturing; mdck-33016pf; pcr; process; production; studies; test; vaccine; virus; viruses cache: cord-252198-gs52k4lq.txt plain text: cord-252198-gs52k4lq.txt item: #188 of 973 id: cord-252268-o63ep08b author: Carolan, Louise A. title: TaqMan real time RT-PCR assays for detecting ferret innate and adaptive immune responses date: 2014-09-01 words: 6668 flesch: 40 summary: We also assessed TNF␣ expression using previously published TaqMan primers and probe (Nakata et al., 2009 ) and SYBR Green primers Rowe et al., 2010) with our samples and the profiles were consistent with those obtained with the TaqMan assay designed in this study (data not shown). The gene stability of housekeeping genes was calculated using geNorm in qbase+ Version 2.5 (Biogazelle) (Vandesompele et al., 2002) . keywords: cells; cytokine; efficiency; et al; expression; ferret; fig; genes; influenza; pcr; rna; taqman; time; virus cache: cord-252268-o63ep08b.txt plain text: cord-252268-o63ep08b.txt item: #189 of 973 id: cord-252347-vnn4135b author: Lee, Wai-Ming title: A Diverse Group of Previously Unrecognized Human Rhinoviruses Are Common Causes of Respiratory Illnesses in Infants date: 2007-10-03 words: 5718 flesch: 46 summary: Selection of the target region To identify a genomic region suitable for molecular typing of HRV, we analyzed all published HRV sequences. These results suggested HRV serotypes are stable and do not undergo influenza virus-like antigenic drift [7] . keywords: hrv; hrvs; human; new; pcr; region; sequences; serotypes; strains cache: cord-252347-vnn4135b.txt plain text: cord-252347-vnn4135b.txt item: #190 of 973 id: cord-252604-1u14i4v1 author: Smith, Alvin W. title: Vesivirus viremia and seroprevalence in humans date: 2006-03-22 words: 5272 flesch: 45 summary: Vesivirus caliciviruses are resistant to environmental degradation; stable in aquatic substrates; multiply to high titer, with an estimated 10 13 virions released into the ocean daily by a single California gray whale (Eschricitus gibbosus) [Matson, 1999] . To test the possibility that sera may contain Vesivirus genomes, as suggested by the clinical evidence of viremia in cases of Vesivirus illness, including humans [Smith et al., 1998a] , three complementary methods targeting three Vesivirus genomic regions were utilized to detect Vesivirus RNA in serum ( Fig. 1 ): dot blot for the ORF1 3C protease region, reverse transcriptionpolymerase chain reaction (RT-PCR) for the 3 0 terminal region of ORF1 encoding a portion of the viral RNA polymerase or for a portion of the viral capsid protein, and nucleotide sequencing of RT-PCR amplicons. keywords: amplicons; blood; donors; et al; hepatitis; marine; pcr; region; smith; smith et; smsv; vesivirus cache: cord-252604-1u14i4v1.txt plain text: cord-252604-1u14i4v1.txt item: #191 of 973 id: cord-252694-36ijqwge author: Heidinger, Benedikt H. title: Radiologische Manifestationen von Lungenerkrankungen bei COVID-19 date: 2020-09-08 words: 2968 flesch: 35 summary: Besteht jedoch der Verdacht auf eine im Rahmen von COVID-19 gehäuft auftretende Pulmonalembolie, sollte eine kontrastmittelunterstützte CT in pulmonalarterieller Phase durchgeführt werden Die schwerste Form der Lungenbeteiligung im Rahmen von COVID-19 manifestiert keywords: auf; bei; chest; covid-19; der; die; disease; einer; imaging; ist; mit; oder; patienten; patients; pcr; pneumonia; sich; und; von cache: cord-252694-36ijqwge.txt plain text: cord-252694-36ijqwge.txt item: #192 of 973 id: cord-252838-av7ducrk author: Lucchi, Naomi W. title: Real-Time Fluorescence Loop Mediated Isothermal Amplification for the Diagnosis of Malaria date: 2010-10-29 words: 4917 flesch: 49 summary: The sensitivity and specificity of RealAmp method was calculated using both microscopy and a nested PCR assay We compared DNA obtained by the standard Qiagen method of DNA isolation and that obtained by direct heating for their performance in RealAmp method. keywords: amplification; dna; falciparum; malaria; method; pcr; realamp; samples cache: cord-252838-av7ducrk.txt plain text: cord-252838-av7ducrk.txt item: #193 of 973 id: cord-253502-v2hh3w3r author: Leung, C.W. title: Clinical picture, diagnosis, treatment and outcome of severe acute respiratory syndrome (SARS) in children date: 2004-11-05 words: 8632 flesch: 40 summary: Important questions to ask in the 'peace time' include: (1) history of recent travel to pre-viously SARS-affected areas or areas with an increased likelihood of animal to human transmission of SARS-CoV infection; (2) close contact with a suspected SARS patient; (3) history of recent hospitalisation or contact with a healthcare facility; (4) individuals who are either healthcare workers or laboratory workers with potential exposure to SARS patients or live SARS-CoV; and (5) link to a cluster of cases of unexplained respiratory illness in the community. Sputum specimens appear to have a higher diagnostic yield but productive cough is uncommon in SARS patients in the early phase of illness and sputum is difficult to obtain in children. keywords: acute; adults; children; clinical; coronavirus; cov; diagnosis; disease; illness; infection; patients; pcr; sars; severe; syndrome; treatment cache: cord-253502-v2hh3w3r.txt plain text: cord-253502-v2hh3w3r.txt item: #194 of 973 id: cord-253826-63dgq551 author: Kim, Jisung title: State of diagnosing infectious pathogens using colloidal nanomaterials date: 2017-08-17 words: 10498 flesch: 34 summary: A novel dengue virus detection method that couples DNAzyme and gold nanoparticle approaches MNAzymes, a versatile new class of nucleic acid enzymes that can function as biosensors and molecular switches A plasmonic DNAzyme strategy for point-ofcare genetic detection of infectious pathogens Terrylenediimide-based intrinsic theranostic nanomedicines with high photothermal conversion efficiency for photoacoustic imaging-guided cancer therapy Size-dependent Ag 2S nanodots for second near-infrared fluorescence/photoacoustics imaging and simultaneous photothermal therapy Diverse applications of nanomedicine Tuning the drug loading and release of DNA-assembled gold-nanorod superstructures Generating heat with metal nanoparticles Significantly improved analytical sensitivity of lateral flow immunoassays by using thermal contrast Thermal contrast amplification reader yielding 8-fold analytical improvement for disease detection with lateral flow assays Integrated quantum dot barcode smartphone optical device for wireless multiplexed diagnosis of infected patients A smartphone dongle for diagnosis of infectious diseases at the point of care Colloidal stability of gold nanoparticles modified with thiol compounds: bioconjugation and application in cancer cell imaging Diagnostic point-of-care tests in resource-limited settings Cheap HIV Test Finds Success as First of its Kind Tested in the Field Microfluidics-based diagnostics of infectious diseases in the developing world Nanotechnology and molecular cytogenetics: the future has not yet arrived Microscopic and macroscopic manipulation of gold nanorod and its hybrid nanostructures Nanomaterialbased electrochemical biosensors formedical applications Sensing colorimetric approaches based on gold and silver nanoparticles aggregation: chemical creativity behind the assay. Nucleic acid based detection can also be problematic because it requires a complex sample preparation step. keywords: assay; detection; diagnosis; diseases; dna; fig; fluorescence; gnps; gold; molecules; nanoparticles; nucleic; pathogens; pcr; probes; properties; qds; quantum; sensitivity; signal; surface; system; target cache: cord-253826-63dgq551.txt plain text: cord-253826-63dgq551.txt item: #195 of 973 id: cord-254064-qxgpehuy author: Chacko, J. title: Hydroxychloroquine in COVID-19: A systematic review and meta-analysis date: 2020-05-19 words: 4038 flesch: 52 summary: We included randomized controlled trials and observational studies in which hydroxychloroquine was adminstered and compared to a control group. Both randomized controlled trials (RCTs) and observational studies with a comparator group were considered for inclusion. keywords: covid-19; hydroxychloroquine; license; patients; preprint; studies cache: cord-254064-qxgpehuy.txt plain text: cord-254064-qxgpehuy.txt item: #196 of 973 id: cord-254101-613aftc1 author: Wang, Ping title: Establishment of a transgenic mouse model with liver-specific expression of secretory immunoglobulin D date: 2012-04-14 words: 4415 flesch: 53 summary: International Hyper-IgD Study Group Molecular analysis of the mevalonate kinase gene in a cohort of patients with the hyper-igd and periodic fever syndrome: its application as a diagnostic tool Carrier frequency of the V377I (1129G>A) MVK mutation, associated with Hyper-IgD and periodic fever syndrome, in the Netherlands Periodic fever syndromes--a clinical overview Hereditary periodic fever Deletion of a single mevalonate kinase (Mvk) allele yields a murine model of hyper-IgD syndrome Diagnostic value of serum immunoglobulinaemia D level in patients with a clinical suspicion of hyper IgD syndrome The recruitment of inflammatory cells using the skin-window technique New insights into the enigma of immunoglobulin D Immunoglobulin D: properties, measurement, and clinical relevance Tissue-specific in vitro transcription from the mouse albumin promoter The rat albumin promoter is composed of six distinct positive elements within 130 nucleotides Determinants of rat albumin promoter tissue specificity analyzed by an improved transient expression system Nummular keratopathy in a patient with Hyper-IgD Syndrome B cell cytopenia in two brothers with hyper-IgD and periodic fever syndrome A patient with hyper-IgD syndrome responding to simvastatin treatment A patient with hyper-IgD syndrome in Antalya The rat albumin promoter: cooperation with upstream elements is required when binding of APF/HNF1 to the proximal element is partially impaired by mutation or bacterial methylation Functional analysis of the trans-acting factor binding sites of the mouse alpha-fetoprotein proximal promoter by site-directed mutagenesis Cell-specific expression of mouse albumin promoter--evidence for cell-specific DNA elements within the proximal promoter region and cis-acting DNA elements upstream of -160 An albumin enhancer located 10-kb upstream functions along with its promoter to direct efficient, liver-specific expression in transgenic mice Functional analyses of albumin expression in a series of hepatocyte cell lines and in primary hepatocytes Rescuing transgene expression by co-integration High level expression of a functional human/mouse chimeric anti-CD20 monoclonal antibody in milk of transgenic mice Transgenic mice secreting coronavirus neutralizing antibodies into the milk Monoclonal IgD. Mouse GAPDH was used as an internal control when we detected the sIgD expression in transgenic mouse liver with Western blotting. keywords: alb; cells; expression; hids; liver; mice; mouse; mvk; pcr; sigd; syndrome; transgenic cache: cord-254101-613aftc1.txt plain text: cord-254101-613aftc1.txt item: #197 of 973 id: cord-254115-hwy962a4 author: Reslova, Nikol title: xMAP Technology: Applications in Detection of Pathogens date: 2017-01-25 words: 11370 flesch: 34 summary: The need for rapid and correct identifications of fungal pathogens was addressed by development of xMAP technology based detection methods (Diaz and Fell, 2004; Page and Kurtzman, 2005; Das et al., 2006; Bovers et al., 2007; Babady et al., 2011; Balada-Llasat et al., 2012; Farooqi et al., 2012; Landlinger et al., 2009) . xMAP technology is applicable in numerous nucleic acid assay formats such as, e.g., gene expression analysis, microRNA analysis, single nucleotide polymorphism (SNP) analysis or specific sequence detection. keywords: assay; ddh; detection; dna; et al; human; identification; luminex; methods; microsphere; multiplex; pathogens; pcr; probes; samples; sensitivity; sequence; simultaneous; specificity; target; technology; viruses; xmap; xtag cache: cord-254115-hwy962a4.txt plain text: cord-254115-hwy962a4.txt item: #198 of 973 id: cord-254250-l0v602x9 author: Hooper, Chantelle title: A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh date: 2020-10-02 words: 6445 flesch: 44 summary: Global scale of freshwater prawn farming A review on the diseases of freshwater prawns with special focus on white tail disease of Macrobrachium rosenbergii Current status and prospects of farming the giant river prawn Macrobrachium rosenbergii (De Man) in Bangladesh Shrimp Research Station Mass larval mortality in a giant freshwater prawn Macrobrachium rosenbergii hatchery: An attempt to detect microbes in the berried and larvae Fishing for prawn larvae in Bangladesh: An important coastal livelihood causing negative effects on the environment Distinctive histopathology of Spiroplasma eriocheiris infection in the giant river prawn Macrobrachium rosenbergii A viral disease associated with mortalities in hatchery-reared postlarvae of the giant freshwater prawn Macrobrachium rosenbergii Extra small virus-like particles (XSV) and nodavirus associated with whitish muscle disease in the giant freshwater prawn, Macrobrachium rosenbergii White tail disease of the giant freshwater prawn Macrobrachium rosenbergii in Thailand Experimental transmission and tissue tropism of Macrobrachium rosenbergii nodavirus (MrNV) and its associated extra small virus (XSV) RT-PCR amplification and sequence analysis of extra small virus associated with white tail disease of Macrobrachium rosenbergii (de Man) cultured in Taiwan Macrobrachium rosenbergii nodavirus infection in a giant freshwater prawn hatchery in Indonesia Isolation and Characterization of a Novel Dicistrovirus Associated with Moralities of the Great Freshwater Prawn, Macrobrachium rosenbergii Infectious hypodermal and haematopoietic necrosis virus (IHHNV) infections in giant freshwater prawn, Macrobrachium rosenbergii Description of a Natural Infection with Decapod Iridescent Virus 1 in Farmed Giant Freshwater Prawn, Macrobrachium rosenbergii Parvo-like virus in the hepatopancreas of freshwater prawns Macrobrachium rosenbergii cultivated in Thailand Tolerance of Macrobrachium rosenbergii to white spot syndrome virus Clearance of white spot syndrome virus (WSSV) and immunological changes in experimentally WSSV-injected Macrobrachium rosenbergii In experimental challenge with infectious clones of Macrobrachium rosenbergii nodavirus (MrNV) and extra small virus (XSV), MrNV alone can cause mortality in freshwater prawn (Macrobrachium rosenbergii) Characterization and pathogenicity studies of Vibrio parahaemolyticus isolated from diseased freshwater prawn A Wrapper Tool around Cutadapt and FastQC to Consistently Apply Quality and Adapter Trimming to FastQ Files A Quality Control Tool for High Throughput Sequence Data Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads Accurate de novo assembly of RNA virus genomes Fast and sensitive protein alignment using DIAMOND MEGAN Community Edition-Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data Fast and accurate short read alignment with Burrows-Wheeler transform Genome Project Data Processing The Sequence Alignment/Map format and SAMtools Integrative genomics viewer Evaluating next-generation sequencing alignment data Prokka: Rapid prokaryotic genome annotation GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Furthermore, RNA viruses can only be visualised indirectly in histology sections (normally associated with damaged host cells and nuclei). keywords: bangladesh; disease; genome; hatcheries; hatchery; larvae; macrobrachium; mortalities; mrgv; prawn; protein; rna; rosenbergii; virus cache: cord-254250-l0v602x9.txt plain text: cord-254250-l0v602x9.txt item: #199 of 973 id: cord-254265-8i86c8kt author: Camps, Marta title: Prevalence of human metapneumovirus among hospitalized children younger than 1 year in Catalonia, Spain date: 2008-06-12 words: 4573 flesch: 34 summary: Integrated software for molecular evolutionary genetics analysis an sequence alignment Detection of human metapneumovirus in clinical samples by immunofluorescence staining of shell vial centrifugation cultures prepared from three different cell lines Realtime reverse transcriptase PCR assay for detection of human metapneumoviruses from all known genetic lineages Reducing the impact of viral respiratory infections in children Respiratory tract reinfections by the new human Metapneumovirus in an immunocompromised child Rapid detection of human metapneumovirus strains in nasopharyngeal aspirates and shell vial cultures by monoclonal antibodies Characterization of human metapneumoviruses isolated from patients in North America Detection and typing by molecular techniques of respiratory viruses in children hospitalized for acute respiratory infection in First detection of human metapneumovirus in children with acute respiratory infection in India: A preliminary report Detection and pathogenicity of human metapneumovirus respiratory infection in pediatric Italian patients during a winterspring season Dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis Bronchiolitis-associated hospitalizations among US children A newly discovered human pneumovirus isolated from young children with respiratory tract disease Absence of human metapneumovirus co-infection in cases of severe respiratory syncytial virus infection Ten years' experience with year-round active surveillance of up to 19 respiratory pathogens in children Estimates of world-wide distribution of child deaths from acute respiratory infections Human metapneumovirus and lower respiratory tract disease in otherwise healthy infants and children Although some studies have detected human metapneumovirus in all age groups, human metapneumovirus infections could be more severe in children, elderly, and immunocompromised patients [Pelletier et al., 2002; Bastien et al., 2003; Cane et al., 2003; Falsey et al., 2003] . keywords: children; et al; human; infection; metapneumovirus; patients; pcr; study; tract; viruses cache: cord-254265-8i86c8kt.txt plain text: cord-254265-8i86c8kt.txt item: #200 of 973 id: cord-254450-ienq3aex author: Kim, Dae-Ki title: Tools to Detect Influenza Virus date: 2013-05-01 words: 4422 flesch: 46 summary: For instance, monkey kidney cells, Madin Darby canine kidney (MDCK) cells and A549 cells are used to detect influenza viruses. One of the major preventions from circulating strains of influenza virus and the complications associated with the viral infection is by vaccination. keywords: detection; diagnosis; h1n1; influenza; pcr; sensitivity; test; virus; viruses cache: cord-254450-ienq3aex.txt plain text: cord-254450-ienq3aex.txt item: #201 of 973 id: cord-254506-cxdklz4u author: Castellvi, J. title: Impact On Clinical Practice Of The Preoperative Screening Of Covid-19 Infection In Surgical Oncological Patients. Prospective Cohort Study date: 2020-08-11 words: 1868 flesch: 48 summary: In the present situation of COVID-19 pandemia, it has been reported that oncological surgical patients have a higher risk of being infected with COVID-19 than other non-oncological surgical patients due to the cancer itself, the immunosuppression related to it as well as to the oncological and surgical treatments [1] [2] Conclusion preoperative screening for COVID-19-infection using medical history and PCR helped the surgeon to decide whether to go ahead or postpone surgery in oncological patients. keywords: covid-19; infection; patients; study cache: cord-254506-cxdklz4u.txt plain text: cord-254506-cxdklz4u.txt item: #202 of 973 id: cord-254825-c5d0wul9 author: Kim, Sei Won title: Containment of a healthcare-associated COVID-19 outbreak in a university hospital in Seoul, Korea: A single-center experience date: 2020-08-14 words: 3562 flesch: 46 summary: Severe symptoms develop in approximately 14% of COVID-19 patients, and the overall mortality is around 2% of confirmed COVID-19 cases [10] . Contact was defined as presence in the same room with COVID-19 confirmed patients, or in the same outpatient clinic or examination room, 30 minutes before and after COVID-19 confirmed patients. keywords: contact; cov-2; covid-19; hospital; outbreak; patients; pcr; sars cache: cord-254825-c5d0wul9.txt plain text: cord-254825-c5d0wul9.txt item: #203 of 973 id: cord-255013-njpuc475 author: He, Xiaocui title: Establishment of Myotis myotis Cell Lines - Model for Investigation of Host-Pathogen Interaction in a Natural Host for Emerging Viruses date: 2014-10-08 words: 4531 flesch: 46 summary: Euro surveillance : bulletin europeen sur les maladies transmissibles Fatal human rabies caused by European bat Lyssavirus type 2a infection in Scotland Emerging diseases in Chiroptera: why bats? Passive surveillance (1987 to 2004) of United Kingdom bats for European bat lyssaviruses Experimental Nipah virus infection in pteropid bats (Pteropus poliocephalus) Experimental hendra virus infectionin pregnant guinea-pigs and fruit Bats (Pteropus poliocephalus) Antiviral immune responses of bats: a review Transmission studies of Hendra virus (equine morbillivirus) in fruit bats, horses and cats Experimental study of European bat lyssavirus type-2 infection in Daubenton's bats (Myotis daubentonii) Bats and viruses: friend or foe? Pathogenesis studies with Australian bat lyssavirus in grey-headed flying foxes (Pteropus poliocephalus) Establishment, immortalisation and characterisation of pteropid bat cell lines Type I interferon reaction to viral infection in interferon-competent, immortalized cell lines from the African fruit bat Eidolon helvum Establishment of cell line from embryonic tissue of Pipistrellus ceylonicus bat species from India & its susceptibility to different viruses Bat airway epithelial cells: a novel tool for the study of zoonotic viruses Interferon production and signaling pathways are antagonized during henipavirus infection of fruit bat cell lines Anti-Lyssaviral Activity of Interferons kappa and omega from the Serotine Bat, Eptesicus serotinus White-nose syndrome fungus: a generalist pathogen of hibernating bats Standardized detection of Simian virus 40 by real-time quantitative polymerase chain reaction in pediatric malignancies Enhanced passive bat rabies surveillance in indigenous bat species from Germany -a retrospective study Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) A broader variety of bat cell lines, particularly European bat cell lines from tissues of immune relevance, is therefore urgently in demand for lyssavirus-host studies. keywords: bats; cell; expression; fig; ifn; infection; lines; lyssavirus; mmbr; myotis; virus cache: cord-255013-njpuc475.txt plain text: cord-255013-njpuc475.txt item: #204 of 973 id: cord-255019-iie8wxb4 author: Chen, Xin title: Acute lower respiratory tract infections by human metapneumovirus in children in Southwest China: A 2‐year study date: 2010-06-25 words: 4009 flesch: 42 summary: In this study, we describe a hospital‐based epidemiological study of hMPV in patients presenting to a children's hospital and show the demographic and clinical characteristics associated with hMPV infection in China, retrospectively. Real-time PCR primers and probe sequences to detect the hMPV F gene (Table 1) were used for the diagnosis of hMPV infection and were selected based on sequence homology with the prototype strain from China (GenBank accession: DQ336144). keywords: children; hmpv; human; infection; metapneumovirus; patients; pcr; rsv; study cache: cord-255019-iie8wxb4.txt plain text: cord-255019-iie8wxb4.txt item: #205 of 973 id: cord-255026-fdp6mies author: Belák, Sándor title: Molecular diagnosis of viral diseases, present trends and future aspects: A view from the OIE Collaborating Centre for the Application of Polymerase Chain Reaction Methods for Diagnosis of Viral Diseases in Veterinary Medicine date: 2007-07-26 words: 5344 flesch: 36 summary: The real-time PCR assays provide novel rapid means of virus detection in the diagnostic laboratories. By introducing single and nested PCR assays as early as 1987-1988, two years after the description of the PCR principle, our laboratory was among the first ones to use this technique for diagnostic purposes [2, 3] . keywords: assays; detection; diagnosis; diseases; methods; pcr; pcr assays; time; time pcr; virus; viruses cache: cord-255026-fdp6mies.txt plain text: cord-255026-fdp6mies.txt item: #206 of 973 id: cord-255043-uxdsjr39 author: Bustin, Stephen A. title: RT-qPCR Testing of SARS-CoV-2: A Primer date: 2020-04-24 words: 4563 flesch: 40 summary: Samples for PCR testing for COVID-19 are usually taken from inside the nose, the mouth or the back of the throat, and careful sampling and nucleic acid preparation are important pre-test considerations. For now, the Coronavirus standards working group (https://jimb.stanford.edu/covid-19-standards), led by the Joint Initiative for Metrology in Biology, is developing a set of guidelines to ensure the availability of common, appropriate standards, controls, validation tests and protocols that are essential for the accuracy of test results. keywords: dna; instruments; min; qpcr; results; rna; run; testing cache: cord-255043-uxdsjr39.txt plain text: cord-255043-uxdsjr39.txt item: #207 of 973 id: cord-255096-27dfbhsl author: Sweet, Michael J. title: Reprint of ‘Diseases in marine invertebrates associated with mariculture and commercial fisheries’ date: 2016-06-19 words: 18109 flesch: 47 summary: Diagnosis and/or treatment: Based on disease signs only at the current time. Diagnosis and/or treatment: Based on disease signs only at the current time. keywords: agent; date; diagnosis; disease; disease signs; epidemiology; et al; hosts; individuals; infection; lobsters; mortality; oie; outbreaks; oysters; pacific; parasite; pathogens; pathology; pcr; populations; shrimp; signs; species; spread; syndrome; tissues; treatment; virus; white; wild cache: cord-255096-27dfbhsl.txt plain text: cord-255096-27dfbhsl.txt item: #208 of 973 id: cord-255384-tljyx6ua author: Decaro, Nicola title: Full-Genome Analysis of a Canine Pneumovirus Causing Acute Respiratory Disease in Dogs, Italy date: 2014-01-06 words: 4647 flesch: 51 summary: The relatedness to other CnPnVs (98.5% of aa identity) was confirmed in the putative N protein (393 aa), which displayed 6 substitutions among canine viruses. In both proteins that were 176 and 98 aa in length, respectively, the Italian CnPnV was more closely related to extant canine viruses than to MPVs (aa identities of 98.9% and 99% in the M2-1 and M2-2 products, respectively). keywords: bari/100; canine; cnpnv; dogs; gene; identity; mpv; pcr; strain; virus cache: cord-255384-tljyx6ua.txt plain text: cord-255384-tljyx6ua.txt item: #209 of 973 id: cord-255465-sc1yzzsn author: Krasteva, Gabriela title: Caveolin-1 and -2 in airway epithelium: expression and in situ association as detected by FRET-CLSM date: 2006-08-11 words: 5696 flesch: 46 summary: Conventional indirect double-labeling immunofluorescence with subsequent FRET-CLSM analysis was conducted to determine whether cav-1 and cav-2 are in close apposition in airway epithelial cells in situ, thereby indicating an association of both proteins and formation of hetero-oligomers. in epithelial cells. keywords: anti; basal; cav-1α; cav-2; caveolae; cells; epithelium; expression; figure; membrane; mice; tracheal cache: cord-255465-sc1yzzsn.txt plain text: cord-255465-sc1yzzsn.txt item: #210 of 973 id: cord-255495-xnoppq3y author: Elrashdy, Fatma title: On the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity date: 2020-07-09 words: 7538 flesch: 35 summary: Disaster Medicine and Public Health Preparedness MERS-coronavirus replication induces severe in vitro cytopathology and is strongly inhibited by cyclosporin A or interferon-a treatment Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn Eleven faces of coronavirus disease Ultrastructural evidence for direct renal infection with SARS-CoV-2 Vaginal delivery in SARS-CoV-2 infected pregnant women in Northern Italy: A retrospective analysis Spread and dynamics of the COVID-19 epidemic in Italy: Effects of emergency containment measures The role of extracellular vesicles as allies of HIV, HCV and SARS viruses Expanding our understanding of the role polyprotein conformation plays in the coronavirus life cycle Modern uses of electron microscopy for detection of viruses Ultrastructural characterization of SARS coronavirus Pathology and pathogenesis of severe acute respiratory syndrome Respiratory viral infection in lung transplantation induces exosomes that trigger chronic rejection Donorderived exosomes with lung self-antigens in human lung allograft rejection The role of extracellular vesicles in COVID-19 virus infection Recurrence of positive SARS-CoV-2 in patients recovered from COVID-19 Retest positive for SARS-CoV-2 RNA of recovered patients with COVID-19: A very interesting case was recently reported, where a 78-year-old woman that was ready to be discharged after the three consecutive PCR tests on her nasopharyngeal swab samples indicated that she was SARS-CoV-2 negative, her conditions were significantly improved, and CT examination showed absorption of pulmonary exudation, but suddenly she fell into the cardiac arrest and died (Yao et al., 2020) . keywords: cells; coronavirus; cov-2; covid-19; dmvs; et al; infection; membrane; particles; patients; pcr; replication; rna; sars; vesicles; virus cache: cord-255495-xnoppq3y.txt plain text: cord-255495-xnoppq3y.txt item: #211 of 973 id: cord-255545-nycdhdsd author: Schoenike, Barry title: Quantitative sense-specific determination of murine coronavirus RNA by reverse transcription polymerase chain reaction date: 1999-03-10 words: 6182 flesch: 37 summary: A striking change in the expected relative or absolute abundance of viral RNA of a given sense may provide clues as to the mode of viral replication in vitro or of viral pathogenesis in vivo. However, in many experiments, particularly with samples obtained in vivo, viral RNA may not be of sufficiently high concentration to allow detection by this technique. keywords: assay; pcr; primers; reaction; rna; rnas; sense; sequences; templates; viral cache: cord-255545-nycdhdsd.txt plain text: cord-255545-nycdhdsd.txt item: #212 of 973 id: cord-255711-8lojw5cz author: Palmu, Arto A. title: Nasal swab bacteriology by PCR during the first 24‐months of life: A prospective birth cohort study date: 2019-01-04 words: 2021 flesch: 28 summary: Pediatr Pulmonol DOI: 10.1002/ppul.24231 sha: doc_id: 255711 cord_uid: 8lojw5cz BACKGROUND: Most respiratory bacterial carriage studies in children are based on cross‐sectional samples or longitudinal studies with infrequent sampling points. 1 Carriage of respiratory bacterial pathogens, such as Streptococcus pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae, is a prerequisite for two important childhood ARIs; acute otitis media, which is the most frequently reported pediatric bacterial infection, 2 and bacterial pneumonia, a leading cause of childhood deaths. keywords: carriage; children; pcr; pneumoniae; streptococcus; study cache: cord-255711-8lojw5cz.txt plain text: cord-255711-8lojw5cz.txt item: #213 of 973 id: cord-255871-dau9tz6u author: Lee, Mi-Kyung title: Survey of Clinical Laboratory Practices for 2015 Middle East Respiratory Syndrome Coronavirus Outbreak in the Republic of Korea date: 2015-12-18 words: 2612 flesch: 43 summary: Clinical laboratories were able to quickly expand their diagnostic capacity in response to the 2015 MERS-CoV outbreak. Our results show that clinical laboratories play an important role in the maintenance and enhancement of laboratory response in preparation for future emerging infections. keywords: cov; laboratories; laboratory; mers; outbreak; pcr cache: cord-255871-dau9tz6u.txt plain text: cord-255871-dau9tz6u.txt item: #214 of 973 id: cord-255975-ymw9avlm author: Ho, Yen‐Peng title: Advances in mass spectrometry for the identification of pathogens date: 2011-05-09 words: 15955 flesch: 26 summary: They proposed a simple method to fabricate IgG functionalized gold nanoparticles as useful probes of the electrostatic interactions between IgG and pathogens (Ho et al., 2004) . Synthesis and characterization of multifunctional nanoclinics for biological applications Characterization of Aspergillus spores by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Behavior of bacteria in the inductively coupled plasma: Atomization and production of atomic ions for mass spectrometry Integration of microfiltration and anion-exchange nano particles-based magnetic separation with MALDI mass spectrometry for bacterial analysis Selective binding of mannose-encapsulated gold nanoparticles to type 1 pili in Escherichia coli Affinity capture using vancomycin-bound magnetic nanoparticles for the MALDI-MS analysis of bacteria Universal sample preparation method for characterization of bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry Affinity capture of uropathogenic Escherichia coli using pigeon ovalbumin-bound Fe 3 O 4 @Al 2 O 3 magnetic nanoparticles Identification of Pseudomonas aeruginosa using functional magnetic nanoparticle-based affinity capture combined with MALDI MS analysis Identification of microbial mixtures by LCselective proteotypic-peptide analysis (SPA) keywords: acid; analysis; approach; bacteria; biomarkers; cells; desorption; detection; et al; flight; gram; identification; ionization; laser; laser desorption; maldi; mass; mass spectrometry; matrix; methods; microbial; microorganisms; ms analysis; pathogens; pcr; protein; samples; species; spectra; spectrometry; time cache: cord-255975-ymw9avlm.txt plain text: cord-255975-ymw9avlm.txt item: #215 of 973 id: cord-255983-3dq99xz9 author: Do, Lien Anh Ha title: A sensitive real-time PCR for detection and subgrouping of human respiratory syncytial virus date: 2012-01-17 words: 4273 flesch: 38 summary: The assay was designed to detect all known RSV strains and to differentiate RSV subgroups A and B. Primers (MTH1 and MTH2B) were selected using Primer Express software v2.0 (Applied Biosystems Inc., Foster city (CA), USA) and a dataset of 45N gene sequences available from the NCBI database (Table 1) to amplify 84 bp for both RSV A and RSV B. RSV subgroups No significant differences in RSV viral load were observed between patients with single infections versus co-infections, or between patients requiring oxygen versus patients who did not. keywords: assay; detection; et al; load; pcr; rsv; virus cache: cord-255983-3dq99xz9.txt plain text: cord-255983-3dq99xz9.txt item: #216 of 973 id: cord-256130-zhlvvuj4 author: Nordén, Rickard title: Quantification of Torque Teno Virus and Epstein-Barr Virus Is of Limited Value for Predicting the Net State of Immunosuppression After Lung Transplantation date: 2018-03-06 words: 4856 flesch: 42 summary: When Tacrolimus was the main immunosuppressive treatment, TTV DNA levels were significantly elevated 6–24 months after transplantation as compared with Cyclosporine treatment. To compare results regarding TTV levels between different transplantation centers, it is vital to reliably quantify the concentrations of TTV-DNA in a standardized manner. keywords: dna; ebv; infection; levels; lung; months; patients; pcr; time; transplantation; ttv; virus cache: cord-256130-zhlvvuj4.txt plain text: cord-256130-zhlvvuj4.txt item: #217 of 973 id: cord-256146-d599uera author: Kuiken, Thijs title: Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome date: 2003-07-26 words: 5704 flesch: 43 summary: Replication in SARS-CoV-infected macaques of pneumonia similar to that in human beings with SARS, combined with the high prevalence of SARS-CoV infection in SARS patients, fulfill the criteria required to prove that SARS-CoV is the primary cause of SARS. Collectively, these results of laboratory studies of SARS patients and experimental infections of macaques prove that the newly discovered SARS-CoV is the primary causal agent of SARS. keywords: cells; coronavirus; cov; human; infection; lung; macaques; metapneumovirus; patients; pcr; samples; sars; virus cache: cord-256146-d599uera.txt plain text: cord-256146-d599uera.txt item: #218 of 973 id: cord-256244-f5zsy56p author: Funakoshi, Yu title: Enterovirus D68 respiratory infection in a children's hospital in Japan in 2015 date: 2019-08-22 words: 3870 flesch: 41 summary: A systematic review Two cases of acute severe flaccid myelitis associated with enterovirus D68 infection in children A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): A retrospective cohort study Acute flaccid paralysis following enterovirus D68 associated pneumonia A cluster of acute flaccid paralysis and cranial nerve dysfunction temporally associated with an outbreak of enterovirus D68 in children in Colorado, USA Acute flaccid myelitis in the United States Neurologic complications in children with enterovirus 71 infection National Institute of Infectious Diseases. 23 Fourth, in the EV-D68 PCR-negative group, some patients infected with EV-D68 might have been missed on PCR due to the long interval between sampling and symptom onset. keywords: asthma; children; d68; enterovirus; patients; pcr; study; symptoms cache: cord-256244-f5zsy56p.txt plain text: cord-256244-f5zsy56p.txt item: #219 of 973 id: cord-256338-ovj63ith author: bhattacharya, b. title: SARS-CoV-2 RT-PCR profile in 298 Indian COVID-19 patients : a retrospective observational study date: 2020-06-20 words: 2148 flesch: 55 summary: Conclusion : This study showed that the average period of PCR positivity is more than 2 weeks in COVID-19 patients; elderly patients have prolonged duration of RT-PCR positivity and requires further follow up. Aim: To analyse the SARS CoV-2 nucleic acid RT-PCR profiles in COVID-19 patients. keywords: license; patients; pcr; preprint cache: cord-256338-ovj63ith.txt plain text: cord-256338-ovj63ith.txt item: #220 of 973 id: cord-256355-muskjaw3 author: Black, Elizabeth M title: A rapid RT-PCR method to differentiate six established genotypes of rabies and rabies-related viruses using TaqMan™ technology date: 2002-05-14 words: 4302 flesch: 47 summary: The N gene was used as the target for the probes as it is well conserved and has been intensively used to genotype rabies isolates. There is a large amount of N gene sequence data available, which, on examination, revealed conserved regions specific to each genotype that could be used to design genotype specific TaqMan™ probes. keywords: et al; genotype; isolates; pcr; probe; rabies; taqman; viruses cache: cord-256355-muskjaw3.txt plain text: cord-256355-muskjaw3.txt item: #221 of 973 id: cord-256456-rg366bk2 author: Kulcsar, Gabor title: Testing for viral contaminants of veterinary vaccines in Hungary date: 2010-05-31 words: 2804 flesch: 44 summary: Vaccinology: past achievements, present roadblocks and future promises Comptes Rendus de l'Academie des Sciences -Series III -Sciences de la Vie Quality control of vaccines Tests for sterility and freedom from contamination of biological materials Genotypes of Pestivirus RNA detected in live virus vaccines for human use Similarity of avian paramyxovirus serotype 1 isolates of low virulence for chickens obtained from contaminated poultry vaccines and from poultry flocks Expression of RD114 virus and its receptor in feline cell lines: potential risk of contamination of live attenuated vaccines by RD114 virus. While these efforts minimise the risk of contamination, vaccine contamination cannot be excluded. keywords: contamination; pcr; ttv; vaccines; virus cache: cord-256456-rg366bk2.txt plain text: cord-256456-rg366bk2.txt item: #222 of 973 id: cord-256608-ajzk86rq author: van Weezep, Erik title: PCR diagnostics: In silico validation by an automated tool using freely available software programs date: 2019-05-13 words: 4953 flesch: 48 summary: To increase the accuracy of the alignment search (see Discussion), large sequences were fragmented in sequences of maximal 3000 nucleotides with an overlap of 50 nucleotides to prevent the loss of hits of primer or probe sequences spanning the split site. Primer and probe sequences were inserted in all possible combinations and orientations potentially initiating amplification ( Fig. 1 ). keywords: pcr; pcrv; primer; probe; sequences; silico; validation; virus cache: cord-256608-ajzk86rq.txt plain text: cord-256608-ajzk86rq.txt item: #223 of 973 id: cord-256702-lwxt4587 author: Song, Lingjie title: A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests date: 2020-04-06 words: 2040 flesch: 54 summary: https://doi.org/10.1101/2020.03.31.20045401 doi: medRxiv preprint The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health -The latest 2019 novel coronavirus outbreak in Wuhan A new coronavirus associated with human respiratory disease in China A novel coronavirus outbreak of global health concern Negative Nasopharyngeal and Oropharyngeal Swab Does Not Rule Out COVID-19 A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. https://doi.org/10.1101/2020.03.31.20045401 doi: medRxiv preprint pathogenic nucleic acid genomes from samples of asymptomatic and occult infected patients is also conducive to studying the virus mutations in the pathogenic genes providing a basis for subsequent virus tracing and epidemiological investigations. keywords: cov-2; license; medrxiv; preprint; sars cache: cord-256702-lwxt4587.txt plain text: cord-256702-lwxt4587.txt item: #224 of 973 id: cord-256931-wj0esjwi author: Gelfer, Gita title: The clinical impact of the detection of potential etiologic pathogens of community-acquired pneumonia date: 2015-08-05 words: 4858 flesch: 44 summary: There were fewer days of antibiotic therapy, P = 0.003, in CAP patients with viral infections and a low serum PCT levels. For detection of viruses, patients were randomized to either a 5-virus laboratory-generated PCR bundle or the 17-virus FilmArray PCR platform. keywords: patients; pcr; pct; pneumoniae; sputum; study cache: cord-256931-wj0esjwi.txt plain text: cord-256931-wj0esjwi.txt item: #225 of 973 id: cord-256982-t6urqus7 author: Wellinghausen, Nele title: Evaluation of the SARS-CoV-2-IgG response in outpatients by five commercial immunoassays date: 2020-09-16 words: 2550 flesch: 41 summary: So, we evaluated the SARS-CoV-2-IgG response (and SARS-CoV-2 total antibody response, respectively, in one immunoassay) in 51 outpatients with past SARS-CoV-2 infection confirmed by RT-PCR as well as 7 asymptomatic contact persons with past positive SARS-CoV-2-PCR. The sensitivity in serum samples, collected at a median of 24 days after onset of symptoms, detected by the Anti-SARS-CoV-2-ELISA IgG (Euroimmun), EDI™ Novel Coronavirus COVID-19 IgG ELISA (Epitope Diagnostics), Liaison(®) SARS-CoV-2 S1/S2 IgG (Diasorin), SARS-CoV-2 IgG on the Architect™ i2000 (Abbott), and Elecsys(®) Anti-SARS-CoV-2 (IgM/IgA/IgG) on the cobas™ e801 (Roche) was 84.3%, 78.4%, 74.5%, 86.3%, and 88.2%, respectively. keywords: cov-2; igg; patients; samples; sars cache: cord-256982-t6urqus7.txt plain text: cord-256982-t6urqus7.txt item: #226 of 973 id: cord-257217-f9sdt7ax author: Nunes, Marta C. title: Clinical Epidemiology of Bocavirus, Rhinovirus, Two Polyomaviruses and Four Coronaviruses in HIV-Infected and HIV-Uninfected South African Children date: 2014-02-03 words: 4642 flesch: 37 summary: A role for Streptococcus pneumoniae in virusassociated pneumonia Respiratory viral and pneumococcal coinfection of the respiratory tract: implications of pneumococcal vaccination A new virus isolated from the human respiratory tract Recovery in tracheal organ cultures of novel viruses from patients with respiratory disease A newly discovered human pneumovirus isolated from young children with respiratory tract disease Cloning of a human parvovirus by molecular screening of respiratory tract samples Identification of a new human coronavirus Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia Identification of a third human polyomavirus A newly reported human polyomavirus, KI virus, is present in the respiratory tract of Australian children Identification of a novel polyomavirus from patients with acute respiratory tract infections The role of rhinovirus in asthma exacerbations Rhinovirus viremia in children with respiratory infections Differing manifestations of respiratory syncytial virus-associated severe lower respiratory tract infections in human immunodeficiency virus type 1-infected and uninfected children Increased burden of respiratory viral associated severe lower respiratory tract infections in children infected with human immunodeficiency virus type-1 Respiratory viruses in HIV-infected patients with suspected respiratory opportunistic infection Contribution of common and recently described respiratory viruses to annual hospitalizations in children in South Africa Human polyomaviruses, WU and KI in HIV exposed children with acute lower respiratory tract infections in hospitals in South Africa Pneumococcal coinfection with human metapneumovirus A trial of a 9-valent pneumococcal conjugate vaccine in children with and those without HIV infection Evaluation of NucliSens easyMAG for automated nucleic acid extraction from various clinical specimens Development of the Respiratory Index of Severity in Children (RISC) score among young children with respiratory infections in South Africa Viral acute respiratory infections among infants visited in a rural hospital of southern Mozambique Accepted for publication) Clinical epidemiology of newly discovered respiratory viruses in HIV-infected and HIVuninfected South African children A preliminary study of pneumonia etiology among hospitalized children in Kenya Viral etiology of severe pneumonia among Kenyan infants and children Human coronavirus NL63 associated with lower respiratory tract symptoms in early life Epidemiology of multiple respiratory viruses in childcare attendees Human respiratory coronavirus HKU1 versus other coronavirus infections in Italian hospitalised patients Detection of four human coronaviruses in respiratory infections in children: a one-year study in Colorado Clinical assessment and improved diagnosis of bocavirus-induced wheezing in children Rationale and expectations of the Pneumonia Etiology Research for Child Health (PERCH) study The impact of dual viral infection in infants admitted to a pediatric intensive care unit associated with severe bronchiolitis Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children The association of newly identified respiratory viruses with lower respiratory tract infections in Korean children Prevention (2012) Severe coinfection with seasonal influenza A (H3N2) virus and Staphylococcus aureus-Maryland Furthermore, respiratory viral infections may heighten the susceptibility to developing a super-imposed bacterial infection resulting in severe pneumonia keywords: children; hiv; infections; lrti; study; viral; viruses cache: cord-257217-f9sdt7ax.txt plain text: cord-257217-f9sdt7ax.txt item: #227 of 973 id: cord-257284-dash9udv author: Decaro, Nicola title: Development and validation of a real-time PCR assay for specific and sensitive detection of canid herpesvirus 1 date: 2010-07-30 words: 3166 flesch: 38 summary: In real-time PCR CHV-1 was detected in the vaginal swab of the dam of pups 257/01-N and 257/01-T and in all the tissues of the three infected pups. For construction of CHV-1 standard DNA, the 136-bp fragment generated by the primers used for real-time PCR was cloned into a pCR ® 4-TOPO ® vector (TOPO TA Cloning ® Kit for Sequencing, Invitrogen srl, Milan, Italy) and propagated in chemically competent Escherichia coli one-shot TOP10 cells, following the manufacturer's instructions. keywords: assay; canine; chv-1; decaro; dna; pcr; time cache: cord-257284-dash9udv.txt plain text: cord-257284-dash9udv.txt item: #228 of 973 id: cord-257316-dmc8wjyl author: Ko, Fanny W.S. title: Viral Etiology of Acute Exacerbations of COPD in Hong Kong date: 2007-09-30 words: 4040 flesch: 38 summary: The relationship between influenza vaccination and the detection rates of influenza viruses in NPA by PCR method is shown in Table 4 . In a study 28 of the viral etiology among 17 patients hospitalized with near-fatal asthma (from endotracheal aspiration), 29 patients with acute asthma (from induced sputum), and 14 patients with COPD (from induced sputum) in Singapore, influenza virus was identified in 36% of the subjects hospitalized with AECOPD. keywords: aecopd; hospital; influenza; npa; patients; pcr; study; virus; viruses cache: cord-257316-dmc8wjyl.txt plain text: cord-257316-dmc8wjyl.txt item: #229 of 973 id: cord-257398-fmkfo5ju author: Meng, Qing-Bin title: Clinical application of combined detection of SARS-CoV-2-specific antibody and nucleic acid date: 2020-10-06 words: 3252 flesch: 43 summary: Of the 652 suspected COVID-19 patients, 237 (36.3%) had positive nucleic acid tests, 311 (47.7%) were positive for IgM, and 592 (90.8%) were positive for IgG. There was a significant difference in the positive detection rate between the IgM and IgG test groups (P < 0.001). Therefore, 366 patients were considered to have COVID-19 with SARS-CoV-2 IgM and/or IgG antibody tests. keywords: cov-2; covid-19; igg; igm; patients; sars; tests cache: cord-257398-fmkfo5ju.txt plain text: cord-257398-fmkfo5ju.txt item: #230 of 973 id: cord-257456-15bm9psj author: Arumugam, Arunkumar title: A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings date: 2020-09-24 words: 5296 flesch: 55 summary: As a reference, we can detect five copies of SARS-CoV-2, positive control plasmid (CDC) per PCR reaction using primer targeting N2. Our findings in this paper with COVID-19 clinical samples suggest that it is possible to eliminate the RNA extraction step in COVID-19 testing without a significant drop in assay sensitivity for samples from symptomatic patients. keywords: cov-2; covid-19; extraction; pcr; rna; samples; sars; time cache: cord-257456-15bm9psj.txt plain text: cord-257456-15bm9psj.txt item: #231 of 973 id: cord-257521-1amcsgmj author: Hirsilä, Maija title: Detection by Reverse Transcription–Polymerase Chain Reaction of Influenza C in Nasopharyngeal Secretions of Adults with a Common Cold date: 2001-04-15 words: 2310 flesch: 51 summary: Influenza viruses Community-acquired influenza C virus infection in children Concepts and procedures for laboratorybased influenza surveillance Detection and identification of human influenza viruses by the polymerase chain reaction Type-specific identification of influenza viruses A, B, and C by the polymerase chain reaction Viruses and bacteria in the etiology of the common cold Sinusitis in the common cold Epidemiology of influenza C virus in man: multiple evolutionary lineages and low rate of change Comparison of enzyme-linked immunosorbent assay and hemagglutination inhibition in a seroepidemiological study of influenza type C infection Influenza C virus infection in France Isolation of influenza C virus during an outbreak of influenza A and B viruses Antibiotics and upper respiratory infection: do some folks think there is a cure for the common cold? key: cord-257521-1amcsgmj authors: Hirsilä, Maija; Kauppila, Jaana; Tuomaala, Katri; Grekula, Birgitta; Puhakka, Tuomo; Ruuskanen, Olli; Ziegler, Thedi title: Detection by Reverse Transcription–Polymerase Chain Reaction of Influenza C in Nasopharyngeal Secretions of Adults with a Common Cold date: 2001-04-15 journal: J Infect Dis DOI: 10.1086/319675 sha: doc_id: 257521 cord_uid: 1amcsgmj The lack of practical methods for a laboratory diagnosis of influenza C virus infections and the seemingly benign nature of the virus contribute to the fact that 50 years after its first isolation, relatively little is known about the epidemiology and the clinical impact of this virus. keywords: influenza; patients; pcr; study; virus cache: cord-257521-1amcsgmj.txt plain text: cord-257521-1amcsgmj.txt item: #232 of 973 id: cord-257600-0plhquk9 author: Calles, Antonio title: Outcomes of COVID-19 in Patients With Lung Cancer Treated in a Tertiary Hospital in Madrid date: 2020-09-16 words: 6983 flesch: 43 summary: We aimed to analyze outcomes of lung cancer patients affected by COVID-19 in a tertiary hospital of a high-incidence region during the pandemic. Conclusions: Lung cancer patients represent a vulnerable population for COVID-19, according to the high rate of hospitalization, onset of ARDS, and high mortality rate. keywords: cancer; cancer patients; cases; cov-2; covid-19; lung; lung cancer; mortality; patients; sars; therapy; treatment cache: cord-257600-0plhquk9.txt plain text: cord-257600-0plhquk9.txt item: #233 of 973 id: cord-257661-iwwzli0w author: Freymuth, François title: Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness date: 2006-09-22 words: 4477 flesch: 39 summary: Retrospective study Sensitivity of NCI-H292 human lung mucoepidermoid cells for respiratory and other human viruses Evaluation of the Prodesse Hexaplex multiplex PCR assay for direct detection of seven respiratory viruses in clinical specimens Mink lung cells and mixed mink lung and A549 cells for rapid detection of influenza virus and other respiratory viruses Persistence of rhinovirus and enterovirus RNA after acute respiratory illness in children Evaluation of the Hexaplex assay for detection of respiratory viruses in children Comparison of real-time PCR assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children Comparison of a multiplex reverse transcription-PCRenzyme hybridization assay with conventional viral culture and immunofluorescence techniques for the detection of seven viral respiratory pathogens Human metapneumovirus infection among children hospitalized with acute respiratory illness Human picornavirus and coronavirus RNA in nasopharynx of children without concurrent respiratory symptoms Direct detection of respiratory syncytial virus, parainfluenza virus, and adenovirus in clinical respiratory specimens by a multiplex reverse transcription-PCR assay Evaluation of a multiplex reverse transcriptase PCR ELISA for the detection of nine respiratory tract pathogens Monoclonal antibodies versus reverse transcription-PCR for detection of respiratory viruses in a patient population with respiratory tract infections admitted to hospital Diagnosis of respiratory tract viruses in 24 hr by immunofluorescent staining of shell vial cultures containing Madin-Darby Canine Kidney (MDCK) cells A sensitive, specific, and costeffective multiplex reverse transcriptase-PCR assay for the detection of seven common respiratory viruses in respiratory samples Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 Respiratory viral infections among pediatric inpatients and outpatients in Taiwan from 1997 to 1999 Development of a PCR-and hybridization-based assay (PCR Adenovirus Consensus 1 ) for the detection and species identification of adenoviruses in respiratory specimens Human Coronavirus NL63, France Superiority of reverse-transcription polymerase chain reaction to conventional viral culture in the diagnosis of acute respiratory tract infections in children Use of A-549 cells in a clinical virology laboratory key: cord-257661-iwwzli0w authors: Freymuth, François; Vabret, Astrid; Cuvillon‐Nimal, Delphine; Simon, Sandrine; Dina, Julia; Legrand, Loïc; Gouarin, Stéphanie; Petitjean, Joëlle; Eckart, Philippe; Brouard, Jacques title: Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness date: 2006-09-22 journal: J Med Virol DOI: 10.1002/jmv.20725 sha: doc_id: 257661 cord_uid: iwwzli0w The performances of four multiplex PCR (m‐PCR) were compared to direct immunofluorescence assay (DFA) and HuH7 cell culture for the detection of viruses in 263 children admitted to hospital with an acute respiratory illness. keywords: children; et al; methods; pcr; viruses cache: cord-257661-iwwzli0w.txt plain text: cord-257661-iwwzli0w.txt item: #234 of 973 id: cord-258008-t78svobg author: Bruijnesteijn van Coppenraet, L.E.S. title: Comparison of two commercial molecular assays for simultaneous detection of respiratory viruses in clinical samples using two automatic electrophoresis detection systems date: 2010-08-05 words: 3524 flesch: 45 summary: Eighty-seven samples with positive culture detections for one of the viral targets (or positive RT-PCR results for coronavirus or hMPV) were submitted and 86 culture-negative samples were matched based on sample type and age of the patients (range 1 week to 90 years old, median age 8 months). However, in both assays the relative peak-height provides information on the viral load compared to that of the internal control and between multiple virus detections. keywords: detection; dpo; mlpa; pcr; samples; virus cache: cord-258008-t78svobg.txt plain text: cord-258008-t78svobg.txt item: #235 of 973 id: cord-258021-xhx74vr6 author: Waterer, Grant W. title: Diagnosing Viral and Atypical Pathogens in the Setting of Community-Acquired Pneumonia date: 2016-12-21 words: 4409 flesch: 27 summary: and related species Oseltamivir overuse at a Chicago hospital during the 2009 influenza pandemic and the poor predictive value of influenza-like illness criteria Detection of 2009 pandemic influenza A(H1N1) virus Infection in different age groups by using rapid influenza diagnostic tests Evaluation of indirect fluorescent antibody assays compared to rapid influenza diagnostic tests for the detection of pandemic influenza A (H1N1) pdm09 Sensitivity of rapid influenza antigen tests in the diagnosis of pandemic (H1N1)2009 compared with the standard rRT-PCR technique during the 2009 pandemic in Turkey Comparison of the performance of direct fluorescent antibody staining, a point-of-care rapid antigen test and virus isolation with that of RT-PCR for the detection of novel 2009 influenza A (H1N1) virus in respiratory specimens Accuracy of rapid influenza diagnostic tests: a meta-analysis Randomised controlled trial and health economic evaluation of the impact of diagnostic testing for influenza, respiratory syncytial virus and Streptococcus pneumoniae infection on the management of acute admissions in the elderly and high-risk 18-to 64-year-olds Performance of rapid influenza diagnostic testing in outbreak settings Evaluation of 3 rapid influenza diagnostic tests during the 2012-2013 epidemic: influences of subtype and viral load Comparison of two new generation influenza rapid diagnostic tests with instrument-based digital readout systems for influenza virus detection Current approaches for diagnosis of influenza virus infections in humans 43-47 A recent metaanalysis of 159 published studies of rapid influenza tests found the pooled sensitivity, sensitivity, specificity, and positive and negative predictive values to be 62%, 98%, 34%, and 38%, respectively. keywords: assays; detection; diagnosis; influenza; legionella; pathogens; pcr; pneumonia; testing; tests cache: cord-258021-xhx74vr6.txt plain text: cord-258021-xhx74vr6.txt item: #236 of 973 id: cord-258057-ti0rpt0q author: Zhao, Kai title: Establishment of a Porcine Parvovirus (PPV) LAMP Visual Rapid Detection Method date: 2020-07-01 words: 3736 flesch: 51 summary: Green I and realized the visual detection for PPV LAMP instead of by the conventional gel electrophoresis analysis or fluorescent detection . J o u r n a l P r e -p r o o f To verify the specificity of PPV detection by LAMP, the DNA (PPV, PCV2, PRV) and cDNA samples (PRRSV, CSFV) were amplified as sample templates by the LAMP reaction at 59.0℃ for 50 min and terminated at 80℃ for 3 min, respectively. keywords: detection; lamp; method; pcr; porcine; ppv cache: cord-258057-ti0rpt0q.txt plain text: cord-258057-ti0rpt0q.txt item: #237 of 973 id: cord-258250-zueo1xfa author: Hirotsu, Yosuke title: Comparison of Automated SARS-CoV-2 Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients date: 2020-08-12 words: 3112 flesch: 47 summary: Antigen tests have been widely applied to detect infection with viruses other than SARS-CoV-2 [16] . Furthermore, both tests are expected to identify the asymptomatic or presymptomatic SARS-CoV-2 infected persons who are likely to have high viral loads. keywords: antigen; cov-2; qpcr; sars; test; viral cache: cord-258250-zueo1xfa.txt plain text: cord-258250-zueo1xfa.txt item: #238 of 973 id: cord-258438-6exkwp52 author: Marcone, Débora N. title: Diagnóstico de virus respiratorios utilizando un sistema automatizado de PCR múltiples (FilmArray) y su comparación con métodos convencionales date: 2015-03-31 words: 3351 flesch: 44 summary: El objetivo de este estudio fue comparar el desempeño de los métodos habitualmente utilizados en nuestro laboratorio (IF y RT-PCR) con el PR-FilmArray para el diagnóstico viral de las IRA en niños. Además, se utilizó la prueba de McNemar para evaluar la concordancia de los resultados obtenidos por ambos métodos. keywords: acuerdo; con; del; filmarray; las; los; muestras; métodos; para; pcr; por; que; respiratorios; una; virus cache: cord-258438-6exkwp52.txt plain text: cord-258438-6exkwp52.txt item: #239 of 973 id: cord-258724-1qhen1bj author: Young, Barnaby E title: Viral dynamics and immune correlates of COVID-19 disease severity date: 2020-08-28 words: 3616 flesch: 43 summary: Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Interventions to mitigate early spread of SARS-CoV-2 in Singapore: a modelling study Clinical and immunological features of severe and moderate coronavirus disease 2019 Dysregulation of Immune Response in Patients With Coronavirus Longitudinal analyses reveal immunological misfiring in severe COVID-19 Longitudinal COVID-19 profiling associates IL-1RA and IL-10 with disease severity and RANTES with mild disease Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease Virological assessment of hospitalized patients with COVID-2019 Severe Acute Respiratory Syndrome Coronavirus 2-Specific Antibody Responses in Coronavirus Disease Patients Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study Kinetics of SARS-CoV-2 specific IgM and IgG responses in COVID-19 patients Neutralizing Antibody Responses to Severe Acute Respiratory Syndrome Coronavirus 2 in Coronavirus Disease 2019 Inpatients and Convalescent Patients Impact of immune enhancement on Covid-19 polyclonal hyperimmune globulin therapy and vaccine development Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Shedding of infectious virus in hospitalized patients with coronavirus disease-2019 (COVID-19): duration and key determinants SARS-CoV-2 Virus Culture and Subgenomic RNA for Respiratory Specimens from Patients with Mild Coronavirus Disease Temporal dynamics in viral shedding and transmissibility of COVID-19 Epidemiologic Features and Clinical Course of Patients Infected With SARS-CoV-2 in Singapore COVID-19 CRF -ISARIC. Studies of COVID-19 patients have described the inflammatory milieu in severe infections, with raised neutrophils, suppressed lymphocytes and elevated inflammatory mediators [3, 4] . keywords: c r; covid-19; disease; patients; pcr; sars; severity; study cache: cord-258724-1qhen1bj.txt plain text: cord-258724-1qhen1bj.txt item: #240 of 973 id: cord-258768-bjjfkfgg author: McElligott, Susan title: Detection and genetic characterization of canine parvoviruses and coronaviruses in southern Ireland date: 2010-11-24 words: 4386 flesch: 48 summary: Infectious Diseases of the Dog and Cat (4 th ed) Isolation and immunisation studies of a canine parvo-like virus from dogs with hemorrhagic enteritis An update on canine coronaviruses: viral evolution and pathobiology The three-dimensional structure of canine parvovirus and its functional implications Canine parvoviruses and coronaviruses in southern Ireland 501 Evolution of canine parvovirus involved loss and gain of feline host range Rapid antigenic-type replacement and DNA evolution of canine parvovirus Evidence for evolution of canine parvovirus type 2 in Italy First detection of canine parvovirus type 2c in pups with haemorrhagic enteritis in Spain High rate of viral evolution associated with the emergence of carnivore parvovirus Canine parvovirus 2c infection in central Portugal Evidence for immunisation failure in vaccinated adult dogs infected with canine parvovirus type 2c Prevalence and genetic characterization of canine parvoviruses in Korea Occurrence of canine parvovirus type 2c in the United States First detection of canine parvovirus type 2c in South America A novel antigenic variant of canine parvovirus from a Vietnamese dog Clinical and virological findings in pups naturally infected by canine parvovirus type 2 Glu-426 mutant Recombinant canine coronaviruses related to transmissible gastroenteritis virus of swine are circulating in dogs Recovery and characterization of a coronavirus from military dogs with diarrhea Genetic diversity of a canine coronavirus detected in pups with diarrhea in Italy Gain, preservation and loss of a group 1a coronavirus accessory glycoprotein The polymerase in its labyrinth: mechanisms and implications of RNA recombination Evolution of positive-strand RNA viruses High frequency RNA recombination of murine coronavirus Experimental infection of dogs with a novel strain of canine coronavirus causing systemic disease and lymphopenia Genotype-specific fluorogenic RT-PCR assays for the detection and quantitation of canine coronavirus type I and type II RNA in faecal samples of dogs Canine distemper and related diseases: report of a severe outbreak in a kennel Infectious canine hepatitis: an 'old' disease reemerging in Italy Fatal coronavirus infection in puppies following canine parvovirus 2b infection Buonavoglia C (2008) Detection and molecular characterization of a canine norovirus The experimental production of diarrhoea in colostrum deprived axenic and gnotoxenic calves with enteropathogenic Escherichia coli, rotavirus, coronavirus and in a combined infection of rotavirus and E. coli Dual infection of gnotobiotic calves with bovine strains of group A and porcinelike group C rotaviruses influences pathogenesis of the group C rotavirus Evolution of canine parvoviruses -a need for new vaccines? Occurrence of severe gastroenteritis in pups after canine parvovirus vaccine administration: A clinical and laboratory diagnostic dilemma Immunogenicity of an intranasally administered modified live canine parvovirus type 2b vaccine in pups with maternally derived antibodies Cloning and expression of two fragments of the S gene of canine coronavirus type I Phylogenetic analysis of a highly conserved region of the polymerase gene from 11 coronaviruses and development of a consensus polymerase chain reaction assay Sequence analysis of divergent canine coronavirus strains present in a UK dog population Bioedit: a user friendly biological sequence alignment and analysis program for Windows 95/98/NT MEGA4: keywords: canine; ccov; cpv; dogs; gene; ire; samples; strains; type cache: cord-258768-bjjfkfgg.txt plain text: cord-258768-bjjfkfgg.txt item: #241 of 973 id: cord-258819-4boe6t1v author: Waller, Joseph V. title: The Limited Sensitivity of Chest Computed Tomography Relative to Reverse Transcription Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus-2 Infection: A Systematic Review on COVID-19 Diagnostics date: 2020-06-16 words: 4452 flesch: 43 summary: Before delving into the results of CT studies, we must first provide context by assessing the reference standard, RT-PCR, as studies using this diagnostic tool are not all free from risk of bias. In addition, overestimation of chest CT sensitivity is evident when patients with pneumonia are assumed to have COVID-19. keywords: covid-19; patients; pcr; sensitivity; studies cache: cord-258819-4boe6t1v.txt plain text: cord-258819-4boe6t1v.txt item: #242 of 973 id: cord-259004-plst2wno author: van Elden, Leontine J. R. title: Frequent Detection of Human Coronaviruses in Clinical Specimens from Patients with Respiratory Tract Infection by Use of a Novel Real-Time Reverse-Transcriptase Polymerase Chain Reaction date: 2004-02-17 words: 3371 flesch: 48 summary: An outbreak of coronavirus OC43 respiratory infection in Normandy, France The common cold in frail older persons: impact of rhinovirus and coronavirus in a senior daycare center Rhinovirus and coronavirus infection-associated hospitalizations among older adults Identification of severe acute respiratory syndrome in Canada A cluster of cases of severe acute respiratory syndrome in Hong Kong Evaluation of nested Real-Time RT-PCR for Detection of HCoV • JID polymerase chain methods for the detection of human coronaviruses 229E and OC43 Direct diagnosis of human respiratory coronaviruses 229E and OC43 by the polymerase chain reaction Neuroinvasion by human respiratory coronaviruses Detection of rhinovirus, respiratory syncytial virus, and coronavirus infections in acute otitis media by reverse transcriptase polymerase chain reaction Sensitive procedure for the amplification of HIV-1 RNA using a combined reverse-transcription and amplification reaction Simultaneous detection of influenza viruses A and B using real-time quantitative PCR Identification of a novel coronavirus in patients with severe acute respiratory syndrome Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome A major outbreak of severe acute respiratory syndrome in Hong Kong Acute viral infections of upper respiratory tract in elderly people living in the community: comparative, prospective, population based study of disease burden We thank H.W. Doerr (Institute of Medical Virology, Johann Wolfgang Goethe University, Frankfurt am Main, Germany) for the gift of severe acute respiratory syndrome-associated coronavirus. The diagnosis of HCoV infections is hampered, in part, by the difficulty to replicate in-cell cultures, whereas serologic testing is time-consuming and therefore has little clinical significance. keywords: hcov; patients; pcr; rti; specimens; time cache: cord-259004-plst2wno.txt plain text: cord-259004-plst2wno.txt item: #243 of 973 id: cord-259324-g8kv4pvq author: Ko, Suk-Min title: Expression of the protective antigen for PEDV in transgenic duckweed, Lemna minor date: 2011-10-28 words: 2336 flesch: 42 summary: First, to determine the appropriate conditions for selecting Lemna transformants, the effect of increasing concentrations of kanamycin was assessed on Lemna fronds (Fig. 1A) . (1998) reported that proliferation of Lemna fronds varied six-fold across the 25 geographic isolates of Lemna collected at various geographical locations around the world. keywords: gene; kanamycin; lemna; pedv; protein cache: cord-259324-g8kv4pvq.txt plain text: cord-259324-g8kv4pvq.txt item: #244 of 973 id: cord-259422-5ex12eun author: Graat, Judith M title: A prospective, community-based study on virologic assessment among elderly people with and without symptoms of acute respiratory infection date: 2003-12-11 words: 3903 flesch: 38 summary: key: cord-259422-5ex12eun authors: Graat, Judith M; Schouten, Evert G; Heijnen, Marie-Louise A; Kok, Frans J; Pallast, Esther G.M; de Greeff, Sabine C; Dorigo-Zetsma, J.Wendelien title: A prospective, community-based study on virologic assessment among elderly people with and without symptoms of acute respiratory infection date: 2003-12-11 journal: J Clin Epidemiol DOI: 10.1016/s0895-4356(03)00171-9 sha: doc_id: 259422 cord_uid: 5ex12eun BACKGROUND AND OBJECTIVE: Community-based elderly studies concerning microbiology of acute respiratory infections are scarce. In a 1-year community-based study, we prospectively investigated the possible virologic cause of acute respiratory infections in 107 symptomatic case episodes and 91 symptom-free control periods. keywords: acute; case; controls; infection; persons; study; symptoms cache: cord-259422-5ex12eun.txt plain text: cord-259422-5ex12eun.txt item: #245 of 973 id: cord-259458-o2yts5pq author: O’Grady, Kerry‐Ann F. title: Successful application of a simple specimen transport method for the conduct of respiratory virus surveillance in remote Indigenous communities in Australia date: 2011-03-21 words: 3642 flesch: 40 summary: A novel gel-based method for self-collection and ambient temperature postal transport of urine for PCR detection of Chlamydia trachomatis Human coronavirus infections in rural Thailand: a comprehensive study using real-time reverse-transcription polymerase chain reaction assays Comparison of nasopharyngeal nylon flocked swabs with universal transport medium and rayon-bud swabs with a sponge reservoir of viral transport medium in the diagnosis of paediatric influenza Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Quantitative stability of DNA after extended storage of clinical specimens as determined by real-time PCR Parent-collected respiratory specimens-a novel method for respiratory virus and vaccine efficacy research Comparing nose-throat swabs and nasopharyngeal aspirates collected from children with symptoms for respiratory virus identification using real-time polymerase chain reaction Bacterial colonization of the nasopharynx predicts very early onset and persistence of otitis media in Australian aboriginal infants Real-time reverse transcription-PCR assay for comprehensive detection of human rhinoviruses Detection of multiple respiratory pathogens during primary respiratory infection: nasal swab versus nasopharyngeal aspirate using realtime polymerase chain reaction Otitis media in young Aboriginal children from remote communities in Northern and Central Australia: a cross-sectional survey Hospitalisation of Indigenous children in the Northern Territory for lower respiratory illness in the first year of life Comparison of nasopharyngeal aspirate and nasal swab specimens for detection of respiratory syncytial virus in different settings in a developing country Detection of human bocavirus in respiratory, fecal, and blood samples by real-time PCR Hospital-based case-control study of bronchiectasis in indigenous children in Central Australia Detection of novel influenza A(H1N1) virus by real-time RT-PCR Neisseria gonorrhoea multi-antigen sequence typing using non-cultured clinical specimens A quantification of human cells using an ERV-3 real time PCR assay Queensland Children's Medical Research Institute, Level 4, Foundation Building, Royal Children's Hospital We thank the staff, residents and Health Council of the community in which this study was conducted. Combined with sensitive molecular techniques, this approach will help us understand the epidemiology of respiratory viruses and bacteria in remote locations, where recurrent infections and persistent carriage may result in chronic lung disease. keywords: clinic; mean; pcr; specimens; study; time; transport; virus; viruses cache: cord-259458-o2yts5pq.txt plain text: cord-259458-o2yts5pq.txt item: #246 of 973 id: cord-259590-ot933axv author: Fielding, Burtram C title: Human coronavirus NL63: a clinically important virus? date: 2011-03-02 words: 4017 flesch: 47 summary: A novel pancoronavirus RTPCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium Croup is associated with the novel coronavirus NL63 Showed that NL63 infections occur frequently in young children with lower respiratory tract infection and showed a strong association with croup Community epidemiology of human metapneumovirus, human coronavirus NL63, and other respiratory viruses in healthy preschoolaged children using parent collected specimens Detection of human coronavirus NL63, human metapneumovirus and respiratory syncytial virus in children with respiratory tract infections in southwest Sweden Coronavirus causes lower respiratory tract infections less frequently than RSV in hospitalized norwegian children Human coronavirus NL63 and 229E seroconversion in children Seroepidemiology of group I human coronaviruses in children HCoV-NL63 causes disease in children, the elderly and the immunocompromised, and has been detected in 1.0–9.3% of respiratory tract infections in children. keywords: children; coronavirus; disease; hcovnl63; human; infections; nl63; tract cache: cord-259590-ot933axv.txt plain text: cord-259590-ot933axv.txt item: #247 of 973 id: cord-259717-e8ljkv2y author: Holtz, Lori R. title: Geographic variation in the eukaryotic virome of human diarrhea date: 2014-11-01 words: 6753 flesch: 42 summary: This result demonstrates that the significant difference between Northern Territory and Melbourne is not due to the higher number of unique reads obtained for Northern Territory samples. Diarrhea samples from the Northern Territory contained more viral families per sample than diarrhea from Melbourne (p¼ 0.0002 (Wilcoxon)). keywords: children; diarrhea; families; human; melbourne; pcr; samples; sequences; sequencing; territory; viruses cache: cord-259717-e8ljkv2y.txt plain text: cord-259717-e8ljkv2y.txt item: #248 of 973 id: cord-259747-sl9q63oc author: Remmelink, Myriam title: Unspecific post-mortem findings despite multiorgan viral spread in COVID-19 patients date: 2020-08-12 words: 4549 flesch: 43 summary: key: cord-259747-sl9q63oc authors: Remmelink, Myriam; De Mendonça, Ricardo; D’Haene, Nicky; De Clercq, Sarah; Verocq, Camille; Lebrun, Laetitia; Lavis, Philomène; Racu, Marie-Lucie; Trépant, Anne-Laure; Maris, Calliope; Rorive, Sandrine; Goffard, Jean-Christophe; De Witte, Olivier; Peluso, Lorenzo; Vincent, Jean-Louis; Decaestecker, Christine; Taccone, Fabio Silvio; Salmon, Isabelle title: Unspecific post-mortem findings despite multiorgan viral spread in COVID-19 patients date: 2020-08-12 journal: Crit Care DOI: 10.1186/s13054-020-03218-5 sha: doc_id: 259747 cord_uid: sl9q63oc BACKGROUND: Post-mortem studies can provide important information for understanding new diseases and small autopsy case series have already reported different findings in COVID-19 patients. Most of the previous post-mortem studies in COVID-19 patients were conducted using needle biopsies and were therefore rather limited in terms of sampling; our complete autopsy analysis identified considerable heterogeneity of SARS-CoV-2 spread through the human body and provides a more accurate description of macroscopic and microscopic organ alterations. keywords: acute; covid-19; findings; lung; organs; patients; pcr; samples; sars; study cache: cord-259747-sl9q63oc.txt plain text: cord-259747-sl9q63oc.txt item: #249 of 973 id: cord-259823-ia1g5dt4 author: Gowin, Ewelina title: Assessment of the Usefulness of Multiplex Real-Time PCR Tests in the Diagnostic and Therapeutic Process of Pneumonia in Hospitalized Children: A Single-Center Experience date: 2017-01-15 words: 3884 flesch: 40 summary: Estimates of world-wide distribution of child deaths from acute respiratory infections Acute respiratory infections in children Procalcitonin, Creactive protein and leukocyte count in children with lower respiratory tract infection British Thoracic Society guidelines for the management of community acquired pneumonia in children: update The management of community-acquired pneumonia in infants and children older than 3 months of age: clinical practice guidelines by the Pediatric Infectious Diseases Society and the Infectious Diseases Society of America Rekomendacje postępowania w pozaszpitalnych zakażeniach układu oddechowego Viral pneumonia Impact of viral infections in children with community-acquired pneumonia: results of a study of 17 respiratory viruses Clinical and socioeconomic impact of different types and subtypes of seasonal influenza viruses in children during influenza seasons Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay Multiplex PCR and emerging technologies for the detection of respiratory pathogens Performance of a novel microarray multiplex PCR for the detection of 23 respiratory pathogens (SYMP-ARI study) Clinical impact of RT-PCR for pediatric acute respiratory infections: a controlled clinical trial Epidemiological investigation of nine respiratory pathogens in hospitalized children in Germany using multiplex reversetranscriptase polymerase chain reaction The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit Etiology of community-acquired pneumonia in hospitalized children based on WHO clinical guidelines Etiology of community-acquired pneumonia in hospitalized school-age children: evidence for high prevalence of viral infections Epidemiology and virology of acute respiratory infections during the first year of life: a birth cohort study in Vietnam Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children Viral infections in immunocompromised patients Frequent detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction Antibiotic therapy for pediatric community-acquired pneumonia: do we know when, what and for how long to treat? New options in the treatment of respiratory syncytial virus disease Successful treatment of parainfluenza virus respiratory tract infection with DAS181 in 4 immunocompromised children Chemotherapy of respiratory syncytial virus infections: the final breakthrough All authors declare that they have no conflict of interests. FTD respiratory pathogens 33 is an in vitro test with eight multiplex real-time PCR reactions for the qualitative detection of the following viruses, bacteria, and fungi causing respiratory infections: influenza A, B, and C; parainfluenza viruses 1 keywords: children; group; patients; pcr; pneumonia; results; tests cache: cord-259823-ia1g5dt4.txt plain text: cord-259823-ia1g5dt4.txt item: #250 of 973 id: cord-259886-j0bpp7iw author: Cho, Hyejin title: Positive control synthesis method for COVID-19 diagnosis by one-step real-time RT-PCR date: 2020-10-12 words: 2327 flesch: 46 summary: Therefore, this approach may be integrated into the molecular diagnosis of COVID-19 and provides a general method for preparing positive controls for diagnosing emerging RNA virus infections. To overcome this problem, a new efficient method for preparing positive controls for COVID-19 detection kits needs to be developed that can be applied to the detection of emerging viruses, such as influenza A (H1N1), human metapneumovirus (HMPT), and keywords: covid-19; gene; pcr; sars; time cache: cord-259886-j0bpp7iw.txt plain text: cord-259886-j0bpp7iw.txt item: #251 of 973 id: cord-259988-3s7b5ovi author: Decaro, Nicola title: Virological and molecular characterization of a mammalian orthoreovirus type 3 strain isolated from a dog in Italy date: 2005-08-10 words: 3371 flesch: 44 summary: In carnivores, MRV infections have been sporadically reported, although all the three serotypes have been isolated from dogs and cats (Binn et al., 1977; Csiza, 1974; Kokubu et al., 1993; Lou and Wenner, 1963; Marshall et al., 1987; Massie and Shaw, 1966; Mochizuki and Uchizono, 1993; Scott et al., 1970) . MRV-2 and MRV-3 have been isolated from dogs with upper respiratory tract disease (Binn et al., 1977) and diarrhea (Kokubu et al., 1993) , respectively. keywords: gene; mrv; pcr; reovirus; sequence; strain; type cache: cord-259988-3s7b5ovi.txt plain text: cord-259988-3s7b5ovi.txt item: #252 of 973 id: cord-260168-rb7j94dh author: Gu, Jiang title: H5N1 infection of the respiratory tract and beyond: a molecular pathology study date: 2007-09-27 words: 6314 flesch: 46 summary: Our comprehensive investigation of the tissue tropism of H5N1 infl uenza virus, based on two adult autopsies and one fetal autopsy, focuses on the localisation of viral genomic sequences and antigens. In cultures of human tracheobronchial epithelial cells, H5N1 infl uenza viruses have been reported to infect mainly ciliated cells, which express mainly avian infl uenza virus receptors (α-2,3-linked sialic acids), although a limited number of non-ciliated cells (<20% of all infected cells) have also been reported to be infected. keywords: cells; gure; h5n1; human; hybridisation; infl; patient; pcr; rna; situ; uenza; virus cache: cord-260168-rb7j94dh.txt plain text: cord-260168-rb7j94dh.txt item: #253 of 973 id: cord-260231-vayxg23a author: Hsien Koh, Tse title: Epidemiology of Clostridium difficile infection in a large teaching hospital in Singapore date: 2007-08-31 words: 3315 flesch: 51 summary: In France, A 2 B + strains comprised 2.7% of toxigenic C. difficile isolates, Most had a 1.7 kb deletion and the same PCR ribotype. The Swedish C. difficile Study Group Molecular epidemiology of hospital-associated and community-acquired Clostridium difficile infection in a Swedish county Epidemiology and molecular characterization of Clostridium difficile strains from patients with diarrhea: low disease incidence and evidence of limited cross-infection in a Swedish teaching hospital Second-look' cytotoxicity: an evaluation of culture plus cytotoxin assay of Clostridium difficile isolates in the laboratory diagnosis of CDAD Laboratory diagnosis of Clostridium difficile-associated diarrhoea: a plea for culture An outbreak of toxin A negative, toxin B positive Clostridium difficile-associated diarrhea in a Canadian tertiary-care hospital Characterization of a toxin Anegative, toxin B-positive strain of Clostridium difficile responsible for a nosocomial outbreak of Clostridium difficile-associated diarrhea Characterization of toxin A-negative, toxin B-positive Clostridium difficile isolates from outbreaks in different countries by amplified fragment length polymorphism and PCR ribotyping International typing study of toxin A-negative, toxin B-positive Clostridium difficile variants Multicenter evaluation of the Clostridium difficile TOX A/B TEST Prevalence of toxin A negative/B positive Clostridium difficile strains Prevalence and genetic characterization of toxin A variant strains of Clostridium difficile among adults and children with diarrhea in France Clonal dissemination of a toxin-A-negative/toxin-B-positive Clostridium difficile strain from patients with antibiotic-associated diarrhea in Poland Antimicrobial susceptibilities and serogroups of clinical strains of Clostridium difficile isolated in France in 1991 and 1997 Antimicrobial susceptibility pattern of Clostridium difficile and its relation to PCR ribotypes in a Swedish university hospital Clindamycin resistant strains of Clostridium difficile isolated from cases of C. difficile associated diarrhea (CDAD) in a hospital in Sweden Reassessment of Clostridium difficile susceptibility to metronidazole and vancomycin ACKNOWLEDGEMENTS This study was funded by a grant from the National Medical Research Council, Singapore. keywords: cases; clindamycin; clostridium; difficile; isolates; strains; toxin cache: cord-260231-vayxg23a.txt plain text: cord-260231-vayxg23a.txt item: #254 of 973 id: cord-260250-t48y27wg author: Decaro, Nicola title: Quantitation of canine coronavirus RNA in the faeces of dogs by TaqMan RT-PCR date: 2004-05-07 words: 3332 flesch: 39 summary: The CCoV fluorogenic RT-PCR assay, which targeted the ORF5 (M gene), was more sensitive than a conventional RT-PCR assay targeting the same gene, showing a detection limit of 10 copies of CCoV standard RNA, and was linear from 10 to 10(8) copies, allowing quantitation of samples with a wide range of CCoV RNA loads. Several RT-PCR based methods have been developed for detecting CCoV RNA in the faeces of dogs, but none of these were designed to be quantitative (Bandai et al., 1999; Naylor et al., 2001; Pratelli et al., 1999 Pratelli et al., , 2002c . keywords: assay; ccov; et al; fluorogenic; pcr; rna cache: cord-260250-t48y27wg.txt plain text: cord-260250-t48y27wg.txt item: #255 of 973 id: cord-260404-leifaqda author: Ishak, Anthony M. title: Prevalence of Mycoplasma haemofelis, ‘Candidatus Mycoplasma haemominutum’, Bartonella species, Ehrlichia species, and Anaplasma phagocytophilum DNA in the blood of cats with anemia date: 2006-07-17 words: 3402 flesch: 34 summary: In this retrospective study, we used polymerase chain reaction (PCR) assays to determine the prevalence rates of Mycoplasma haemofelis, ‘Candidatus M haemominutum’, A phagocytophilum, Ehrlichia species, and Bartonella species DNA in the blood of cats with anemia and a control group of healthy cats. However, to our knowledge, the Bartonella species prevalence rates as determined by PCR assay results have not been determined in cats with anemia and compared to results from healthy cats. keywords: anemia; bartonella; cats; dna; species cache: cord-260404-leifaqda.txt plain text: cord-260404-leifaqda.txt item: #256 of 973 id: cord-260431-eksl7pp8 author: Sun, Heting title: Isolation and Identification of Feline Herpesvirus Type 1 from a South China Tiger in China date: 2014-02-28 words: 2526 flesch: 47 summary: Challenged cats exhibited uniform clinical symptoms and shed FHV-1 virus. Our finding extends the host range of FHV-1 and has implications for FHV-1 infection and South China tiger conservation. keywords: cats; china; feline; fhv-1; pcr; tiger; virus cache: cord-260431-eksl7pp8.txt plain text: cord-260431-eksl7pp8.txt item: #257 of 973 id: cord-260457-m1jbpo5l author: Allander, Tobias title: Human Bocavirus and Acute Wheezing in Children date: 2007-04-01 words: 3715 flesch: 46 summary: As part of a randomized, placebo-controlled clinical trial evaluating the efficacy of systemic corticosteroids for the treatment of acute expiratory wheezing in children, we performed extensive diagnostic evaluations for respiratory virus infection. We investigated the prevalence of HBoV and the genome HBoV load in the respiratory tract and blood specimens obtained from children who had been hospitalized for acute expiratory wheezing-the most common manifestation of lower respiratory tract infection in children-to investigate the association between HBoV infection and acute respiratory tract illness. keywords: acute; children; hbov; infection; samples; serum; virus; wheezing cache: cord-260457-m1jbpo5l.txt plain text: cord-260457-m1jbpo5l.txt item: #258 of 973 id: cord-260481-twk5kvd3 author: Täufer, Matthias title: Rapid, large-scale, and effective detection of COVID-19 via non-adaptive testing date: 2020-08-18 words: 3855 flesch: 55 summary: However, pool testing is typically performed via an adaptive testing strategy which requires a feedback loop in the lab and at least two PCR runs to confirm positive results. A small modification of our strategy might furthermore allow for an improvement of the false negative rate -even compared to usual adaptive pool testing strategies: even though commonly used, pooling samples can potentially dilute samples close to the identification threshold of the PCR and increase the probaility of false negatives. keywords: pool; positive; size; testing cache: cord-260481-twk5kvd3.txt plain text: cord-260481-twk5kvd3.txt item: #259 of 973 id: cord-260647-7bjhobg7 author: Coudray-Meunier, Coralie title: A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date: 2016-01-29 words: 5584 flesch: 39 summary: This information is available on line on the web site of the Institut de Veille Sanitaire (IVS) at http://www. invs.sante.fr/content/download/6498/42945/version/2/file/fiche_info_patient.pdf for HAV samples and on the web site of the NRC at www.cnr-ve.org for enteric virus samples. Sensitive and quantitative detection of human enteric viruses is typically achieved through quantitative RT-PCR (RT-qPCR). keywords: array; assays; detection; dpcr; qpcr; rna; samples; time; viruses cache: cord-260647-7bjhobg7.txt plain text: cord-260647-7bjhobg7.txt item: #260 of 973 id: cord-260690-h5pjv2dw author: Druce, Julian title: Laboratory diagnosis and surveillance of human respiratory viruses by PCR in Victoria, Australia, 2002–2003 date: 2004-11-12 words: 3805 flesch: 38 summary: The availability of new classes of drugs active against both influenza A and B viruses , preclinical and clinical trials of drugs targeted at respiratory viruses other than influenza [Hayden et al., 2003; Cianci et al., 2004; Uckun et al., 2004] , and the potential for new vaccines [Power et al., 2001] has encouraged further a shorter diagnostic turnaround time for the detection of respiratory viruses. The results of a 2-year retrospective study of respiratory viruses in more than 4,200 specimens obtained from individuals living in Victoria, Australia are presented. keywords: influenza; patients; pcr; specimens; virus; viruses cache: cord-260690-h5pjv2dw.txt plain text: cord-260690-h5pjv2dw.txt item: #261 of 973 id: cord-260700-u12aa739 author: Kainulainen, Leena title: Recurrent and persistent respiratory tract viral infections in patients with primary hypogammaglobulinemia date: 2010-06-10 words: 3695 flesch: 43 summary: The occurrence of respiratory tract viral infections in patients with primary hypogammaglobulinemia has not been studied. Despite adequate immunoglobulin replacement therapy, patients with primary hypogammaglobulinemia have increased susceptibility to respiratory tract viral infections. keywords: hypogammaglobulinemia; infections; nasal; patients; respiratory; rhinoviral; sputum; tract; viruses cache: cord-260700-u12aa739.txt plain text: cord-260700-u12aa739.txt item: #262 of 973 id: cord-260728-4w23kwzu author: Timmermans, Ans title: Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia date: 2016-03-30 words: 7426 flesch: 44 summary: Previous studies have attributed the etiology of acute viral respiratory infections in Cambodia to rhinovirus, respiratory syncytial virus (RSV), parainfluenza virus (PIV), influenza virus A and B, human metapneumovirus (HMPV), bocavirus, adenovirus, enterovirus, and coronavirus Influenza virus efficiently escapes from host antibodies through an accumulation of mutations/single amino acid changes (antigenic drift) at the antigenic sites (epitopes) in surface glycoproteins of the hemagglutinin (HA) gene, and to a lesser extent, neuraminidase (NA) genes [8] . keywords: acid; amino; antigenic; cambodia; changes; gene; influenza; isolates; pcr; samples; sequences; sites; specimens; study; table; virus cache: cord-260728-4w23kwzu.txt plain text: cord-260728-4w23kwzu.txt item: #263 of 973 id: cord-260791-2gmrsm8q author: Iwata, Takanori title: PCR detection and new therapies for COVID-19 date: 2020-06-23 words: 409 flesch: 53 summary: Although members of the general public may consider PCR testing to be an absolutely reliable method, false positives and false negatives can take place. In addition, since PCR testing only detects the RNA fragments of severe acute respiratory syndrome coronavirus 2, the virus that causes COVID-19, it is impossible to distinguish whether the virus is viable using PCR. keywords: covid-19; pcr cache: cord-260791-2gmrsm8q.txt plain text: cord-260791-2gmrsm8q.txt item: #264 of 973 id: cord-260866-bzdd4f5h author: Barceló, Damià title: Wastewater-Based Epidemiology to Monitor COVID-19 Outbreak: Present and Future Diagnostic Methods to be in Your Radar date: 2020-09-14 words: 4680 flesch: 44 summary: Shortly afterwards, the National Medical Products Administration (NMPA) announced nucleic acid testing as the gold standard for virus detection. Most importantly is to encourage the scientists involved in virus detection in WBE to think outside the PCR box by considering other complementary ways to detect COVID-19 outbreak in wastewaters . keywords: biomarkers; biosensors; cov-2; covid-19; detection; methods; pcr; sars; virus; viruses; wastewater; wbe cache: cord-260866-bzdd4f5h.txt plain text: cord-260866-bzdd4f5h.txt item: #265 of 973 id: cord-261089-aul4ifso author: Yuan, Wen title: Development of a duplex real-time RT-PCR for the simultaneous detection and differentiation of Theiler’s murine encephalomyelitis virus and rat theilovirus date: 2016-07-07 words: 4524 flesch: 44 summary: In addition, serologic assays to detect antibodies to RTV in rats have historically used mouse TMEV strains as antigens, exploiting the antigenic cross-reactivity of these viruses with RTV (Easterbrook et al., 2008; Pritchett-Corning et al., 2009) . In the presence of 1 × 10 6 copies/ng of RTV genomic RNA, the TMEV standard curves were similar to those generated from the standard dilutions alone (Fig. 5A) . keywords: assay; duplex; pcr; rna; rtv; time; tmev cache: cord-261089-aul4ifso.txt plain text: cord-261089-aul4ifso.txt item: #266 of 973 id: cord-261128-j55v4clu author: Gagliardi, T.B. title: Concurrent detection of other respiratory viruses in children shedding viable human respiratory syncytial virus date: 2013-07-16 words: 4624 flesch: 38 summary: The children had HRSV infections associated with shedding of viable HRSV, as opposed to HRSV detection only by RT-PCR or rapid antigen detection methods. Cloning of a human parvovirus by molecular screening of respiratory tract samples Acute respiratory viral infections in ambulatory children of urban northeast Brasil Magnetic purification of biotinylated cDNA removes false priming and ensures strand-specificity of RT-PCR for enteroviral RNAs Two-year prospective study of single infections and coinfections by respiratory syncytial virus and viruses identified recently in infants with acute respiratory disease Occurrence and severity of infections caused by subgroup A and B respiratory syncytial virus in children in southest Brazil Respiratory syncytial virus and metapneumovirus Severity of viral coinfection in hospitalized infants with respiratory syncytial virus infection Simultaneous detection and identification of human parainfluenza viruses 1: 2 and 3 from clinical samples by multiplex PCR Human metapneumovirus infections in young and elderly adults Correlation of viral load of respiratory pathogens and co-infections with disease severity in children hospitalized for lower respiratory tract infection Human bocavirus respiratory infections in children in southeast Brazil Prevalence and clinical characteristics of human metapneumovirus infections in hospitalized infants in spain Human metapneumovirus in severe respiratory syncytial virus bronchiolitis Detection of adenovirus in clinical specimens by polymerase chain reaction and liquid-phase hybridization quantitated by time-resolved fluorometry Persistence of adenovirus nucleic acids in nasopharyngeal secretions: A diagnostic conundrum Multiple versus single virus respiratory infections: Viral load and clinical disease severity in hospitalized children Nosocomial respiratory syncytial virus infections in children's wards High rate of viral identification and coinfections in infants with acute bronchiolitis Mixed respiratory virus infections Circulation patterns of genetically distinct group A and B strains of human respiratory syncytial virus in a communities Circulation patterns of group A and B human respiratory syncytial virus genotypes in 5 communities in North America Detection of rhinovirus in sinus brushings of patientes with acute community-acquired sinusits by reverse transcription-PC Detection of human bocavirus mRNA in respiratory secretions correlates with high viral load and concurrent diarrhea Comparison of the directgen flu A þ B test, the QuickVue influenza test, and clinical definition to viral culture and reverse transcription-PCR for rapid diagnosis of influenza virus infection Dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis Viral co-detection in infants hospitalized with respiratory disease: Is it important to detect? Severity of respiratory syncytial virus infection is related to virus strain Comparison of human metapneumovirus, respiratory syncytial virus and influenza A virus lower respiratory tract infections in hospitalized young children Strain-specific reverse transcriptase PCR assay: Means to distinguish candidate vaccine from wild-type strains of respiratory syncytial virus keywords: children; detection; disease; hrsv; infections; patients; pcr; samples; viruses cache: cord-261128-j55v4clu.txt plain text: cord-261128-j55v4clu.txt item: #267 of 973 id: cord-261134-zarq507s author: Pulford, David title: Amplification refractory mutation system PCR assays for the detection of variola and Orthopoxvirus date: 2004-02-13 words: 3803 flesch: 40 summary: When a variola virus specific primer was used with a consensus primer in an ARMS assay with different Orthopoxvirus genomes, a PCR product was only amplified from variola virus DNA. Incorporating a second consensus primer into the assay produced a multiplex PCR that provided Orthopoxvirus generic and variola-specific products with variola virus DNA. keywords: assays; dna; multiplex; orthopoxvirus; pcr; primer; specific; virus cache: cord-261134-zarq507s.txt plain text: cord-261134-zarq507s.txt item: #268 of 973 id: cord-261160-g92zhv19 author: Rowland, Raymond R.R title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date: 2003-10-30 words: 6389 flesch: 42 summary: A unique aspect of this study was the thorough analysis of virus replication in pig tissues during asymptomatic infection (Roman numeral III, Fig. 2 ). key: cord-261160-g92zhv19 authors: Rowland, Raymond R.R; Lawson, Steven; Rossow, Kurt; Benfield, David A title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date: 2003-10-30 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2003.07.006 sha: doc_id: 261160 cord_uid: g92zhv19 The ability of porcine reproductive and respiratory syndrome virus (PRRSV) to establish a persistent infection is the principal contributing factor to the world-wide spread of the disease. keywords: days; infection; pigs; porcine; positive; prrsv; replication; syndrome; virus cache: cord-261160-g92zhv19.txt plain text: cord-261160-g92zhv19.txt item: #269 of 973 id: cord-261237-0hbijukt author: Hou, Peili title: Development of a recombinase polymerase amplification combined with lateral-flow dipstick assay for detection of bovine ephemeral fever virus date: 2017-12-26 words: 4870 flesch: 45 summary: This work was partially supported by grants from National Natural Science Fund of China (31502064, 31672556), Taishan Bovine ephemeral fever in Taiwan Bovine ephemeral fever: a review Bovine ephemeral fever in Australia and the world Preliminary observations on the epidemiology of bovine ephemeral fever in China Large-scale serological survey of bovine ephemeral fever in China A comparison of the epidemiology of bovine ephemeral fever in South Korea and south-western Japan A large-scale outbreak of bovine ephemeral fever in Turkey Bovine ephemeral fever and rhabdoviruses endemic to Australia Epidemiology and control of bovine ephemeral fever Bovine ephemeral fever in beef cattle herds in the Jordan Valley, Israel Epidemiological investigation of bovine ephemeral Fever outbreaks in Israel Development of a reliable assay protocol for identification of diseases (RAPID)-bioactive amplification with probing (BAP) for detection of bovine ephemeral fever virus Antigenic characterization of bovine ephemeral fever rhabdovirus G and GNS glycoproteins expressed from recombinant baculoviruses Phylogenetic relationships of the G gene sequence of bovine ephemeral fever virus isolated in Japan Phylogenetic relationships of the glycoprotein gene of bovine ephemeral fever virus isolated from mainland China Development and application of G1-ELISA for detection of antibodies against bovine ephemeral fever virus Bovine ephemeral fever in Iran: diagnosis, isolation and molecular characterization Characterization of a recombinant Newcastle disease virus expressing the glycoprotein of bovine ephemeral fever virus Expression of G1-epitope of bovine ephemeral fever virus in E. coli : a novel candidate to develop ELISA kit Bovine ephemeral fever: the reaction of cattle to different strains of ephemeral fever virus and the antigenic comparison of two strains of virus The isolation of bovine ephemeral fever virus in cell cultures and evidence for autointerference Application of indirect immunofluorescent assay for the detection of bovine ephemeral fever virus A reverse-transcription PCR method for detecting all known ephemeroviruses in clinical samples Occurrence of bovine ephemeral fever in Okinawa Prefecture, Japan, in 2012 and development of a reverse-transcription polymerase chain reaction assay to detect bovine ephemeral fever virus gene A real-time RTquantative(q)PCR for the detection of bovine ephemeral fever virus A blocking ELISA for the detection of specific antibodies to bovine ephemeral fever virus DNA detection using recombination proteins Recombinase polymerase and enzyme-linked immunosorbent assay as a DNA amplification-detection strategy for food analysis An aptamer-based bio-barcode assay with isothermal recombinase polymerase amplification for cytochrome-c detection and anti-cancer drug screening Multiplex isothermal solid-phase recombinase polymerase amplification for the specific and fast DNAbased detection of three bacterial pathogens Recombinase polymerase amplification assay for rapid detection of Rift Valley fever virus Rapid detection of Plasmodium falciparum with isothermal recombinase polymerase amplification and lateral flow analysis Isothermal Recombinase Polymerase amplification (RPA) of Schistosoma haematobium DNA and oligochromatographic lateral flow detection Recombinase polymerase amplification (RPA) combined with lateral flow (LF) strip for equipment-free detection of Cryptosporidium spp. A report on bovine ephemeral fever virus in Turkey: antigenic variations of different strains of EFV in the 1985 and 2012 outbreaks using partial glycoprotein gene sequences A reverse-transcription, loop-mediated isothermal amplification assay for detection of bovine ephemeral fever virus in the blood of infected cattle Factors influencing Recombinase polymerase amplification (RPA) assay outcomes at point of care Rapid detection of infectious bovine rhinotracheitis virus using recombinase polymerase amplification assays Application of a flow type quartz crystal microbalance immunosensor for real time determination of cattle bovine ephemeral fever virus in liquid Application of a realtime polymerase chain reaction assay to the diagnosis of bovine ephemeral fever during an outbreak in New South Wales and northern Victoria in 2009-10 Not applicable. keywords: amplification; assay; befv; bovine; detection; fever; lfd; pcr; reaction; rpa; virus cache: cord-261237-0hbijukt.txt plain text: cord-261237-0hbijukt.txt item: #270 of 973 id: cord-261279-6mef38eo author: Chu, Daniel K W title: Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date: 2020-01-31 words: 2999 flesch: 49 summary: Interestingly, several bat coronaviruses that are genetically similar to human SARS coronavirus were detected in horseshoe bats. This virus is genetically similar to SARS coronavirus and bat SARS-like coronaviruses. keywords: assays; coronavirus; human; ncov; patients; rna; samples; sars cache: cord-261279-6mef38eo.txt plain text: cord-261279-6mef38eo.txt item: #271 of 973 id: cord-261329-k1p7fo0e author: Nidzworski, Dawid title: Detection and differentiation of virulent and avirulent strains of Newcastle disease virus by real-time PCR date: 2010-12-28 words: 3159 flesch: 50 summary: key: cord-261329-k1p7fo0e authors: Nidzworski, Dawid; Rabalski, Lukasz; Gromadzka, Beata title: Detection and differentiation of virulent and avirulent strains of Newcastle disease virus by real-time PCR date: 2010-12-28 journal: J Virol Methods DOI: 10.1016/j.jviromet.2010.12.015 sha: doc_id: 261329 cord_uid: k1p7fo0e A rapid diagnostic method based on the melting curve SYBR Green The results obtained in this study demonstrate the possible applications for melting curve real-time PCR analysis in laboratory practice for the diagnosis and differentiation of avirulent and virulent strains of Newcastle disease virus. keywords: disease; ndv; newcastle; pcr; strains; time; virus cache: cord-261329-k1p7fo0e.txt plain text: cord-261329-k1p7fo0e.txt item: #272 of 973 id: cord-261419-8dcqnifn author: Ma, Qing-Hu title: Overexpression of a wheat jasmonate-regulated lectin increases pathogen resistance date: 2009-12-01 words: 4678 flesch: 46 summary: Our data showed that Ta-JA1 was a mannose-specific lectin protein (Table 1) . Plant lectins can be classified into 12 families according to their molecular structures, biochemical properties and sugar-binding specificities. keywords: disease; gene; ja1; jasmonate; jrl; lectins; pcr; plant; protein; resistance; tobacco; transgenic cache: cord-261419-8dcqnifn.txt plain text: cord-261419-8dcqnifn.txt item: #273 of 973 id: cord-261442-r4vgt0h3 author: Huh, Hee Jae title: Comparison of the AnyplexTM II RV16 and Seeplex® RV12 ACE assays for the detection of respiratory viruses date: 2014-08-31 words: 2492 flesch: 45 summary: The monoplex PCR and sequencing for the samples with discrepant results revealed that majority of the results were concordant with the results from RV16 assays. The overall results of monoplex PCR and sequencing revealed that majority of the samples that were identified as positive from RV16 assays also exhibited positive results, except INF A (Table 2) . keywords: assay; detection; pcr; results; rv12; rv16; samples cache: cord-261442-r4vgt0h3.txt plain text: cord-261442-r4vgt0h3.txt item: #274 of 973 id: cord-261735-03hvi4el author: Rodrigues, R. title: Development of a one step real time RT-PCR assay to detect and quantify Dugbe virus date: 2011-06-14 words: 2642 flesch: 52 summary: Hazara virus, a new agent isolated from Ixodes redikorzevi ticks from the Kaghan Valley, W. Pakistan Structure and morphogenesis of Dugbe virus (Bunyaviridae Nairovirus) studied by immunogold electron microscopy of ultrathin cryosection Pathogenesis of Dugbe virus infection in wild-type and interferon-deficient mice Dugbe nairovirus S segment: correction of published sequence and comparison of five isolates Investigation of tick-borne viruses as pathogens of humans in South Africa and evidence of Dugbe virus infection in a patient with prolonged thrombocytopenia Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays Supplement to the catalogue of Arthropod-borne viruses Kupe virus, a new virus in the family bunyaviridae, genus nairovirus Dugbe virus: a tick-borne arbovirus from Nigeria Nairobi sheep disease Bunyaviridae Seroprevalence of five arboviruses in Zebu cattle in the Central African Republic Dugbe nairovirus M RNA:nucleotide sequence and coding strategy Large RNA segment of Dugbe nairovirus encodes the putative RNA polymerase Differential activation profiles of Crimean-Congo hemorrhagic fever virus versus Dugbe virus infected antigen presenting cells Tickborne arbovirus surveillance in marquet livestock Epidemiologic and clinical features of Crimean-Congo hemorrhagic fever in southern Africa CLUSTALW: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice Ticks of Domestic Animals in Africa: A Guide to Identification of Species Detection of an arbovirus in an invertebrate and a vertebrate host using the polymerase chain reaction Expression of the nucleocapsid protein of Dugbe virus and antigenic crossreactions with other nairoviruses This work was partly funded by IRBA and Fondation Mérieux. Dugbe virus (DUGV), a member of the genus Nairovirus of the Bunyaviridae family, was first isolated in 1964 from the Amblyomma variegatum tick in Nigeria (Causey, 1970) . keywords: assay; dugv; pcr; rna; virus cache: cord-261735-03hvi4el.txt plain text: cord-261735-03hvi4el.txt item: #275 of 973 id: cord-261823-pgluidj8 author: Wang, Ji title: Novel One-Step Single-Tube Nested Quantitative Real-Time PCR Assay for Highly Sensitive Detection of SARS-CoV-2 date: 2020-05-22 words: 3586 flesch: 57 summary: In addition, the median time from illness onset to PCR testing was 9.85 days (range, 1−19 days). However, digital PCR often needs unique supporting reagents, instruments, and professional operators, making the cost very high with moderate throughput. keywords: assay; cov-2; detection; pcr; samples; sars cache: cord-261823-pgluidj8.txt plain text: cord-261823-pgluidj8.txt item: #276 of 973 id: cord-261867-6n0g3bz5 author: Evermann, James F. title: Canine Reproductive, Respiratory, and Ocular Diseases due to Canine Herpesvirus date: 2011-10-28 words: 8827 flesch: 38 summary: Nonspecific clinical signs associated with CHV ocular infection in mature dogs include blepharospasm, photophobia, and ocular discharge. Nonulcerative keratitis is a less frequent lesion reported with CHV ocular infection. keywords: canine; chv; chv infection; colleagues; corneal; disease; dogs; herpesvirus; infected; infection; lesions; pcr; reactivation; shedding; virus cache: cord-261867-6n0g3bz5.txt plain text: cord-261867-6n0g3bz5.txt item: #277 of 973 id: cord-262328-q7mt0xve author: Wajnberg, Ania title: Humoral response and PCR positivity in patients with COVID-19 in the New York City region, USA: an observational study date: 2020-09-25 words: 4421 flesch: 46 summary: An understanding of the duration of potential infectiousness and the time to IgG antibody response is crucial to the containment of SARS-CoV-2 and the plans for widespread antibody testing over the coming months. 19 To study the duration of IgG antibody response to SARS-CoV-2, we plan to follow our cohort for the next 6 months to track titre levels. keywords: antibody; cov-2; days; participants; pcr; resolution; sars; symptom cache: cord-262328-q7mt0xve.txt plain text: cord-262328-q7mt0xve.txt item: #278 of 973 id: cord-262467-epqqd8n8 author: Chen, Jun title: COVID-19 infection: the China and Italy perspectives date: 2020-06-08 words: 7608 flesch: 41 summary: Other symptoms including rhinorrhoea, sore throat, fatigue, dyspnea, muscle weakness, dizziness, and headache are also often reported in COVID-19 patients. As a viral pneumonia, respiratory tract specimens from COVID-19 patients are first of choice to collect for the detection of viral nuclear acid. keywords: cases; china; clinical; coronavirus; cov-2; covid-19; disease; hcq; infection; patients; plasma; sars; study; tests; treatment cache: cord-262467-epqqd8n8.txt plain text: cord-262467-epqqd8n8.txt item: #279 of 973 id: cord-262485-sx2q5ol4 author: Davda, Jayeshkumar Narsibhai title: An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance date: 2020-06-08 words: 3259 flesch: 48 summary: 6 In order to compare the performance of RT-nPCR with that of standard RT-qPCR we tested RNA samples that had tested positive by RT-qPCR. Based on E gene result RdRp and Orf1b were tested with 5 µl of RNA sample by following Confirmatory assay given by ICMR-NIV https://main.icmr.nic.in/sites/default/files/upload_documents/2_SOP_for_Confirmatory_As say_for_2019_nCoV.pdf. keywords: npcr; pcr; rna; samples; sars; test; testing cache: cord-262485-sx2q5ol4.txt plain text: cord-262485-sx2q5ol4.txt item: #280 of 973 id: cord-262592-0rdiosxd author: Cuevas, José M. title: Human norovirus hyper-mutation revealed by ultra-deep sequencing date: 2016-04-17 words: 5847 flesch: 44 summary: To more directly test for hyper-mutation, we performed transfection assays in which the production of mutations was restricted to a single cell infection cycle. Two of the samples showing hyper-mutation belonged to newborns, whereas the other two belonged to adults, with no significant association between age and hyper-mutation at this low sample size (Fisher's exact test, P = 0.547). keywords: base; et al; hyper; mutation; pcr; reads; region; rna; virus cache: cord-262592-0rdiosxd.txt plain text: cord-262592-0rdiosxd.txt item: #281 of 973 id: cord-262599-19aj551d author: Fongaro, Gislaine title: Evaluation and molecular characterization of human adenovirus in drinking water supplies: viral integrity and viability assays date: 2013-05-28 words: 4315 flesch: 42 summary: Water samples were collected, concentrated and HAdV quantified by real-time PCR. The PA value (PFU/mL) equivalence, when compared to ICC-RT-qPCR values (GC/mL) immediately after the concentration of water samples and after a series of decimal dilutions (10 0 to 10 -8 ), is shown in Figure 1 . keywords: cell; detection; hadv; human; icc; molecular; particles; qpcr; samples; viruses; water cache: cord-262599-19aj551d.txt plain text: cord-262599-19aj551d.txt item: #282 of 973 id: cord-262730-1dxeg8ci author: Barón-Sánchez, J. title: Smell and taste disorders in Spanish patients with mild COVID-19 date: 2020-10-08 words: 3510 flesch: 49 summary: Some authors suggest that smell disorders may be mediated by direct infection of the olfactory mucosa, which would result in destruction of olfactory sensory neurons; recovery would therefore be slower, with olfactory alterations lasting longer and even a risk of permanent deficits. Furthermore, recovery of olfactory function was faster than and independent of recovery of gustatory function in most cases; most individuals with smell disorders experienced complete recovery. keywords: cov-2; covid-19; olfactory; participants; patients; sars; smell; taste cache: cord-262730-1dxeg8ci.txt plain text: cord-262730-1dxeg8ci.txt item: #283 of 973 id: cord-262826-2usqmujy author: She, Rosemary C. title: Performance of diagnostic tests to detect respiratory viruses in older adults date: 2010-07-31 words: 2896 flesch: 35 summary: The role of viruses in the aetiology of communityacquired pneumonia in adults Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections Clinical and financial benefits of rapid detection of respiratory viruses: an outcomes study Lack of sensitivity of rapid antigen tests for the diagnosis of respiratory syncytial virus infection in adults Sensitivity of respiratory virus culture when screening with R-mix fresh cells Detection of respiratory syncytial virus and human metapneumovirus by reverse transcription polymerase chain reaction in adults with and without respiratory illness Evaluation of four methods for the diagnosis of respiratory syncytial virus infection in older adults Acute respiratory tract infection in daycare centers for older persons Viral pneumonia in older adults Viral lower respiratory tract infection in the elderly: a prospective in-hospital study A prospective, community-based study on virologic assessment among elderly people with and without symptoms of acute respiratory infection Rhinovirus and coronavirus infections Practical implementation of a multiplex PCR for acute respiratory tract infections in children Respiratory syncytial virus infections within families Two outbreaks of severe respiratory disease in nursing homes associated with rhinovirus Identification of respiratory viruses in asymptomatic subjects: asymptomatic respiratory viral infections Incidence and characteristics of viral community-acquired pneumonia in adults Comparison of real-time PCR assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children Rapid multiplex nested PCR for detection of respiratory viruses Surveillance for outbreaks of respiratory tract infections in nursing homes Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay Evaluation of a multiplexed PCR assay for detection of respiratory viral pathogens in a public health laboratory setting Impact of rapid detection of viral and atypical bacterial pathogens by real-time polymerase chain reaction for patients with lower respiratory tract infection The burden of infection in long-term care Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza a and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 Improved diagnosis of the etiology of community-acquired pneumonia with real-time polymerase chain reaction Is clinical recognition of respiratory syncytial virus infection in hospitalized elderly and high-risk adults possible? Although many studies have examined the utility of the various methods used for diagnosis of respiratory virus infections, to our knowledge, none have systematically and concurrently examined the performance characteristics of DFA, culture, rapid antigen testing, and PCR on an older adult population (Barenfanger et al., 2000; Falsey et al., 1996 Falsey et al., , 1995 Lam et al., 2007; Templeton et al., 2004) . keywords: culture; et al; pcr; rvp; specimens cache: cord-262826-2usqmujy.txt plain text: cord-262826-2usqmujy.txt item: #284 of 973 id: cord-263118-6sf41rsj author: Landry, Marie L. title: Real-time PCR compared to Binax NOW and cytospin-immunofluorescence for detection of influenza in hospitalized patients date: 2008-07-18 words: 2587 flesch: 50 summary: Two samples testing positive for influenza B by all three methods, tested falsely positive for influenza A by Binax. Two samples positive for influenza B by all three methods tested falsely positive for influenza A by Binax. keywords: binax; dfa; influenza; pcr; samples cache: cord-263118-6sf41rsj.txt plain text: cord-263118-6sf41rsj.txt item: #285 of 973 id: cord-263134-0p4zy5t2 author: de Paz, Hector David title: Molecular isothermal techniques for combating infectious diseases: towards low-cost point-of-care diagnostics date: 2014-07-23 words: 6478 flesch: 30 summary: An integrated system combining RNA purification (previously extracted from bacteria), NASBA and amplification detection This review describes the state-ofthe-art and new directions in the development of isothermal amplification technologies for diagnosis of infectious diseases with particular focus on those susceptible to be integrated in inexpensive molecular POC tests. keywords: amplification; assay; detection; device; dna; isothermal; lamp; loop; nucleic; pcr; poc; polymerase; reaction; techniques; tests; time cache: cord-263134-0p4zy5t2.txt plain text: cord-263134-0p4zy5t2.txt item: #286 of 973 id: cord-263142-o8qbqxhx author: Cavalcante, Liliane T. F. title: Clinical and Molecular Features of Feline Foamy Virus and Feline Leukemia Virus Co-Infection in Naturally-Infected Cats date: 2018-12-11 words: 9139 flesch: 47 summary: Moreover, FeLV regressive cats with undetectable antigenemia, but that are immune to vaccination, are often equivocally vaccinated [59] . Moreover, FeLV regressive cats with undetectable antigenemia, but that are immune to vaccination, are often equivocally vaccinated [59] . keywords: cats; cell; copies; feline; felv; ffv; fiv; infection; pbmc; pcr; pvl; pvls; study; virus cache: cord-263142-o8qbqxhx.txt plain text: cord-263142-o8qbqxhx.txt item: #287 of 973 id: cord-263279-afdmegq0 author: Uhteg, Katharine title: Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays date: 2020-04-26 words: 3181 flesch: 42 summary: As SARS CoV-2 assays became available for testing on existing molecular platforms, laboratories devoted unprecedented energy and resources into evaluating the analytical performance of the new tests and in some cases developed their own diagnostic assays under FDA-EUA guidance. Many questions remains to be answered about the clinical sensitivity of PCR assays for the diagnosis of COVID-19 and the minimum acceptable analytical sensitivity. keywords: cov-2; covid-19; pcr; realstar; sars; specimens cache: cord-263279-afdmegq0.txt plain text: cord-263279-afdmegq0.txt item: #288 of 973 id: cord-263302-z5uhrta5 author: Zhang, Xuming title: Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date: 2000-12-05 words: 8057 flesch: 52 summary: Three intergenic regions of coronavirus mouse hepatitis virus strain A59 genome RNA contain a common nucleotide sequence that is homologous to the 3Ј-end of the viral mRNA leader sequence Analysis of a recombinant mouse hepatitis virus expressing a foreign gene reveals a novel aspect of coronavirus transcription TGEV coronavirus ORF4 encodes a membrane protein that is incorporated into virions Replication and plaque formation of mouse hepatitis virus (MHV-2) in mouse cell line DBT culture Characterization of an internal ribosome entry site within mRNA5 of murine hepatitis virus Cellular factors in the transcription and replication of viral RNA genomes: a parallel to DNA-dependent RNA transcription Characterization of leader RNA sequences on the virion and mRNAs of mouse hepatitis virus-a cytoplasmic RNA virus The molecular biology of coronaviruses Mouse hepatitis virus A59: Our findings thus support the notion that base-pairing between the leader (or antileader) and the IG is not the sole mechanism in subgenomic RNA transcription. keywords: cat; fig; ig5; leader; mrna5; pcr; primer; rna; sequence; subgenomic; transcription cache: cord-263302-z5uhrta5.txt plain text: cord-263302-z5uhrta5.txt item: #289 of 973 id: cord-263389-m6x9gxwe author: AlGhounaim, M. title: Diagnostic yield and clinical impact of routine cell culture for respiratory viruses among children with a negative multiplex RT-PCR result date: 2017-07-29 words: 1931 flesch: 38 summary: We aimed to estimate the yield and clinical impact of routine respiratory virus culture among children with a negative PCR result. We aimed to estimate the yield of routine respiratory virus culture among children with a negative PCR and to describe the impact of a positive cell culture result on their care. keywords: cell; culture; pcr; respiratory; viruses cache: cord-263389-m6x9gxwe.txt plain text: cord-263389-m6x9gxwe.txt item: #290 of 973 id: cord-263417-jgu8kc5k author: Yan, Yong title: A multiplex liquid-chip assay based on Luminex xMAP technology for simultaneous detection of six common respiratory viruses date: 2017-06-17 words: 4662 flesch: 39 summary: Superiority of reverse-transcription polymerase chain reaction to conventional viral culture in the diagnosis of acute respiratory tract infections in children Near patient testing for influenza in children in primary care: comparison with laboratory test Comparison of a rapid antigen test with nucleic acid testing during cocirculation of pandemic influenza A/H1N1 2009 and seasonal influenza A/H3N2 Comparison of real-time PCR assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children Rapid semi-automated quantitative multiplex tandem PCR (MT-PCR) assays for the differential diagnosis of influenza-like illness Comparison of a multiplex real-time PCR assay with a multiplex Luminex assay for influenza virus detection Development and evaluation of a Luminex multiplex serology assay to detect antibodies to bovine herpes virus 1, parainfluenza 3 virus, bovine viral diarrhoea virus, and bovine respiratory syncytial virus, with comparison to existing ELISA detection methods Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection High-throughput multiplexed xMAP Luminex array panel for detection of twenty two medically important mosquito-borne arboviruses based on innovations in synthetic biology Multiplex reverse transcription PCR Luminex assay for detection and quantitation of viral agents of gastroenteritis Development of a bead-based Luminex assay using lipopolysaccharide specific monoclonal antibodies to detect biological threats from Brucella species Comparison of the Luminex Respiratory Virus Panel fast assay with in-house real-time PCR for respiratory viral infection diagnosis Simultaneous detection and high-throughput identification of a panel of RNA viruses causing respiratory tract infections respiratory viral panel fast for diagnosis of respiratory virus infections Sensitive and specific quantitative detection of rotavirus A by onestep real-time reverse transcription-PCR assay without antecedent double-stranded-RNA denaturation A one-step multiplex real-time RT-PCR assay for rapid and simultaneous detection of human norovirus genogroup I, II and IV Development of high-throughput liquid chips for respiratory virus detection Development of a Luminex assay for the simultaneous detection of human enteric viruses in sewage and river water ACS Commitee on Environmental Improvement. keywords: assay; detection; luminex; mers; multiplex; pcr; rmla; time; time rt cache: cord-263417-jgu8kc5k.txt plain text: cord-263417-jgu8kc5k.txt item: #291 of 973 id: cord-263426-l32gyiky author: Najafi, Hamideh title: Molecular and clinical study on prevalence of feline herpesvirus type 1 and calicivirus in correlation with feline leukemia and immunodeficiency viruses date: 2014 words: 3439 flesch: 51 summary: 5, 11 In other studies, FCV and FHV-1 prevalence were 0 to 29.00% and 0 to 54.00% in healthy cats, 3,13,14 and 20.0 to 53.00% and 10.0 to 34.00% in cats with URTD, 5 which are less than the prevalence levels found in our study. Fenner's veterinary virology Feline herpesvirus 1, feline calicivirus infections in heterogeneous cat population of a rescue shelter Isolation of feline herpesvirus 1 and feline calicivirus from healthy cats in Swedish breeding catteries Factors associated with upper respiratory tract disease caused by feline herpesvirus, feline calicivirus, Chlamydophila felis and Bordetella bronchiseptica in cats: Experience from 218 European catteries Detection of feline calicivirus, feline herpesvirus 1 and Chlamidia psittaci mucosal swabs by multiplex RT-PCR/PCR Feline leukemia virus infection as a potentiating cofactor for the primary and secondary stages of experimentally induced feline immunodeficiency virus infection Detection of bacterial and viral organisms from the conjunctiva of cats with conjunctivitis and upper respiratory tract disease Early events in the immunopathogenesis of feline retrovirus infections Evaluation of novel nested PCR for the routine diagnosis of feline leukemia virus (FeLV) and feline immunodeficiency virus(FIV) Feline immunodeficiency virus, feline leukemia virus, and toxoplasma gondii in stray and household cats in Kerman-Iran: Seroprevalence and correlation with clinical and laboratory findings Evaluation of a p30 gene-based real-time reverse transcriptase polymerase chain reaction assay for detection of feline caliciviruses Chronic oral infections of cats and their relationship to persistent oral carriage of feline calici, immunodeficiency, or leukemia viruses Prevalence of feline herpesvirus 1, feline calicivirus and Chlamydophila felis in clinically normal cats at a Korean animal shelter Detection of active and latent feline herpesvirus 1 infection using the polymerase chain reaction Diagnosis of feline leukemia virus infection by semiquantitative real-time polymerase chain reaction Prevalence of feline immunodeficiency virus and feline leukemia virus among client-owned cats and risk factors for infection in Germany Prevalence of feline leukemia virus and feline immunodeficiency virus infections in cats in Sydney Seroprevalence of Bartonella henselae, Toxoplasma gondii, FIV and FeLV infections in domestic cats in Japan Molecular diagnosis of feline immunodeficiency virus in cerebrospinal fluid (CSF) and blood by RT-PCR and PCR methods among stray cats and relationships with clinical signs A case-controlled study of FeLV infected cats in Tehran, Iran, confirmed by immunochromatography and RT-PCR and correlation with clinical and hematological findings Case-control study of infection by feline immunodeficiency virus in cats by immunechromatography and PCR methods in Tehran, Iran Antibody detection to feline immunodeficiency virus in stray cats in Ahvaz, southwestern Iran Seroprevalence of viral infections in damestic cats in Costa Rica Prevalence and risk factors for heartworm infection in cats from northern Florida Naturally acquired feline immunodeficiency virus (FIV) infection in cats from western Canada: Prevalence, disease associations, and survival analysis Prevalence of feline leukemia virus and antibodies to feline immunodeficiency virus and feline coronavirus in stray cats sent to an RSPCA hospital Seroepidemiologic survey of feline immunodeficiency virus infection in cats of Wake County, North Carolina Seroepidemiologic study of FIV in cats referred to small animal teaching hospital, Faculty of Veterinary Medicine We would like to thank Mohammad Mahdi Ghaffari and Iraj Ashrafi Tamai for their technical assistance. keywords: cats; fcv; feline; felv; fhv-1; fiv; pcr; prevalence cache: cord-263426-l32gyiky.txt plain text: cord-263426-l32gyiky.txt item: #292 of 973 id: cord-263538-0wozg085 author: Cooch, P. B. title: Supervised self-collected SARS-CoV-2 testing in indoor summer camps to inform school reopening date: 2020-10-23 words: 4441 flesch: 45 summary: The methods we describe suggest a scalable approach for return to school testing. Eligible participants were campers, up to two adult household contacts, and camp staff. keywords: camp; collection; cov-2; license; preprint; sars; school; self; staff; testing cache: cord-263538-0wozg085.txt plain text: cord-263538-0wozg085.txt item: #293 of 973 id: cord-263567-6uacorpp author: Collignon, C. title: Polyarthrite associée à une leishmaniose chez un jeune chien date: 2009-03-31 words: 3627 flesch: 50 summary: Par ailleurs, lors de suspicion de syndrome néphrotique débutant (protéinurie massive objectivée par un rapport protéine/créatine urinaire, associée à une hypoalbuminémie et une hypercholestérolémie), le dosage de l'antithrombine III doit être effectué. Cependant, elle peut être également due à une monoarthrite [8, 14] , une hyperkératose des coussinets, des ulcères interdigités, une onychogriphose sévère, des lésions ostéolytiques, une polymyosite ou encore une neuralgie keywords: canine; chien; dans; des; est; leishmaniasis; leishmaniose; les; mois; par; pcr; que; sur; traitement; une cache: cord-263567-6uacorpp.txt plain text: cord-263567-6uacorpp.txt item: #294 of 973 id: cord-263570-6notzm6s author: Elia, Gabriella title: Detection of infectious canine parvovirus type 2 by mRNA real-time RT-PCR date: 2007-08-10 words: 3997 flesch: 45 summary: A sensitive one-step real-time PCR for detection of avian influenza viruses using a MGB probe and an internal positive control Antibody levels and protection to canine parvovirus type 2 Detection of canine distemper virus in dogs by real-time RT-PCR Different patterns of restriction to B19 parvovirus replication in human blast cell lines Comparison of isolates of canine parvovirus by monoclonal antibody and restriction-enzyme analysis Sensitive detection of canine parvovirus DNA by the nested polymerase chain reaction Defective viral genomes The natural host range shift and subsequent evolution of canine parvovirus resulted from virus-specific binding to the canine transferring receptor An enteric disease of dogs resembling feline panleukopenia Isolation and genetic characterization of two G3P5A[3] canine rotavirus strains in Italy Antigenic and genomic variabilities among recently prevalent parvoviruses of canine and feline origin in Japan Comparison of polymerase chain reaction with virus isolation and haemagglutination assays for the detection of canine parvoviruses in faecal specimens A novel antigenic variant of canine parvovirus from a Vietnamese dog Canine and feline parvoviruses can use human or feline transferrin receptors to bind, enter, and infect cells Antigenic relationships between canine parvovirus type 2, feline panleukopenia virus and mink enteritis virus using conventional antisera and monoclonal antibodies RNA extraction from mammalian tissues Molecular characterisation of canine parvovirus in Brazil by polymerase chain reaction assay Antigenic characterization of canine parvovirus strains isolated in Italy A simple touch-down polymerase chain reaction for the detection of canine parvovirus and feline panleukopenia virus in feces Detection by PCR of wild-type canine parvovirus which contaminates dog vaccines Persistence of human parvovirus B19 in human tissues A case report Identification of types of canine parvovirus circulating in Spain Maternally derived antibodies in pups and protection from canine parvovirus infection Virological and molecular characterization of a type 3 mammalian reovirus strain isolated from a dog with diarrhea in Italy A real-time PCR assay for rapid detection and quantitation of canine parvovirus type 2 DNA in the feces of dogs Genotyping-specific fluorogenic RT-PCR assays for the detection and quantitation of canine coronavirus type I and II RNA in faecal samples of dogs Infectious canine hepatitis: an old disease reemerging in Italy Characterisation of the canine parvovirus type 2 variants using minor groove binder probe technology First detection of canine parvovirus type 2c in pups with haemorrhagic enteritis in Spain Tissue distribution of the antigenic variants of canine parvovirus type 2 in dogs Canine parvovirus infection: which diagnostic test for virus? keywords: assay; canine; detection; dna; et al; mrna; parvovirus; pcr; time cache: cord-263570-6notzm6s.txt plain text: cord-263570-6notzm6s.txt item: #295 of 973 id: cord-263735-sos2ovng author: Li, K. title: Diagnostic performance of CT and its key signs for COVID-19: A systematic review and meta-analysis date: 2020-05-26 words: 5256 flesch: 63 summary: Moreover, the sample size and time interval between reference standard and CT did not show an effect on CT sensitivity (p = 0.68-0.84). key: cord-263735-sos2ovng authors: Li, K.; Wu, X.; Zhong, Y.; Qin, W.; Zhang, Z. title: Diagnostic performance of CT and its key signs for COVID-19: A systematic review and meta-analysis date: 2020-05-26 journal: nan DOI: 10.1101/2020.05.24.20111773 sha: doc_id: 263735 cord_uid: sos2ovng Abstract Purpose: To evaluate the diagnostic value of chest CT in 2019 novel coronavirus disease (COVID-19), using the reverse transcription polymerase chain reaction(RT-PCR)as a reference standard. keywords: author; medrxiv; perpetuity; preprint; review cache: cord-263735-sos2ovng.txt plain text: cord-263735-sos2ovng.txt item: #296 of 973 id: cord-263763-a8wgvgz2 author: Çelik, Ersin title: Treatment Approach to Coronavirus Disease (COVID-19) Seen Early After Open Heart Surgery. Case Report date: 2020-07-02 words: 1540 flesch: 45 summary: We aimed to present our approach to high probability COVID-19 pneumonia which developed on early postoperative period in our patient after coronary artery bypass grafting (CABG) operation, which was not reported in the literature before. We should assume and keep in mind that there are also pandemic and asymptomatic carriers, especially in elderly patients who undergo open heart surgery with many additional risk factors. keywords: covid-19; patient; pcr cache: cord-263763-a8wgvgz2.txt plain text: cord-263763-a8wgvgz2.txt item: #297 of 973 id: cord-263976-b9shffb3 author: Shaukat, Shahzad title: Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA date: 2014-08-12 words: 3694 flesch: 40 summary: Emerg Infect Dis Identification of human parechovirus genotype, HPeV-12, in a paralytic child with diarrhea Human parechovirus 3 and neonatal infections Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis Detection and genetic differentiation of human astroviruses: phylogenetic grouping varies by coding region Molecular epidemiology of human astrovirus diarrhea among children from a periurban community of Mexico City Evidence of a recombinant wild-type human astrovirus strain from a Kenyan child with gastroenteritis Emergence of unique variants and inter-genotype recombinants of human astroviruses infecting infants, children and adults in Kolkata Use of nucleotide composition analysis to infer hosts for three novel picorna-like viruses A new arenavirus in a cluster of fatal transplantassociated diseases Metagenomic analysis of human diarrhea: viral detection and discovery Applications of next-generation sequencing technologies to diagnostic virology Molecular identification and characterization of a new type of Bovine Enterovirus A newly identified bocavirus species in human stool A highly prevalent and genetically diversified Picornaviridae genus in South Asian children Rapid group-, serotype-, and vaccine strain-specific identification of poliovirus isolates by realtime reverse transcription-PCR using degenerate primers and probes containing deoxyinosine residues Rapid and simple method for purification of nucleic acids Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription Species-specific RT-PCR amplification of human enteroviruses: a tool for rapid species identification of uncharacterized enteroviruses Human parechovirus infections in Dutch children and the association between serotype and disease severity MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0 A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA Here, we show that in the majority of virus cultures simplified-VIDISCA can quickly reveal the infecting agent. keywords: human; identification; parechovirus; pcr; samples; sequences; type; vidisca; viral; viruses cache: cord-263976-b9shffb3.txt plain text: cord-263976-b9shffb3.txt item: #298 of 973 id: cord-264071-hg0qslyx author: Camelo-Castillo, Anny title: Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects date: 2019-01-28 words: 7158 flesch: 32 summary: In addition, IPD samples presented significantly higher levels of Veillonella (Figure 2C) , which is a bacterium that uses lactate as a carbon source, as a consequence of which it is usually found physically and functionally associated to lactate producers like Streptococcus (Dige et al., 2014; Gaspar et al., 2014) . Nasopharyngeal samples were taken from cases after a mean of 92 h of fever (IQR 48-408 h) and all of them except two (one patient with necrotizing pneumonia and another one with fatal fulminant sepsis and viral respiratory coinfection), were exposed to beta-lactamic antibiotic treatment, during a mean period of 4 days. keywords: cases; children; controls; disease; et al; human; ipd; microbiota; nasopharyngeal; pneumococcal; samples; species; streptococcus cache: cord-264071-hg0qslyx.txt plain text: cord-264071-hg0qslyx.txt item: #299 of 973 id: cord-264107-6doie8pj author: Marando, Marco title: False-Negative Nasopharyngeal Swab RT-PCR Assays in Typical COVID-19: Role of Ultra-low-dose Chest CT and Bronchoscopy in Diagnosis date: 2020-04-24 words: 1852 flesch: 44 summary: CT imaging of the 2019 novel coronavirus (2019-nCoV) pneumonia Chest CT for typical 2019-nCoV pneumonia: relationship to negative RT-PCR testing Updated effective doses in radiology Ultra-low-dose CT of the thorax using iterative reconstruction: evaluation of image quality and radiation dose reduction Sensitivity of chest CT for Covid-19: comparison to RT-PCR Accuracy and reproducibility of low-dose submillisievert chest CT for the diagnosis of COVID-19 Evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections. Standard chest CT findings have a sensitivity of up to 97% compared with RT-PCR assays, but lack specificity keywords: chest; nasopharyngeal; pcr cache: cord-264107-6doie8pj.txt plain text: cord-264107-6doie8pj.txt item: #300 of 973 id: cord-264261-98h1bmb2 author: Caruana, Giorgia title: Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results date: 2020-06-25 words: 1419 flesch: 32 summary: WHO guidelines for 396 the global surveillance of severe acute respiratory syndrome (SARS): updated 397 recommendations Serological assays for emerging 401 coronaviruses: challenges and pitfalls Novel antibody epitopes dominate the antigenicity of spike 403 glycoprotein in SARS-CoV-2 compared to SARS-CoV Potent binding of 2019 novel coronavirus spike protein by a SARS 407 coronavirus-specific human monoclonal antibody Lateral flow assays SARS-CoV-2 viral load in 413 upper respiratory specimens of infected patients Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 China: a report of 1014 cases Fecal specimen diagnosis 2019 Samples like blood and urines were found to be weakly-to-none sensitive, while the virus was 231 also found in feces and perineal swabs of patients with gastro-intestinal symptoms [44] [45] , Improved molecular diagnosis of COVID-19 by the novel, highly sensitive 316 and specific COVID-19-RdRp/Hel real-time reverse transcription-polymerase chain 317 reaction assay validated in vitro and with clinical specimens Ten years of R&D and full automation 320 in molecular diagnosis Letter to the editor: 322 SARS-CoV-2 detection by real-time RT-PCR Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction-Based 330 SARS-CoV-2 Tests by Time Since Exposure Sources of pre-analytical, analytical and post-analytical errors in 332 the microbiology laboratory PCR inhibitors-occurrence, 336 properties and removal SARS-COV-2 diagnostic pipeline Xpert® Xpress SARS-CoV-2 has received FDA 340 Purification and enrichment of 343 virus samples utilizing magnetic beads on a microfluidic system High-speed RNA microextraction technology 346 using magnetic oligo-dT beads and lateral magnetophoresis Parallel RNA extraction 349 using magnetic beads and a droplet array Viral DNA/RNA 96 Kit; c2020 351 EZ1 Advanced XL; c2020 IDEAL96 Automated Extraction Robot; c2020 Multifunctional device for 360 nucleic acid extraction based on magnetic separation and its co-working with liquid 361 handling system for high throughput sample preparation A simple 364 magnetic nanoparticles-based viral RNA extraction method for efficient detection of 365 Profile of specific antibodies to the SARS-associated 369 coronavirus Antibody responses to SARS-CoV-2 in patients of 373 novel coronavirus disease 2019 Longitudinal Monitoring of SARS-CoV-2 IgM and IgG Seropositivity 378 to Detect COVID-19 Antibody 387 responses to SARS-CoV-2 in patients with COVID-19 Kinetics of serologic responses to MERS coronavirus infection in humans, South 392 Korea Antigenic relationships amongst coronaviruses. keywords: coronavirus; cov-2; pcr; protein; sars cache: cord-264261-98h1bmb2.txt plain text: cord-264261-98h1bmb2.txt item: #301 of 973 id: cord-264392-he1vekrt author: Lambeth, L. S. title: Complete genome sequence of Nariva virus, a rodent paramyxovirus date: 2008-12-23 words: 4373 flesch: 48 summary: This was then followed by PCR to fill in the 'gaps' using specific primers designed from NarPV Nariva virus genome 201 sequences obtained from the cDNA subtraction or degenerate primers designed using highly conserved consensus sequences of known paramyxoviruses in the subfamily Paramyxovirinae. c Alignment of the V-specific protein sequences NarPV F protein, SGRNK, is dibasic and does not conform to the consensus sequence motif for cleavage by furin, R-X-K/R-R keywords: cdna; genome; members; mospv; narpv; paramyxovirinae; paramyxoviruses; pcr; protein; sequence; subfamily; virus cache: cord-264392-he1vekrt.txt plain text: cord-264392-he1vekrt.txt item: #302 of 973 id: cord-264716-igl25jhg author: Koo, B.S. title: Molecular survey of enteric viruses in commercial chicken farms in Korea with a history of enteritis date: 2013-11-01 words: 4986 flesch: 38 summary: A molecular survey was performed for a broad range of enteric viruses, namely CAstV, ANV, IBV, AvRV, ARV, and FAdV, in commercial chicken flocks suffering from enteritis. In this study, a molecular survey was performed for a broad range of enteric viruses including CAstV, ANV, ChPV, IBV, AvRV, ARV, and FAdV in intestine samples from commercial chicken flocks suffering from enteritis. keywords: anv; castv; chicken; et al; flocks; ibv; viruses cache: cord-264716-igl25jhg.txt plain text: cord-264716-igl25jhg.txt item: #303 of 973 id: cord-264880-0tmd9knh author: Li, Zhao title: Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids date: 2016-04-13 words: 5361 flesch: 42 summary: The blade was held at a 40-60°angle relative to the chip carrier so that the edge of silica gel was placed at the end of PWA chip. Silanization of the PWA chip to avoid cross-contamination The manufactured finished PWA chip was 20.8 mm × 16 mm, with 27,000 closely packed microwells. keywords: amplification; chip; detection; digital; dna; drpa; fig; isothermal; pcr; pwa; reaction; rpa; time cache: cord-264880-0tmd9knh.txt plain text: cord-264880-0tmd9knh.txt item: #304 of 973 id: cord-264944-7xj27r98 author: Koopmans, Marion title: Optimization of extraction and PCR amplification of RNA extracts from paraffin-embedded tissue in different fixatives date: 1993-07-31 words: 5186 flesch: 46 summary: In the work reported here we used paraffin-embedded torovirus-infected cell pellets to compare the effect of different fixatives and RNA extraction methods on RT-PCR amplification of tissue extracts. Dewaxing of tissue sections had no effect on the yield and quality of RNA extractions, and further purification of the extracts using gel filtration did not improve the results. keywords: actin; amplification; extraction; method; pcr; primers; results; rna; torovirus cache: cord-264944-7xj27r98.txt plain text: cord-264944-7xj27r98.txt item: #305 of 973 id: cord-265221-qtkwciym author: Bahadur, Gulam title: SARS-CoV-2: diagnostic and design conundrums, and the male factor infertility date: 2020-06-03 words: 3268 flesch: 39 summary: There is also a report relating to SARS infection and orchitis (Xu et al. 2006) . A complication of severe acute respiratory syndrome (SARS) COVID-19: should we continue to cryopreserve sperm during the pandemic? Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes keywords: cov-2; infection; patients; pcr; sars; semen; virus cache: cord-265221-qtkwciym.txt plain text: cord-265221-qtkwciym.txt item: #306 of 973 id: cord-265237-sxh2nqre author: Weile, Jan title: Current applications and future trends of molecular diagnostics in clinical bacteriology date: 2009-04-18 words: 4557 flesch: 35 summary: Furthermore, for other complex resistance problems such as detection of hundreds of different ESBL variants in tem, oxa, shv, and ctx-m genes, or MRSA and other clinical relevant resistances in Staphylococci, DNA microarray assays were published [103, 104] All these assays, although needing further optimization regarding implementation in routine clinical laboratories, are characterized by comparable short time requirements (4-5 h) compared to conventional methods. There are many different real-time PCR instruments and detection probe formats available. keywords: amplification; assays; clinical; detection; diagnostics; dna; identification; methods; pcr; probes; resistance; sequencing; time cache: cord-265237-sxh2nqre.txt plain text: cord-265237-sxh2nqre.txt item: #307 of 973 id: cord-265258-2rmtsyns author: Domanska‐Blicharz, K. title: Specific detection of GII‐1 lineage of infectious bronchitis virus date: 2017-07-03 words: 3414 flesch: 46 summary: The intra and interassay precision of the new method were assessed using serial dilutions of D1466 IBV RNA ranging from 8Á2 9 10 6 down to 5Á6 9 10 1 copies. The standard curve and linear regression analysis were performed using serial dilutions of known quantity of GII-1 IBV RNA (Fig. 1) . keywords: assay; bronchitis; ibv; pcr; rna; time; virus cache: cord-265258-2rmtsyns.txt plain text: cord-265258-2rmtsyns.txt item: #308 of 973 id: cord-265268-5xu9hj2n author: Ahmed, W. title: Evaluation of Glass Wool Filters and Hollow-Fiber Ultrafiltration Concentration Methods for qPCR Detection of Human Adenoviruses and Polyomaviruses in River Water date: 2016-08-13 words: 4972 flesch: 42 summary: The method involves concentrating water samples using a Hemoflow HF80S dialysis filter (Fresenius Medical Care, Bad Homberg, Germany). Therefore, we recommended that HFUF method should be used to concentrate water samples for MST field studies. keywords: dna; hadvs; hpyvs; human; recovery; river; samples; viruses; wastewater; water cache: cord-265268-5xu9hj2n.txt plain text: cord-265268-5xu9hj2n.txt item: #309 of 973 id: cord-265634-7n4cvgs4 author: Dhar, Arun K. title: Quantitative assay for measuring the Taura syndrome virus and yellow head virus load in shrimp by real-time RT-PCR using SYBR Green chemistry date: 2002-03-26 words: 5192 flesch: 52 summary: The analytical sensitivity of SYBR Green PCR was determined by using a serial dilution of TSV and YHV plasmid DNA as template for amplification. The standard curve for TSV (A) and YHV (B) obtained by SYBR Green PCR using plasmid DNA as template. keywords: actin; amplification; ef-1a; green; pcr; shrimp; sybr; tsv; virus; yhv cache: cord-265634-7n4cvgs4.txt plain text: cord-265634-7n4cvgs4.txt item: #310 of 973 id: cord-265978-i0fu8e0p author: Amer, Haitham M. title: Development of a SYBR Green I based real-time RT-PCR assay for detection and quantification of bovine coronavirus date: 2011-06-30 words: 4812 flesch: 45 summary: The concentration of BCoV RNA in the analyzed positive samples varied from 2  10 4 to 1.56  10 8 copies/ml for the fecal samples, and 3.77  10 2 to 1.56  10 8 copies/ ml for the nasal samples. This implies that co-amplification of the IPC does not affect the detection and quantification of BCoV RNA. keywords: assay; bcov; bovine; detection; fecal; nasal; pcr; reaction; samples; time cache: cord-265978-i0fu8e0p.txt plain text: cord-265978-i0fu8e0p.txt item: #311 of 973 id: cord-266025-bkm486jd author: Tao, Ying title: Genomic characterization of seven distinct bat coronaviruses in Kenya() date: 2012-04-26 words: 3917 flesch: 43 summary: The four clusters of Kenya bat CoVs represented by BtKY22, BtKY41, BtKY43, and BtKY24 respectively, most likely belonged to novel CoV species, the two clusters represented by BtKY27 and BtKY33 were likely members of Bat-CoV 1A, and the cluster represented by BtKY06 was likely a member of Bat-CoV HKU9 species. However, because of the examples of host switching among CoVs after relatively minor sequence changes in S1 domain of spike protein, a further surveillance in animal reservoirs and understanding the interface between host susceptibility is critical for predicting and preventing the potential threat of bat CoVs to public health. keywords: bat; bats; coronavirus; covs; et al; kenya; orfs; sequence; species cache: cord-266025-bkm486jd.txt plain text: cord-266025-bkm486jd.txt item: #312 of 973 id: cord-266036-qhlo99l7 author: Axell-House, Dierdre B. title: The Estimation of Diagnostic Accuracy of Tests for COVID-19: A Scoping Review date: 2020-08-31 words: 5764 flesch: 36 summary: A review of methods Using a combination of reference tests to assess the accuracy of a new diagnostic test Value of composite reference standards in diagnostic research Diagnostic test evaluation methodology: A systematic review of methods employed to evaluate diagnostic tests in the absence of gold standard -An update Food and Drug Administration CfDaRH. However, our scoping review also uncovered imperfect methods for estimating diagnostic test performance in the absence of a gold standard and demonstrate that the accuracy of these tests should be interpreted with caution. keywords: cov-2; pcr; reference; rrt; sars; standard; studies; table; test cache: cord-266036-qhlo99l7.txt plain text: cord-266036-qhlo99l7.txt item: #313 of 973 id: cord-266150-wox7pnkr author: Torres, Juan Pablo title: SARS-CoV-2 antibody prevalence in blood in a large school community subject to a Covid-19 outbreak: a cross-sectional study date: 2020-07-10 words: 4206 flesch: 46 summary: The median percent of antibody positive students per classroom was 8.3% (IQR 1.6-14.3%). Certainly, school related outbreak studies from other settings and situations, especially after the first wave, are required to further increase our knowledge of transmission dynamics within M a n u s c r i p t 10 schools, in order to pinpoint recommendations which may end up being most effective. keywords: antibody; cases; children; covid-19; outbreak; positivity; school; staff; students; test cache: cord-266150-wox7pnkr.txt plain text: cord-266150-wox7pnkr.txt item: #314 of 973 id: cord-266156-xmf4emln author: Miller, Tyler E. title: Clinical sensitivity and interpretation of PCR and serological COVID‐19 diagnostics for patients presenting to the hospital date: 2020-08-28 words: 4336 flesch: 38 summary: We modeled a linear daily regression trend after first positive PCR test, to estimate the time when PCR sensitivity reaches zero (foot-point analysis). Second, we also modeled how PCR sensitivity decreases over time after the first positive PCR test (Figures S3 and S5 ). keywords: cov-2; days; infection; onset; patients; pcr; sars; sensitivity; symptom; test cache: cord-266156-xmf4emln.txt plain text: cord-266156-xmf4emln.txt item: #315 of 973 id: cord-266175-4jyltfus author: Brendish, Nathan J title: Clinical impact of molecular point-of-care testing for suspected COVID-19 in hospital (COV-19POC): a prospective, interventional, non-randomised, controlled study date: 2020-10-08 words: 5487 flesch: 39 summary: In addition to testing symptomatic acute admissions to hospital, point-of-care testing could also be used for assessing elective hospital admissions, primary care patients, hospital staff, and care home staff and residents, as well as for airport screening, school screening, and even population-level screening. Initially, laboratory PCR testing used the PHE RdRp gene assay alone and subsequently used the PHE RdRp and E gene assays combined. keywords: care; care testing; cov-2; covid-19; group; patients; point; respiratory; sars; study; testing cache: cord-266175-4jyltfus.txt plain text: cord-266175-4jyltfus.txt item: #316 of 973 id: cord-266466-5sgfx7oq author: Mansour, Amani title: First Case of an Infant with COVID-19 in the Middle East date: 2020-04-03 words: 1508 flesch: 51 summary: Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period SARS-CoV-2 infection in children Detection of covid-19 in children in early An epidemiological study on COVID-19: a rapidly spreading disease Coronavirus disease (COVID-19) and pediatric patients: a review of epidemiology, symptomatology, laboratory and imaging results to guide the development of a management algorithm A bibliometric analysis of COVID-19 research activity: a call for increased output A 55-day-old female infant infected with COVID 19: presenting with pneumonia, liver injury, and heart damage Novel coronavirus infection in hospitalized infants under 1 year of age in China A case series of children with 2019 novel coronavirus infection: clinical and epidemiological features Clinical and CT features in pediatric patients with COVID-19 infection: different points from adults Epidemiological characteristics of 2143 pediatric patients with 2019 coronavirus disease in China Clinical characteristics of COVID-19 patients with digestive symptoms in Hubei, China: a descriptive, cross-sectional, multicenter study Health communication research in the Arab world: a bibliometric analysis COVID-19 related pediatric symptoms can exhibit an array of presentations, including diarrhea. keywords: children; covid-19; patient; symptoms cache: cord-266466-5sgfx7oq.txt plain text: cord-266466-5sgfx7oq.txt item: #317 of 973 id: cord-266499-g1lajsp8 author: Han, Jae-Ik title: A multiplex quantitative real-time polymerase chain reaction panel for detecting neurologic pathogens in dogs with meningoencephalitis date: 2015-09-21 words: 3083 flesch: 36 summary: Next, the performance of the mqPCR panel and singleplex PCR for each of the eight pathogens were compared directly to identify any negative effects of multiplexing on PCR detection. The results of singleplex and multiplex PCR were identical except for CDV, and CT differences between PCR reactions were not significant, demonstrating that multiplexing did not have a significant negative effect on sensitivity of the PCR. keywords: dogs; mqpcr; panel; pcr; time cache: cord-266499-g1lajsp8.txt plain text: cord-266499-g1lajsp8.txt item: #318 of 973 id: cord-266523-qd5asgg8 author: Wilson, N. title: Estimating the Impact of Control Measures to Prevent Outbreaks of COVID-19 Associated with Air Travel into a COVID-19-free country: A Simulation Modelling Study date: 2020-06-12 words: 5838 flesch: 48 summary: This was increased to 2.2 years after adding in exit screening upon leaving Australia; to 3.3 years by adding in mask use on flights; and to 3.5 years by adding in entry screening on arrival in New Zealand. Additional results with the time to last PCR test extended up to day 15 in New Zealand (Table 4 ), indicate the particularly important benefit from mask use, then symptom self-reporting, and then contact tracing/isolation. keywords: covid-19; flight; mask; new; passengers; pcr; preprint; use; zealand cache: cord-266523-qd5asgg8.txt plain text: cord-266523-qd5asgg8.txt item: #319 of 973 id: cord-266670-jxgywvwx author: Wong, Mark title: Chapter 13 Recent Advances and Future Needs in Environmental Virology date: 2007-09-06 words: 5843 flesch: 30 summary: A large waterborne viral hepatitis E epidemic in Kanpur DNA microarray technique for detection and identification of seven flaviviruses pathogenic for man Virulence signatures: microarray-based approaches to discovery and analysis Detection of adenovirus outbreak at a municipal swimming pool by nested PCR amplification Global illness and deaths caused by rotavirus disease in children Prevalence of vaccinederived polioviruses in sewage and river water in South Africa Light-generated oligonucleotide arrays for rapid DNA sequence analysis Rapid detection and identification of human adenovirus species by adenoplex, a multiplex PCR-enzyme hybridization assay Viral Pollution in the environment and in shellfish: human adenovirus detection by PCR as an index of human viruses Detection of adenoviruses and enteroviruses in polluted waters by nested PCR amplification Human-blind probes and primers for dengue virus identification Comparison of PCR, enzyme immunoassay and conventional culture for adenovirus detection in bone marrow transplant patients with hemorrhagic cystitis Detection of adenoviruses in shellfish by means of conventional-PCR, nested-PCR, and integrated cell culture PCR (ICC/PCR) A simple and rapid single-step multiplex RT-PCR to detect norovirus, astrovirus and adenovirus in clinical stool samples OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach Microarray assay for detection and discrimination of orthopoxvirus species Comprehensive detection and serotyping of human adenoviruses by PCR and sequencing Quantitative monitoring of gene expression patterns with a complementary DNA microarray Molecular detection and identification of influenza viruses by oligonucleotide microarray hybridization Nested and multiplex PCR, which are variations of the conventional PCR, have also been applied to virus detection in water samples. keywords: adenoviruses; cell; culture; detection; dna; environmental; et al; microarray; pcr; samples; time; viruses; water cache: cord-266670-jxgywvwx.txt plain text: cord-266670-jxgywvwx.txt item: #320 of 973 id: cord-266738-8xx1xm2d author: None title: cord-266738-8xx1xm2d date: None words: 14692 flesch: 44 summary: Increasing reports on human PRV infection cases in China have recently indicated that PRV poses a significant threat to public health in China, especially in people in close contact with sick pigs and/or related pork products/contaminants. 3 , 8 Here we explored a simple data-driven, Boltzmann functionbased approach for estimation only based on the daily cumulative number of confirmed cases of SARS-CoV-2 (Note: the rational for Boltzmann function-based regression analysis is presented in supporting information (SI) file). keywords: 2019; cases; china; colistin; control; data; disease; gene; health; human; infection; isolates; laboratory; novel; number; outbreak; patients; pcr; pertussis; pjp; pneumoniae; prv; resistance; table; time; treatment cache: cord-266738-8xx1xm2d.txt plain text: cord-266738-8xx1xm2d.txt item: #321 of 973 id: cord-267671-ys43n672 author: Whary, Mark T. title: Biology and Diseases of Mice date: 2015-07-10 words: 63704 flesch: 37 summary: If an endogenous retrovirus is still infectious to other mouse cell targets, it is termed ecotropic, whereas if it is no longer infectious for mouse cells, but can infect cells of other species, it is termed xenotropic. Recombinant viruses have recently been discovered that can infect mouse cells and heterologous cells and are associated with spontaneous leukemia development in high leukemia strains such as AKR mice. keywords: acute; adult mice; age; animal; bacterial; blood; breeding; c mice; c57bl/6 mice; cause; cells; chronic; clinical; colonies; common; complications; control; days; detection; development; diagnosis; differential; difficile; disease; eggs; epithelium; epizootiology; et al; etiology; feces; female; fig; gene; genome; hair; helicobacter; hepaticus; high; host; humans; hyperplasia; immune; immunity; immunodeficient mice; infant mice; infection; inflammation; inoculation; intestine; laboratory mice; lesions; lines; liver; lymph; male; medicine; mhv; mice; mouse; mouse colonies; mouse strains; murine; necrosis; organisms; pathology; pcr; potential; prevention; primary; rats; research; responses; results; scid; signs; skin; species; specific; spleen; strains; studies; susceptibility; system; tissues; tract; transmission; treatment; tumors; type; virus; virus infection; viruses; weeks cache: cord-267671-ys43n672.txt plain text: cord-267671-ys43n672.txt item: #322 of 973 id: cord-267928-dflkggjt author: Kantola, Kalle title: Merkel cell polyomavirus DNA in tumor-free tonsillar tissues and upper respiratory tract samples: Implications for respiratory transmission and latency date: 2009-05-22 words: 2735 flesch: 46 summary: MCPyV DNA was detected in 14 samples altogether; 8 of 229 (3.5%) tonsillar tissues, 3 of 140 (2.1%) NPAs, 2 of 106 (1.9%) nasal swabs and 1 of 840 (0.1%) sera. MCPyV DNA occurs in tonsils more frequently in adults than in children. keywords: children; dna; kipyv; mcpyv; pcr; samples; wupyv cache: cord-267928-dflkggjt.txt plain text: cord-267928-dflkggjt.txt item: #323 of 973 id: cord-268094-ubz0q7e9 author: Curland, N. title: Investigation into diseases in free-ranging ring-necked pheasants (Phasianus colchicus) in northwestern Germany during population decline with special reference to infectious pathogens date: 2018-02-06 words: 8172 flesch: 41 summary: In 11.9% (n = 19) of investigated pheasants, dermal abrasions or lacerations were diagnosed, which probably were caused by trauma. Myositis was detected in 10.0% (n = 23) of investigated pheasants. keywords: avian; birds; cases; disease; et al; germany; n =; pathogens; pcr; pheasants; population; samples; spp; study; tissue; virus cache: cord-268094-ubz0q7e9.txt plain text: cord-268094-ubz0q7e9.txt item: #324 of 973 id: cord-268251-mcg1v24t author: Martins, Ronaldo Bragança title: Detection of respiratory viruses by real-time polymerase chain reaction in outpatients with acute respiratory infection date: 2014-09-17 words: 3162 flesch: 40 summary: Cloning of a human parvovirus by molecular screening of respiratory tract samples Respiratory tract viral infections Acute respiratory viral infections in ambulatory children of urban Northeast Brazil Viral potentiation of bacterial superinfection of the respiratory tract Clinical and financial benefits of rapid detection of respiratory viruses: an outcomes study Acute respiratory infection and influenza-like illness viral etiologies in Brazilian adults Viral and atypical bacterial detection in acute respiratory infection in children under five years Multiplex real-time PCR for detection of respiratory tract infections Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens -duration of symptoms significantly affects detection rate WHO estimates of the causes of death in children Treatment of naturally acquired common colds with zinc: a structures review Severe lower respiratory tract infection in infants and toddlers from a non-affluent population: viral etiology and co-detection as risk factors Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay Respiratory syncytial virus infection: immune response, immunopathogenesis and treatment Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Serial viral infections in infants with recurrent respiratory illnesses A novel multiplex realtime RT-PCR assay with FRET hybridization probes for the detection and quantitation of 13 respiratory viruses The complication of coinfection Human bocavirus infections in hospitalized children and adults Human bocavirus -insights into a newly identified respiratory virus Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay Detection of respiratory viruses by molecular methods Informe epidemiológico: influenza pandêmica (H1N1) New respiratory viruses of humans Hospitalization of influenza-like illness patients recommended by general practitioners in France between Rhinoviruses: important respiratory pathogens High rates of detection of respiratory viruses in tonsillar tissues from children with chronic adenotonsillar disease Laboratory diagnosis, epidemiology and clinical outcomes of pandemic influenza A and community respiratory viral infections in southern Brazil Comparison of fast-track diagnostics respiratory pathogens multiplex real-time RT-PCR assay with in-house singleplex assay for comprehensive detection of human respiratory viruses Clinical evaluation of multiplex real-time PCR panels for rapid detection of respiratory viral infections Osterhaus AD 2001. keywords: age; detection; multiplex; pcr; study; viruses cache: cord-268251-mcg1v24t.txt plain text: cord-268251-mcg1v24t.txt item: #325 of 973 id: cord-268455-btuzihsy author: de Santiago, Javier title: COVID-19: gynecologic cancer surgery at a single center in Madrid date: 2020-07-07 words: 2970 flesch: 42 summary: MD Anderson Cancer Center Madrid, given its characteristics and focus on the treatment of cancer patients, can be comparatively considered as a relatively COVID-19 free center. Although there are no specific reports in cancer patients regarding the incidence of COVID-19, they are considered high risk due to older age, increased incidence of comorbidities, and lower immunity. keywords: cancer; covid-19; infection; pandemic; patients; study; surgery cache: cord-268455-btuzihsy.txt plain text: cord-268455-btuzihsy.txt item: #326 of 973 id: cord-268468-036i1082 author: Asif, Muhammad title: The role of biosensors in COVID-19 outbreak date: 2020-09-18 words: 3210 flesch: 32 summary: The more precise and targeted detection of the virus can be carried out using biosensor based approaches. A pneumonia outbreak associated with a new coronavirus of probable bat origin Differential Sensitivities of Severe Acute Respiratory Syndrome (SARS) keywords: antibodies; biosensors; coronavirus; cov-2; covid-19; detection; diagnosis; patients; sars; surface cache: cord-268468-036i1082.txt plain text: cord-268468-036i1082.txt item: #327 of 973 id: cord-268567-2xoubkxb author: Samannodi, Mohammed title: Compliance with international guidelines in adults with encephalitis date: 2020-04-14 words: 3278 flesch: 40 summary: We hope that this study will increase awareness of encephalitis guidelines among clinicians with goals to improve the care and outcomes of this devastating disease. The epidemiology, clinical features, and long-term prognosis of Japanese encephalitis in Central Sarawak Results of a multinational study suggest the need for rapid diagnosis and early antiviral treatment at the onset of herpetic meningoencephalitis The neurocognitive and MRI outcomes of West Nile virus infection: preliminary analysis using an external control group In search of encephalitis etiologies: diagnostic challenges in the California encephalitis project Causes of encephalitis and differences in their clinical presentation in England: a multicenter, population-based prospective study Challenge of the unknown. keywords: csf; encephalitis; guidelines; hsv; patients; pcr; study; virus cache: cord-268567-2xoubkxb.txt plain text: cord-268567-2xoubkxb.txt item: #328 of 973 id: cord-268721-n6dsc4ig author: Pawlowski, Colin title: Inference from longitudinal laboratory tests characterizes temporal evolution of COVID-19-associated coagulopathy (CAC) date: 2020-08-17 words: 6970 flesch: 32 summary: However, the observations that DIC was formally diagnosed in only five of 2232 COVID pos patients and emphasizes that consumptive coagulopathy is an exception rather than the rule as it pertains to thrombotic phenotypes in COVID-19 patients. During each time window, we then compared the distribution of results from COVID pos versus COVID neg (matched) patients, allowing us to identify any lab tests which were significantly altered in COVID pos patients during any time of disease acquisition, onset, and/or progression. keywords: cohort; covid; covid pos; covid-19; days; lab; patients; pcr; pos; test; time cache: cord-268721-n6dsc4ig.txt plain text: cord-268721-n6dsc4ig.txt item: #329 of 973 id: cord-268817-wx96wwpg author: Karp, Donna Grace title: Sensitive and Specific Detection of SARS-CoV-2 Antibodies Using a High-Throughput, Fully Automated Liquid-Handling Robotic System date: 2020-08-20 words: 3619 flesch: 42 summary: Here, we present an ultrasensitive and high-throughput automated liquid biopsy assay based on the Hamilton Microlab ADAP STAR automated liquid-handling platform, which was developed and validated for the qualitative detection of total antibodies against spike protein 1 (S1) of SARS-CoV-2 that uses as little as 4 µL of serum. The S1 protein is a high-quality antigen in that it shares less homology with other coronaviruses (~64% with S1 protein from SARS 2003), 11 whereas the nucleocapsid (N) protein shares extremely high homology (~91% with SARS 2003). keywords: adap; antibodies; antibody; assay; cov-2; covid-19; sars; specimens; total cache: cord-268817-wx96wwpg.txt plain text: cord-268817-wx96wwpg.txt item: #330 of 973 id: cord-268977-hcg2rrhl author: Feikin, Daniel R. title: Etiology and Incidence of Viral and Bacterial Acute Respiratory Illness among Older Children and Adults in Rural Western Kenya, 2007–2010 date: 2012-08-24 words: 6449 flesch: 43 summary: The percentage of malaria blood smears positive among ARI patients ranged from (13) 1041 (10) 341 (8) 3406 (11) -1194 (62) 2212 (8) 489 (14) 802 (7) CFR a for ARI cases (5) 15 (4) 73 (2) -69 For ARI patients, blood, nasopharyngeal and oropharyngeal specimens using polyester-tipped swabs, and urine were collected. keywords: adults; ari; cases; controls; hiv; incidence; influenza; pathogen; patients; pneumonia; study; virus; years cache: cord-268977-hcg2rrhl.txt plain text: cord-268977-hcg2rrhl.txt item: #331 of 973 id: cord-269194-b1wlr3t7 author: Engstrom-Melnyk, Julia title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 words: 12555 flesch: 22 summary: Determining a patient's HIV viral load is indicated prior to entry into care, at the initiation of ART, at 2-8 weeks after ART initiation, and then typically every 3-4 months while on treatment: (1) to establish a baseline level of HIV viral load; (2) to establish viral response to the therapy to assess the virologic efficacy of ART; and (3) to monitor for abnormalities that may be associated with antiretroviral drugs (DHHS HIV, 2014) . (A) HIV viral loads will fluctuate as patients are on treatment, and, in most instances, will remain 'undetectable' (at or below dotted line); viral 'blips' are not uncommon and will result in transient 'detectable' and even quantifiable results (above the dashed line). keywords: assays; chronic; clinical; cmv; disease; et al; fda; hcv; hiv; infection; laboratory; load; molecular; patients; pcr; results; rna; testing; tests; therapy; time; time pcr; transplant; treatment; virus cache: cord-269194-b1wlr3t7.txt plain text: cord-269194-b1wlr3t7.txt item: #332 of 973 id: cord-269407-6i66zf0e author: Rutvisuttinunt, Wiriya title: Retrospective use of next-generation sequencing reveals the presence of Enteroviruses in acute influenza-like illness respiratory samples collected in South/South-East Asia during 2010–2013 date: 2017-07-14 words: 3869 flesch: 42 summary: We sought to determine if we could identify a pathogen in CPE positive samples despite the samples testing negative using antibody panels for common respiratory samples. Regional map displaying the distribution of respiratory viral pathogens identified by NGS from respiratory specimens collected during metagenomic data Discovery of STL polyomavirus, a polyomavirus of ancestral recombinant origin that encodes a unique T antigen by alternative splicing Prevalence and characterization of enterovirus infections among pediatric patients with hand foot mouth disease, herpangina and influenza like illness in Thailand Metagenomics study of viral pathogens in undiagnosed respiratory specimens and identification of human enteroviruses at a Thailand hospital Public health strategies to prevent genital herpes: where do we stand? Age-specific prevalence of infection with herpes simplex virus types 2 and 1: a global review Seroprevalence of HSV1 and HSV2 infections in family planning clinic attenders Clusters of acute respiratory illness associated with human enterovirus 68-Asia, Europe, and United States The use of next generation sequencing in the diagnosis and typing of respiratory infections The diagnosis of infectious diseases by whole genome next generation sequencing: a new era is opening Next-generation sequencing technologies in diagnostic virology Next-generation sequencing technology in clinical virology Temporal response of the human virome to immunosuppression and antiviral therapy Sequence analysis of the human virome in febrile and afebrile children We would like to thank Dr. Simon Pollett and Dr. Damon Ellison for comments on the manuscript; Dr. Kimberly Bishop-Lilly, Mr. Gregory Rice, Ms. Ragina Cer, Dr. Patrick Chain for advices in bioinformatics; Ms. Thidarat Intararit and the clinical research coordinator team for the support on the clinical information; Mr. Chitchai Hemachudha, Ms. Angkana Huang, Ms. Tipawan Thipwong and the project management section for specimen processing and demographic data on study subjects;Ms. keywords: cpe; ngs; pathogens; pcr; pools; positive; respiratory; samples; sequencing; virus cache: cord-269407-6i66zf0e.txt plain text: cord-269407-6i66zf0e.txt item: #333 of 973 id: cord-269627-mx1mjdqc author: Thiry, Etienne title: Feline herpesvirus infection. ABCD guidelines on prevention and management date: 2009-07-31 words: 3939 flesch: 41 summary: 2 Passive immunity acquired via colostrum Maternally derived antibodies protect kittens against disease during the first weeks of life, but in general levels are low in FHV infections. 18 Viral DNA has also been detected in the aqueous humour of a larger proportion of cats suffering from uveitis, as compared with 19 Chronic rhinosinusitis, a frequent cause of sneezing and nasal discharge, has been associated with FHV infection. keywords: cats; disease; feline; fhv; herpesvirus; infection; signs; vaccination; virus cache: cord-269627-mx1mjdqc.txt plain text: cord-269627-mx1mjdqc.txt item: #334 of 973 id: cord-269726-z0frgm7s author: Gidari, Anna title: Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date: 2020-10-10 words: 6714 flesch: 47 summary: Long-term effects of COVID-19 in a patient on maintenance dialysis Glucocorticoid-induced relapse of COVID-19 in a patient with sarcoidosis Reevaluation of retested nucleic acid-positive cases in recovered COVID-19 patients: Report from a designated transfer hospital in Chongqing Recurrence of positive SARS-CoV-2 RNA in COVID-19: a case report Clinical recurrences of COVID-19 symptoms after recovery: viral relapse, reinfection or inflammatory rebound? Positive SARS-CoV-2 RNA recurs repeatedly in a case recovered from COVID-19: dynamic results from 108 days of follow-up Persistent SARS-COV-2 RNA positivity in a patient for 92 days after disease onset: a case report Positive conversion of COVID-19 after two consecutive negative RT-PCR results: a role of low-dose CT Recurrent presence of SARS-CoV-2 RNA in a 33-year-old man Repositive cases of nucleic acid tests in discharged patients with COVID-19: a follow-up study Positive SARS-Cov-2 test in a woman with COVID-19 at 22 days after hospital discharge: a case report Low humoral immune response and ineffective clearance of SARS-Cov-2 in a COVID-19 patient with CLL during a 69-day follow-up Recurrent positive nucleic acid detection in a recovered COVID-19 patient: a case report and literature review Successful recovery of recurrence of positive SARS-CoV-2 RNA in COVID-19 patient with systemic lupus erythematosus: a case report and review Clinical characteristics of severe acute respiratory syndrome coronavirus 2 reactivation Absent immune response to SARS-CoV-2 in a 3-month recurrence of coronavirus disease 2019 (COVID-19) case Recurrence of SARS-CoV-2 infection with a more severe case after mild COVID-19, reversion of RT-qPCR for positive and late antibody response: case report Repeated COVID-19 relapse during post-discharge surveillance with viral shedding lasting for 67 days in a recovered patient infected with SARS-CoV-2 COVID-19 infection recurrence presenting with meningoencephalitis Post discharge positive re-tests in COVID-19: common but clinically non-significant Progressive CT findings and positive RT-PCR again of recovered and discharged patients with COVID-19 Changes in RT-PCR test results and symptoms during the menstrual cycle of female individuals infected with SARS-CoV-2: report of two cases Incidence, clinical course and risk factor for recurrent PCR positivity in discharged COVID-19 patients in Guangzhou, China: a prospective cohort study COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing The treatment and follow-up of 'recurrence' with discharged COVID-19 patients: data from Guizhou Recurrent recurrence of positive SARS-CoV-2 RNA in a COVID-19 patient Recurrence or relapse of COVID-19 in older patients: a description of three cases Recurrent pneumonia in a patient with new coronavirus infection after discharge from hospital for insufficient antibody production: a case report A case presentation for positive SARS-CoV-2 RNA recurrence in a patient with a history of type 2 diabetes that had recovered from severe COVID-19 Clinical features of discharged COVID-19 patients with an extended SARS-CoV-2 RNA positive signal in respiratory samples The dilemma of COVID-19 recurrence after clinical recovery Persistent positivity and fluctuations of SARS-CoV-2 RNA in clinically-recovered COVID-19 patients Probable causes and risk factors for positive SARS-CoV-2 test in recovered patients: evidence from Brunei Darussalam Epidemiological characteristics of COVID-19 patients in convalescence period Chest CT study of fifteen COVID-19 patients with positive RT-PCR retest results after discharge Rate of re-positive RT-PCR test among patients recovered from COVID-19 Discontinuation of antiviral drugs may be the reason for recovered COVID-19 patients testing positive again Changes in serum virus-specific IgM/IgG antibody in asymptomatic and discharged patients with reoccurring positive COVID-19 nucleic acid test (RPNAT) Chest CT and clinical follow-up of discharged patients with COVID-19 in Wenzhou City A cluster of the Corona Virus Disease 2019 caused by incubation period transmission in Wuxi Re-positive coronavirus disease 2019 PCR test: could it be a reinfection? Diagnostic testing and screening for SARS-CoV-2 Growth kinetics of SARS-coronavirus in Vero E6 cells Detection and isolation of SARS-CoV-2 in serum, urine, and stool specimens of COVID-19 patients from the Republic of Korea Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement Positive result of Sars-Cov-2 in faeces and sputum from discharged patient with COVID-19 in Yiwu Song S Recurrence of positive SARS-CoV-2 viral RNA in recovered COVID-19 patients during medical isolation observation Positive RT-PCR test results in discharged COVID-19 patients: reinfection or residual Coronavirus disease (COVID-19) in a paucisymptomatic patient: Epidemiological and clinical challenge in settings with limited community transmission Seven discharged patients turning positive again for SARS-CoV-2 on quantitative RT-PCR Serial CT features in discharged COVID-19 patients with positive RT-PCR re-test A case series of recurrent viral RNA positivity in recovered COVID-19 Chinese patients The clinical features and outcomes of discharged coronavirus disease 2019 patients: a prospective cohort study Re-infection by COVID-19: a real threat for the future management of pandemia? Letter to the Editor: Three cases of re-detectable positive SARS-CoV-2 RNA in recovered COVID-19 Microbiol Infect Dis patients with antibodies Two cases of COVID-19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: a rising concern Persistent viral RNA positivity during recovery period of a patient with SARS-CoV-2 infection Recurrent PCR positivity after hospital discharge of people with coronavirus disease 2019 (COVID-19) Rehospitalization of a recovered coronavirus disease 19 (COVID-19) child with positive nucleic acid detection keywords: assay; cases; cov-2; covid-19; nasopharyngeal; patients; pcr; positive; recurrence; rna; sars; swab cache: cord-269726-z0frgm7s.txt plain text: cord-269726-z0frgm7s.txt item: #335 of 973 id: cord-269839-jxqs51o5 author: Bitome-Essono, Paul-Yannick title: Tracking zoonotic pathogens using blood-sucking flies as 'flying syringes' date: 2017-03-28 words: 5877 flesch: 49 summary: The omnipresence of hematophagous flies in certain habitats and their opportunistic blood-feeding behaviour (Muturi et al., 2011; Muzari et al., 2010; Späth, 2000) make of them compelling candidates to obtain blood meals from different vertebrate hosts for pathogen detection. Specifically, blood meals were from 20 vertebrate species, including 12 families and 8 orders (Figure 1b and Tables 2 and 3). keywords: blood; dna; et al; flies; hosts; meals; parasites; pathogens; pcr; species; system; tsetse cache: cord-269839-jxqs51o5.txt plain text: cord-269839-jxqs51o5.txt item: #336 of 973 id: cord-269948-zfbu9646 author: Teo, Jeanette title: VereFlu™: an integrated multiplex RT-PCR and microarray assay for rapid detection and identification of human influenza A and B viruses using lab-on-chip technology date: 2011-04-19 words: 3856 flesch: 44 summary: key: cord-269948-zfbu9646 authors: Teo, Jeanette; Pietro, Patrizia Di; Biagio, Floriana San; Capozzoli, Monica; Deng, Yi-Mo; Barr, Ian; Caldwell, Natalie; Ong, Kian-Leong; Sato, Mitsuharu; Tan, Rosemary; Lin, Raymond title: VereFlu™: an integrated multiplex RT-PCR and microarray assay for rapid detection and identification of human influenza A and B viruses using lab-on-chip technology date: 2011-04-19 journal: Arch Virol DOI: 10.1007/s00705-011-0999-7 sha: doc_id: 269948 cord_uid: zfbu9646 Threatening sporadic outbreaks of avian influenza and the H1N1 pandemic of 2009 highlight the need for rapid and accurate detection and typing of influenza viruses. Therefore, the looming threat of pandemics from influenza viruses cannot be overlooked, and assays that enable rapid, accurate identification and subtyping of influenza viruses is pertinent for surveillance and outbreak management. keywords: assay; detection; h1n1; influenza; pcr; rna; vereflu; virus; viruses cache: cord-269948-zfbu9646.txt plain text: cord-269948-zfbu9646.txt item: #337 of 973 id: cord-270526-o4hsr4pm author: An, Dong-Jun title: An immunochromatography assay for rapid antemortem diagnosis of dogs suspected to have canine distemper date: 2007-10-24 words: 3326 flesch: 52 summary: Antemortem diagnosis of CDV infection by RT-PCR in distemper dogs with neurological deficits without the typical clinical presentation Virus Infections of Carnivores A sample standardised protocol for the production of monoclonal antibodies against viral and bacterial antigens Detection of canine distemper virus nucleoprotein RNA by reverse transcription-PCR using serum, whole blood, and cerebrospinal fluid from dogs with distemper Infectious diseases of the dog and cat Rinderpest and other animal morbillivirus infections: comparative aspects and recent developments A comparison of in situ hybridisation, reverse transcriptase-polymerase chain reaction (RT-PCR) and in situ-RT-PCR for the detection of canine distemper virus RNA in Paget's disease Immunochromatographic test for simultaneous serodiagnosis of Babesia caballi and B. equi infections in horses Comparison of the immunofluorescence assay with RT-PCR and nested PCR in the diagnosis of canine distemper Comparison of tissue and fluid samples for the early detection of canine distemper virus in experimentally infected dogs The evaluation of diagnostic procedures for the detection of canine distemper virus infection One-step immunochromatography assay kit for detecting antibodies to canine parvovirus Histopathological features of canine distemper recently observed in Japan Morbillivirus infections of aquatic mammals: newly identified members of the genus Comparison of one-step RT-PCR and a nested PCR for the detection of canine distemper virus in clinical samples Neurological manifestation of canine distemper virus infection Detection of canine parvovirus antigens with antibodies to synthetic peptides This research was supported in part by the Joint HBI Corporation, Anyang, Kyunggi-do. The CDV detection limits of the IC and nested PCR assays were tested by using the Rockborn CDV strain and diluting it serially 10-fold. keywords: assay; cdv; conjunctival; dogs; pcr; samples cache: cord-270526-o4hsr4pm.txt plain text: cord-270526-o4hsr4pm.txt item: #338 of 973 id: cord-270579-rf933a0y author: van Kruijssen, Alida M. title: Detection of respiratory pathogens by real-time PCR in children with clinical suspicion of pertussis date: 2006-12-20 words: 514 flesch: 48 summary: However, 21 out of 38 cases that met the clinical definition of pertussis were negative for B. pertussis. This would prompt more appropriate treatment of B. pertussis and other atypical bacteria, differentiating them from viral infections as well as use of vaccination to prevent spread of pertussis. keywords: pcr; pertussis cache: cord-270579-rf933a0y.txt plain text: cord-270579-rf933a0y.txt item: #339 of 973 id: cord-270929-utn21ce1 author: Wise, Annabel G. title: Molecular characterization of a novel coronavirus associated with epizootic catarrhal enteritis (ECE) in ferrets date: 2006-05-25 words: 6117 flesch: 47 summary: BLAST analysis of the entire FECV-MSU1 N gene sequence consistently demonstrated significant similarities to reported coronavirus N gene sequences in the GenBank database. The deduced amino acid sequence of the FECV-MSU1 N protein was aligned with corresponding coronavirus sequences from GenBank, representing each of the coronavirus antigenic groupings. keywords: coronavirus; et al; fecv; ferrets; gene; group; min; msu1; orf; pcr; protein; sequence cache: cord-270929-utn21ce1.txt plain text: cord-270929-utn21ce1.txt item: #340 of 973 id: cord-270964-kxze0470 author: Lau, Kwok-Kwong title: Possible Central Nervous System Infection by SARS Coronavirus date: 2004-02-17 words: 1559 flesch: 51 summary: Cerebrospinal fluid tested positive for SARS coronavirus (SARS-CoV) by reverse transcriptase–polymerase chain reaction. Emerg Infect Dis DOI: 10.3201/eid1002.030638 sha: doc_id: 270964 cord_uid: kxze0470 On day 22 of illness, generalized tonic-clonic convulsion developed in a 32-year-old woman with severe acute respiratory syndrome (SARS). keywords: cov; day; patient; sars; serum cache: cord-270964-kxze0470.txt plain text: cord-270964-kxze0470.txt item: #341 of 973 id: cord-271130-6s79q1c1 author: Filoni, Claudia title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) date: 2017-11-17 words: 6586 flesch: 42 summary: The outcomes of FeLV infection in domestic cats vary according to host susceptibility, virus strain, and infectious challenge dose. We previously reported on FeLV infections in jaguarundis. keywords: animals; antibodies; cats; feline; felv; infection; jaguarundis; leukemia; loads; pcr; proviral; rna; time; virus; wild cache: cord-271130-6s79q1c1.txt plain text: cord-271130-6s79q1c1.txt item: #342 of 973 id: cord-271339-wt5o9sgm author: Chen, Chao-Ju title: Optimization of the CDC Protocol of Molecular Diagnosis of COVID-19 for Timely Diagnosis date: 2020-05-21 words: 2094 flesch: 48 summary: The event rate of nonspecific signals in E gene assay was significantly reduced from 63.1% (301/477) to 12% (226/1890) after adding BSA. Diagnostics 2020, 10, x FOR PEER REVIEW 3 of 6 The event rate of nonspecific signals in E gene assay was significantly reduced from 63.1% (301/477) to 12% (226/1890) after adding BSA. keywords: assay; coronavirus; covid-19; gene; pcr cache: cord-271339-wt5o9sgm.txt plain text: cord-271339-wt5o9sgm.txt item: #343 of 973 id: cord-271341-fszljnax author: Lei, Pinggui title: COVID-19 Carrier or Pneumonia: Positive Real-Time Reverse-Transcriptase Polymerase Chain Reaction but Negative or Positive Chest CT Results date: 2020-05-06 words: 1013 flesch: 32 summary: However, several questions need to be answered to support the proposed hypotheses: 1) the potential infectivity of true hidden carriers; 2) if the subclinical chest abnormalities present in true hidden carriers; 3) the value and feasibility of CT examination compared to rRT-PCR in screening hidden carriers from perspectives of patients and social resources; 4) the proportions of hidden carriers and hidden carriers with subclinical chest abnormalities; 5) the composition of subclinical chest abnormalities; 6) the performance of a deployed DL-based AI system in detecting these subclinical chest abnormalities; and 7) distinguishing the mild natural symptomatic presentation and subclinical CT abnormalities. Considering the rare understanding of asymptomatic hidden carriers and potential false-negative results in rRT-PCR tests, more studies on hidden carriers and validation on other possible screening approaches are worth exploring. keywords: carriers; pcr; rrt cache: cord-271341-fszljnax.txt plain text: cord-271341-fszljnax.txt item: #344 of 973 id: cord-271421-4dk7mkut author: Balsalobre-Arenas, Luz title: Rapid diagnosis of gastrointestinal tract infections due to parasites, viruses, and bacteria date: 2017-07-31 words: 6338 flesch: 39 summary: There are various other antigen detection techniques that are valid alternatives, such as IFD, ELISA or ICT techniques, that have shown specificity and sensitivity values higher than those of microscopic observation. While antigen detection techniques are widely used in Clinical Microbiology laboratories, for the diagnosis of viruses, some parasites and some bacteria, molecular techniques are routinely used only for some pathogens (such as Clostridium difficile). keywords: antigen; detection; diagnosis; helicobacter; infection; methods; patients; pcr; pylori; samples; sensitivity; specificity; techniques; test; use cache: cord-271421-4dk7mkut.txt plain text: cord-271421-4dk7mkut.txt item: #345 of 973 id: cord-271427-af71cum9 author: Yazici, Zafer title: Circulation of Indigenous Bovine Respiratory Syncytial Virus Strains in Turkish Cattle: The First Isolation and Molecular Characterization date: 2020-09-20 words: 4466 flesch: 59 summary: Evidence for the circulation of new divergent clades Recombinant bovine respiratory syncytial virus with deletion of the SH gene induces increased apoptosis and pro-inflammatory cytokines in vitro, and is attenuated and induces protective immunity in calves Evolution of Bovine Respiratory Syncytial Virus Genetic analysis of bovine respiratory syncytial virus in Croatia Molecular characterization of Brazilian wild-type strains of Bovine respiratory syncytial virus reveals genetic diversity and putative subgroup of the virus Molecular Epidemiology and Evolution of Bovine Respiratory Syncytial Virus Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil Detection of bovine respiratory syncytial virus infections in young dairy and beef cattle in Poland Bovine respiratory disease complex associated mortality and morbidity rates in feedlot cattle from southeastern Brazil The first serological report for genotype C bovine parainfluenza 3 virus in ruminant species of mid-northern Turkey: The detection of etiological agents by direct immunofluorescence technique Seroprevalence of bovine respiratory viruses in North-Western Turkey Detection of bovive respiratory syncytial virus in experimentally infected balb/c mice Live-cell characterization and analysis of a clinical isolate of bovine respiratory syncytial virus, using molecular beacons Weis Arns, C.; Issa Samara, S. Detection of an untyped strain of bovine respiratory syncytial virus in a dairy herd The antigenic and genetic variability of bovine respiratory syncytial virus with emphasis on the G protein Potential risk of regional disease spread in West Africa through cross-border cattle trade Molecular detection and phylogenetic analysis of bovine respiratory syncytial virus (BRSV) in swabs and lung tissues of adult cattle Bovine respiratory syncytial virus lacking the virokinin or with a mutation in furin cleavage site RA(R/K)R109 induces less pulmonary inflammation without impeding the induction of protective immunity in calves Virokinin, a bioactive peptide of the tachykinin family, is released from the fusion protein of bovine respiratory syncytial virus An investigation of the seroprevalence of crimean-congo hemorrhagic fever and lumpy skin disease in domesticated water buffaloes in Northern Turkey keywords: analysis; bovine; brsv; isolates; pcr; turkey; virus cache: cord-271427-af71cum9.txt plain text: cord-271427-af71cum9.txt item: #346 of 973 id: cord-271504-t3y1w9ef author: Luo, Zichao title: Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date: 2020-06-16 words: 14501 flesch: 38 summary: Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol New small-molecule drug design strategies for fighting resistant influenza A Characteristics of arbidol-resistant mutants of influenza virus: implications for the mechanism of anti-influenza action of arbidol Mechanism of inhibition of enveloped virus membrane fusion by the antiviral drug arbidol Membranotropic effects of arbidol, a broad antiviral molecule, on phospholipid model membranes Clinical characteristics and therapeutic procedure for four cases with 2019 novel coronavirus pneumonia receiving combined Chinese and Western medicine treatment Discovering drugs to treat coronavirus disease 2019 (COVID-19) Effects of chloroquine on viral infections: an old drug against today's diseases Effect of weak bases on the intralysosomal pH in mouse peritoneal macrophages Mechanisms of action of hydroxychloroquine and chloroquine: implications for rheumatology Chloroquine inhibits autophagic flux by decreasing autophagosomelysosome fusion New insights into the antiviral effects of chloroquine Anti-HIV effects of chloroquine: inhibition of viral particle glycosylation and synergism with protease inhibitors Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro Chloroquine is a potent inhibitor of SARS coronavirus infection and spread In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro Breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies Chloroquine and hydroxychloroquine as available weapons to fight COVID-19 In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Effects of chronic exposure to hydroxychloroquine or chloroquine on inner retinal structures Animal toxicity and pharmacokinetics of hydroxychloroquine sulfate Retroviral proteases and their roles in virion maturation Host cell proteases: critical determinants of coronavirus tropism and pathogenesis Influenza and SARS-coronavirus activating proteases TMPRSS2 and HAT are expressed at multiple sites in human respiratory and gastrointestinal tracts Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases Virusencoded proteinases and proteolytic processing in the Nidovirales The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide Simultaneous treatment of human bronchial epithelial cells with serine and cysteine protease inhibitors prevents severe acute respiratory syndrome coronavirus entry Protease inhibitors targeting coronavirus and filovirus entry Efficacy of camostat mesilate compared with famotidine for treatment of functional dyspepsia: is camostat mesilate effective? Camostat mesilate attenuates pancreatic fibrosis via inhibition of monocytes and pancreatic stellate cells activity Recent research by Hoffmann et al. showed a promising in vitro inhibitory effect of this serine protease inhibitor in SARS-CoV and 2019-nCoV on human lung cells, showing potential as a viable option for COVID-19 treatment [113] . keywords: amplification; antibodies; antiviral; cells; china; chloroquine; coronavirus; covid-19; crispr; detection; disease; dna; drug; genome; host; infection; lamp; mers; ncov; novel; nucleic; patients; pcr; potential; protease; protein; rna; sars; syndrome; therapeutic; treatment cache: cord-271504-t3y1w9ef.txt plain text: cord-271504-t3y1w9ef.txt item: #347 of 973 id: cord-271669-dkg6229j author: Han, Seung Beom title: Respiratory Viral Infections in Children and Adolescents with Hematological Malignancies date: 2019-01-01 words: 3775 flesch: 36 summary: Pediatr Blood Cancer Respiratory tract viral infections in bone marrow transplant patients Respiratory viral infections in adults with hematologic malignancies and human stem cell transplantation recipients: a retrospective study at a major cancer center Respiratory virus infections after stem cell transplantation: a prospective study from the Infectious Diseases Working Party of the European Group for Blood and Marrow Transplantation Detection of respiratory viruses with a multiplex polymerase chain reaction assay (MultiCode-PLx Respiratory Virus Panel) in patients with hematologic malignancies Respiratory viral infections and coinfections in children with cancer, fever and neutropenia: clinical outcome of infections caused by different respiratory viruses Prospective detection of respiratory pathogens in symptomatic children with cancer Acute respiratory viral infections in pediatric cancer patients undergoing chemotherapy Efficacy and safety of withholding antimicrobial treatment www.mjhid.org in children with cancer, fever and neutropenia, with a demonstrated viral respiratory infection: a randomized clinical trial Nasopharyngeal detection of respiratory viruses in febrile neutropenic children Human rhinovirus and coronavirus detection among allogeneic hematopoietic stem cell transplantation recipients A guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2018 update by the Infectious Diseases Society of America and the The impact of RSV, adenovirus, influenza, and parainfluenza infection in pediatric patients receiving stem cell transplant, solid organ transplant, or cancer chemotherapy Molecular characterization of strains of respiratory syncytial virus identified in a hematopoietic stem cell transplant outpatient unit over 2 years: community or nosocomial infection? Detection and control of a nosocomial respiratory syncytial virus outbreak in a stem cell transplantation unit: the role of palivizumab Control of an outbreak of human parainfluenza virus 3 in hematopoietic stem cell transplant recipients Impact of aerosolized ribavirin on mortality in 280 allogeneic haematopoietic stem cell transplant recipients with respiratory syncytial virus infections How I treat respiratory viral infections in the setting of intensive chemotherapy or hematopoietic cell transplantation Parainfluenza virus lower respiratory tract disease after hematopoietic cell transplant: viral detection in the lung predicts outcome Human rhinovirus detection in the lower respiratory tract of hematopoietic cell transplant recipients: association with mortality Parainfluenza virus infections in hematopoietic cell transplant recipients and hematologic malignancy patients: A systematic review Immunodeficiency scoring index to predict poor outcomes in hematopoietic cell transplant recipients with RSV infections Respiratory viral infections in immunocompetent and immunocompromised persons Mediterr J Hematol Infect Dis DOI: 10.4084/mjhid.2019.006 sha: doc_id: 271669 cord_uid: dkg6229j BACKGROUND: Despite the introduction of a polymerase chain reaction (PCR) test for the diagnosis of respiratory viral infection (RVI), guidance on the application of this test and the management of RVI in immunocompromised children is lacking. keywords: children; infection; patients; pcr; respiratory; rvi; study cache: cord-271669-dkg6229j.txt plain text: cord-271669-dkg6229j.txt item: #348 of 973 id: cord-271915-nvilxnzl author: Adachi, D. title: Comprehensive detection and identification of human coronaviruses, including the SARS-associated coronavirus, with a single RT-PCR assay date: 2004-12-01 words: 3599 flesch: 43 summary: Identification of a novel coronavirus in patients with severe acute respiratory syndrome Case cluster of the severe acute respiratory syndrome Koch's postulates fulfilled for SARS virus A previously undescribed coronavirus associated with respiratory disease in humans Molecular epidemiology of the novel coronavirus that causes severe acute respiratory syndrome Coronaviruses Comprehensive PCR-based assay for detection and species identification of human herpesviruses A novel coronavirus associated with severe acute respiratory syndrome Severe acute respiratory syndrome (SARS) in a liver transplant recipient and guidelines for donor SARS screening A major outbreak of severe acute respiratory syndrome in Hong Kong Mounting lab accidents raise SARS fears Coronavirus as a possible cause of severe acute respiratory syndrome Clinical progression and viral load in a community outbreak of coronavirus associated SARS pneumonia: a prospective study National Microbiology Laboratory, Canada, Canadian Severe Acute Respiratory Syndrome Study Team Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infections Comparison of immunofluorescence with monoclonal antibodies and RT-PCR for the detection of human coronaviruses 229E and OC43 in cell culture Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage Interpretation of diagnostic laboratory tests for severe acute respiratory syndrome: the Toronto experience The ClustalX Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools A cluster of cases of severe acute respiratory syndrome in Hong Kong TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment Identification of a new human coronavirus SARS in Northern Vietnam Update: severe acute respiratory syndrome-Toronto World Health Organization Multicentre Collaborative Network for Severe Acute Respiratory Syndrome (SARS) Diagnosis, 2003. key: cord-271915-nvilxnzl authors: Adachi, D.; Johnson, G.; Draker, R.; Ayers, M.; Mazzulli, T.; Talbot, P.J.; Tellier, R. title: Comprehensive detection and identification of human coronaviruses, including the SARS-associated coronavirus, with a single RT-PCR assay date: 2004-12-01 journal: J Virol Methods DOI: 10.1016/j.jviromet.2004.07.008 sha: doc_id: 271915 cord_uid: nvilxnzl The SARS-associated human coronavirus (SARS-HCoV) is a newly described, emerging virus conclusively established as the etiologic agent of the severe acute respiratory syndrome (SARS). keywords: assay; coronavirus; hcov; pcr; sars; sequence cache: cord-271915-nvilxnzl.txt plain text: cord-271915-nvilxnzl.txt item: #349 of 973 id: cord-271919-pbs95hy0 author: Desenclos, Jean-Claude title: Introduction of SARS in France, March–April, 2003 date: 2004-02-17 words: 3414 flesch: 49 summary: Global Surveillance of Severe acute respiratory syndrome (SARS) SARS emergence from uncertainty Use of laboratory methods for SARS diagnosis World Health Organization. Four contacts of SARS cases had an episode of transient, mild or low-grade fever without other signs, including three healthcare workers of the hospital where patient D had been admitted and the passenger seated next to patient A during the AF171 flight. keywords: case; contact; days; patient; pcr; persons; sars cache: cord-271919-pbs95hy0.txt plain text: cord-271919-pbs95hy0.txt item: #350 of 973 id: cord-271920-1dzkgt6w author: Carpenter, Christopher R. title: Diagnosing COVID‐19 in the Emergency Department: A Scoping Review of Clinical Exam, Labs, Imaging Accuracy and Biases date: 2020-06-16 words: 7256 flesch: 41 summary: For example, among COVID-19 patients from cruise ships evaluated with CT, those with symptoms more commonly had COVID-19 CT findings than those without symptoms (80% vs. 40%). Emergency departments (ED) encountered decreased patient volumes before some in Seattle, New York City, New Orleans, and Detroit experienced waves of COVID-19 patients mixed with asymptomatic patients or those concerned about potential exposures. keywords: accuracy; article; copyright; coronavirus; cov-2; covid-19; disease; negative; patients; pcr; rrt; sars; sensitivity; tests cache: cord-271920-1dzkgt6w.txt plain text: cord-271920-1dzkgt6w.txt item: #351 of 973 id: cord-272104-i79b79un author: Chen, Yan title: Re-evaluation of retested nucleic acid-positive cases in recovered COVID-19 patients: Report from a designated transfer hospital in Chongqing, China date: 2020-06-07 words: 1612 flesch: 59 summary: He was diagnosed with novel coronavirus pneumonia on January 30, 2020, according to typical respiratory symptoms, positive oropharyngeal swab results and radiological ground-glass opacification. The remaining patients showed positive anal swab results three days after discharge. keywords: days; discharge; hospital; patients cache: cord-272104-i79b79un.txt plain text: cord-272104-i79b79un.txt item: #352 of 973 id: cord-272696-1jg46veg author: Tang, An title: Detection of Novel Coronavirus by RT-PCR in Stool Specimen from Asymptomatic Child, China date: 2020-06-17 words: 1726 flesch: 46 summary: By using the number of cumulative cases on February 21 as the denominator for the adjusted case-fatality risk (aCFR), we assumed that half of the additional cumulative reported deaths on March 5 could be matched with cases reported on February 21. Our result for China, excluding Hubei Province, is similar to a previous estimate of 0.9% (95% CI 0.6%-1.3%) by using a time-delay adjusted case-fatality risk for the same area (K. Mizumoto We estimated the case-fatality risk for coronavirus disease cases in China (3.5%); China, excluding Hubei Province (0.8%); 82 countries, territories, and areas (4.2%); and on a cruise ship (0.6%). keywords: china; coronavirus; pcr; specimens; stool cache: cord-272696-1jg46veg.txt plain text: cord-272696-1jg46veg.txt item: #353 of 973 id: cord-272955-kkkrkgg1 author: Belsy, Acosta title: Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes date: 2009-03-12 words: 4225 flesch: 35 summary: Rapid and sensitive diagnosis of human adenovirus infections by a generic polymerase chain reaction Outcome and clinical course of 100 patients with adenovirus infection following bone marrow transplantation Family Adenoviridae Infections in 18, 000 infants and children in a controlled study of respiratory tract disease. This research identified 49 confirmed cases of human adenovirus infection by PCR and/or viral culture. keywords: acute; adenovirus; cases; children; hadv; human; infection; patients; pcr; serotype; species cache: cord-272955-kkkrkgg1.txt plain text: cord-272955-kkkrkgg1.txt item: #354 of 973 id: cord-273179-bpnak9ov author: Ma, Fen-lian title: Quantitative detection of human Malawi polyomavirus in nasopharyngeal aspirates, sera, and feces in Beijing, China, using real-time TaqMan-based PCR date: 2017-08-14 words: 4130 flesch: 55 summary: Sixteen specimens were positive for MWPyV, including 13 (1.47%) respiratory samples and three (1.7%) fecal samples. These findings are supported by other studies that frequently detected MWPyV in respiratory samples from acutely ill patients and babies with upper respiratory symptoms [13, 17] . keywords: children; fecal; human; mwpyv; pcr; polyomavirus; samples; study cache: cord-273179-bpnak9ov.txt plain text: cord-273179-bpnak9ov.txt item: #355 of 973 id: cord-273343-als886fe author: McClenahan, Shasta D. title: Discovery of a Bovine Enterovirus in Alpaca date: 2013-08-12 words: 4603 flesch: 45 summary: Viral diseases of new world camelids Census of Agriculture Chronic weight loss in an immunodeficient adult llama Camelid immunoglobulins and their importance for the newborn-a review Evaluation of bovine viral diarrhea virus in New World camelids Bovine viral diarrhea virus in New World camelids Isolation of bovine viral diarrhea virus from an alpaca BVDV in British alpacas Genotyping and phylogenetic analysis of bovine viral diarrhea virus isolates from BVDV infected alpacas in North America Prevalence of bovine viral diarrhea virus infections in alpacas in the United States Persistent infection with bovine viral diarrhea virus in an alpaca Update on llama medicine. [1, 3, 4] and bovine viral diarrhea virus keywords: alpaca; bovine; enterovirus; min; pcr; sequences; serotypes; virus; viruses cache: cord-273343-als886fe.txt plain text: cord-273343-als886fe.txt item: #356 of 973 id: cord-273608-dxx3p1x5 author: Deng, Jikui title: Respiratory virus multiplex RT-PCR assay sensitivities and influence factors in hospitalized children with lower respiratory tract infections date: 2013-04-11 words: 3481 flesch: 39 summary: Multiplex RT-PCR; Respiratory viral loads; Cell culture; Lower respiratory tract infection Lower respiratory tract infections (LRTIs) are the most frequent cause of hospitalization among children worldwide (Ahn K M, et al., 1999; Garbino J, et al., 2004; Ruuskanen O, et al., 2011; Sung C C, et al., 2011; Thompson W W, et al., 2003; van Woensel J B, et al., 2003) . One NPS aliquot was used for a panel of respiratory viral pathogen detection by the ResPlex II Panel (Qiagen, Germany) (Li H, et al., 2007) . keywords: et al; multiplex; pcr; resplex cache: cord-273608-dxx3p1x5.txt plain text: cord-273608-dxx3p1x5.txt item: #357 of 973 id: cord-273829-t5cuop5c author: Görgülü, Özkan title: rRT-PCR Results of a Covid-19 Diagnosed Geriatric Patient date: 2020-10-17 words: 1490 flesch: 46 summary: The nucleic acid test functions as the gold standard method for confirming the SARS-COV-2 infection; however, some recent studies have detected false negative results of real-time reverse transcriptase polymerase chain reaction (rRT-PCR) Both lung and cardiovascular injuries are common in the management of COVID-19 infections, especially those with only cardiovascular disease symptoms [7] . keywords: covid-19; patient; pcr; rrt; test cache: cord-273829-t5cuop5c.txt plain text: cord-273829-t5cuop5c.txt item: #358 of 973 id: cord-273840-jjm7y07m author: Vabret, Astrid title: Detection of the New Human Coronavirus HKU1: A Report of 6 Cases date: 2006-03-01 words: 3080 flesch: 51 summary: Human coronavirus HKU1 (HCoV-HKU1), a new group 2 coronavirus, was first characterized in 2005 from 2 adults with pneumonia in Hong Kong, China. We are able to detect HKU1 in respiratory samples and stool specimens, indicating that this virus can be excreted in this way. keywords: coronavirus; hcov; hku1; patients; pcr; samples cache: cord-273840-jjm7y07m.txt plain text: cord-273840-jjm7y07m.txt item: #359 of 973 id: cord-273846-l0elcfe8 author: Ganapathy, Kannan title: Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes date: 2005-02-24 words: 2442 flesch: 51 summary: key: cord-273846-l0elcfe8 authors: Ganapathy, Kannan; Cargill, Peter Walker; Jones, Richard Charles title: Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes date: 2005-02-24 journal: J Virol Methods DOI: 10.1016/j.jviromet.2005.01.024 sha: doc_id: 273846 cord_uid: l0elcfe8 In order to test the survivability of infectious bronchitis virus (IBV) in dead chicken carcasses during 24 h of cold storage, 7 week-old specific-pathogen-free chickens were infected with virulent IBV Massachusetts strain M41, and were killed humanely 10 days later. Early pathogenesis in chicks of infection with an enterotropic strain of infectious bronchitis virus Co-circulation of four types of infectious bronchitis virus (793/B 624/1, B1648 and Massachusetts) Infectious bronchitis Longitudinal field studies on infectious bronchitis and avian pneumovirus in broiler using type-specific PCR Coronaviridae The use of chicken tracheal organ cultures for the isolation and assay of avian infectious bronchitis virus Comparative growth kinetic studies on avian infectious bronchitis virus in different systems Detection of infectious bronchitis Local antibody production in the oviduct and gut of hens infected with a variant strain of infectious bronchitis virus Infectious bronchitis virus: immunopathogenesis of infection in chicken Microwave or autoclave treatments destroy the infectivity of infectious bronchitis virus and avian pneumovirus but allow detection by reverse transcriptasepolymerase chain reaction Rapid diagnosis of avian infectious bronchitis virus by the polymerase chain reaction Inactivated rabies vaccine control and release: use of an ELISA method A Laboratory Manual for the Isolation and Identification of Avian Pathogens Local antibody response in avian infectious bronchitis: virus-neutralizing antibody in tracheobronchial secretions Local immunity to avian infectious bronchitis in tracheal organ culture Presence of viral antigens and antibody in the trachea of chickens infected with avian infectious bronchitis virus Further development and use of a molecular serotype identification test for infectious bronchitis virus Polymerase chain reaction a biotin-labelled DNA probe for detection of infectious bronchitis virus in chickens Tissue tropism of three cloacal isolates and Massachusetts strain of infectious bronchitis virus keywords: bronchitis; ibv; storage; virus cache: cord-273846-l0elcfe8.txt plain text: cord-273846-l0elcfe8.txt item: #360 of 973 id: cord-273859-tr4s5i7h author: Luis García Garmendia, José title: DETECCIÓN VIRAL Y RESPUESTA SEROLÓGICA EN PACIENTES CRÍTICOS INTUBADOS CON SARS-CoV-2. IMPLICACIONES PARA RETIRADA DE AISLAMIENTO date: 2020-04-29 words: 1382 flesch: 46 summary: El CDC propone como una pauta segura la determinación de 2 rRT-PCR negativas consecutivas para valorar la necesidad de aislamiento de los pacientes con COVID-19 (8). Tabla 1: Características y pruebas diagnósticas de los casos de pacientes críticos con SARS-CoV-2 con ventilación mecánica Figura 1. keywords: con; del; los; pacientes; pcr; sars cache: cord-273859-tr4s5i7h.txt plain text: cord-273859-tr4s5i7h.txt item: #361 of 973 id: cord-274127-12x5cc8i author: Jeong, Ji Hun title: Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses date: 2014-05-06 words: 2721 flesch: 46 summary: Nasopharyngeal versus oropharyngeal sampling Optimal sampling sites and methods for detection of pathogens possibly causing community-acquired lower respiratory tract infections Epidemiology of viral respiratory infections Laboratory detection of respiratory viruses by automated techniques Diagnosis of influenza in intensive care units: Lower respiratory tract samples are better than nose-throat swabs Diagnostic virology Comparison of different methods of total RNA extraction for viral detection in sputum Etiology and clinical characterization of respiratory virus infections in adult patients attending an emergency department in Beijing High incidence of multiple viral infections identified in upper respiratory tract infected children under three years of age in We thank Seegene Company for providing us with AnyplexTM II RV16. Molecular techniques have been used currently for respiratory virus detection with improved sensitivity, and multiplex real-time reverse transcription-polymerase chain reaction (RT-PCR) methods can detect simultaneously a number of viruses in a single assay. keywords: detection; nasopharyngeal; samples; sputum; swabs; viruses cache: cord-274127-12x5cc8i.txt plain text: cord-274127-12x5cc8i.txt item: #362 of 973 id: cord-274128-kgtr77e7 author: Hochstetter, Axel title: Lab-on-a-Chip Technologies for the Single Cell Level: Separation, Analysis, and Diagnostics date: 2020-04-29 words: 14659 flesch: 45 summary: For an overview of the pros and cons of DEP in the context of single cell separation and diagnostics, refer to Table 2 . For an overview of the pros and cons of DEP in the context of single cell separation and diagnostics, refer to Table 2 . keywords: amplification; analysis; array; blood; cell; chip; devices; diagnostics; dld; dna; droplet; e.g.; field; figure; flow; force; index; microfluidics; paper; particle; phase; sample; separation; techniques cache: cord-274128-kgtr77e7.txt plain text: cord-274128-kgtr77e7.txt item: #363 of 973 id: cord-274184-hm516x6p author: Elli, Luca title: Endoscopy during the Covid-19 outbreak: experience and recommendations from a single center in a high-incidence scenario date: 2020-04-27 words: 4847 flesch: 44 summary: To face the new scenario all the hospitals have been re-organised in order to reduce all the outpatient services and to devote almost all their personnel and resources to the management of Covid-19 patients. Establishing maximum prevention within the endoscopy unit is a necessary countermeasure to the large spectrum of signs and symptoms expressed by Covid-19 patients (fever, cough but also, in smaller percentages, nausea, vomiting, diarrhoea and even neurological symptoms) and the large quantity of asymptomatic carriers [1, 2, 27, 28] . keywords: coronavirus; cov-2; covid-19; endoscopy; infection; outbreak; patients; pcr; risk; route; sars cache: cord-274184-hm516x6p.txt plain text: cord-274184-hm516x6p.txt item: #364 of 973 id: cord-274289-8g9tuyrc author: Liang, Xiao title: Evaluation of Fast Technology Analysis (FTA) Cards as an improved method for specimen collection and shipment targeting viruses associated with Bovine Respiratory Disease Complex date: 2014-06-15 words: 3438 flesch: 31 summary: The lower detection sensitivity for FTA card samples generated from archived case material is presumed to be due to the dilution of the original swab material in viral transport media prior to archiving, as opposed to collecting directly onto FTA Cards at the time of sampling. In a recent field study (Foster et al., unpublished) 100% agreement was shown for FTA Card samples collected from nasal cavities of known BVDV PI and direct contact animals (n = 69) when compared to EDTA blood from the same animals. keywords: bovine; cards; fta; media; nucleic; pcr; specimens; transport; virus cache: cord-274289-8g9tuyrc.txt plain text: cord-274289-8g9tuyrc.txt item: #365 of 973 id: cord-274438-tgslabi2 author: Schnee, Sarah Valerie title: Performance of the Alere i RSV assay for point-of-care detection of respiratory syncytial virus in children date: 2017-12-13 words: 3124 flesch: 48 summary: Expert review of respiratory medicine Lack of sensitivity of rapid antigen tests for the diagnosis of respiratory syncytial virus infection in adults Diagnostic accuracy of rapid antigen detection tests for respiratory Syncytial virus infection: systematic review and meta-analysis Evaluation of Alere i RSV for rapid detection of respiratory syncytial virus in children hospitalized with acute respiratory tract infection Alere i RSV test results are available A limitation of our study is the use of VTM for Alere i RSV testing instead of directly inserting the swab to the Alere test base. keywords: alere; assay; children; pcr; respiratory; rsv; test cache: cord-274438-tgslabi2.txt plain text: cord-274438-tgslabi2.txt item: #366 of 973 id: cord-274567-xd37wxxf author: Monpoeho, S. title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid date: 2002-07-13 words: 3286 flesch: 42 summary: The variability observed with 50 copies of EV RNA standard was acceptable, and the detection limit of the RT-PCR is therefore 50 copies of EV RNA standard per reaction. Only duration of hospitalization showed a statistically significant decrease from 2.7 days for patients with negative PCR results to 1.8 days for patients with positive PCR results (P=0.042). keywords: amplification; csf; culture; meningitis; pcr; rna cache: cord-274567-xd37wxxf.txt plain text: cord-274567-xd37wxxf.txt item: #367 of 973 id: cord-274568-flqc3jjd author: Naguib, Michael title: The use of radiological imaging alongside reverse transcriptase PCR in diagnosing novel coronavirus disease 2019: a narrative review date: 2020-07-08 words: 2828 flesch: 45 summary: Coronavirus disease (COVID-19) pandemic Coronavirus disease 2019: what we know? Discusses the clinical features, diagnosis and treatment of COVID-19, with a brief commentary on the epidemiology and pathology based on the current evidence Relation between chest CT findings and clinical conditions of coronavirus disease (COVID-19) pneumonia: a multicenter study Chest radiographic and CT findings of the 2019 novel coronavirus disease (COVID-19): analysis of nine patients treated in Korea The majority of patients had ground-glass opacities with a patchy to confluent or nodular shape bilaterally in peripheral posterior lungs Chest CT findings in 2019 novel coronavirus (2019-nCoV) infections from Wuhan, China: key points for the radiologist CT imaging features of 4,121 patients with COVID-19: a meta-analysis • A meta-analysis of 34 retrospective studies reports the common CT findings as well as the sensitivity of CT scan CT imaging features of 2019 novel coronavirus (2019-nCoV) Emerging 2019 novel coronavirus (2019-nCoV) pneumonia Radiology of COVID-19-Imaging the pulmonary damage Sensitivity of chest CT for COVID-19: comparison to RT-PCR Diagnosing COVID-19: the disease and tools for detection Chest CT for detecting COVID-19: a systematic review and meta-analysis of diagnostic accuracy Chest CT for typical 2019-nCoV pneumonia: relationship to negative RT-PCR testing Essentials for radiologists on COVID-19: an update-radiology scientific expert panel Systematic review and meta-analysis on the value of chest CT in the diagnosis of coronavirus disease (COVID-19): Sol Scientiae, Illustra Nos Asymptomatic novel coronavirus pneumonia patient outside Wuhan: the value of CT images in the course of the disease Performance of radiologists in differentiating COVID-19 from viral pneumonia on chest CT Compares the accuracy of distinguishing COVID-19 pneumonia on CT between seven radiologists COVID-Net: a tailored deep convolutional neural network design for detection of COVID-19 cases from chest X-Ray images Frequency and distribution of chest radiographic findings in COVID-19 positive patients Center for Disease Control and Prevention. Many studies have reported high sensitivities of CT scans and suggested that they can be used in the diagnosis of COVID-19 alongside reverse transcriptase PCR. keywords: covid-19; disease; patients; pcr cache: cord-274568-flqc3jjd.txt plain text: cord-274568-flqc3jjd.txt item: #368 of 973 id: cord-274644-gr1eaj6k author: Chen, Zhao-Chi title: Thermally stable and uniform DNA amplification with picosecond laser ablated graphene rapid thermal cycling device date: 2019-12-15 words: 5170 flesch: 54 summary: Moreover, surface property of MLG PCR device with hydrophilic pattern sites here was required to be the use of forensic DNA evidence. The fabrication process of a hole-array rapid thermal cycling (HA-RTC) PCR device is illustrated in Fig. keywords: bkv; device; dna; et al; film; graphene; laser; mlg; pcr; rtc; surface; temperature cache: cord-274644-gr1eaj6k.txt plain text: cord-274644-gr1eaj6k.txt item: #369 of 973 id: cord-274656-dngumjns author: Mori, Masahiro title: Detection of mumps virus RNA in cerebrospinal fluid of patients with neuromyelitis optica date: 2011-04-06 words: 1991 flesch: 45 summary: Childhood infection by mumps virus has been reported not to be associated with increased risk of MS later in life [21] , and mumps virus genome has been not been detected in autopsy specimen lesions [26] . Although many infectious agents, including mumps virus, are postulated to have a role in the pathogenesis of multiple sclerosis (MS), the relationship between NMO and infectious agents remains uncertain. keywords: mumps; nmo; patients; pcr; virus cache: cord-274656-dngumjns.txt plain text: cord-274656-dngumjns.txt item: #370 of 973 id: cord-274676-wtizb7hk author: Lee, Seung-Hun title: Multilocus typing of Cryptosporidium spp. in young calves with diarrhea in Korea date: 2016-10-15 words: 4380 flesch: 48 summary: Subtyping of C. parvum by using gp60 All sequences obtained from C. parvum gp60 belonged to IIa according to phylogenetic analysis (Fig. 4) . In Table 3 Detection of Cryptosporidium parvum and C. bovis/ryanae using PCR analysis and ELISA. keywords: cryptosporidium; et al; parvum; pcr; prevalence; samples; spp cache: cord-274676-wtizb7hk.txt plain text: cord-274676-wtizb7hk.txt item: #371 of 973 id: cord-274707-mxh38hwd author: Laureano, Ana Flávia Santarine title: The different tests for the diagnosis of COVID-19 - A review in Brazil so far date: 2020 words: 3741 flesch: 42 summary: Most rapid tests use colloidal gold particles in a technique known as immunochromatography, also called lateral flow immunoassay, a type of sandwich assay that relies on a pair of antibodies used to recognize two independent epitopes of a protein, and therefore it can achieve high specificity (Zhou et al., 2012) . This kind of test is being used for pregnancy (Puertas et al., 2010) , HIV (Granade et al., 2010) , bacterial infections (Huang, 2007) , drugs of abuse (Gonzalez et al., 2011) , food contaminants and dengue virus (Cuzzubbo et al., 2001) , and many tests are commercially available (Zhou et al., 2012) . keywords: antibody; coronavirus; covid-19; dna; igm; pcr; sars; tests cache: cord-274707-mxh38hwd.txt plain text: cord-274707-mxh38hwd.txt item: #372 of 973 id: cord-274805-b3mqkfhh author: Onodera, Kenji title: Selection for 3′ end triplets for polymerase chain reaction primers date: 2004-12-31 words: 2272 flesch: 55 summary: We analyzed 3′ end triplets of PCR primer sequences obtained from refereed journal articles, to test those recommendations and to make empirical recommendations for primer design. key: cord-274805-b3mqkfhh authors: Onodera, Kenji; Melcher, Ulrich title: Selection for 3′ end triplets for polymerase chain reaction primers date: 2004-12-31 journal: keywords: end; frequencies; pcr; primer; triplets cache: cord-274805-b3mqkfhh.txt plain text: cord-274805-b3mqkfhh.txt item: #373 of 973 id: cord-274828-67yeag50 author: Dybkær, Karen title: Identification of acute myeloid leukemia patients with diminished expression of CD13 myeloid transcripts by competitive reverse transcription polymerase chain reaction (RT-PCR) date: 2000-04-21 words: 6052 flesch: 45 summary: We relate CD13 transcript levels with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) transcript levels in order to normalise the content of CD13 mRNA for variation in sample degradation and handling. Observed normalised CD13 transcript levels are correlated to CD13 surface expression and various clinical, pathological, and cytogenetic findings. keywords: aml; cd13; cells; expression; gapdh; high; levels; low; normalised; patients; pcr; surface; transcript cache: cord-274828-67yeag50.txt plain text: cord-274828-67yeag50.txt item: #374 of 973 id: cord-274892-a6fscyjf author: Smith, Joseph A. title: Identification and isolation of a novel herpesvirus in a captive mob of eastern grey kangaroos (Macropus giganteus) date: 2008-06-22 words: 4609 flesch: 41 summary: Iguanid herpesvirus 2 (GenBank accession no. AY236869) was designated as the outgroup due to its early divergence from other herpesvirus (Wellehan et al., 2003; . The herpesvirus sequence in this study is from a conserved region, and these differences together with host species are significant enough to differentiate this from other known herpesvirus species. keywords: analysis; cloacal; grey; herpesvirus; kangaroos; lesions; mob; pcr; samples; sequence cache: cord-274892-a6fscyjf.txt plain text: cord-274892-a6fscyjf.txt item: #375 of 973 id: cord-274954-06c3ymc3 author: Huang, Yu-Liang title: Development of a reverse transcription multiplex real-time PCR for the detection and genotyping of classical swine fever virus date: 2009-05-04 words: 5738 flesch: 53 summary: 2. Virological studies Detection of classical swine fever vaccine virus in blood and tissue samples of pigs vaccinated either with a conventional C-strain vaccine or a modified live marker vaccine Cost-effective real-time reverse transcriptase PCR (RT-PCR) to screen for Dengue virus followed by rapid single-tube multiplex RT-PCR for serotyping of the virus Detection and quantitative pathogenesis study of classical swine fever virus using a real time RT-PCR assay World Organisation for Animal Health. Among CSFV strains were 10-fold serially diluted and CSFV was detected from viral isolation, RT-PCR, RT-nPCR, and RT-MRT-PCR. keywords: csfv; genotype; mrt; pcr; pigs; samples; strain; viral; virus cache: cord-274954-06c3ymc3.txt plain text: cord-274954-06c3ymc3.txt item: #376 of 973 id: cord-275232-0sg0hv9w author: Yeung, Siu-Wai title: A DNA biochip for on-the-spot multiplexed pathogen identification date: 2006-09-25 words: 3243 flesch: 36 summary: Miniaturised nucleic acid analysis Microfabricated systems for nucleic acid analysis DNA-based bioanalytical microsystems for handheld device applications Electrochemical DNA sensors Electrochemical nucleic acid biosensors Nanomaterial-based electrochemical biosensors Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection Microfabricated PCR-electrochemical device for simultaneous DNA amplification and detection An integrated nanoliter DNA analysis device Effects of gold nanoparticle and electrode surface properties on electrocatalytic silver deposition for electrochemical DNA hybridization detection Preparation of a DNA matrix via an electrochemically directed copolymerization of pyrrole and oligonucleotides bearing a pyrrole group Gold nanoparticle-catalyzed silver electrodeposition on an indium tin oxide electrode and its application in DNA hybridization transduction Results of the two different types of electrodes (functionalized with E.coli and B.subtilis detection capture probe) when subjected to different sample solutions. (7) successfully demonstrated a fully integrated biochip for cell isolation and lysis, target amplification, as well as electrochemical amplicon detection. keywords: capture; detection; dna; e.coli; electrodes; microchamber; probe; sample; target; temperature cache: cord-275232-0sg0hv9w.txt plain text: cord-275232-0sg0hv9w.txt item: #377 of 973 id: cord-275275-wy8d6cw3 author: Rovida, Francesca title: Molecular detection of gastrointestinal viral infections in hospitalized patients date: 2013-09-12 words: 2598 flesch: 42 summary: key: cord-275275-wy8d6cw3 authors: Rovida, Francesca; Campanini, Giulia; Piralla, Antonio; Adzasehoun, Kodjo Messan Guy; Sarasini, Antonella; Baldanti, Fausto title: Molecular detection of gastrointestinal viral infections in hospitalized patients date: 2013-09-12 journal: Diagn Microbiol Infect Dis DOI: 10.1016/j.diagmicrobio.2013.07.020 sha: doc_id: 275275 cord_uid: wy8d6cw3 Gastrointestinal viral syndromes are a common cause of morbidity and mortality in humans worldwide. Human bocavirus and human coronavirus, mainly involved in infections of the respiratory tract, are also implicated in gastrointestinal infections (Clark and McKendrick, 2004; Khan and Bass, 2010) . keywords: gastroenteritis; infections; patients; pcr; viruses cache: cord-275275-wy8d6cw3.txt plain text: cord-275275-wy8d6cw3.txt item: #378 of 973 id: cord-275413-e2rhioty author: Rowland, Raymond R.R. title: The interaction between PRRSV and the late gestation pig fetus date: 2010-09-09 words: 6192 flesch: 42 summary: The IHC staining procedure included two sets of negative controls: tissue thin sections from non-infected fetuses and from infected fetuses stained with only secondary antibody. This scenario as a cause of severe interstitial pnuemonia in the PRRSV-infected newborn requires further investigation, but has obvious implications in the etiology of postnatal pulmonary complications following virus infections of the fetus. keywords: cells; fetuses; ifn-; infection; lymph; pcr; porcine; prrsv; syndrome; virus cache: cord-275413-e2rhioty.txt plain text: cord-275413-e2rhioty.txt item: #379 of 973 id: cord-275519-98qxf6xo author: Chun, Jong-Yoon title: Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene date: 2007-02-07 words: 3293 flesch: 43 summary: In addition, DPO primers detected the influenza A virus in patient 1 (lane 6), which was not detected using the conventional primer system (lane 1). DPO primers are easier to design than conventional primers. keywords: -segment; annealing; dpo; pcr; primer; priming cache: cord-275519-98qxf6xo.txt plain text: cord-275519-98qxf6xo.txt item: #380 of 973 id: cord-275787-5s442sy2 author: Banerjee, Arinjay title: Generation and Characterization of Eptesicus fuscus (Big brown bat) kidney cell lines immortalized using the Myotis polyomavirus large T-antigen date: 2016-09-14 words: 5831 flesch: 50 summary: Establishing bat cell lines enable researchers to study relevant virus-host interactions in a system that more closely resembles the reservoir host. Interferon response in terms of interferon beta transcript upregulation by bat cell lines, mostly cell lines from fruit bats, has been demonstrated before (Hagmaier et al., 2007; Crameri et al., 2009; Biesold et al., 2011; Virtue et al., 2011) . keywords: antigen; bat; bats; beta; cells; clones; cov; interferon; line; pcr; replication; usa; viruses cache: cord-275787-5s442sy2.txt plain text: cord-275787-5s442sy2.txt item: #381 of 973 id: cord-276271-3nz3169p author: Deborggraeve, Stijn title: T. cruzi OligoC-TesT: A Simplified and Standardized Polymerase Chain Reaction Format for Diagnosis of Chagas Disease date: 2009-06-02 words: 4736 flesch: 48 summary: key: cord-276271-3nz3169p authors: Deborggraeve, Stijn; Coronado, Ximena; Solari, Aldo; Zulantay, Ines; Apt, Werner; Mertens, Pascal; Laurent, Thierry; Leclipteux, Thierry; Stessens, Tim; Dujardin, Jean-Claude; Herdewijn, Piet; Büscher, Philippe title: T. cruzi OligoC-TesT: A Simplified and Standardized Polymerase Chain Reaction Format for Diagnosis of Chagas Disease date: 2009-06-02 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0000450 sha: doc_id: 276271 cord_uid: 3nz3169p BACKGROUND: PCR has evolved into one of the most promising tools for T. cruzi detection in the diagnosis and control of Chagas disease. We here present the development and phase I evaluation of the T. cruzi OligoC-TesT, a simple and standardized dipstick format for detection of PCR amplified T. cruzi DNA. keywords: blood; chagas; control; cruzi; detection; dna; oligoc; pcr; t. cruzi; test cache: cord-276271-3nz3169p.txt plain text: cord-276271-3nz3169p.txt item: #382 of 973 id: cord-276368-c9e93h0u author: Hosmillo, Myra D.T. title: Development of universal SYBR Green real-time RT-PCR for the rapid detection and quantitation of bovine and porcine toroviruses date: 2010-06-15 words: 4791 flesch: 52 summary: Comparison of the detection rates of BToV by real-time RT-PCR, conventional RT-PCR, and nested PCR assay. Comparison of the detection rates of PToV by real -time RT-PCR, conventional RT-PCR, and nested PCR assay. keywords: btov; detection; pcr; ptov; time; time rt cache: cord-276368-c9e93h0u.txt plain text: cord-276368-c9e93h0u.txt item: #383 of 973 id: cord-276542-lxwls664 author: Pan, Zhongzhou title: Development of a TaqMan-probe-based multiplex real-time PCR for the simultaneous detection of emerging and reemerging swine coronaviruses date: 2020-06-03 words: 4721 flesch: 49 summary: Improvements in detection method can bring many benefits. Pathogen monitoring nowadays largely relies on laboratory detection methods. keywords: copies; coronaviruses; detection; method; pcr; porcine; ptov; time cache: cord-276542-lxwls664.txt plain text: cord-276542-lxwls664.txt item: #384 of 973 id: cord-276718-3lujp0oy author: Neeraja, M. title: Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Hyderabad, India date: 2014-10-24 words: 6153 flesch: 45 summary: b RT-LAMP and CDC real time RT-PCR assay detected 8 samples which were negative for NS1 Ag by ELISA and NS1 RT PCR assay. All the primers were assessed for specificity before use in LAMP assays with a BLAST search with sequences in the Gen Bank (Table 1) . keywords: amplification; assay; dengue; denv; detection; lamp; ns1; pcr; serotype; time cache: cord-276718-3lujp0oy.txt plain text: cord-276718-3lujp0oy.txt item: #385 of 973 id: cord-276739-84vf5bts author: Sakurai, Akira title: Rapid typing of influenza viruses using super high-speed quantitative real-time PCR date: 2011-08-22 words: 3315 flesch: 44 summary: Clinical diagnostic tests for influenza viruses in outpatient departments or clinics are typically based on immunochromatographic detection of influenza virus antigens (Chan et al., 2007) . The analysis targeted the nucleotide sequences of the matrix protein segment of influenza virus A (A-MP), influenza virus B (B-MP), and hemagglutinin (HA) of the 2009 pandemic S-OIV and H5N1 avian influenza viruses. keywords: detection; influenza; pcr; reaction; rna; shrt; time; viruses cache: cord-276739-84vf5bts.txt plain text: cord-276739-84vf5bts.txt item: #386 of 973 id: cord-276978-xl4u7n6r author: Jonassen, Christine Monceyron title: Detection and Sequence Characterization of the 3′-End of Coronavirus Genomes Harboring the Highly Conserved RNA Motif s2m date: 2007-11-28 words: 2884 flesch: 55 summary: Cycle sequencing is performed using BigDye Terminator version 3.1, for long PCR product sequencing, with the following reagents: 4 l BigDye Terminator mix, 1.3 l coronavirus-specific reverse primer 2 (2.5 M), and 4.7 l PCR product. It is therefore important to use a PCR enzyme with a proofreading activity, in order to get PCR products from the longer cDNA molecules as well. keywords: pcr; primer; sequencing cache: cord-276978-xl4u7n6r.txt plain text: cord-276978-xl4u7n6r.txt item: #387 of 973 id: cord-277025-gmy51dx4 author: Pfefferle, Susanne title: Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Northern Germany date: 2020-06-04 words: 954 flesch: 48 summary: After 1 h at 37°C, the ESwab medium was replaced by cell culture medium (Dulbecco's modified Eagle's medium containing 3% fetal calf serum, 1% penicillinstreptomycin, 1% L-glutamine A novel coronavirus from patients with pneumonia in China The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Infection control and virological assessment of the first cluster of COVID-19 in northern Germany Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system Trimmomatic: a flexible trimmer for Illumina sequence data Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing NCBI Prokaryotic Genome Annotation Pipeline Haplotype-based variant detection from shortread sequencing We are grateful to Svenja Reucher and Kerstin Reumann for excellent technical assistance. keywords: coronavirus; cov-2; genome; reads; sars cache: cord-277025-gmy51dx4.txt plain text: cord-277025-gmy51dx4.txt item: #388 of 973 id: cord-277057-ww41t4k2 author: Sakthivel, Senthilkumar K. title: Comparison of fast-track diagnostics respiratory pathogens multiplex real-time RT-PCR assay with in-house singleplex assays for comprehensive detection of human respiratory viruses() date: 2012-07-11 words: 4955 flesch: 36 summary: In contrast, FTDRP RV assay failed to detect 5 RV positive samples with low Ct values by the corresponding in-house assay. Of 9 samples positive by the in-house EV assay and negative by the FTDRP EV/PeV assay, all were strongly positive for RV (Ct < 30) by both in-house and FTDRP RV assays and were confirmed positive for RV species A or C by VP1 and/or VP4/2 sequences. keywords: assays; ftdrp; house; pcr; specimens; time; virus; viruses cache: cord-277057-ww41t4k2.txt plain text: cord-277057-ww41t4k2.txt item: #389 of 973 id: cord-277125-s11obc7w author: Kim, Hyeong Rae title: An integrated system of air sampling and simultaneous enrichment for rapid biosensing of airborne coronavirus and influenza virus date: 2020-09-26 words: 3929 flesch: 58 summary: In this study, airborne virus particles were collected to a degree above the limit of detection (LOD) for a real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). key: cord-277125-s11obc7w authors: Kim, Hyeong Rae; An, Sanggwon; Hwang, Jungho title: An integrated system of air sampling and simultaneous enrichment for rapid biosensing of airborne coronavirus and influenza virus date: 2020-09-26 journal: Biosens Bioelectron DOI: 10.1016/j.bios.2020.112656 sha: doc_id: 277125 cord_uid: s11obc7w Point-of-care risk assessment (PCRA) for airborne viruses requires a system that can enrich low-concentration airborne viruses dispersed in field environments into a small volume of liquid. keywords: air; ath; enrichment; pcr; viruses cache: cord-277125-s11obc7w.txt plain text: cord-277125-s11obc7w.txt item: #390 of 973 id: cord-277265-p8pns7r9 author: Malik, Yashpal Singh title: Biotechnological innovations in farm and pet animal disease diagnosis date: 2019-09-20 words: 7289 flesch: 29 summary: Although, yet not been adopted for animal disease diagnosis, but novel platforms such as smartphonebased diagnosis (which expands nucleic acid-based detection assays toward POCD) like RT-LAMP and fluorescent lateral flow immunoassay (already developed for Zika virus and Dengue virus) provide exciting opportunities for veterinary diagnostics in the near future (Rong et al., 2019) . The real-time PCR (qPCR) is a well-established tool with high sensitivity of pathogens detection and recently, qPCR has been transitioned into POCD platform. keywords: acid; amplification; animal; assays; detection; diagnosis; diseases; dna; elisa; et al; isothermal; methods; nucleic; pathogens; pcr; techniques; time; virus cache: cord-277265-p8pns7r9.txt plain text: cord-277265-p8pns7r9.txt item: #391 of 973 id: cord-277276-j2qzhvzi author: Al-Ayed, Mohamed S. title: Viral etiology of respiratory infections in children in southwestern Saudi Arabia using multiplex reverse-transcriptase polymerase chain reaction date: 2014 words: 2987 flesch: 44 summary: The burden of acute respiratory infections in crisisaffected populations: a systematic review Respiratory pathogens in children with and without respiratory symptoms Diagnostic value of respiratory virus detection in symptomatic children using real-time PCR Respiratory viruses in children hospitalized for acute lower respiratory tract infection in Ghana Virological and clinical characterizations of respiratory infections in hospitalized children Emerging respiratory agents: new viruses for old diseases? Novel respiratory virus infections in children Epidemiology and etiology of childhood pneumonia Treatment of the common cold in children and adults Detecting respiratory viruses in asymptomatic children Comparative evaluation of the Seegene Seeplex RV15 and real-time PCR for respiratory virus detection Rapid detection of respiratory tract viral infections and coinfections in patients with influenza-like illnesses by use of reverse transcription-PCR DNA microarray systems Detection and genotyping of human respiratory viruses in clinical specimens from children with acute respiratory tract infections Human metapneumovirus and human coronavirus infection and pathogenicity in Saudi children hospitalized with acute respiratory illness Detection of bocavirus in children suffering from acute respiratory tract infections in Saudi Arabia Prevalence of respiratory syncytial virus infection in Riyadh during the winter season 2007-2008 and different risk factors impact World Health Organization. Geneva (CH): World Health Organization Basic Laboratory Procedures in Clinical Microbiology Viral etiology of acute respiratory infection in Gansu Province Viral etiology of acute febrile respiratory illnesses in hospitalized children younger than 24 months Aetiology of influenza-like illness in adults includes parainfluenzavirus type 4 Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children Epidemiology of respiratory viral infection using multiplex rt-PCR in Update on rhinovirus and coronavirus infections Frequent detection of respiratory viruses without symptoms: toward defining clinically relevant cutoff values Role of emerging respiratory viruses in children with severe acute wheezing Respiratory viral infections in infants: causes, clinical symptoms, virology, and immunology Human metapneumovirus: review of an important respiratory pathogen Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Brookline (MA): ProMed, International Society for Infectious Diseases keywords: children; detection; hrv; infections; pcr; saudi; study; viruses cache: cord-277276-j2qzhvzi.txt plain text: cord-277276-j2qzhvzi.txt item: #392 of 973 id: cord-277357-lpurk7pe author: González-González, Everardo title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date: 2020-08-13 words: 4008 flesch: 44 summary: The blueGel1 has several important advantages and represents a valid and portable solution for detecting PCR amplification products. Our results suggest that using a commercial plate reader to determine the extent of advance of PCR amplifications is a practical, reliable, reproducible, and robust alternative to the use of gel electrophoresis. keywords: amplification; cov-2; covid-19; detection; fluorescence; minipcr; plate; reader; sars cache: cord-277357-lpurk7pe.txt plain text: cord-277357-lpurk7pe.txt item: #393 of 973 id: cord-277359-za2hh71g author: Chae, Kum Ju title: Positive conversion of COVID-19 after two consecutive negative RT-PCR results: A role of low-dose CT date: 2020-06-09 words: 602 flesch: 50 summary: [1] recently published an article describes serial CT features in discharged COVID-19 patients with positive RT-PCR re-tests, giving us a lesson that follow-up CT after discharge is essential. Serial CT features in discharged COVID-19 patients with positive RT-PCR re-test SARS-CoV-2 RNA more readily detected in induced sputum than in throat swabs of convalescent COVID-19 patients Positive RT-PCR Test Results in Patients Recovered From COVID-19 Korea Center for Disease Control & Prevention, Updates on 2019 novel coronavirus: for press release keywords: pcr cache: cord-277359-za2hh71g.txt plain text: cord-277359-za2hh71g.txt item: #394 of 973 id: cord-277659-afysef1e author: Hamilton, F. title: Kinetics and performance of the Abbott Architect SARS-CoV-2 IgG antibody assay date: 2020-07-04 words: 3098 flesch: 47 summary: Total nucleic acids were recovered from nose and throat swabs in viral transport medium or lower respiratory samples using a KingFisher Flex (Thermofisher) and tested for SARS CoV-2 RNA by real time PCR. For PCR confirmed hospitalised patients (n = 114), early sensitivity was low: <5 days: 44.4% (95%CI: 18.9%-73.3%), 5-9 days: 32.6% (95%CI, 20.5%-47.5%), 10-14 days: 65.2% (95% CI 44.9%-81.2%), 15-20 days: 66.7% (95% CI: 39.1%-86.2%) but by day 20, sensitivity was 100% (95%CI, 86.2-100%). keywords: assay; days; pcr; preprint; sars; sensitivity cache: cord-277659-afysef1e.txt plain text: cord-277659-afysef1e.txt item: #395 of 973 id: cord-277804-ujabzic4 author: Yuk, Seong-su title: Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs date: 2016-01-21 words: 4161 flesch: 46 summary: United States Department of Agriculture Animal and Plant Health Inspection Service Protection induced by infectious laryngotracheitis virus vaccines alone and combined with Newcastle disease virus and/or infectious bronchitis virus vaccines Understanding interobserver agreement: the kappa statistic Respiratory signs, immunity response, and interference from vaccination with monovalent and multivalent infectious bronchitis vaccines This work was supported by a grant from the Agricultural Biotechnology Development Program, Ministry of Agriculture, Food and Rural Affairs, Republic of Korea (no. 314017-03). key: cord-277804-ujabzic4 authors: Yuk, Seong-su; Kwon, Jung-Hoon; Noh, Jin-Yong; Hong, Woo-tack; Gwon, Gyeong-Bin; Jeong, Jei-Hyun; Jeong, Sol; Youn, Ha-Na; Heo, Yong-Hwan; Lee, Joong-Bok; Park, Seung-Yong; Choi, In-Soo; Song, Chang-Seon title: Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs date: 2016-01-21 journal: J Virol Methods DOI: 10.1016/j.jviromet.2016.01.008 sha: doc_id: 277804 cord_uid: ujabzic4 A sensitive and specific method for measuring the vaccine titer of infectious bronchitis virus (IBV) is important to commercial manufacturers for improving vaccine quality. keywords: eggs; ibv; index; pcr; results; time cache: cord-277804-ujabzic4.txt plain text: cord-277804-ujabzic4.txt item: #396 of 973 id: cord-277838-931sco95 author: Erles, Kerstin title: Detection of a group 2 coronavirus in dogs with canine infectious respiratory disease date: 2003-06-05 words: 5089 flesch: 54 summary: The virus was provisionally called canine respiratory coronavirus (CRCV). Serological analysis showed that the presence of antibodies against CRCV on the day of entry into the kennel decreased the risk of developing respiratory disease. keywords: canine; coronavirus; crcv; disease; dogs; gene; pcr; respiratory; samples cache: cord-277838-931sco95.txt plain text: cord-277838-931sco95.txt item: #397 of 973 id: cord-277909-rn1dow26 author: Gunson, R.N. title: Practical experience of high throughput real time PCR in the routine diagnostic virology setting date: 2006-02-07 words: 6856 flesch: 51 summary: There are numerous chemistries available to carry out real time PCR. Unlike traditional systems, which rely upon endpoint analysis, real time PCR assays visualise the reaction as it is taking place allowing quantification and reaction analysis keywords: assay; control; number; pcr; positive; primer; probe; reaction; samples; sensitivity; time; use cache: cord-277909-rn1dow26.txt plain text: cord-277909-rn1dow26.txt item: #398 of 973 id: cord-277988-dhzln0n3 author: Mcheik, Jiad N. title: Infantile hypertrophic pyloric stenosis: Are viruses involved? date: 2010-10-27 words: 2449 flesch: 45 summary: Pyloric stenosis and maternal Bendectin exposure Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses Inheritance of congenital pyloric stenosis Helicobacter pylori and infantile hypertrophic pyloric stenosis: Is there a possible relationship Simultaneous detection and identification of human parainfluenza viruses 1, 2, and 3 from clinical samples by multiplex PCR Structural immaturity of the pylorus muscle in infantile hypertrophic pyloric stenosis Quantitation of respiratory syncytial virus RNA in nasal aspirates of children by real-time RT-PCR assay Infantile hypertrophic pyloric stenosis Detection of adenovirus in clinical specimens by polymerase chain reaction and liquid-phase hybridization quantitated by time-resolved fluorometry Falle Von Angeborener Pylorustenose Low plasma nitrite in infantile hypertrophic pyloric stenosis patients Study of insulin-like growth factor-1 (IGF-1) and plateletderived endothelial cell growth (PDEGF) expression in children with infantile hypertrophic pyloric stenosis Absence of Epstein-Barr virus in smooth muscle cells of idiopathic hypertrophic pyloric stenosis Pyloric stenosis: New histopathologic perspective using confocal laser scanning Viruses in the stools Disseminated adenovirus disease in immunocompromised and immunocompetent children Infantile hypertrophic pyloric stenosis Abnormalities of elastin and elastic fibers in infantile hypertrophic pyloric stenosis New insights into the pathogenesis of infantile pyloric stenosis Is Helicobacter pylori a cause of infantile hypertrophic pyloric stenosis? Infantile hypertrophic pyloric stenosis: A comparative study of incidence and other epidemiological characteristics in seven European regions Phylogenetic analysis of rhinovirus isolates collected during successive epidemic seasons Infantile hypertrophic pyloric stenosis: An infectious cause? Risk of infantile hypertrophic pyloric stenosis after maternal postnatal use of macrolides Multiplex PCR for typing and subtyping influenza and respiratory syncytial viruses Enterovirus in neonates Direct diagnosis of human respiratory coronaviruses 229E and OC43 by the polymerase chain reaction Study of the interstitial cells of Cajal in infantile hypertrophic pyloric stenosis Hypertrophic pyloric stenosis in twins: Same genes or same environments? Prevalence of infantile hypertrophic pyloric stenosis in Texas Infantile hypertrophic pyloric stenosis in South Glamorgan 1970-9. Effects of changes in feeding practice key: cord-277988-dhzln0n3 authors: Mcheik, Jiad N.; Dichamp, Isabelle; Levard, Guillaume; Ragot, Stéphanie; Beby‐Defaux, Agnès; Grosos, Céline; Couvrat, Véronique; Agius, Gérard title: Infantile hypertrophic pyloric stenosis: Are viruses involved? date: 2010-10-27 journal: J Med Virol DOI: 10.1002/jmv.21913 sha: doc_id: 277988 cord_uid: dhzln0n3 Infantile hypertrophic pyloric stenosis (IHPS) is characterized by abnormal thickening of the internal circular muscle layer. keywords: ihps; infantile; muscle; pyloric; stenosis; viruses cache: cord-277988-dhzln0n3.txt plain text: cord-277988-dhzln0n3.txt item: #399 of 973 id: cord-278176-o9glkhyv author: Houng, Huo-Shu H title: Development and evaluation of an efficient 3′-noncoding region based SARS coronavirus (SARS-CoV) RT-PCR assay for detection of SARS-CoV infections date: 2004-09-01 words: 4788 flesch: 45 summary: Detection of yellow fever virus: a comparison of quantitative real-time PCR and plaque assay Clinical features and short-term outcomes of 144 patients with SARS in the greater Toronto area CDC update: outbreak of severe acute respiratory syndrome-worldwide Severe acute respiratory syndrome-Singapore A simple micro-culture method for the study of group B arboviruses Identification of a novel coronavirus in patients with severe acute respiratory syndrome Quantitative RT-PCR: pitfalls and potential Detection of specific polymerase chain reaction product by utilizing the 5 -3 exonuclease activity of Thermus aquaticus DNA polymerase Quantitative detection of dengue 2 virus using fluorogenic RT-PCR based on 3 -noncoding sequence Development of a fluorogenic RT-PCR system for quantitative identification of dengue virus serotypes 1-4 using conserved and serotype-specific 3 -noncoding sequences The SARS working group Coronavirus confirmed as cause of SARS A major outbreak of severe acute respiratory syndrome in Hong Kong Dengue virus structural differences that correlate with pathogenesis Transmission dynamics and control of severe acute respiratory syndrome Real-time PCR in virology Molecular and in vitro analysis of eight dengue type 2 viruses isolated from patients exhibiting different disease severities The Genome Sequence of the SARS-associated Coronavirus Epidemic spread of adenovirus type 4-associated acute respiratory disease between US Army installations Theoretical uncertainty of measurements using quantitative polymerase chain reaction Coronavirus as a possible cause of severe acute respiratory syndrome Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays Early diagnosis of SARS coronavirus infection by real-time RT-PCR A plaque technique for the titration of yellow fever virus and antisera Transmission dynamics of the etiological agent of SARS in Hong Kong: impact of public health interventions Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection A single nucleotide change in the E protein gene of dengue virus 2 Mexican strain affects neurovirulence in mice Effectiveness of precautions against droplets and contact in prevention of nosocomial transmission of severe acute respiratory syndrome (SARS) SARS-CoV could be isolated and cultivated from sputum specimens and respiratory secretions of SARS patients using Vero cell cultures before the appearance of SARS-specific antibodies in serum, average 21 days following exposure (Peiris et al., 2003b; Booth et al., 2003) . keywords: assay; cdna; cov; patients; pcr; pfu; sars; study cache: cord-278176-o9glkhyv.txt plain text: cord-278176-o9glkhyv.txt item: #400 of 973 id: cord-278635-vwdxr1bl author: Świętoń, Edyta title: Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date: 2020-08-28 words: 5436 flesch: 41 summary: A defective interfering influenza RNA inhibits infectious influenza virus replication in human respiratory tract cells: a potential new human antiviral Cell culture-based production of defective interfering particles for influenza antiviral therapy Influenza virus DI particles: Defective interfering or delightfully interesting? Characterization of virulent and avirulent A/chicken/Pennsylvania/83 influenza A viruses: potential role of defective interfering RNAs in nature Defective viral genomes arising in vivo provide critical danger signals for the triggering of lung antiviral immunity Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients Interfering vaccine: a novel antiviral that converts a potentially virulent infection into one that is subclinical and immunizing Protection of mice from lethal influenza: evidence that defective interfering virus modulates the immune response and not virus multiplication Defective interfering influenza virus confers only short-lived protection against influenza virus disease: evidence for a role for adaptive immunity in DI virus-mediated protection in vivo Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing Defective interfering virus associated with A/Chicken/Pennsylvania/83 influenza virus Avian influenza in Poland Manual of diagnostic tests and vaccines for terrestrial animals chapter Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses Viral population analysis and minority-variant detection using short read next-generation sequencing Trimmomatic: a flexible trimmer for Illumina sequence data Fast and accurate short read alignment with Burrows-Wheeler transform The sequence alignment/map format and SAMtools VarScan: variant detection in massively parallel sequencing of individual and pooled samples Droplet digital PCR: A novel method for detection of influenza virus defective interfering particles convenient online submission • thorough peer review by experienced researchers in your field • rapid publication on acceptance • support for research data, including large and complex data types • gold Open Access which fosters wider collaboration and increased citations maximum visibility for your research: over 100M website views per year • At BMC Development and evaluation of a one-step real-time RT-PCR assay for universal detection of influenza A viruses from avian and mammal species Identification of sensitive and specific avian influenza polymerase chain reaction methods through blind ring trials organized in the European Union Pathogenesis and pathobiology of avian influenza virus infection in birds Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys Infectivity, transmission and pathogenicity of H5 highly pathogenic avian influenza clade 2344 (H5N8 and H5N2) United States index viruses in Pekin ducks and Chinese geese Different pathogenicity of two strains of clade 2.3.4.4c H5N6 highly pathogenic avian influenza viruses bearing different PA and NS gene in domestic ducks Ghedin E; INSIGHT FLU002 Study Group; INSIGHT FLU003 Study Group (2013) In: Swayne DE (ed) Diseases of poultry Influenza virus RNA polymerase: insights into the mechanisms of viral RNA synthesis Population diversity and collective interactions during influenza virus infection The defective component of viral populations Incomplete forms of influenza virus Functional characterization of naturally occurring variants of human hepatitis B virus containing the core internal deletion mutation Defective interfering viral particles in acute dengue infections Internally deleted WNV genomes isolated from exotic birds in New Mexico: function in cells, mosquitoes, and mice SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection Influenza defective interfering viral RNA is formed by internal deletion of genomic RNA Segment-specific noncoding sequences of the influenza virus genome RNA are involved in the specific competition between defective interfering RNA and its progenitor RNA segment at the virion assembly step Defective interfering influenza virus RNAs: time to reevaluate their clinical potential as broad-spectrum antivirals? keywords: birds; contact; dpi; high; infection; influenza; low; particles; segments; turkeys; virus cache: cord-278635-vwdxr1bl.txt plain text: cord-278635-vwdxr1bl.txt item: #401 of 973 id: cord-278833-wlhmcdcn author: Rutschke, Nils title: Hot start reverse transcriptase: an approach for improved real-time RT-PCR performance date: 2015-06-21 words: 2283 flesch: 48 summary: Simplified hot start PCR The elimination of primer-dimer accumulation in PCR Selection of high-affinity RNA ligands to reverse transcriptase: inhibition of cDNA synthesis and RNase H activity Inhibitory RNA ligand to reverse transcriptase from feline immunodeficiency virus Prevention of pre-PCR mis-priming and primer dimerization improves low-copy-number amplifications Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections qPCR inhibition and amplification of difficult templates Sequencing needs for viral diagnostics RNA aptamers selected against DNA polymerase ß inhibit the polymerase activities of DNA polymerases ß and k A novel method for real time quantitative RT-PCR Preanalytic removal of human DNA eliminates false signals in general 16S rDNA In summary, we could demonstrate that hot start RT has the potential to improve the sensitivity of real-time RT-PCR assays. keywords: aptamer; pcr; time cache: cord-278833-wlhmcdcn.txt plain text: cord-278833-wlhmcdcn.txt item: #402 of 973 id: cord-279101-c763gzq2 author: Xu, Sen title: Identification and characterization of a novel L-type lectin (MjLTL2) from kuruma shrimp (Marsupenaeus japonicus) date: 2020-01-13 words: 4813 flesch: 51 summary: As indicated by a previous study, the homolog of ATFα from M. japonicus is vital for WSSV replication, and UPR in M. japonicus may facilitate WSSV infection In the presence of WSSV infection, MjLTL2 knockdown by RNA interference resulted in a 7-day lower cumulative mortality of M. japonicus. keywords: expression; japonicus; mjltl2; protein; shrimp; type; virus; wssv cache: cord-279101-c763gzq2.txt plain text: cord-279101-c763gzq2.txt item: #403 of 973 id: cord-279223-qvih5qas author: Hascoët, Jean-Michel title: Case Series of COVID-19 Asymptomatic Newborns With Possible Intrapartum Transmission of SARS-CoV-2 date: 2020-09-29 words: 3064 flesch: 44 summary: Front Pediatr DOI: 10.3389/fped.2020.568979 sha: doc_id: 279223 cord_uid: qvih5qas Background: Despite the pandemic, data are limited regarding COVID-19 infection in pregnant women and newborns. However, limited data are available regarding pregnant women with COVID-19 infection and their newborns (1) . keywords: baby; covid-19; infection; mother; pcr cache: cord-279223-qvih5qas.txt plain text: cord-279223-qvih5qas.txt item: #404 of 973 id: cord-279229-2226jnfl author: Savan, R title: Loop‐mediated isothermal amplification: an emerging technology for detection of fish and shellfish pathogens date: 2005-11-22 words: 4191 flesch: 38 summary: Furthermore, LAMP detection was superior to PCR when spleen DNA extracted from infected fish was used as template. Recently, PCR detection has been possible for nocardiosis (Kono, Ooyama, Chen & Sakai 2001; Miyoshi & Suzuki 2002) . keywords: amplification; detection; dna; fish; isothermal; lamp; loop; method; pcr; reaction; virus cache: cord-279229-2226jnfl.txt plain text: cord-279229-2226jnfl.txt item: #405 of 973 id: cord-279496-3be5tlnw author: Losurdo, Michele title: Long-term shedding of Canine alphaherpesvirus 1 in naturally infected newborn pups date: 2018-07-06 words: 2569 flesch: 40 summary: Our findings demonstrated that in neonatal pups, CaHV-1 shedding occurs mainly by the nasal route, especially in the first phase of infection. A duplex real-time PCR assay based on TaqMan technology for simultaneous detection and differentiation of canine adenovirus types 1 and 2 Detection of canine distemper virus in dogs by real-time RT-PCR Canine reproductive, respiratory, and ocular diseases due to canine herpesvirus Identification of bovine and porcine rotavirus G types by PCR Design and evaluation of a primer pair that detects both Norwalk-and Sapporo-like caliciviruses by RT-PCR Prevalence of canid herpesvirus-1 infection in stillborn and dead neonatal puppies in Denmark Detection of reovirus by reverse transcription-polymerase chain reaction using primers corresponding to conserved regions of the viral L1 genome segment Experimental primary ocular canine herpesvirus-1 infection in adult dogs Experimental reactivation of latent canine herpesvirus-1 and induction of recurrent ocular disease in adult dogs Frequency of spontaneous canine herpesvirus-1 reactivation and ocular viral shedding in latently infected dogs and canine herpesvirus-1 reactivation and ocular viral shedding induced by topical administration of cyclosporine and systemic administration of corticosteroids What is your diagnosis? keywords: cahv-1; canine; days; pups; shedding cache: cord-279496-3be5tlnw.txt plain text: cord-279496-3be5tlnw.txt item: #406 of 973 id: cord-279551-py2awuav author: Willi, Barbara title: Clinical and molecular investigation of a canine distemper outbreak and vector-borne infections in a group of rescue dogs imported from Hungary to Switzerland date: 2015-07-16 words: 6271 flesch: 49 summary: Canine distemper spillover in domestic dogs from urban wildlife Canine distemper in terrestrial carnivores: a review Canine distemper virus-a morbillivirus in search of new hosts? Serological and demographic evidence for domestic dogs as a source of canine distemper virus infection for Serengeti wildlife Pathogenesis of canine distemper Inactivation of laboratory animal RNA-viruses by physicochemical treatment Lymphocyte-mediated immune cytotoxicity in dogs infected with virulent canine distemper virus Canine distemper virus Canine distemper virus uses both the anterograde and the hematogenous pathway for neuroinvasion Acute canine distemper encephalitis is associated with rapid neuronal loss and local immune activation Infectious Diseases of the Dog and Cat Neurological manifestations of canine distemper virus infection Vaccination of dogs with modified distemper virus Distemper epidemic in Switzerland: epidemiology and anamnesis of vaccination Emergence of canine distemper virus strains with modified molecular signature and enhanced neuronal tropism leading to high mortality in wild carnivores Real-time reverse transcription polymerase chain reaction method for detection of Canine distemper virus modified live vaccine shedding for differentiation from infection with wild-type strains Whole genome sequence analysis of the arctic-lineage strain responsible for distemper in Italian wolves and dogs through a fast and robust next generation sequencing protocol Vaccine use and disease prevalence in dogs and cats GST) und Schweizerische Vereinigung für Kleintiermedizin (SVK) Duration of immunity induced by companion animal vaccines Age and long-term protective immunity in dogs and cats Detection of canine distemper virus in dogs by real-time RT-PCR Comparison of the immunofluorescence assay with RT-PCR and nested PCR in the diagnosis of canine distemper Comparison of tissue and fluid samples for the early detection of canine distemper virus in experimentally infected dogs Occurrence of different Canine distemper virus lineages in Italian dogs An outbreak of dog distemper among seals (2) Baikal seal virus Comparison of two morbilliviruses isolated from seals during outbreaks of distemper in north west Europe and Siberia Genetic diversity of Hungarian canine distemper virus strains Heterogeneity within the hemagglutinin genes of canine distemper virus (CDV) strains detected in Italy Arctic lineage-canine distemper virus as a cause of death in Apennine wolves (Canis lupus) in Italy Canine and feline dirofilariasis: life cycle, pathophysiology, and diagnosis Guidelines for diagnosis and clinical classification of leishmaniasis in dogs Pediatric clinical pathology Feline leukemia virus and other pathogens as important threats to the survival of the critically endangered Iberian lynx (Lynx pardinus) High viral loads despite absence of clinical and pathological findings in cats experimentally infected with feline coronavirus (FCoV) type I and in naturally FCoV-infected cats Quantitative real-time PCR for the measurement of 11beta-HSD1 and 11beta-HSD2 mRNA levels in tissues of healthy dogs Emergence of canine distemper in Bavarian wildlife associated with a specific amino acid exchange in the haemagglutinin protein Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data Prospects for inferring very large phylogenies by using the neighbor-joining method A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences Molecular Evolutionary Genetics Analysis version 6.0 Cross-species recombination in the haemagglutinin gene of canine distemper virus Evaluation of enzyme-linked immunosorbent assays, an immunofluorescent-antibody test, and two rapid tests (immunochromatographic-dipstick and gel tests) for serological diagnosis of symptomatic and asymptomatic Leishmania infections in dogs Submit your next manuscript to BioMed Central and take full advantage of: • Convenient online submission • Dogs that develop an adequate immune response can clear the virus from most tissues, whereas in dogs that show an intermediate immune response, CDV infects the epithelial tissues and induces clinical signs. keywords: animal; canine; cdv; distemper; dogs; infection; months; pcr; switzerland; table; time; vaccination; virus cache: cord-279551-py2awuav.txt plain text: cord-279551-py2awuav.txt item: #407 of 973 id: cord-279563-4lu1n0s7 author: Gorzalski, Andrew J. title: High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2 date: 2020-06-10 words: 1722 flesch: 39 summary: Reports of false negative results from real time PCR testing indicate that even the high analytical sensitivity of RT-PCR may be challenged by the pathology of COVID-19 (6, 7) . The Hologic Panther SARS-CoV-2 transcription mediated amplification test showed higher analytical sensitivity when compared to real time PCR for the detection of SARS-CoV-2. keywords: cov-2; detection; pcr; sars; specimens cache: cord-279563-4lu1n0s7.txt plain text: cord-279563-4lu1n0s7.txt item: #408 of 973 id: cord-279576-wt4crton author: Fajardo, Álvaro title: Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples date: 2020-05-13 words: 4858 flesch: 42 summary: Since all these protocols are based on the use of fluorogenic probes and one-step reagents (cDNA synthesis followed by PCR amplification in the same tube), these techniques can be difficult to perform given the limited supply of reagents in low and middle income countries. Since all these protocols are based on the use of fluorogenic probes and one-step reagents (cDNA synthesis followed by PCR amplification in the same tube), these techniques are limited to the use of more specific reagents and can be quite expensive. keywords: amplification; cov-2; detection; green; qpcr; samples; sars; sybr; time cache: cord-279576-wt4crton.txt plain text: cord-279576-wt4crton.txt item: #409 of 973 id: cord-279577-iwqr2d0r author: Kaur, Taranjit title: Descriptive epidemiology of fatal respiratory outbreaks and detection of a human‐related metapneumovirus in wild chimpanzees (Pan troglodytes) at Mahale Mountains National Park, Western Tanzania date: 2008-06-11 words: 6212 flesch: 43 summary: Finding human-related paramyxoviruses, like RSV and hrcMPV, in habituated chimpanzee populations is not unforeseen. At Kibale National Park in Uganda, Escherichia coli isolates in the feces of habituated chimpanzees were found to be genetically more similar to isolates from the feces of humans employed in research and tourism than those obtained from humans in a local village who had no regular interactions with them keywords: chimpanzees; disease; et al; groups; hmpv; human; metapneumovirus; outbreak; park; pcr; samples; signs; virus; years cache: cord-279577-iwqr2d0r.txt plain text: cord-279577-iwqr2d0r.txt item: #410 of 973 id: cord-279644-g9cr9m96 author: Abedi Kiasari, Bahman title: Merkel cell polyomavirus DNA in immunocompetent and immunocompromised patients with respiratory disease date: 2011-10-19 words: 2470 flesch: 48 summary: The presence of MCPyV in the respiratory tract suggests that the respiratory tract may be a route of transmission just as JC and BK are suspected of being transmitted by inhalation and are occasionally detected in respiratory samples The aim of this study was to determine the prevalence of MCPyV in respiratory specimens collected from immunocompetent and immunocompromised patients and evaluate the possible of contribution of the virus in respiratory disease alone, or in combination with other respiratory viruses. keywords: cell; mcpyv; patients; pcr; samples cache: cord-279644-g9cr9m96.txt plain text: cord-279644-g9cr9m96.txt item: #411 of 973 id: cord-279980-49yv65gm author: WANARATANA, S. title: The potential of house flies to act as a vector of avian influenza subtype H5N1 under experimental conditions date: 2010-12-01 words: 4329 flesch: 51 summary: The AI H5N1-exposed flies collected from each time period were washed three times and homogenized as previously described, to determine the presence of AI H5N1 viruses. Therefore, we suggest that the experimental infection with AI H5N1 virus exposed house flies in chickens should be further performed. keywords: flies; fluid; fly; h5n1; house; influenza; pcr; virus cache: cord-279980-49yv65gm.txt plain text: cord-279980-49yv65gm.txt item: #412 of 973 id: cord-280442-jtvez46y author: Wu, Xuan title: Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date: 2019-11-01 words: 5316 flesch: 47 summary: NDV detection assays were specific to the NDV templates ( Figure 4B ). As for NDV detection assays, positive results were observed only when NDV templates existed. keywords: assays; detecting; detection; ibv; lamp; lfd; mrt; ndv; pcr; virus cache: cord-280442-jtvez46y.txt plain text: cord-280442-jtvez46y.txt item: #413 of 973 id: cord-280846-bbv6f5gf author: Greninger, Alexander L. title: A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America date: 2010-10-18 words: 8040 flesch: 37 summary: Treatment with DNase twice yielded the best percentage recovery of However, despite very low viral titers, H1N1 influenza was still detectable by deep sequencing, with 270 and 18 reads aligning to influenza for Cal-UC12 and BC-59, respectively (Table 1) . Emergence of a novel swine-origin influenza A (H1N1) virus in humans Triplereassortant swine influenza A (H1) in humans in the United States Pandemic potential of a strain of influenza A (H1N1): early findings Rapid-test sensitivity for novel swine-origin influenza A (H1N1) virus in humans Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic Metagenomics for the discovery of novel human viruses Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult Microarray-based detection and genotyping of viral pathogens Characterization of a novel coronavirus associated with severe acute respiratory syndrome Viral discovery and sequence recovery using DNA microarrays Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections Achalasia and viral infection: new insights from veterinary medicine Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children Identification of a novel astrovirus (astrovirus VA1) associated with an outbreak of acute gastroenteritis The complete genome of klassevirus -a novel picornavirus in pediatric stool Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces Genetic detection and characterization of Lujo virus, a new hemorrhagic feverassociated arenavirus from southern Africa A new arenavirus in a cluster of fatal transplant-associated diseases Influenza vaccine-outmaneuvering antigenic shift and drift Broadspectrum respiratory tract pathogen identification using resequencing DNA microarrays Robust sequence selection method used to develop the FluChip diagnostic microarray for influenza virus Panmicrobial oligonucleotide array for diagnosis of infectious diseases Experimental evaluation of the FluChip diagnostic microarray for influenza virus surveillance Detection in 2009 of the swine origin influenza A (H1N1) virus by a subtyping microarray Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays Identifying influenza viruses with resequencing microarrays Detection of molecular markers of drug resistance in the 2009 pandemic influenza A (H1N1) viruses using pyrosequencing Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/ 2009) by de novo sequencing using a next-generation DNA sequencer California Pandemic Working G (2010) Severe 2009 H1N1 influenza in pregnant and postpartum women in California E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics The NIH Human Microbiome Project Xenotropic Murine Leukemia Virus-related Gammaretrovirus in Respiratory Tract Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome Antiviral actions of interferons Clonal integration of a polyomavirus in human Merkel cell carcinoma Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals Streptococcus pneumoniae coinfection is correlated with the severity of H1N1 pandemic influenza RNA viral community in human feces: prevalence of plant pathogenic viruses Substantial biases in ultra-short read data sets from high-throughput DNA sequencing Inefficient control of host gene expression by the 2009 pandemic H1N1 influenza A virus NS1 protein Real-time DNA sequencing from single polymerase molecules The next generation becomes the now generation The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing Kleine-Levin syndrome: a systematic study of 108 patients PANTHER pathway: an ontology-based pathway database coupled with data analysis tools SSAHA: a fast search method for large DNA databases Multiple sequence alignment using ClustalW and ClustalX We thank Aurora París at the Ministry of Health BSL-3 state laboratory in Veracruz for providing 2009 H1N1 samples from Mexico. keywords: analysis; data; detection; genome; h1n1; human; influenza; novel; pcr; reads; samples; sequence; sequencing; virochip; virus; viruses cache: cord-280846-bbv6f5gf.txt plain text: cord-280846-bbv6f5gf.txt item: #414 of 973 id: cord-280865-shwxhak9 author: Zhang, Dan title: Clinical evaluation of a panel of multiplex quantitative real-time reverse transcription polymerase chain reaction assays for the detection of 16 respiratory viruses associated with community-acquired pneumonia date: 2018-06-30 words: 2550 flesch: 43 summary: II RV16 and Seeplex RV12 ACE assays for the detection of respiratory viruses Evaluation of the AdvanSure real-time RT-PCR compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses Clinical evaluation of a single-tube multiple RT-PCR assay for the detection of 13 common virus types/ subtypes associated with acute respiratory infection A two-tube multiplex reverse transcription PCR assay for simultaneous detection of sixteen human respiratory virus types/subtypes Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster Added value of an oropharyngeal swab in detection of viruses in children hospitalized with lower respiratory tract infection Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children Comparison of fast-track diagnostics respiratory pathogens multiplex real-time RT-PCR assay with in-house singleplex assays for comprehensive detection of human respiratory viruses Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses Parainfluenza Virus Types 1, 2, and 3 in pediatric patients with acute respiratory infections in Beijing during Epidemiology and clinical presentation of the four human parainfluenza virus types Seasonal trends of human parainfluenza viral infections: United States Outbreak of pneumonia in a long-term care facility: antecedent human parainfluenza virus 1 infection may predispose to bacterial pneumonia Epidemiology and clinical characteristics of human coronaviruses OC43, 229E, NL63, and HKU1: a study of hospitalized children with acute respiratory tract infection in Guangzhou, China Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method We acknowledge the Children's Hospital, Zhejiang University School of Medicine, and the Center for Disease Control and Prevention of Zhejiang province for providing sputum. The mqRT-PCR assay performed comparably with the two-tube assay for most viruses, offering the advantages of quantitative analysis, easier performance, lower susceptibility to contamination, and shorter turnaround time in laboratories equipped with conventional real-time PCR instrumentation, and it could therefore be a valuable tool for routine surveillance of respiratory virus infections in China. keywords: assay; detection; mqrt; panel; pcr; respiratory; tube; viruses cache: cord-280865-shwxhak9.txt plain text: cord-280865-shwxhak9.txt item: #415 of 973 id: cord-281162-2pu7x5rj author: Etemadi, Mohammad Reza title: Diversity of respiratory viruses detected among hospitalized children with acute lower respiratory tract infections at Hospital Serdang, Malaysia date: 2019-03-22 words: 4908 flesch: 40 summary: The burden of respiratory syncytial virus infection in young children Currently used nucleic acid amplification tests for the detection of viruses and atypicals in acute respiratory infections Use of monoclonal antibodies for rapid diagnosis of respiratory viruses in a community hospital Respiratory picornaviruses and respiratory syncytial virus as causative agents of acute expiratory wheezing in children Viral etiology of acute respiratory tract infections in children presenting to hospital: role of polymerase chain reaction and demonstration of multiple infections Etiology of acute respiratory infections in children in tropical southern India Respiratory virus infections Serious respiratory illness associated with rhinovirus infection in a pediatric population Methodological and quality issues in epidemiological studies of acute lower respiratory infections in children in developing countries Prospective comparison of R-mix (TM) shell vial system with direct antigen tests and conventional cell culture for respiratory virus detection Clinical and molecular epidemiology of human rhinovirus C in children and adults in Hong Kong reveals a possible distinct human rhinovirus C subgroup A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illnesses in infants Clinical severity of respiratory adenoviral infection by serotypes in Korean children over 17 consecutive years (1991-2007) Effect of rapid viral diagnosis on the management of children hospitalized with lower respiratory tract infection Cloning of a human parvovirus by molecular screening of respiratory tract samples Cloning of a human parvovirus by molecular screening of respiratory tract samples Identification of a third human polyomavirus Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections Human bocavirus infection Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses Detection of new respiratory viruses in hospitalized infants with bronchiolitis: a three-year prospective study Molecular identification of adenoviruses in clinical samples by analyzing a partial hexon genomic region Viral aetiology of lower respiratory tract infection in young Malaysian children Respiratory adenoviral infections in children: a study of hospitalized cases in Southern Taiwan in 2001-2002 Detection of viruses identified recently in children with acute wheezing Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-PCR assay Simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested PCR assays First detected human bocavirus in a malaysian child with pneumonia and pre-existing asthma: a case report Human metapneumovirus infection in young children hospitalized with respiratory tract disease Human bocavirus in children Correlation of viral load of respiratory pathogens and co-infections with disease severity in children hospitalized for lower respiratory tract infection Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Risk Factors for Respiratory Syncytial Virus Bronchiolitis Hospital Admission in New Zealand 136 Practical implementation of a multiplex PCR for acute respiratory tract infections in children keywords: children; detection; infections; methods; respiratory; samples; study; viruses cache: cord-281162-2pu7x5rj.txt plain text: cord-281162-2pu7x5rj.txt item: #416 of 973 id: cord-281174-3c1vue0y author: Greene, Shermalyn R title: Evaluation of the NucliSens® Basic Kit assay for detection of Norwalk virus RNA in stool specimens date: 2003-01-16 words: 5258 flesch: 39 summary: key: cord-281174-3c1vue0y authors: Greene, Shermalyn R; Moe, Christine L; Jaykus, Lee-Ann; Cronin, Mike; Grosso, Lynell; Aarle, Pierre van title: Evaluation of the NucliSens® Basic Kit assay for detection of Norwalk virus RNA in stool specimens date: 2003-01-16 journal: J Virol Methods DOI: 10.1016/s0166-0934(02)00286-0 sha: doc_id: 281174 cord_uid: 3c1vue0y Norwalk-like viruses (NLVs) are a genetically diverse group of human caliciviruses that are the most common cause of epidemic gastroenteritis and are detected typically in stool by reverse transcription (RT)-PCR or electron microscopy (EM). Primers and probes for the NLV Basic Kit assay were based on the RNA polymerase region of the prototype NLV, Norwalk virus (NV) genome and could consistently detect 10(4) RT-PCR detectable units of NV RNA in a stool filtrate. keywords: amplification; assay; basic; detection; kit; nasba; nuclisens; pcr; rna cache: cord-281174-3c1vue0y.txt plain text: cord-281174-3c1vue0y.txt item: #417 of 973 id: cord-281529-2rec51xg author: Haagmans, Bart L title: Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation date: 2013-12-17 words: 4037 flesch: 51 summary: Global Alert and Response (GAR): novel coronavirus infection-update Ecology, evolution and classifi cation of bat coronaviruses in the aftermath of SARS Close relative of human Middle East respiratory syndrome coronavirus in bat Human betacoronavirus 2c EMC/2012-related viruses in bats, Ghana and Europe Genetic characterization of betacoronavirus lineage C viruses in bats revealed marked sequence divergence in the spike protein of pipistrellus bat coronavirus HKU5 in Japanese pipistrelle: implications on the origin of the novel Middle East Respiratory Syndrome Coronavirus Human coronavirus EMC does not require the SARS-coronavirus receptor and maintains broad replicative capability in mammalian cell lines Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection Transmission scenarios for Middle East respiratory syndrome coronavirus (MERS-CoV) and how to tell them apart Recovery from severe novel coronavirus infection Family cluster of Middle East respiratory syndrome coronavirus infections Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study Seroepidemiology for MERS coronavirus using microneutralisation and pseudoparticle virus neutralisation assays reveal a high prevalence of antibody in dromedary camels in Egypt Alert and Response (GAR): novel coronavirus infection-update Alert and Response (GAR): novel coronavirus infection-update Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction Assays for laboratory confi rmation of novel human coronavirus (hCoV-EMC) infections SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building Specifi c serology for emerging human coronaviruses by protein microarray Middle East respiratory syndrome coronavirus in bats, Saudi Arabia MERS coronavirus: data gaps for laboratory preparedness We thank WHO and the Food and Agriculture Organization of the United Nations for their generous help in organisation of the study, Theo Bestebroer for providing Middle East respiratory syndrome coronavirus specifi c primer sets, Berend Jan Bosch for providing antigens for the microarray, and Jeroen Cremer for technical support. Viral sequences from the two human cases were isolated (with the same techniques as for camel cases) in the Reference Department, Public Health England, London, UK. keywords: camels; cases; coronavirus; cov; data; farm; human; infection; mers; pcr; samples cache: cord-281529-2rec51xg.txt plain text: cord-281529-2rec51xg.txt item: #418 of 973 id: cord-281653-zogtpm7a author: Thurman, Kathleen A. title: Detection of Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella spp. in clinical specimens using a single-tube multiplex real-time PCR assay() date: 2011-03-11 words: 3318 flesch: 37 summary: PCR assays have also been developed (Gullsby et al., 2008; Loens et al., 2008; McDonough et al., 2005; Miyashita et al., 2004; Welti et al., 2003) . A retrospective review of 103 hospitalised children Guidelines for the management of adults with community-acquired pneumonia: diagnosis, assessment of severity, antimicrobial therapy, and prevention Comparison of real-time PCR protocols for differential laboratory diagnosis of amebiasis Diagnostic testing for community-acquired pneumonia ) prospective study of communityacquired pneumonia of bacterial etiology in adults Prevalence of Chlamydia pneumoniae and Mycoplasma pneumoniae immunoglobulin G and A antibodies in a healthy Finnish population as analyzed by quantitative enzyme immunoassays Mycoplasma pneumoniae and its role as a human pathogen Population prevalence antibody to Chlamydia pneumoniae strain TWAR Development of a multiplex real-time quantitative PCR assay to detect Chlamydia pneumoniae, Legionella pneumophila and Mycoplasma pneumoniae in respiratory tract secretions Evaluation of three real-time PCR assays for detection of Mycoplasma pneumoniae in an outbreak investigation keywords: assay; multiplex; pcr; pneumoniae; specimens; time cache: cord-281653-zogtpm7a.txt plain text: cord-281653-zogtpm7a.txt item: #419 of 973 id: cord-281844-c0uhcatg author: Costa, Lusmaia D.C. title: Exacerbation of asthma and airway infection: is the virus the villain? date: 2014-12-31 words: 6550 flesch: 37 summary: The impact of viral respiratory infection on the severity and recovery from an asthma exacerbation Symptomatic viral infection is associated with impaired response to treatment in children with acute asthma Newly identified respiratory viruses in children with asthma exacerbation not requiring admission to hospital Understanding the September asthma epidemic Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center Innate immunity in the pathogenesis of virus-induced asthma exacerbations Sentinel surveillance of influenza and other respiratory viruses, Brazil Variação sazonal nos atendimentos de emergência por asma em Gama Effect of seasonality on the occurrence of respiratory symptoms in a Brazilian city with a tropical climate Prevalência dos atendimentos por crises de asma nos serviços públicos do Município de Juiz de Fora (MG) Study of modifiable risk factors for asthma exacerbations: virus infection and allergen exposure increase the risk of asthma hospital admissions in children Risk factors for wheezing in a subtropical environment: Role of respiratory viruses and allergen sensitization Associations between environmental exposures and asthma control and exacerbations in young children: a systematic review Smoke-free legislation and hospitalizations for childhood asthma Personal exposure to nitrogen dioxide (NO 2 ) and the severity of virus-induced asthma in children Health effects of indoor nitrogen dioxide and passive smoking on urban asthmatic children Environmental tobacco smoke exposure and nocturnal symptoms among inner-city children with asthma Results of a home-based environmental intervention among urban children with asthma Guidelines reduce X-ray and blood gas utilization in acute asthma Basic Research on virus-induced asthma exacerbation: inhibition of inflammatory chemokine expression by fluticasone propionate Respiratory viral infections in children with asthma: do they matter and can we prevent them? 4 Considering the possibility of a causal relationship between respiratory virus infection and the triggering of asthma attacks in children, the implications of this association, as well as the possibility of specific prophylaxis and therapy for these agents, special attention to this subject is justified. keywords: association; asthma; children; detection; exacerbations; hrv; infection; patients; pcr; studies; viruses; years cache: cord-281844-c0uhcatg.txt plain text: cord-281844-c0uhcatg.txt item: #420 of 973 id: cord-281871-3j64de2i author: Sinagra, G title: Viral presence guided immunomodulation in lymphocytic myocarditis: An update date: 2020-07-19 words: 2747 flesch: 24 summary: These findings were not confirmed in the study by Belkaya et al 11 , where genetic mutations in interferon-mediated immunity investigated in human-induced pluripotent stem cell-derived cardiomyocytes did not result in increased susceptibility to viral myocarditis, though the study did note a potential association between myocarditis and defects in cardiac structural Accepted Article proteins. Lastly, enteroviruses are established viral myocarditis causative agents in animals and in humans 9 ; conversely, the role of other viruses (particularly PVB19 and HHV-6) is at present controversial and requires further scrutiny. keywords: acute; emb; immunosuppression; myocarditis; patients; presence cache: cord-281871-3j64de2i.txt plain text: cord-281871-3j64de2i.txt item: #421 of 973 id: cord-281887-b511bjdy author: Ribeiro, Reitan title: Perioperative Cancer Care in the Context of Limited Resources during the COVID-19 Pandemic: Brazilian Society of Surgical Oncology Recommendations date: 2020-09-26 words: 4744 flesch: 40 summary: The rational use of resources to reduce the risk of surgical cancer patients being operated on during the incubation period of a corona virus infection is important in this context. We present a protocol, focused on the patients’ outcomes, for safe and rational use of resources to reduce the risk of surgical cancer patients being operated on during the virus incubation period, in the context of areas with limited resources. Discussion. keywords: areas; cancer; covid-19; pandemic; patients; prevalence; resources; risk; screening; surgery; testing cache: cord-281887-b511bjdy.txt plain text: cord-281887-b511bjdy.txt item: #422 of 973 id: cord-282155-6jp9yx47 author: Zhao, Li title: A highly sensitive 1-tube nested real-time RT-PCR assay using LNA-modified primers for detection of respiratory syncytial virus date: 2018-09-08 words: 4106 flesch: 35 summary: LNA modification has been used in many applications including single-nucleotide polymorphism analysis (Karmakar and Hrdlicka, 2013) , real-time PCR probes (Osterback et al., 2013; Sun et al., 2007) , antisense oligonucleotides (Wahlestedt et al., 2000) , microarray probes (Castoldi et al., 2008) , and PCR primers (Chen et al., 2016; Latorra et al., 2003) . Some studies have reported performing nested PCR in a single tube using fluorescent probes, gel electrophoresis, or spatial separation of outer and inner primer sets (Brisco et al., 2011; Dey et al., 2012; Hu and Arsov, 2014; Moser et al., 2012) . keywords: assay; otnrt; pcr; pcr assay; rsv; step cache: cord-282155-6jp9yx47.txt plain text: cord-282155-6jp9yx47.txt item: #423 of 973 id: cord-282278-q7jp224a author: Thorburn, Fiona title: The use of next generation sequencing in the diagnosis and typing of respiratory infections date: 2015-08-31 words: 3015 flesch: 45 summary: Further examination of the relationship between the numbers of viral sequenced reads and the threshold cycle (Ct) value provided by the RT-PCR assay is shown in Fig. 4 . Similar to other studies we also found a correlation between NGS sequence reads and RT-PCR cycle thresholds [16, 17] . keywords: ngs; pcr; reads; respiratory; samples; sequences; sequencing cache: cord-282278-q7jp224a.txt plain text: cord-282278-q7jp224a.txt item: #424 of 973 id: cord-282321-svoshzz8 author: Eboigbodin, Kevin title: Reverse transcription strand invasion based amplification (RT-SIBA): a method for rapid detection of influenza A and B date: 2016-04-11 words: 4417 flesch: 42 summary: The best performing seeding region was then chosen for subsequent SIBA influenza A experiments and adopted for influenza B SIBA assay design. In order to test our hypothesis, SIBA influenza A assay IOs containing seeding regions that differed in length and nucleotide composition were designed and tested, and the results are depicted in Fig. keywords: amplification; assays; detection; influenza; pcr; region; rna; seeding; siba cache: cord-282321-svoshzz8.txt plain text: cord-282321-svoshzz8.txt item: #425 of 973 id: cord-282449-7mxp3sdy author: A, Amouroux title: Evidence for and against vertical transmission for SARS-CoV-2 (COVID-19) date: 2020-05-04 words: 1512 flesch: 45 summary: We identified 12 articles published between February 10th and April 4th 2020 reporting on 68 deliveries and 71 neonates with maternal infection in the third trimester of pregnancy. The dynamic of the pandemic has not allowed for any meaningful cohort following maternal infection in the second trimester of pregnancy to be reported with perinatal outcomes, and the largest numbers relate to cases of infection and delivery in the third trimester of pregnancy. keywords: infection; sars cache: cord-282449-7mxp3sdy.txt plain text: cord-282449-7mxp3sdy.txt item: #426 of 973 id: cord-282968-kjvvoveq author: Qu, Renjun title: Selection of reference genes for the quantitative real-time PCR normalization of gene expression in Isatis indigotica fortune date: 2019-03-25 words: 6295 flesch: 42 summary: Choose BMC and benefit from: sweetpotato cultivars subjected to abiotic stress conditions Genomewide identification and testing of superior reference genes for transcript normalization in Arabidopsis Identification and validation of reference genes and their impact on normalized gene expression studies across cultivated and wild cicer species Reliable reference genes for normalization of gene expression in cucumber grown under different nitrogen nutrition Selection of reference genes for diurnal and developmental time-course real-time PCR expression analyses in lettuce Comparison of the response of ion distribution in the tissues and cells of the succulent plants Aloe vera and Salicornia europaea to saline stress Selection of suitable reference genes for qRT-PCR normalization during leaf development and hormonal stimuli in tea plant (Camellia sinensis) Identification of stable reference genes for quantitative PCR in koalas Analysis of relative gene expression data using real-time quantitative PCR and the 2 −ΔΔCT method Not applicable. key: cord-282968-kjvvoveq authors: Qu, Renjun; Miao, Yujing; Cui, Yingjing; Cao, Yiwen; Zhou, Ying; Tang, Xiaoqing; Yang, Jie; Wang, Fangquan title: Selection of reference genes for the quantitative real-time PCR normalization of gene expression in Isatis indigotica fortune date: 2019-03-25 journal: BMC Mol Biol DOI: 10.1186/s12867-019-0126-y sha: doc_id: 282968 cord_uid: kjvvoveq BACKGROUND: keywords: analysis; expression; genes; indigotica; mub; normalization; pcr; reference; reference genes; results; samples; stress; tissues cache: cord-282968-kjvvoveq.txt plain text: cord-282968-kjvvoveq.txt item: #427 of 973 id: cord-283309-ovx5fzsg author: Yang, Yong-Le title: Characterization of a novel bat-HKU2-like swine enteric alphacoronavirus (SeACoV) infection in cultured cells and development of a SeACoV infectious clone date: 2019-08-09 words: 5450 flesch: 42 summary: Two viral genes, SeACoV N and the nonstructural protein 3 (Nsp3) acidic domain (Ac) of ORF1a, were expressed as soluble products in the bacteria; the SeACoV spike subunit 1 (S1) was expressed in insect cells, secreting into the cultured medium. The availability of the SeACoV infectious clone and a panel of antibodies against different viral proteins will facilitate further studies on understanding the molecular mechanisms of SeACoV replication and pathogenesis. keywords: analysis; anti; cells; coronavirus; fig; ns7a; pcr; protein; seacov; vero; virus cache: cord-283309-ovx5fzsg.txt plain text: cord-283309-ovx5fzsg.txt item: #428 of 973 id: cord-283409-ynwgdz52 author: Baggett, Travis P. title: Clinical Outcomes, Costs, and Cost-effectiveness of Strategies for People Experiencing Sheltered Homelessness During the COVID-19 Pandemic date: 2020-10-20 words: 1742 flesch: 37 summary: After acquiring SARS-CoV-2 infection, individuals may progress through the following health states (eFigure 1): • Pre-infectious latency • Asymptomatic infection • Mild/moderate illness: symptomatic • Severe illness: dyspnea and/or hypoxemia ideally managed in a hospital with standard supplemental oxygen but not requiring intensive care unit (ICU) • Critical illness: ideally managed in an ICU with high-flow supplemental oxygen, non-invasive positive pressure ventilation, or invasive mechanical ventilation • Recuperation: for those recuperating from critical illness and improving while remaining in the hospital or other health care facility • Recovered Individuals in the asymptomatic infection, mild/moderate illness, and severe illness states can transition directly to the recovered state. This nominal transmission rate captures the ratio of daily infectivity stratified by illness states. keywords: illness; individuals; infection; pcr cache: cord-283409-ynwgdz52.txt plain text: cord-283409-ynwgdz52.txt item: #429 of 973 id: cord-283641-2u16otbf author: Vainionpää, R. title: Diagnostic Techniques: Serological and Molecular Approaches date: 2015-03-06 words: 4400 flesch: 38 summary: IgM and IgG antibody determinations from cerebrospinal fluid are used for diagnosis of virus infections in the central nervous system although new molecular methods are increasingly replacing them. POC tests are nowadays available for antibody screening of an increasing number of virus infections (HIV, hepatitis C virus (HCV), varicella-zoster virus (VZV), cytomegalovirus (CMV), Epstein-Barr virus (EBV)). keywords: antibodies; antibody; assays; detection; igg; infections; pcr; test; virus cache: cord-283641-2u16otbf.txt plain text: cord-283641-2u16otbf.txt item: #430 of 973 id: cord-283786-d65njv7b author: Toptan, Tuna title: Optimized qRT-PCR Approach for the Detection of Intra- and Extra-Cellular SARS-CoV-2 RNAs date: 2020-06-20 words: 5268 flesch: 45 summary: We and others [8] (personal communication) determined certain drawbacks of the two-step PCR protocol recommended by the WHO, including unspecific signals for E-gene PCR arising due to a combination of several factors including primer dimers, the unspecific binding of the primers and probes, the RT-PCR kit and thermocycler-dependent differences. We and others [8] (personal communication) determined certain drawbacks of the two-step PCR protocol recommended by the WHO, including unspecific signals for E-gene PCR arising due to a combination of several factors including primer dimers, the unspecific binding of the primers and probes, the RT-PCR kit and thermocycler-dependent differences. keywords: cov-2; figure; gene; gene pcr; pcr; rdrp; rna; sars cache: cord-283786-d65njv7b.txt plain text: cord-283786-d65njv7b.txt item: #431 of 973 id: cord-284037-nj5jo1ev author: Kwee, Thomas C. title: Chest CT in COVID-19: What the Radiologist Needs to Know date: 2020-10-23 words: 7673 flesch: 29 summary: The authors describe imaging and managing care of patients with COVID-19, with topics including (a) chest CT protocol, (b) chest CT findings of COVID-19 and its complications, (c) the diagnostic accuracy of chest CT and its role in diagnostic decision making and prognostication, and (d) reporting and communicating chest CT findings. In this article, we provide an overview of chest CT in imaging and managing care of patients with COVID-19 and discuss topics including (a) chest CT protocol, (b) chest CT findings in COVID-19 and its complications, (c) the diagnostic accuracy of chest CT and its role in diagnostic decision making and prognostication, and (d) reporting and communicating chest CT findings. keywords: chest; chest ct; coronavirus; covid-19; disease; findings; imaging; patients; pcr; pneumonia; sars; test cache: cord-284037-nj5jo1ev.txt plain text: cord-284037-nj5jo1ev.txt item: #432 of 973 id: cord-284262-lddmo1sv author: Li, Linlin title: Circovirus in Tissues of Dogs with Vasculitis and Hemorrhage date: 2013-04-17 words: 4176 flesch: 37 summary: Samples from the sentinel dog (dog 1) and 3 other dogs (dogs 2-4) were positive for DogCV by ISH analysis. In dogs 1 and 2, the hemorrhage was associated with the gastrointestinal tract (Figure 2 , panels A, C); dog 2 had additional multifocal to coalescing regions of hemorrhage in the kidneys (Figure 2, panel B) . keywords: analysis; canine; circovirus; disease; dogcv; dogs; genome; pcv2; porcine; samples; tissue; vasculitis cache: cord-284262-lddmo1sv.txt plain text: cord-284262-lddmo1sv.txt item: #433 of 973 id: cord-284275-bqo203pf author: Lu, Roujian title: Characterization of Human Coronavirus Etiology in Chinese Adults with Acute Upper Respiratory Tract Infection by Real-Time RT-PCR Assays date: 2012-06-15 words: 2979 flesch: 50 summary: Update on rhinovirus and coronavirus infections Identification of a new human coronavirus Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia Identification of a novel coronavirus in patients with severe acute respiratory syndrome A novel coronavirus associated with severe acute respiratory syndrome A previously undescribed coronavirus associated with respiratory disease in humans Viruses and bacteria in the etiology of the common cold A cluster of cases of severe acute respiratory syndrome in Hong Kong Croup is associated with the novel coronavirus NL63 Respiratory coronavirus infections in children younger than two years of age Coronavirus 229E-related pneumonia in immunocompromised patients Coronavirus HKU1 infection in the United States Human respiratory coronavirus HKU1 versus other coronavirus infections in Italian hospitalised patients Detection of human coronavirus NL63, human metapneumovirus and respiratory syncytial virus in children with respiratory tract infections in southwest Sweden Evidence of human coronavirus HKU1 and human bocavirus in Australian children Detection of human coronavirus-NL63 in children in Japan Human coronaviruses infections in rural Tailand: A comprehensive study using real-time reverse-transcription polymerase chain reaction assays Detection of Four Human Coronaviruses in Respiratory Infections in Children: A One-Year Study in Colorado Impact of human coronavirus infections in otherwise healthy children who attended an emergency department Human coronavirus and acute respiratory illness in older adults with chronic obstructive pulmonary disease Coronavirus infection and hospitalizations for acute respiratory illness in young children An outbreak of coronavirus OC43 respiratory infection in Normandy, France Epidemiology and Clinical Presentations of the Four Human Coronaviruses 229E, HKU1, NL63, and OC43 Detected over 3 Years Using a Novel Multiplex Real-Time PCR Method Prevalence of Human Coronaviruses in Adults With Acute Respiratory Tract Infections in Beijing Laboratory Diagnosis and Surveillance of Human Respiratory Viruses by PCR in Etiology and clinical characterization of respiratory virus infections in adult patients attending an emergency department in Beijing Molecular assays for detection of human metapneumovirus Epidemiological profil and clinical associations of human bocavirus and other human parvoviruses Coronavirus HKU1 and other coronavirus infections in Hong Kong Human (nonsevere acute respiratory syndrome) coronavirus infections in hospitalized children in France Clinical disease in children associated with newly described coronavirus subtypes Detection of human coronaviruses in children with acute gastroenteritis A prospective hospital-based study of the clinical impact of non-severe acute respiratory syndrome (Non-SARS)-related human coronavirus infection Seroepidemiology of group I human coronaviruses in children Acute respiratory infection and influenza-like illness viral etiologies in Brazilian adults The common cold Molecular diagnosis of respiratory virus infections Use of sensitive, broad-spectrum molecular assays and human airway epithelium cultures for detection of respiratory pathogens Our results suggest that testing algorithms that include sensitive HCoVs detection contribute to the likelihood of obtaining a laboratory diagnosis when respiratory virus infection is suspected [26, [37] keywords: coronavirus; hcovs; hku1; human; infection; patients; pcr cache: cord-284275-bqo203pf.txt plain text: cord-284275-bqo203pf.txt item: #434 of 973 id: cord-284313-rg3krh7d author: Wood, Lisa G. title: Persistent Airway Obstruction After Virus Infection Is Not Associated With Airway Inflammation date: 2007-02-28 words: 3832 flesch: 36 summary: Methods:Subjects (n = 40) were recruited at hospital admission for acute asthma exacerbation. Persistent airway obstruction following acute asthma exacerbation is a significant clinical problem. keywords: airway; asthma; exacerbation; group; obstruction; postexacerbation; recovery; subjects; virus cache: cord-284313-rg3krh7d.txt plain text: cord-284313-rg3krh7d.txt item: #435 of 973 id: cord-284366-snajbvr9 author: Han, Zhiyong title: Discharged COVID‐19 Patients Testing Positive Again for SARS‐CoV‐2 RNA: A Minireview of Published Studies from China date: 2020-07-01 words: 2020 flesch: 53 summary: To better understand what is happening and to provide public health policy planners and clinicians timely information, we have searched and reviewed published studies about discharged patients testing positive again for the SARS‐CoV‐2 RNA. Our review of these reports indicates the presence of discharged patients who remain asymptomatic but test positive. keywords: discharged; patients; pcr; sars cache: cord-284366-snajbvr9.txt plain text: cord-284366-snajbvr9.txt item: #436 of 973 id: cord-284367-cy61pjcb author: MULEYA, Walter title: Molecular Epidemiology of Paramyxoviruses in Frugivorous Eidolon helvum Bats in Zambia date: 2013-12-31 words: 1566 flesch: 44 summary: The viruses identified in this study were shown to originate from wide geographical areas, and their presence in fruit bat species might pose a public health risk and as such, continued surveillance of these viruses in fruit bats in essential. key: cord-284367-cy61pjcb authors: MULEYA, Walter; SASAKI, Michihito; ORBA, Yasuko; ISHII, Akihiro; THOMAS, Yuka; NAKAGAWA, Emiko; OGAWA, Hirohito; HANG’OMBE, Bernard; NAMANGALA, Boniface; MWEENE, Aaron; TAKADA, Ayato; KIMURA, Takashi; SAWA, Hirofumi title: Molecular Epidemiology of Paramyxoviruses in Frugivorous Eidolon helvum Bats in Zambia date: 2013-12-31 journal: J Vet Med Sci DOI: 10.1292/jvms.13-0518 sha: doc_id: 284367 cord_uid: cy61pjcb In this study, we describe the detection of novel paramyxoviruses from the Eidolon helvum species of fruit bats. keywords: bats; fruit; novel; paramyxoviruses; pcr; samples cache: cord-284367-cy61pjcb.txt plain text: cord-284367-cy61pjcb.txt item: #437 of 973 id: cord-284372-v95fzp8n author: Coyle, Peter V title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections date: 2004-10-25 words: 4719 flesch: 36 summary: key: cord-284372-v95fzp8n authors: Coyle, Peter V; Ong, Grace M; O'Neill, Hugh J; McCaughey, Conall; De Ornellas, Dennis; Mitchell, Frederick; Mitchell, Suzanne J; Feeney, Susan A; Wyatt, Dorothy E; Forde, Marian; Stockton, Joanne title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections date: 2004-10-25 journal: BMC Microbiol DOI: 10.1186/1471-2180-4-41 sha: doc_id: 284372 cord_uid: v95fzp8n BACKGROUND: Immunofluorescence and virus culture are the main methods used to diagnose acute respiratory virus infections. [3, 4] are the main methods used to diagnose acute respiratory virus infections. keywords: immunofluorescence; infections; influenza; parainfluenza; primer; specimens; strip; touchdown; type; virus; viruses cache: cord-284372-v95fzp8n.txt plain text: cord-284372-v95fzp8n.txt item: #438 of 973 id: cord-284376-plwyjhl8 author: Fu, Xinmiao title: Simulating and forecasting the cumulative confirmed cases of SARS-CoV-2 in China by Boltzmann function-based regression analyses date: 2020-05-31 words: 14755 flesch: 44 summary: Increasing reports on human PRV infection cases in China have recently indicated that PRV poses a significant threat to public health in China, especially in people in close contact with sick pigs and/or related pork products/contaminants. Potential total numbers of confirmed cases in different regions were estimated. keywords: 2019; cases; china; colistin; control; data; disease; gene; health; human; infection; isolates; laboratory; novel; number; outbreak; patients; pcr; pertussis; pjp; pneumoniae; resistance; sars; table; time; treatment cache: cord-284376-plwyjhl8.txt plain text: cord-284376-plwyjhl8.txt item: #439 of 973 id: cord-284423-fzz8g3rq author: Wang, Hui-yu title: Establishment and optimization of a liquid bead array for the simultaneous detection of ten insect-borne pathogens date: 2018-07-31 words: 4672 flesch: 49 summary: Liquid array detection showed that the MFI for RVFV, SBV, EBV, WNV and BTV was relatively higher (mainly > 4000) when the ratio of forward/reverse primers was 1:2, 1:3 or 1:4. The parameters of the system were optimized, including ratio of forward/reverse primers (1:2), hybridization temperature (50 °C) and duration (30 min) and quantity of PCR product (2 μl). keywords: array; detection; hybridization; liquid; pathogens; pcr; system; virus cache: cord-284423-fzz8g3rq.txt plain text: cord-284423-fzz8g3rq.txt item: #440 of 973 id: cord-284608-ba7wq52t author: Sias, Catia title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date: 2019-03-04 words: 5652 flesch: 51 summary: Currently, there are no guidelines recommending HPV oral cavity screening as a mandatory test, and it remains unknown which HPV types should be included in HPV screening programs. In addition, it remains unknown which HPV types should be included in oral cavity screening. keywords: anal; detection; hiv; hpv; human; prevalence; samples; swabs; types cache: cord-284608-ba7wq52t.txt plain text: cord-284608-ba7wq52t.txt item: #441 of 973 id: cord-284625-to6w5hm2 author: Duan, Xiaopei title: A retrospective study of the initial 25 COVID-19 patients in Luoyang, China date: 2020-05-26 words: 3357 flesch: 52 summary: GGO was the typical chest CT findings of COVID-19 patients. In addition, COVID-19 patients were not found to have combined a On the admission day, the unenhanced CT scan shows diffuse bilateral multiple patchy GGO (white arrow), and the partial boundary is clear while some have unclear boundaries, which are especially significant in the lower lobes of both lungs; strip consolidative opacities (black arrow) are in the focal area. keywords: ggo; patients; pcr; results; sars; symptoms cache: cord-284625-to6w5hm2.txt plain text: cord-284625-to6w5hm2.txt item: #442 of 973 id: cord-284644-9k2oox64 author: Sharma, Vikrant title: Evaluation of clinical applicability of reverse transcription-loop-mediated isothermal amplification assay for detection and subtyping of Influenza A viruses date: 2017-12-15 words: 4491 flesch: 38 summary: Virus isolation using egg embryo culture or cell culture is considered as 'gold standard' for influenza virus detection but the whole process is labour intensive and lengthy taking 3-7 days for obtaining results (Ellis and Zambon, 2002) . Influenza viruses belong to the family Orthomyxoviridae, characterized by segmented, negative-sense, single stranded RNA genome (Shaw and Palese, 2013) . keywords: assay; detection; h1n1; influenza; lamp; pcr cache: cord-284644-9k2oox64.txt plain text: cord-284644-9k2oox64.txt item: #443 of 973 id: cord-284777-z7bd3a91 author: Sun, Ning title: Reverse transcription recombinase polymerase amplification with lateral flow dipsticks for detection of influenza A virus and subtyping of H1 and H3 date: 2018-10-27 words: 4307 flesch: 47 summary: A viruses Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans The evolving history of influenza viruses and influenza vaccines Advances in the development of influenza virus vaccines Implications of antiviral resistance of influenza viruses Time lines of infection and disease in human influenza: a review of volunteer challenge studies Influenza diagnosis and treatment in children: a review of studies on clinically useful tests and antiviral treatment for influenza Cost-effectiveness of newer treatment strategies for influenza Low sensitivity of rapid diagnostic test for influenza Management of influenza symptoms in healthy children: cost-effectiveness of rapid testing and antiviral therapy Detection of influenza A viruses from different species by PCR amplification of conserved sequences in the matrix gene A multiplex PCR assay for the detection of five influenza viruses using a dual priming oligonucleotide system Single-step multiplex reverse transcription-polymerase chain reaction (RT-PCR) for influenza A virus subtype H5N1 detection Detection and identification of human influenza viruses by the polymerase chain reaction A matrix gene-based multiplex real-time RT-PCR for detection and differentiation of 2009 pandemic H1N1 and other influenza A viruses in North America Application of a fluorogenic PCR assay for typing and subtyping of influenza viruses in respiratory samples Integrated centrifugal reverse transcriptase loop-mediated isothermal amplification microdevice for influenza A virus detection An immunoassay-based reverse-transcription loopmediated isothermal amplification assay for the rapid detection of avian influenza H5N1 virus viremia DNA detection using recombination proteins Rapid detection of HIV-1 proviral DNA for early infant diagnosis using recombinase polymerase amplification Early detection of dengue virus by use of reverse transcription-recombinase polymerase amplification Development of a rapid recombinase polymerase amplification assay for detection of Brucella in blood samples Preliminary application of Tem-PCR combined with luminex for detection of four common respiratory viruses World Health Organization, WHO information for molecular diagnosis of influenza virus -update Multiplexed recombinase polymerase amplification assay to detect intestinal protozoa Identification of single-nucleotide polymorphisms by the oligonucleotide ligation reaction: a DNA biosensor for simultaneous visual detection of both alleles Phylogenetic analysis reveals the global migration of seasonal influenza A viruses Update: influenza activity in the United States during the 2017-18 season and composition of the 2018-19 influenza vaccine Quantitative RT-PCR evaluation of a rapid influenza antigen test for efficient diagnosis of influenza virus infection Detection of respiratory viruses in sputum from adults by use of automated multiplex PCR Design and performance testing of quantitative real time PCR assays for influenza A and B viral load measurement Loop-mediated isothermal amplification using self-avoiding molecular recognition systems and antarctic thermal sensitive uracil-DNA-glycosylase for detection of nucleic acid with prevention of carryover contamination Development of recombinase polymerase amplification assays for detection of Orientia tsutsugamushi or Rickettsia typhi A rapid isothermal assay for the detection of Hop stunt viroid in hop plants (Humulus lupulus), and its application in disease surveys Detection of root-infecting fungi on cool-season turfgrasses using loop-mediated isothermal amplification and recombinase polymerase amplification Picoliter well array chip-based digital recombinase polymerase amplification for absolute quantification of nucleic acids We acknowledge the Pediatrics Outpatient Department of Jinling Hospital, Nanjing, China, for collecting pharyngeal swab specimens. Influenza viruses are common and major pathogens that cause viral respiratory infections. keywords: assays; detection; influenza; lfd; pcr; rpa; virus cache: cord-284777-z7bd3a91.txt plain text: cord-284777-z7bd3a91.txt item: #444 of 973 id: cord-285203-ilxd0ih9 author: Paradiso, Angelo Virgilio title: Clinical meanings of rapid serological assay in patients tested for SARS-Co2 RT-PCR date: 2020-04-06 words: 3079 flesch: 43 summary: Results Rapid serological test showed a sensitivity of 30% and a specificity of 89% with respect to the standard assay but, interestingly, these performances improve after 8 days of symptoms appearance. After 10 days of symptoms the predictive value of rapid serological test is higher than that of standard assay. keywords: cov-2; covid-19; igg; igm; preprint; sars; test cache: cord-285203-ilxd0ih9.txt plain text: cord-285203-ilxd0ih9.txt item: #445 of 973 id: cord-285323-473d7zvg author: Jang, Hyesun title: Altered pro-inflammatory cytokine mRNA levels in chickens infected with infectious bronchitis virus date: 2013-09-01 words: 4817 flesch: 39 summary: Interleukin-6 expression after infectious bronchitis virus infection in chickens Proinflammatory cytokine responses induced by influenza A (H5N1) viruses in primary human alveolar and bronchial epithelial cells Proinflammatory cytokine response and viral replication in mouse bone marrow derived macrophages infected with influenza H1N1 and H5N1 viruses Newly isolated serotypes of infectious bronchitis virus: Their role in disease Avian Immunology Biologic basis for interleukin-1 in disease New insights on infectious bronchitis virus pathogenesis: Characterization of Italy 02 serotype in chicks and adult hens A choice of death-The signal-transduction of immune-mediated beta-cell apoptosis A novel chicken lung epithelial cell line: Characterization and response to low pathogenicity avian influenza virus Variant serotypes of infectious bronchitis virus isolated from commercial layer and broiler chickens The TNF-TNF receptor system Antigenic differences among isolates of avian infectious bronchitis virus Molecular cloning and characterization of chicken lipopolysaccharide-induced TNF-alpha factor (LITAF) Susceptibility of three genetic lines of chicks to infection with a nephropathogenic T strain of avian infectious bronchitis virus Pro-inflammatory responses in chicken spleen and brain tissues after infection with very virulent plus Marek's disease virus Inflammatory cytokines and lipopolysaccharide induce Fas-mediated apoptosis in renal tubular cells Analysis of chicken mucosal immune response to Eimeria tenella and Eimeria maxima infection by quantitative reverse transcription-PCR Genetic diversity of avian infectious bronchitis virus isolates in Korea between Live attenuated nephropathogenic infectious bronchitis virus vaccine provides broad cross protection against new variant strains Genetic diversity of avian infectious bronchitis coronavirus strains isolat A bovine herpesvirus type 1 mutant virus specifying a carboxylterminal truncation of glycoprotein E is defective in anterograde neuronal transport in rabbits and calves Genetic diversity of avian infectious bronchitis coronavirus in recent years in China IL-1b, TNF-a and IL-6 release from monocytes in haemodialysis patients in relation to dialytic age Rapid differentiation of current infectious bronchitis virus vaccine strains and field isolates in Australia Chemokine and cytokine gene expression profiles in chickens inoculated with Mycoplasma gallisepticum strains Rlow or GT5 challenge group inoculated with an isolate of the KIIa genotype (kr/ADL110002/2011, group 2), and challenge group inoculated with an isolate of the ChVI genotype dpi = days postinoculation AGP level in the serum (arithmetic mean ± SD) Therapy, Design of Vaccines, and Epidemiology Viral Immunol A novel lipopolysaccharide-induced transcription factor regulating tumor necrosis factor alpha gene expression: Molecular cloning, sequencing, characterization, and chromosomal assignment Comparison of the susceptibility to avian infectious bronchitis virus infection of two inbred lines of White Leghorn chickens Re-emergence of fatal human influenza A subtype H5N1 disease H5N1 and 1918 pandemic influenza virus infection results in early and excessive infiltration of macrophages and neutrophils in the lungs of mice Infectious bronchitis virus: Immunopathogenesis of infection in the chicken Transcriptional profiling reveals a possible role for the timing of the inflammatory response in determining susceptibility to a viral infection Sequence analysis of the S1 glycoprotein of infectious bronchitis viruses Differential cytokine mRNA expression in heterophils isolated from Salmonella-resistant and -susceptible chickens Comparative host gene transcription by microarray analysis early after infection of the Huh7 cell line by severe acute respiratory syndrome coronavirus and human coronavirus 229E LPS induces the interaction of a transcription factor, LPS-induced TNF-alpha factor, and STAT6(B) with effects on multiple cytokines Interferon and cytokine responses to SARS-coronavirus infection Pathology of fatal human infection associated with avian influenza A H5N1 virus Tumor necrosis factor and interleukin-1 induce expression of the verocytotoxin receptor globotriaosylceramide on human endothelial cells: Implications for the pathogenesis of the hemolytic uremic syndrome Viral diseases of respiratory system Rapid expression of chemokines and proinflammatory cytokines in newly hatched chickens infected with Salmonella enterica serovar Typhimurium Plasma inflammatory cytokines and chemokines in severe acute respiratory syndrome keywords: chickens; dpi; genotype; group; infection; kiia; response; virus cache: cord-285323-473d7zvg.txt plain text: cord-285323-473d7zvg.txt item: #446 of 973 id: cord-285527-1mceq6v0 author: Kinloch, Natalie N title: Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results date: 2020-06-28 words: 1917 flesch: 41 summary: We used droplet digital PCR (ddPCR) to demonstrate that human DNA levels, a stable molecular marker of sampling quality, were significantly lower in samples from 40 confirmed or suspected COVID-19 cases that yielded negative diagnostic test results (i.e. suspected false-negative test results) compared to a representative pool of 87 specimens submitted for COVID-19 testing. As diagnoses may not have been made in a consistent manner across treating physicians, these samples may be less likely to represent false negative results. keywords: test cache: cord-285527-1mceq6v0.txt plain text: cord-285527-1mceq6v0.txt item: #447 of 973 id: cord-285587-rggfg60a author: Meligy, Bassant title: Detection of viral acute lower respiratory tract infection in hospitalized infants using real-time PCR date: 2015-12-30 words: 3537 flesch: 45 summary: World Health Organization Factsheet no Comparison of Anyplex II RV16 with the xTAG respiratory viral panel and Seeplex RV15 for detection of respiratory viruses World Health Organization: the global burden of disease: 2004 update Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Evaluation of a novel real-time RT-PCR using TOCE technology compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses Narkevicˇi ut_ key: cord-285587-rggfg60a authors: Meligy, Bassant; Sayed, Amal; Ismail, Dalia Kadry; Kamal, Dina; Abdel-Latif, Walaa; Erfan, Dina M. title: Detection of viral acute lower respiratory tract infection in hospitalized infants using real-time PCR date: 2015-12-30 journal: Gaz Egypt Paediatr Assoc DOI: 10.1016/j.epag.2015.11.005 sha: doc_id: 285587 cord_uid: rggfg60a INTRODUCTION: keywords: cases; children; hospital; patients; pcr; study; virus; viruses cache: cord-285587-rggfg60a.txt plain text: cord-285587-rggfg60a.txt item: #448 of 973 id: cord-286065-x0g67pnb author: Metzgar, David title: The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood date: 2016-07-06 words: 5932 flesch: 34 summary: PCR-based rapid sepsis diagnosis effectively guides clinical treatment in patients with new onset of SIRS Laboratory detection of sepsis: biomarkers and molecular approaches EPISEPSIS: a reappraisal of the epidemiology and outcome of severe sepsis in French intensive care units Burden of illness imposed by severe sepsis in Germany Epidemiology of severe sepsis in the United States: analysis of incidence, outcome, and associated costs of care Initiation of inappropriate antimicrobial therapy results in a fivefold reduction of survival in human septic shock The potential for PCR based testing to improve diagnosis and treatment of sepsis Community-acquired bloodstream infection in critically ill adult patients: impact of shock and inappropriate antibiotic therapy on survival Multiplex real-time PCR and blood culture for identification of bloodstream pathogens in patients with suspected sepsis Benefit of appropriate empirical antibiotic treatment: thirty-day mortality and duration of hospital stay Delaying the empiric treatment of Candida bloodstream infection until positive blood culture results are obtained: a potential risk factor for hospital mortality Improved detection of blood stream pathogens by real-time PCR in severe sepsis Blood cultures: key elements for best practices and future directions A comprehensive model to optimize the strategy for diagnosing bacteremia The clinical and prognostic importance of positive blood cultures in adults Blood culture contamination: persisting problems and partial progress A critical appraisal of the role of the clinical microbiology laboratory in the diagnosis of bloodstream infections Interference testing in clinical chemistry; approved guideline. keywords: assay; bac; bac bsi; blood; bsi; bsi assay; culture; iridica; iridica bac; negative; organisms; pcr; samples; species cache: cord-286065-x0g67pnb.txt plain text: cord-286065-x0g67pnb.txt item: #449 of 973 id: cord-286096-h275nner author: Huijskens, Elisabeth G. W. title: Viral and bacterial aetiology of community‐acquired pneumonia in adults date: 2012-08-22 words: 3715 flesch: 42 summary: Year-round inclusion is important to cover the complete spectrum of respiratory virus infections, because several viruses are known to be found only in particular months of the year. InfA has been found as the second most frequent pathogen in CAP patients and the most common viral pathogen in all the age groups. keywords: antigen; community; pathogens; patients; pneumoniae; samples; sputum; viruses cache: cord-286096-h275nner.txt plain text: cord-286096-h275nner.txt item: #450 of 973 id: cord-286343-s8n1ldol author: Martin, Javier title: Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic date: 2020-10-09 words: 5931 flesch: 44 summary: We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations. keywords: concentration; cov-2; npcr; nucleotide; results; rna; samples; sars; sequences; sewage; viral; virus; wastewater cache: cord-286343-s8n1ldol.txt plain text: cord-286343-s8n1ldol.txt item: #451 of 973 id: cord-286360-wrrqb387 author: Pratelli, A title: Development of a nested PCR assay for the detection of canine coronavirus date: 1999-06-02 words: 1682 flesch: 52 summary: Our principal interest was to develop both PCR and n-PCR as methods to rapidly differentiate CCV infections from other canine enteric pathogens which cause similar clinical illness. key: cord-286360-wrrqb387 authors: Pratelli, A; Tempesta, M; Greco, G; Martella, V; Buonavoglia, C title: Development of a nested PCR assay for the detection of canine coronavirus date: 1999-06-02 journal: J Virol Methods DOI: 10.1016/s0166-0934(99)00017-8 sha: doc_id: 286360 cord_uid: wrrqb387 A diagnostic test for canine coronavirus (CCV) infection based on a nested polymerase chain reaction (n-PCR) assay was developed and tested using the following coronavirus strains: CCV (USDA strain), CCV (45/93, field strain), feline infectious peritonitis virus (FIPV, field strain), trasmissible gastroenteritis virus (TGEV, Purdue strain), bovine coronavirus (BCV, 9WBL-77 strain), infectious bronchitis virus (IBV, M-41 strain) and fecal samples of dogs with CCV enteritis. keywords: ccv; coronavirus; dogs; pcr cache: cord-286360-wrrqb387.txt plain text: cord-286360-wrrqb387.txt item: #452 of 973 id: cord-286443-t0asknzu author: Emerson, Julia title: Home Self-Collection of Nasal Swabs for Diagnosis of Acute Respiratory Virus Infections in Children With Cystic Fibrosis date: 2013-07-14 words: 4010 flesch: 39 summary: Severe viral respiratory infections in infants with cystic fibrosis Respiratory viruses in children with cystic fibrosis: viral detection and clinical findings Effects of upper respiratory tract infections in patients with cystic fibrosis Effects of viral lower respiratory tract infection on lung function in infants with cystic fibrosis Effect of respiratory virus infections including rhinovirus on clinical status in cystic fibrosis Prevalence and impact of respiratory viral infections in young children with cystic fibrosis: prospective cohort study Association of respiratory viral infections with pulmonary deterioration in patients with cystic fibrosis The role of respiratory viruses in cystic fibrosis Importance of viruses and Legionella pneumophila in respiratory exacerbations of young adults with cystic fibrosis The effect of respiratory viral infections on patients with cystic fibrosis Influenza-associated cystic fibrosis pulmonary exacerbations Rhinovirus C and respiratory exacerbations in children with cystic fibrosis Role of respiratory viruses in pulmonary exacerbations in children with cystic fibrosis Detection of viral and bacterial respiratory pathogens in patients with cystic fibrosis Comparing nosethroat swabs and nasopharyngeal aspirates collected from children with symptoms for respiratory virus identification using real-time polymerase chain reaction Detection of multiple respiratory pathogens during primary respiratory infection: nasal swab versus nasopharyngeal aspirate using real-time polymerase chain reaction Comparative study of nasopharyngeal aspirate and nasal swab specimens for diagnosis of acute viral respiratory infection Non-invasive sample collection for respiratory virus testing by multiplex PCR E-mail-based symptomatic surveillance combined with self-collection of nasal swabs: a new tool for acute respiratory infection epidemiology Monitoring the emergence of community transmission of influenza A/H1N1 2009 in England: a cross sectional opportunistic survey of self sampled telephone callers to NHS Direct Collection by trained pediatricians or parents of mid-turbinate nasal flocked swabs for the detection of influenza viruses in childhood Community epidemiology of human metapneumovirus, human coronavirus NL63, and other respiratory viruses in healthy preschool-aged children using parent-collected specimens Parent-collected respiratory specimens-a novel method for respiratory virus and vaccine efficacy research Self-collected midturbinate swabs for the detection of respiratory viruses in adults with acute respiratory illnesses Self-collection of foam nasal swabs for respiratory virus detection by pcr among immunocompetent subjects and hematopoietic cell transplant recipients Clinical disease in children associated with newly described coronavirus subtypes Detection and quantification of human metapneumovirus in pediatric specimens by real-time RT-PCR Comparison of realtime PCR assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children Evaluation of quantitative and type-specific real-time RT-PCR assays for detection of respiratory syncytial virus in respiratory specimens from children Real-time reverse transcription-PCR assay for comprehensive detection of human rhinoviruses Respiratory virus infection among hematopoietic cell transplant recipients: evidence for asymptomatic parainfluenza virus infection Linking syndromic surveillance with virological self-sampling Self-Collection of Nasal Swabs for Viral Diagnosis in Cystic Fibrosis 351 Home self-collection is feasible and well tolerated for timely respiratory virus diagnosis and provides a novel approach for clinical diagnostics and surveillance of respiratory virus infections among CF patients. keywords: clinic; collection; foam; home; nasal; swabs; virus cache: cord-286443-t0asknzu.txt plain text: cord-286443-t0asknzu.txt item: #453 of 973 id: cord-286451-ujo72w06 author: Bennett, Susan title: The development of a multiplex real-time PCR for the detection of herpes simplex virus 1 and 2, varizella zoster virus, adenovirus and Chlamydia trachomatis from eye swabs date: 2012-09-18 words: 2039 flesch: 45 summary: Primers and probes were then compared to all sequences available in BLAST (www.ncbi.nlm.nih.gov/blast) and shown to only detect all serovars of C. trachomatis including the Swedish variant (sw C. trachomatis) discovered in 2006. A multiplex real-time PCR assay for rapid and simultaneous detection of HSV 1 and 2, VZV, adenovirus and Chlamydia trachomatis (C. trachomatis) from eye swabs was developed and evaluated. keywords: assay; multiplex; pcr; trachomatis cache: cord-286451-ujo72w06.txt plain text: cord-286451-ujo72w06.txt item: #454 of 973 id: cord-286555-rz88g3ze author: Petrovan, Vlad title: Evaluation of Commercial qPCR Kits for Detection of SARS-CoV-2 in Pooled Samples date: 2020-07-11 words: 3549 flesch: 50 summary: One such alternative is sample pooling. Sample pooling represents one of the approaches that can easily be applied in order to increase the number of tests. keywords: gene; kit; pcr; rdrp; samples cache: cord-286555-rz88g3ze.txt plain text: cord-286555-rz88g3ze.txt item: #455 of 973 id: cord-287054-zmxpuynv author: Li, Ning title: Molecular diagnosis of COVID-19: Current situation and trend in China (Review) date: 2020-08-25 words: 6832 flesch: 30 summary: Nucleic acid detection technology. Due to antibody preparation requiring additional time, faster breakthroughs are expected in pathogen nucleic acid detection technology (79) . keywords: acid; amplification; coronavirus; cov-2; detection; diagnosis; epidemic; ncov; novel; nucleic; patients; pcr; sars; sequencing; technology cache: cord-287054-zmxpuynv.txt plain text: cord-287054-zmxpuynv.txt item: #456 of 973 id: cord-287104-4k8pqbc0 author: Lee, J. Y. title: Development of Rapid and Specific Detection for the Human Aichivirus A Using the Loop-Mediated Isothermal Amplification from Water Samples date: 2019-04-04 words: 2019 flesch: 44 summary: Virus taxonomy at the XIth international congress of virology Aichi virus strains in children with gastroenteritis Isolation of cytopathic small round virus (Aichi virus) from Pakistani children and Japanese travelers from Southeast Asia Isolation of cytopathic small round viruses with BS-C-1 cells from patients with gastroenteritis Epidemiology of human parechovirus, Aichi virus and salivirus in fecal samples from hospitalized children with gastroenteritis in Hong Kong Aichi virus shedding in high concentrations in patients with acute diarrhea Molecular characterization of the first Aichi viruses isolated in Europe and in South America Detection and genomic characterization of Aichi viruses in stool samples from children in Monastir, Tunisia Etiological role of viruses in outbreaks of acute gastroenteritis in The Netherlands from 1994 through Aichi virus, norovirus, astrovirus, enterovirus, and rotavirus involved in clinical cases from a french oysterrelated gastroenteritis outbreak Isolation and molecular characterization of Aichi viruses from fecal specimens collected in Japan, Bangladesh, Thailand, and Vietnam Molecular detection and nucleotide sequence analysis of a new Aichi virus closely related to canine kobuvirus in sewage samples Aichi virus in sewage and surface water, the Netherlands Molecular detection and characterization of Aichi viruses in sewage-polluted waters of venezuela Prevalance and genetic diversity of Aichi viruses in wastewater and river water in japan Aichi virus 1: Enviromental Occurrence and Behavior. In addition, confirm system of positive LAMP reaction was developed by using the restriction enzyme Aci I and Hae III. keywords: aiv; lamp; pcr; primer; samples cache: cord-287104-4k8pqbc0.txt plain text: cord-287104-4k8pqbc0.txt item: #457 of 973 id: cord-287228-0qm939ve author: Hong, Ke title: Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness date: 2020-10-27 words: 3623 flesch: 45 summary: Our study has its limitation that a relatively small number of patients were included, which makes it difficult to associate any demographic features with increased risk of prolonged viral RNA in COVID-19 patients. Infectiousness in COVID-19 patients with prolonged presence of viral nucleic acid should not solely be evaluated by RT–PCR. keywords: cov-2; covid-19; infection; patients; pcr; rna; sars cache: cord-287228-0qm939ve.txt plain text: cord-287228-0qm939ve.txt item: #458 of 973 id: cord-287447-5lzzobl3 author: Keyaerts, Els title: In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine date: 2004-10-08 words: 2170 flesch: 46 summary: Summary of probable SARS cases with onset of illness from 1 Identification of a novel coronavirus in patients with severe acute respiratory syndrome SARS Working Group, A novel coronavirus associated with severe acute respiratory syndrome Coronavirus as a possible cause of severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome Treatment of severe acute respiratory syndrome with lopinavir/ ritonavir: a multicentre retrospective matched cohort study Role of lopinavir/ritonavir in the treatment of SARS: initial virological and clinical findings Role of interferons in the treatment of severe acute respiratory syndrome Antiviral treatment of SARS: can we draw any conclusions? Glycyrrhizin, an active component of liquorice roots, and replication of SARS-associated coronavirus Inhibition of severe acute respiratory syndrome coronavirus replication by niclosamide HIV protease inhibitor nelfinavir inhibits replication of SARS-associated coronavirus Inhibition of SARS-coronavirus infection in vitro by S-nitroso-N-acetylpenicillamine, a nitric oxide donor compound Effects of chloroquine on viral infections: an old drug against todayÕs diseases? Inhibition of human immunodeficiency virus infectivity by chloroquine Chloroquine inhibits HIV-1 replication in human peripheral blood lymphocytes The anti-HIV-1 activity of chloroquine Treatment of chronic active hepatitis B (CAH B) with chloroquine: a preliminary report Mechanism of enhancement of the antiviral action of interferon against herpes simplex virus-1 by chloroquine Human Coronavirus HCoV-229E enters susceptible cells via the endocytic pathway A method for the rapid construction of cRNA standard curves in quantitative real-time reverse transcription polymerase chain reaction Rapid and automated tetrazolium-based colorimetric assay for the detection of anti-HIV compounds Microculture tetrazolium assays: a comparison between two new tetrazolium salts, XTT and MTS Proliferative growth of SARS coronavirus in Vero E6 cells Treatment of Plasmodium falciparum malaria in Africa (except cerebral malaria Chloroquine treatment in rheumatoid arthritis. Severe acute respiratory syndrome (SARS) has recently emerged as a new highly contagious human disease with a major impact all over the world [1] . keywords: antiviral; chloroquine; coronavirus; cov; replication; sars; treatment cache: cord-287447-5lzzobl3.txt plain text: cord-287447-5lzzobl3.txt item: #459 of 973 id: cord-287466-ag5y781z author: Cowley, J.A. title: Nidoviruses of Fish and Crustaceans date: 2016-09-09 words: 17742 flesch: 23 summary: A constant-temperature RT loop-mediated isothermal amplification (RT-LAMP) test with a sensitivity of ~5 RNA copies has also been developed for FHMNV diagnosis and surveillance (Zhang et al., 2014) . While toroviruses (28.0-28.5 kb) (Snijder et al., 2013) , bafiniviruses (26.6-27.3 kb) (Schütze et al., 2006; Batts et al., 2012) and roniviruses (26.2-26.6 kb) (Cowley et al., 2000a; Cowley and Walker, 2002; Sittidilokratna et al., 2002 Sittidilokratna et al., , 2008 possess similarly long genomes, those of mesoniviruses (20.2 kb) (Nga et al., 2011; Zirkel et al., 2011 Zirkel et al., , 2013 Lauber et al., 2012) and arteriviruses (12.7-15.7 kb) (Snijder et al., 2013) are more compact. keywords: cells; cowley et; detection; disease; dsrna; et al; flegel et; gav; gene; genome; gill; head; head virus; infection; lightner; monodon; nadala et; pcr; penaeus; penaeus monodon; rna; sequence; shrimp; sithigorngul et; sittidilokratna et; soowannayan et; spann et; species; virions; virus; viruses; wijegoonawardane et; yellow; yhv cache: cord-287466-ag5y781z.txt plain text: cord-287466-ag5y781z.txt item: #460 of 973 id: cord-287843-snra23sy author: Lee, Wan‐Ji title: Prevalence and molecular epidemiology of human coronavirus HKU1 in patients with acute respiratory illness date: 2012-11-14 words: 2718 flesch: 49 summary: The novel human coronaviruses NL63 and HKU1 Prevalence of human coronaviruses in adults with acute respiratory tract infections in Beijing Human (non-severe acute respiratory syndrome) coronavirus infections in hospitalized children in France Identification of a new human coronavirus Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia Phylogenetic and recombination analysis of coronavirus HKU1, a novel coronavirus from patients with pneumonia Comparative analysis of 22 coronavirus HKU1 genomes reveals a novel genotype and evidence of natural recombination in coronavirus HKU1 More and more a coronaviruses: Human coronavirus HKU1 HCoV-NL63 was discovered in 2004 as a minor pathogen of HCoV infections in humans keywords: acute; coronavirus; hcov; hku1; pcr cache: cord-287843-snra23sy.txt plain text: cord-287843-snra23sy.txt item: #461 of 973 id: cord-287931-cxqzac4a author: Huang, Weiwei title: An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens date: 2013-09-20 words: 5170 flesch: 42 summary: The predominant techniques for identification of microbial pathogens depend on conventional clinical microbiology monitoring approaches. Since the first application of a high-throughput, rapid, and unbiased microarray for detecting viral pathogens in 2002 keywords: analysis; china; eopm; microarray; pathogens; pcr; probes; rna; samples; sequences; species; virus cache: cord-287931-cxqzac4a.txt plain text: cord-287931-cxqzac4a.txt item: #462 of 973 id: cord-288253-wqrhiq08 author: Park, Jung-Eun title: Development of transgenic mouse model expressing porcine aminopeptidase N and its susceptibility to porcine epidemic diarrhea virus date: 2015-02-02 words: 5336 flesch: 42 summary: We thus generated porcine APN transgenic mice expressing porcine APN in the brush borders of their small intestines and various tissues (lungs and kidneys). PEDV replication in the small intestines of porcine APN transgenic mice Both wild type and porcine APN transgenic mice were infected with PEDV orally on day 0. keywords: anti; apn; cells; coronavirus; et al; mice; mouse; pcr; pedv; porcine; porcine apn; transgenic cache: cord-288253-wqrhiq08.txt plain text: cord-288253-wqrhiq08.txt item: #463 of 973 id: cord-288306-0chcsqe7 author: Wang, Lihua title: Recent Advances in the Diagnosis of Classical Swine Fever and Future Perspectives date: 2020-08-15 words: 5836 flesch: 36 summary: A multiplex reverse transcription PCR and automated electronic microarray assay for detection and differentiation of seven viruses affecting swine Detection system based on magnetoelastic sensor for classical swine fever virus Diagnosis of mixed infections with swine viruses using an integrated microfluidic platform Next-generation sequencing in veterinary medicine: How can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases? Next-generation sequencing as diagnostic tool in veterinary research Molecular epidemiology of current classical swine fever virus isolates of wild boar in Germany Sequencing approach to analyze the role of quasispecies for classical swine fever Virus adaptation and selection following challenge of animals vaccinated against classical swine fever virus Classical swine fever virus biology, clinicopathology, diagnosis, vaccines and a meta-analysis of prevalence: A review from the Indian Perspective Pigs immunized with a novel E2 subunit vaccine are protected from heterologous classical swine fever virus challenge Towards the development of a one-dose classical swine fever subunit vaccine: Antigen titration, onset and duration of immunity Plant-made E2 glycoprotein single-dose vaccine protects pigs against classical swine fever A neutralizing monoclonal antibody-based competitive ELISA for classical swine fever C-strain post-vaccination monitoring Development of a high-throughput serum neutralization test using recombinant pestiviruses possessing a small reporter tag Detection of antibodies against classical swine fever virus in swine sera by indirect ELISA using recombinant envelope glycoprotein E2 Direct coating of culture medium from cells secreting classical swine fever virus E2 antigen on ELISA plates for detection of E2-specific antibodies Development of a competitive ELISA using a truncated E2 recombinant protein as antigen for detection of antibodies to classical swine fever virus Development of single dilution immunoassay to detect E2 protein specific classical swine fever virus antibody A multiplex nested RT-PCR for the detection and differentiation of wild-type viruses from C-strain vaccine of classical swine fever virus Evaluation of a multiplex real-time RT-PCR for quantitative and differential detection of wild-type viruses and C-strain vaccine of Classical swine fever virus Differentiation of C-strain Riems or CP7_E2alf vaccinated animals from animals infected by classical swine fever virus field strains using real-time RT-PCR A generic real-time TaqMan assay for specific detection of lapinized Chinese vaccines against classical swine fever Development of a triplex TaqMan real-time RT-PCR assay for differential detection of wild-type and HCLV vaccine strains of classical swine fever virus and bovine viral diarrhea virus 1 Differential detection of classical swine fever virus challenge strains in C-strain vaccinated pigs Comparison of two real-time RT-PCR assays for differentiation of C-strain vaccinated from classical swine fever infected pigs and wild boars Development of a reverse-transcription polymerase chain reaction assay with fluorogenic probes to discriminate Korean wild-type and vaccine isolates of Classical swine fever virus Rapid detection and differentiation of wild-type and three attenuated lapinized vaccine strains of classical swine fever virus by reverse transcription polymerase chain reaction Genetic differentiation of infected from vaccinated animals after implementation of an emergency vaccination strategy against classical swine fever in wild boar Evaluation of classical swine fever virus antibody detection assays with an emphasis on the differentiation of infected from vaccinated animals Antibody responses of pigs to defined E rns fragments after infection with classical swine fever virus Development of a classical swine fever subunit marker vaccine and companion diagnostic test Enzyme-linked immunosorbent assay using a virus type-specific peptide based on a subdomain of envelope protein Erns for serologic diagnosis of pestivirus infections in swine Laboratory diagnosis, epizootiology, and efficacy of marker vaccines in classical swine fever: A review Evaluation of an Erns-based enzyme-linked immunosorbent assay to distinguish Classical swine fever virus-infected pigs from pigs vaccinated with CP7_E2alf The double-antigen ELISA concept for early detection of E rns -specific classical swine fever virus antibodies and application as an accompanying test for differentiation of infected from marker vaccinated animals Differentiation of classical swine fever virus infection from CP7_E2alf marker vaccination by a multiplex microsphere immunoassay Discrimination within epitope specific antibody populations against classical swine fever virus is a new means of differentiating infection from vaccination Enhanced expression of the Erns protein of classical swine fever virus in yeast and its application in an indirect enzyme-linked immunosorbent assay for antibody differentiation of infected from vaccinated animals Bossis, I. keywords: antibody; assay; csfv; detection; diagnosis; fever; pcr; pigs; strain; swine; time; virus cache: cord-288306-0chcsqe7.txt plain text: cord-288306-0chcsqe7.txt item: #464 of 973 id: cord-288327-r20zowty author: Coiras, M.T. title: Oligonucleotide array for simultaneous detection of respiratory viruses using a reverse‐line blot hybridization assay date: 2005-04-15 words: 5928 flesch: 43 summary: The preparation of reagents, processing of samples, aliquots of the respiratory specimens, and nested PCR assays were performed in safety cabinets located in separate laboratories, isolated from the area for the analysis of the amplified products. Therefore, comparison of the results obtained by both RLB and nested PCR assays, showed a 96% correlation (see Table III and Fig. 4) . keywords: assay; coiras; detection; et al; pcr; rlb; viruses cache: cord-288327-r20zowty.txt plain text: cord-288327-r20zowty.txt item: #465 of 973 id: cord-288556-o8i6j3b2 author: Li, Yanpeng title: Virome of a Feline Outbreak of Diarrhea and Vomiting Includes Bocaviruses and a Novel Chapparvovirus date: 2020-05-04 words: 5875 flesch: 48 summary: FeBoV1 was first discovered in multiple tissues of cats in Hong Kong [53] and subsequently reported in cat feces in the US, Japan, Europe and China Using metagenomics, we found FeBoV1, 2, and 3 and a novel chaphamaparvovirus we named fechavirus in a large fraction of fecal samples and fechavirus in all vomit samples from sick cats in a multi-facility outbreak. keywords: animals; cats; days; diarrhea; dna; fechavirus; feline; novel; outbreak; pcr; samples; shelter; viruses cache: cord-288556-o8i6j3b2.txt plain text: cord-288556-o8i6j3b2.txt item: #466 of 973 id: cord-288692-v471648u author: Yip, Shea Ping title: Use of Dual TaqMan Probes to Increase the Sensitivity of 1-Step Quantitative Reverse Transcription-PCR: Application to the Detection of SARS Coronavirus date: 2005-10-01 words: 2401 flesch: 34 summary: This simple modification using dual TaqMan probes for quantification has wide applications in areas in which ultrasensitivity is critically required. In conclusion, we report the use of dual TaqMan probes for quantification purposes and apply it to the detection of Clinical Chemistry 51, No. 10, 2005 SARS-CoV with a detection limit of 1 copy RNA per reaction. keywords: assay; coronavirus; detection; pcr; probe; rna; sars; taqman cache: cord-288692-v471648u.txt plain text: cord-288692-v471648u.txt item: #467 of 973 id: cord-288701-nx9fg4yn author: Mari, Viviana title: Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date: 2015-12-17 words: 4836 flesch: 33 summary: The prototype strain (HoBi D32/00) of this emerging group of pestiviruses, also known as BVDV-3 or atypical pestiviruses (Larska et al., 2012; Liu et al., 2009) , was detected as contaminant of a batch of fetal bovine serum (FBS) imported from Brazil (Schirrmeier et al., 2004) . A recently developed real-time RT-PCR assay is able to detect HoBi-like pestiviruses without providing any simultaneous detection of BVDV-1 and BVDV-2 (Liu et al., 2008) . keywords: assay; bovine; bvdv-2; decaro; et al; hobi; like; pcr; pestivirus; rna; samples; time cache: cord-288701-nx9fg4yn.txt plain text: cord-288701-nx9fg4yn.txt item: #468 of 973 id: cord-288962-jgtoehcr author: Andréoletti, Laurent title: Differential detection of rhinoviruses and enteroviruses RNA sequences associated with classical immunofluorescence assay detection of respiratory virus antigens in nasopharyngeal swabs from infants with bronchiolitis date: 2000-06-06 words: 3713 flesch: 29 summary: [1988] , that demonstrated by cell culture assays the low prevalence of human rhinovirus respiratory infection in childhood bronchiolitis. Interestingly, positive human rhinovirus and enterovirus RT-PCR results were obtained in 8 of 84 (9.5%) and in 7 of 84 (8.3%) nasopha-ryngeal aspirates samples, and were the only evidence of respiratory viral infection in 15 patients with obstructive bronchiolitis ( Table I) . keywords: assay; bronchiolitis; detection; pcr; respiratory; rhinovirus; viral cache: cord-288962-jgtoehcr.txt plain text: cord-288962-jgtoehcr.txt item: #469 of 973 id: cord-289017-vwye3pk9 author: Comach, Guillermo title: Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date: 2012-09-11 words: 6275 flesch: 44 summary: Influenza viruses, including pandemic H1N1 2009, were the most frequently detected pathogens, accounting for 67.4% (97/144) of the viruses detected. CONCLUSIONS/SIGNIFICANCE: Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. keywords: detection; ili; influenza; pandemic; pcr; ph1n1; study; surveillance; venezuela; viral; viruses cache: cord-289017-vwye3pk9.txt plain text: cord-289017-vwye3pk9.txt item: #470 of 973 id: cord-289050-9w7ks01n author: Donoso, Alejandro F. title: Fatal hemorrhagic pneumonia caused by human metapneumovirus in an immunocompetent child date: 2008-08-25 words: 1783 flesch: 43 summary: This agent causes acute respiratory tract infections in children and adults. Although the spectrum of clinical manifestations of hMPV infection is not completely defi ned as yet, the most frequent manifestations include cough, coryza and pharyngitis. keywords: children; hmpv; human; metapneumovirus; patient; respiratory cache: cord-289050-9w7ks01n.txt plain text: cord-289050-9w7ks01n.txt item: #471 of 973 id: cord-289114-ifnk41oq author: Singh, Angaraj title: Effect of pre‐existing diseases on COVID‐19 infection and role of new sensors and biomaterials for its detection and treatment date: 2020-10-28 words: 6903 flesch: 48 summary: All rights reserved Treatment of severe acute respiratory syndrome with lopinavir/ritonavir: a multicentre retrospective matched cohort study Use of convalescent plasma therapy in SARS patients in Hong Kong Clinical Trials. All rights reserved A novel human coronavirus: Middle East respiratory syndrome human coronavirus Loneliness as a public health issue: the impact of loneliness on health care utilization among older adults Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor The mechanism of resistance to favipiravir in influenza The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus Critical care utilization for the COVID-19 outbreak in Lombardy, Italy: early experience and forecast during an emergency response Isolation and characterization of viruses related to the SARS coronavirus from animals in Southern China Myocardial injury may be key in predicting COVID-19 fatalities The origin, transmission and clinical therapies on coronavirus disease-2019 (COVID-19) outbreak -an update on the Status Expression of elevated levels of pro-inflammatory cytokines in SARS-CoV-infected ACE2 cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan, China: a descriptive study Clinical features of patients infected with 2019 novel coronavirus in Wuhan Accepted Article keywords: article; copyright; coronavirus; cov-2; covid-19; detection; et al; infection; novel; patients; pcr; plasma; rights; sars; treatment cache: cord-289114-ifnk41oq.txt plain text: cord-289114-ifnk41oq.txt item: #472 of 973 id: cord-289200-6yhz1a23 author: Yang, Ziyi title: Vertical Transmission of Severe Acute Respiratory Syndrome Coronavirus 2: A Systematic Review date: 2020-05-13 words: 1899 flesch: 42 summary: Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn Microbial vertical transmission during human pregnancy Viral infections during pregnancy Mother-to-infant transmission of hepatitis B virus: challenges and perspectives Single-cell RNA expression profiling of ACE2 and AXL in the human maternal-fetal interface Pregnant women with new coronavirus infection: a clinical characteristics and placental pathological analysis of three cases ubella infection in pregnancy Expert consensus for managing pregnant women and neonates born to mothers with suspected or confirmed novel coronavirus (COVID-19) infection Safe delivery for COVID-19 infected pregnancies Pregnant women complicated with corona virus disease 2019 (COVID-19): a clinical analysis of 3 cases Impact of COVID-19 infection on pregnancy outcomes and the risk of maternal-to-neonatal intrapartum transmission of COVID-19 during natural birth Emergency cesarean section on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) confirmed patient Clinical characteristics of COVID-19 in pregnancy: analysis of nine cases Lack of vertical transmission of severe acute respiratory syndrome coronavirus 2, China. 6yhz1a23 Objective The aim of this study is to summarize currently available evidence on vertical transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). keywords: coronavirus; infection; pcr; transmission cache: cord-289200-6yhz1a23.txt plain text: cord-289200-6yhz1a23.txt item: #473 of 973 id: cord-289216-g4kqi560 author: Malecki, M. title: Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account date: 2020-09-23 words: 1931 flesch: 45 summary: Ever since the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the causative agent of the coronavirus disease 2019 (COVID-19), the number of commercial kits detecting the virus from clinical samples keeps growing (1, 2) . Clinical samples may be reported falsely as negative, unlike indicated by the sensitivity values published in predated studies. keywords: cov-2; pcr; preprint; samples; sars cache: cord-289216-g4kqi560.txt plain text: cord-289216-g4kqi560.txt item: #474 of 973 id: cord-289612-4x5t4c5u author: Alsuliman, Tamim title: COVID-19 paraclinical diagnostic tools: Updates and future trends date: 2020-06-20 words: 7370 flesch: 45 summary: Therefore, it may be important to routinely detect viral RNA in stool specimens of COVID-19 patients during the hospitalization and recovery stage, and to perform transmission-based precautions for patients until the negative conversion of viral RNA in feces. Probably, combining RNA and antibody detections may significantly improve the sensitivity of pathogenic diagnosis for COVID-19 patients (p < 0.001), even in the early phase of 1-week since onset (p = 0.007). keywords: assay; cases; coronavirus; cov-2; covid-19; diagnosis; disease; infection; patients; pcr; results; rna; rrt; sars; study cache: cord-289612-4x5t4c5u.txt plain text: cord-289612-4x5t4c5u.txt item: #475 of 973 id: cord-289676-tjy7f9rk author: Park, Sang-Ik title: Development of SYBR Green real-time RT-PCR for rapid detection, quantitation and diagnosis of unclassified bovine enteric calicivirus date: 2009-03-14 words: 4148 flesch: 51 summary: In addition, the sensitivity and specificity of the developed SYBR Green real-time RT-PCR was evaluated and compared to conventional RT-PCR and nested PCR assays reported previously (Park et al., 2008) . Diarrheic specimens (n = 118) collected from 2004 to 2005 were subjected to RT-PCR, nested PCR and SYBR Green real-time RT-PCR. keywords: green; pcr; sybr; time; time rt cache: cord-289676-tjy7f9rk.txt plain text: cord-289676-tjy7f9rk.txt item: #476 of 973 id: cord-289735-iw3uq2z9 author: Tsou, P. title: Association between multiple respiratory viral infections and pediatric intensive care unit admission among infants with bronchiolitis date: 2019-11-25 words: 3865 flesch: 33 summary: key: cord-289735-iw3uq2z9 authors: Tsou, P.; Vadivelan, A.; Kovvuri, M.; Garg, N.; Thangavelu, M.; Wang, Y.; Raj, S. title: Association between multiple respiratory viral infections and pediatric intensive care unit admission among infants with bronchiolitis date: 2019-11-25 journal: Arch Pediatr DOI: 10.1016/j.arcped.2019.11.006 sha: doc_id: 289735 cord_uid: iw3uq2z9 BACKGROUND: It is unclear whether multiple respiratory viral infections are associated with more severe bronchiolitis requiring pediatric intensive care unit (PICU) admission. We aimed to identify the association between multiple respiratory viral infections and PICU admission among infants with bronchiolitis. keywords: admission; bronchiolitis; infants; infections; patients; picu cache: cord-289735-iw3uq2z9.txt plain text: cord-289735-iw3uq2z9.txt item: #477 of 973 id: cord-289744-suiqh3gv author: Lafolie, Jérémy title: Assessment of blood enterovirus PCR testing in paediatric populations with fever without source, sepsis-like disease, or suspected meningitis: a prospective, multicentre, observational cohort study date: 2018-10-30 words: 4728 flesch: 42 summary: 27, 28 Accordingly, the concentrations of circulating mono nuclear cells at different ages and the ability of entero virus genotypes to replicate in these cells can affect the sensitivity of blood enterovirus detection. This finding substantiates those of previous single-centre studies [7] [8] [9] and lends support to use of blood enterovirus testing as a diagnostic adjunct to rapidly identify newborn babies and infants admitted with fever without source, sepsislike disease, or suspected meningitis whose antibiotic treatment can be discontinued and who are eligible for discharge. keywords: blood; csf; enterovirus; infants; meningitis; patients; pcr; samples; sepsis; study cache: cord-289744-suiqh3gv.txt plain text: cord-289744-suiqh3gv.txt item: #478 of 973 id: cord-289745-qtorq2qq author: Esper, Frank title: Evidence of a Novel Human Coronavirus That Is Associated with Respiratory Tract Disease in Infants and Young Children date: 2005-02-15 words: 3634 flesch: 50 summary: Both our study and those in The Netherlands screened respiratory specimens submitted to a diagnostic virology laboratory and used a PCR-based approach for screening. The etiological agents responsible for a substantial proportion of respiratory tract diseases have not been identified. keywords: children; disease; hcov; infection; novel; primers; specimens cache: cord-289745-qtorq2qq.txt plain text: cord-289745-qtorq2qq.txt item: #479 of 973 id: cord-290456-cgrn5c36 author: Soliman, Mohamed A. R. title: Endoscopic endonasal skull base surgery during the COVID-19 pandemic: A developing country perspective date: 2020-09-25 words: 4110 flesch: 42 summary: Now in the midst of the pandemic, health-care facilities in developing countries are overwhelmed by COVID-19 patients. [38] In positive COVID-19 patients, all health-care personnel that dealt with the patient should be quarantined for 14 days. keywords: care; chest; countries; covid-19; health; pandemic; patients; pcr; surgery cache: cord-290456-cgrn5c36.txt plain text: cord-290456-cgrn5c36.txt item: #480 of 973 id: cord-290513-ygqin14x author: Stevens, Barry J. title: Reporting radiographers’ interpretation and use of the British Society of Thoracic Imaging’s coding system when reporting COVID-19 chest x-rays date: 2020-06-18 words: 2445 flesch: 46 summary: This study was a retrospective review of ED chest x-ray reports authored by three Reporting Radiographers in a National Health Service (NHS) district general hospital in the West Midlands region of the UK. The findings from this retrospective review indicate that Reporting Radiographers can adequately utilise and apply the BSTI classification system when reporting COVID-19 CXRs. keywords: cases; covid-19; pcr; reporting cache: cord-290513-ygqin14x.txt plain text: cord-290513-ygqin14x.txt item: #481 of 973 id: cord-290540-r0d6oaez author: Rottier, Peter J.M. title: The molecular dynamics of feline coronaviruses date: 1999-09-01 words: 3821 flesch: 53 summary: They compared sequences of FIPV viruses from different geographic areas with those of FECV viruses from these same areas and concluded that the viruses isolated from FIP cases are most similar to the coronaviruses from the area where this particular case of FIP occurred. On the other hand we have the virulent strains which cause feline infectious peritonitis (FIP), and we then talk about FIP viruses (FIPV). keywords: coronaviruses; feline; fipv; infection; pcr; protein; type; viruses cache: cord-290540-r0d6oaez.txt plain text: cord-290540-r0d6oaez.txt item: #482 of 973 id: cord-290867-akurajpf author: Legrand, Loïc title: Epidemiological and phylogenic study of human metapneumovirus infections during three consecutive outbreaks in Normandy, France date: 2011-01-24 words: 4072 flesch: 47 summary: Genetic variability of human metapneumovirus infection: Evidence of a shift in viral genotype without a change in illness Prospective evaluation of rapid antigen tests for diagnosis of respiratory syncytial virus and human metapneumovirus infections Human metapneumovirus infection in the Canadian population Sequence analysis of the N, P, M and F genes of Canadian human metapneumovirus strains Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses Virological features and clinical manifestations associated with human metapneumovirus: A new paramyxovirus responsible for acute respiratory-tract infections in all age groups Global genetic diversity of human metapneumovirus fusion gene Human metapneumovirus infections in hospitalized children Detection of human metapneumovirus RNA sequences in nasopharyngeal aspirates of young French children with acute bronchiolitis by real-time reverse transcriptase PCR and phylogenetic analysis Human metapneumovirusassociated respiratory tract infections in the Republic of Ireland during the influenza season of Epidemiological survey of human metapneumovirus infection in a large pediatric tertiary care center Human metapneumovirus and respiratory syncytial virus Evolutionary dynamics of human and avian metapneumoviruses Detection of influenza A and B in respiratory secretions with the polymerase chain reaction Seroprevalence of human metapneumovirus in Japan Detection of human metapneumovirus antigens in nasopharyngeal secretions by an immunofluorescent-antibody test A 1-year experience with human metapneumovirus in children aged <5 years Human metapneumovirus infections in young and elderly adults Detection of human metapneumovirus in two Tunisian children Human metapneumovirus infection in young children hospitalized with respiratory tract disease Presence of the new human metapneumovirus in French children with bronchiolitis Replication of respiratory viruses, particularly influenza virus, rhinovirus, and coronavirus in HuH7 hepatocarcinoma cell line Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Simultaneous detection and typing of human metapneumovirus strains in nasopharyngeal secretions and cell cultures by monoclonal antibodies Changing circulation rate of human metapneumovirus strains and types among hospitalized paediatric patients during three consecutive winter-spring seasons Multi-year study of human metapneumovirus infection at a large US Midwestern Medical Referral Center Detection and characterisation of human metapneumovirus from children with acute respiratory symptoms in north-west England Evaluation of real-time RT-PCR compared with conventional RT-PCR for detecting human metapneumovirus RNA from clinical specimens Detection of human metapneumovirus in clinical samples by immunofluorescence staining of shell vial centrifugation cultures prepared from three different cell lines Human metapneumovirus genetic variability Molecular assays for detection of human metapneumovirus Use of the P gene to genotype human metapneumovirus identifies 4 viral subtypes Genetic diversity of human metapneumovirus over 4 consecutive years in Australia Realtime reverse transcriptase PCR assay for detection of human metapneumoviruses from all known genetic lineages Epidemiological and virological assessment of influenza activity in Europe, during the 2004-2005 winter Human metapneumovirus: A not so new virus Human metapneumovirus infection among children hospitalized with acute respiratory illness Evidence of human metapneumovirus in Australian children Epidemiology and genetic variability of human Metapneumovirus during a 4-year-long study in southeastern Brazil Heterogeneous influenza activity across Europe during the winter of Children with respiratory disease associated with metapneumovirus in Hong Kong Respiratory tract reinfections by the new human Metapneumovirus in an immunocompromised child Characterization of human metapneumoviruses isolated from patients in North America Human metapneumovirus genotypes and severity of disease in young children (n¼100) during a 7-year study in Dijon hospital, France Characterization of human metapneumovirus infections in Israel Detection and pathogenicity of human metapneumovirus respiratory infection in pediatric Italian patients during a winter-spring season Human metapneumovirus as a cause of community-acquired respiratory illness Direct diagnosis of human respiratory coronaviruses 229E and OC43 by the polymerase chain reaction Human metapneumovirus and lower respiratory tract disease in otherwise healthy infants and children Human infections occur mainly during the winter period and affect, in particular, young children, elderly people, and immunocompromised patients Bastien et al., 2003a; Falsey et al., 2003] . keywords: children; et al; hmpv; human; metapneumovirus; respiratory; winter cache: cord-290867-akurajpf.txt plain text: cord-290867-akurajpf.txt item: #483 of 973 id: cord-290976-dhwlr2ui author: Lednicky, John A title: Isolation and genetic characterization of human coronavirus NL63 in primary human renal proximal tubular epithelial cells obtained from a commercial supplier, and confirmation of its replication in two different types of human primary kidney cells date: 2013-06-27 words: 7817 flesch: 51 summary: Following 2-3 weeks of propagation without antibiotics, the plasmocin-treated cell lines and RPTEC cells were tested by PCR for the presence of mycoplasma DNA using a Takara PCR Mycoplasma Detection kit (Fisher Scientific, Pittsburgh, PA) The Art of animal cell culture for virus isolation Methods for detection and frequency of contamination of fetal calf serum with bovine viral diarrhea virus and antibodies against bovine viral diarrhea virus Bovine viral diarrhea disease associated with a contaminated vaccine Demonstration and genotyping of pestivirus RNA from mammalian cell lines Bovine viral diarrhea virus contamination of nutrient serum, cell cultures and viral vaccines Identification of pestiviruses contaminating cell lines and fetal calf sera Bovine polyomavirus, a frequent contaminant of calf serum Bovine polyomavirus, a frequent contaminant of calf sera A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species Identification of novel porcine and bovine parvoviruses closely related to human parvovirus 4 The association of calf serum with the contamination of BHK21 clone 13 suspension cells by a parvovirus serologically related to the minute virus of mice (MVM) Replication of bovine herpesvirus type 4 in human cells in vitro Bovine herpesvirus type 4: a special herpesvirus (review article) keywords: bovine; cells; cmv; coronavirus; cpe; figure; hcov; human; kidney; lines; llc; mk2; nl63; pcr; rptec; virus; viruses cache: cord-290976-dhwlr2ui.txt plain text: cord-290976-dhwlr2ui.txt item: #484 of 973 id: cord-291026-99cit4ig author: Lung, O. title: Insulated Isothermal Reverse Transcriptase PCR (iiRT‐PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus date: 2015-01-27 words: 4574 flesch: 44 summary: In this study, we describe validation of a new probe‐based insulated isothermal reverse transcriptase PCR (iiRT‐PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user‐friendly device (POCKIT (™) Nucleic Acid Analyzer) that does not need data interpretation by the user. Classical swine fever virus (CSFV) is a member of the genus Pestivirus of the family Flaviviridae (Wengler 1991) . keywords: assay; csfv; detection; iirt; pcr; samples; swine; time; virus cache: cord-291026-99cit4ig.txt plain text: cord-291026-99cit4ig.txt item: #485 of 973 id: cord-291029-oldket3n author: Sefers, Susan E. title: QIAamp MinElute Virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs() date: 2005-07-21 words: 3537 flesch: 46 summary: GG167 Influenza Study Group A distinctive property of Tth DNA polymerase: enzymatic amplification in the presence of phenol Identification of human immunodeficiency virus sequences by using in vitro enzymatic amplification and oligomer cleavage detection Evaluation of realtime PCR versus PCR with liquid-phase hybridization for detection of enterovirus RNA in cerebrospinal fluid Measurement of human cytomegalovirus loads by quantitative real-time PCR for monitoring clinical intervention in transplant recipients Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Bedside diagnosis of influenzavirus infections in hospitalized children Impact of a diagnostic cerebrospinal fluid enterovirus polymerase chain reaction test on patient management Recovery efficiencies on nucleic acid extraction kits as measured by quantitative LightCycler PCR Diagnosis of enteroviral meningitis by using PCR with a colorimetric microwell detection assay Monoclonal antibodies versus reverse transcription-PCR for detection of respiratory viruses in a patient population with respiratory tract infections admitted to hospital Acyclovir versus vidarabine in herpes simplex encephalitis. Cost per test was calculated for each extraction kit, which included test kit and additional materials and reagents used for nucleic acid extraction. keywords: dna; extraction; minelute; pcr; rna; rnazol cache: cord-291029-oldket3n.txt plain text: cord-291029-oldket3n.txt item: #486 of 973 id: cord-291281-ygrh8ces author: Durner, J. title: Critical Questions when Interpreting Coronavirus PCR Diagnostics date: 2020-06-14 words: 1914 flesch: 52 summary: At this time, it cannot be clarified for SARS-CoV-2 whether or not there is a risk that can be eliminated of infection for contact persons despite PCR detection of the virus. This indicates that a healing of COVID-19 cannot be proven by PCR examination. keywords: medrxiv; pcr; preprint; sars; sensitivity cache: cord-291281-ygrh8ces.txt plain text: cord-291281-ygrh8ces.txt item: #487 of 973 id: cord-291360-z19ri377 author: Lan, Fan-Yun title: COVID-19 symptoms predictive of healthcare workers’ SARS-CoV-2 PCR results date: 2020-06-26 words: 4357 flesch: 45 summary: Positive assay results represented detection of SARS--CoV2 RNA, while for negative results, the virus was not detected. Table 3 shows the counts and percentages of HCWs with positive and negative assays, and age-and sex-adjusted odds ratios for increasing numbers of total reported symptoms. keywords: assays; cov-2; covid-19; hcws; pcr; sars; symptoms cache: cord-291360-z19ri377.txt plain text: cord-291360-z19ri377.txt item: #488 of 973 id: cord-291486-5h96msv1 author: Kistler, Amy title: Pan-Viral Screening of Respiratory Tract Infections in Adults With and Without Asthma Reveals Unexpected Human Coronavirus and Human Rhinovirus Diversity date: 2007-09-15 words: 4484 flesch: 39 summary: All viral-positive calls were confirmed by recovery of viral sequence. Between 50% and 80% of asthma exacerbations are associated with viral respiratory tract infections (RTIs), yet the influence of viral pathogen diversity on asthma outcomes is poorly understood because of the limited scope and throughput of conventional viral detection methods. keywords: analysis; asthma; detection; hcov; hrv; isolates; pcr; sequence; study; virochip; viruses cache: cord-291486-5h96msv1.txt plain text: cord-291486-5h96msv1.txt item: #489 of 973 id: cord-291729-4l4v9jxd author: de Salazar, Adolfo title: Sample pooling for SARS-COV-2 RT-PCR screening date: 2020-09-10 words: 2642 flesch: 42 summary: SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Viral load of SARS-CoV-2 in clinical samples The Detection of Defective Members of Large Populations Improved matrix pooling A methodology for deriving the sensitivity of pooled testing, based on viral load progression and pooling dilution Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR COVID-19 diagnosis and management: a comprehensive review Screening tests: Can we get more by doing less Pooling Strategies to Reduce the Cost of HIV-1 RNA Load Monitoring in a Resource-Limited Setting Pooled Nucleic Acid Testing to Detect Antiretroviral Treatment Failure in Mexico Occult HBV infection in HIV-infected adults and evaluation of pooled NAT for HBV Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources Pooled-sample analysis strategies for COVID-19 mass testing: a simulation study Sample Pooling as a Strategy to Detect Community Transmission of SARS-CoV-2 Evaluation of COVID-19 RT-qPCR test in multi-sample pools Pooling of nasopharyngeal swab specimens for SARS-CoV-2 detection by RT-PCR Evaluating the efficiency of specimen pooling for PCR-based detection of COVID-19 Pooling of samples for testing for SARS-CoV-2 in asymptomatic people False Negative Tests for SARS-CoV-2 Infection -Challenges and Implications Predicting infectious SARS-CoV-2 from diagnostic samples Optimization of group size in pool testing strategy for SARS-CoV-2: A simple mathematical model Simulation of Pool Testing to Identify Patients With Coronavirus Disease 2019 key: cord-291729-4l4v9jxd authors: de Salazar, Adolfo; Aguilera, Antonio; Trastoy, Rocio; Fuentes, Ana; Alados, Juan Carlos; Causse, Manuel; Galán, Juan Carlos; Moreno, Antonio; Trigo, Matilde; Pérez-Ruiz, Mercedes; Roldán, Carolina; José Pena, Ma; Bernal, Samuel; Serrano-Conde, Esther; Barbeito, Gema; Torres, Eva; Riazzo, Cristina; Cortes-Cuevas, Jose Luis; Chueca, Natalia; Coira, Amparo; Sanchez-Calvo, Juan M.; Marfil, Eduardo; Becerra, Federico; Gude, María José; Pallarés, Ángeles; Pérez Del Molino, María Luisa; García, Federico title: Sample pooling for SARS-COV-2 RT-PCR screening date: 2020-09-10 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.008 sha: doc_id: 291729 cord_uid: 4l4v9jxd OBJECTIVE: To evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of COVID-19, by using different commercial platforms for nucleic acid extraction and amplification. keywords: pooling; pools; samples; sars; strategy; testing cache: cord-291729-4l4v9jxd.txt plain text: cord-291729-4l4v9jxd.txt item: #490 of 973 id: cord-291749-revhbd0q author: Mongan, Arthur Elia title: Portable sequencer in the fight against infectious disease date: 2019-10-03 words: 3742 flesch: 38 summary: Sequencing technique has been around since 1975 by the works of Frederick Sanger, Allan Maxam, and Walter Gilbert Although the running cost of other sequencing platform is cheaper than MinION (for example, $67.82 for MiSeq compared with $71.56 for MinION per sample [28] ), MinION has significantly lower cost to set up. keywords: amplification; disease; dna; genome; minion; nanopore; pcr; resistance; rna; sequencing; virus cache: cord-291749-revhbd0q.txt plain text: cord-291749-revhbd0q.txt item: #491 of 973 id: cord-291860-dw1sfzqx author: van Boheemen, Sander title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date: 2019-12-16 words: 5406 flesch: 35 summary: Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study Global and regional burden of hospital admissions for severe acute lower respiratory infections in young children in 2010: a systematic analysis Deaths due to respiratory tract infections in Africa: a review of autopsy studies CDC EPIC Study Team: Community-acquired pneumonia requiring hospitalization among U.S. adults The common cold Aetiology of lower respiratory tract infection in adults in primary care: a prospective study in 11 European countries Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Exploring the potential of next-generation sequencing in detection of respiratory viruses A primer on metagenomics Beer M: Novel orthobunyavirus in cattle Neurobrucellosis: unexpected answer from metagenomic nextgeneration sequencing Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans Protocol for metagenomic virus detection in clinical specimens Application of next generation sequencing for the detection of human viral pathogens in clinical specimens Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique Sequence analysis of the human virome in febrile and afebrile children Diagnosis of human metapneumovirus and rhinovirus in patients with respiratory tract infections by an internally controlled multiplex real-time RNA PCR Validation of clinical application of cytomegalovirus plasma DNA load measurement and definition of treatment criteria by analysis of correlation to antigen detection Zincmediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq Cutadept removes adapter sequences from high-throughput sequencing reads Centrifuge: rapid and sensitive classification of metagenomic sequences Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation Interactive metagenomic visualization in a Web browser Genome Detective: an automated system for virus identification from high-throughput sequencing data. The amount of internal control reads and target virus reads has been reported to be dependent on the amount of background reads (negative correlation). keywords: database; detection; dna; mngs; pathogens; pcr; protocol; reads; rna; samples; sensitivity; sequencing; viruses cache: cord-291860-dw1sfzqx.txt plain text: cord-291860-dw1sfzqx.txt item: #492 of 973 id: cord-291916-5yqc3zcx author: Hozhabri, Hossein title: The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date: 2020-08-05 words: 16799 flesch: 39 summary: This form of adaptation required a series of amino acid changes in the RBD within the S protein of SARS viruses that circulated in bats [56, 68] . Strategies for controlling emerging coronaviruses A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice Cross-species transmission of the newly identified coronavirus 2019-nCoV Towards a solution to MERS: keywords: ace2; acute; cases; cell; china; coronavirus; cov-2; covid-19; days; diagnosis; disease; figure; genome; host; human; infection; mers; novel; patients; pneumonia; protein; receptor; rna; sars; study; symptoms; syndrome; transmission; vaccine cache: cord-291916-5yqc3zcx.txt plain text: cord-291916-5yqc3zcx.txt item: #493 of 973 id: cord-291954-wormplcu author: Sakulkonkij, Parichart title: A family cluster of diagnosed coronavirus disease 2019 (COVID‐19) kidney transplant recipient in Thailand date: 2020-08-08 words: 4433 flesch: 41 summary: The majority of COVID-19 patients in the general population have leukopenia with lymphocytopenia (70%) as similar to transplant recipients. A familial cluster, including a kidney transplant recipient Aerosol and surface stability of SARS-CoV-2 as compared with SARS-CoV Postdischarge surveillance and positive virus detection in two medical staff recovered from coronavirus disease 2019 (COVID-19), China Epidemiologic features and clinical course of patients infected with SARS-CoV-2 in Singapore Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study Factors associated with prolonged viral shedding in patients with avian influenza A(H7N9) virus infection Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia Improved molecular diagnosis of COVID-19 by the novel, highly sensitive and specific COVID-19-RdRp/Hel real-time reverse transcription-PCR assay validated in vitro and with clinical specimens Laboratory diagnosis of COVID-19: current issues and challenges Detection of SARS-CoV-2 in different types of clinical specimens Early clinical and CT manifestations of coronavirus disease 2019 (COVID-19) pneumonia Relation between chest CT findings and clinical conditions of coronavirus disease (COVID-19) pneumonia: a multicenter study Frequency and distribution of chest radiographic findings in COVID-19 positive patients Radiological Society of North America Expert Consensus Statement on Reporting Chest CT Findings Related to COVID-19. keywords: case; coronavirus; covid-19; disease; patients; pneumonia; recipients; sars; transplant cache: cord-291954-wormplcu.txt plain text: cord-291954-wormplcu.txt item: #494 of 973 id: cord-291958-g4jlg9pw author: Silva, Camila S title: Human Respiratory Coronaviruses Detected In Patients with Influenza-Like Illness in Arkansas, USA date: 2014-03-26 words: 4264 flesch: 53 summary: Antivir Ther A novel coronavirus associated with severe acute respiratory syndrome Identification of a novel coronavirus in patients with severe acute respiratory syndrome Cultivation of viruses from a high proportion of patients with colds Identification of a new human coronavirus Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Identification of a novel coronavirus from a beluga whale by using a panviral microarray Feline aminopeptidase N serves as a receptor for feline, canine, porcine, and human coronaviruses in serogroup I Coronavirus genome structure and replication Broadly targeted multiprobe QPCR for detection of coronaviruses: Coronavirus is common among mallard ducks (Anas platyrhynchos) Coronavirus diversity, phylogeny and interspecies jumping Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the Coronavirus Study Group SYBR Green real-time reverse transcription-polymerase chain reaction assay for the generic detection of coronaviruses A one step quantitative RT-PCR for detection of SARS coronavirus with an internal control for PCR inhibitors A pancoronavirus RT-PCR assay for detection of all known coronaviruses Detection of four human coronaviruses in respiratory infections in children: a one-year study in Colorado Human coronavirus NL-63 infections in children: a 1-year study Persistence and transmission of natural type I feline coronavirus infection CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method Development of a real-time TaqMan RT-PCR assay for the detection of infectious bronchitis virus in chickens, and comparison of RT-PCR and virus isolation Understanding Human Coronavirus HCoV-NL63 Human coronavirus NL63: a clinically important virus? Clinical disease in children associated with newly described coronavirus subtypes Human coronavirus in young children hospitalized for acute respiratory illness and asymptomatic controls The neighbor-joining method: a new method for reconstructing phylogenetic trees Confidence Limits on Phylogenies: An Approach Using the Bootstrap Prospects for inferring very large phylogenies by using the neighborjoining method Samples and age distribution of coronavirus in influenza negative human respiratory samples during the 2009-2010 influenza season in Arkansas Author manuscript; available in PMC Strain distribution of respiratory coronavirus in Arkansas by age group and number of cases. keywords: coronavirus; cov; hcov; human; oc43; pcr; positive; samples; strains cache: cord-291958-g4jlg9pw.txt plain text: cord-291958-g4jlg9pw.txt item: #495 of 973 id: cord-291961-usl8z6ep author: Zheng, Wen-zhi title: Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China date: 2015-10-13 words: 2937 flesch: 50 summary: The full-length HPyV6 sequence was aligned with the sequences of other HPyVs and other HPyV6 strains available in GenBank with DNAStar software. All 15 HPyV6-positive patients were coinfected with other respiratory viruses, of which influenza virus A (IFVA) (8/15, 53.3 %) and respiratory syncytial virus (7/15, 46.7 %) were most common. keywords: children; genome; hpyv6; patients; pcr; polyomavirus; time cache: cord-291961-usl8z6ep.txt plain text: cord-291961-usl8z6ep.txt item: #496 of 973 id: cord-292031-weiwksh6 author: Ramírez-Castillo, Flor Yazmín title: Waterborne Pathogens: Detection Methods and Challenges date: 2015-05-21 words: 7362 flesch: 27 summary: Even though culture dependent methods are extensively used for pathogens detection in water, these methods are limited by their low sensitivity and the excessive time needed to obtain reliable results. The Microbiology of the Water Distribution System A Report on an American Academy of Microbiology Colloquium Recommended advanced techniques for waterborne pathogen detection in developing countries Dei-Cas, E. Microbial agents associated with waterborne diseases Global Water, Sanitation, and Hygiene (WASH) Progress on Sanitation and Drinking-Water Contamination of water resources by pathogenic bacteria Millennium Development Goals: Progress towards the Health-Related Millennium Development Goals Waterborne outbreaks reported in the United States Causes of outbreaks associated with drinking water in the United States from A fatal waterborne disease epidemic in Walkerton, Ontario: Comparison with other waterborne outbreaks in the developed world Surveillance for waterborne disease outbreaks associated with drinking water and other nonrecreational water-United States Epidemiology of cholera in the Philippines The 2010 cholera outbreak in Haiti: How science solved a controversy Lessons learned during public health response to cholera epidemic in Haiti and the Dominican Republic Shiga toxin-producing Escherichia coli O104:H4: A new challenge for microbiology Annual Epidemiological Report Food-and Waterborne Diseases and Zoonoses Self-reported diarrhea in a control group: A strong association with reporting of low-pressure events in tap water Global Drinking Water Management and Conservation Optimal Decision-Making Surveillance for waterborne-disease outbreaks associated with drinking water--United States Emerging waterborne pathogens: Can we kill them all? Where do emerging pathogens come from? keywords: analysis; assessment; cells; coli; detection; dna; drinking; health; methods; microarray; microbial; pathogens; pcr; risk; sample; time; water; waterborne cache: cord-292031-weiwksh6.txt plain text: cord-292031-weiwksh6.txt item: #497 of 973 id: cord-292172-aqsc9fbl author: Al Amin, Md. title: Screening of commercial meat products from supermarket chains for feline derivatives using SP-PCR-RLFP and lab-on-a-chip date: 2020-06-09 words: 4861 flesch: 50 summary: Lower priced meat are deliberately mixed in commercial meat products (Amin et al., 2016) and the food forgeries were reported in a number of meat products such as frankfurters, dried meats, burgers, ground meat, nuggets, meatballs and sausage (Kane and Hellberg, 2016) . key: cord-292172-aqsc9fbl authors: Al Amin, Md.; Mahfujur Rahman, Md.; Razimi, Mohd Shahril Ahmad; Chowdhury, Zaira Zaman; Hussain, Muhammad Nasri Md.; Desa, Mohd Nasir Mohd title: Screening of commercial meat products from supermarket chains for feline derivatives using SP-PCR-RLFP and lab-on-a-chip date: 2020-06-09 journal: J Food Compost Anal DOI: 10.1016/j.jfca.2020.103565 sha: doc_id: 292172 cord_uid: aqsc9fbl Determination of feline meat in food products is an important issue for social, health, economic and religious concern. keywords: dna; feline; frankfurters; meat; nuggets; pcr; products; species cache: cord-292172-aqsc9fbl.txt plain text: cord-292172-aqsc9fbl.txt item: #498 of 973 id: cord-292281-fui9all6 author: Pratelli, A. title: High‐cell‐passage canine coronavirus vaccine providing sterilising immunity date: 2007-09-14 words: 3537 flesch: 48 summary: key: cord-292281-fui9all6 authors: Pratelli, A. title: High‐cell‐passage canine coronavirus vaccine providing sterilising immunity date: 2007-09-14 journal: J Small Anim Pract DOI: 10.1111/j.1748-5827.2007.00416.x sha: doc_id: 292281 cord_uid: fui9all6 Objectives: To evaluate the ability of a high‐cell‐passage canine coronavirus vaccine to immunise dogs against challenge with a field isolate of the virus. Both vaccinated and control dogs were challenged two weeks after the second vaccination with a field canine coronavirus strain. keywords: canine; ccov; coronavirus; days; dogs; pcr; pratelli; vaccine; virus cache: cord-292281-fui9all6.txt plain text: cord-292281-fui9all6.txt item: #499 of 973 id: cord-292312-cwrqorn1 author: Sales, M. J. T. title: Fernando de Noronha: how an island controlled the community transmission of COVID-19 in Brazil date: 2020-10-27 words: 4333 flesch: 52 summary: This is especially critical in Brazil, until recently, the country with the second largest number of COVID-19 cases in the world 2 . The findings were compared to national estimates and with experience on other islands of similar size. keywords: brazil; cases; covid-19; fna; health; island; measures; pcr; preprint; study cache: cord-292312-cwrqorn1.txt plain text: cord-292312-cwrqorn1.txt item: #500 of 973 id: cord-292347-d7xq7x5g author: Carter, Linda J. title: Assay Techniques and Test Development for COVID-19 Diagnosis date: 2020-04-30 words: 3437 flesch: 38 summary: This type of testing requires cell culture facilities, 470 and in the case of SARS coronavirus, Biosafety Level 3 (BSL3) 471 laboratories. These tests have a huge potential for the epide-397 miology of COVID-19, 32,42−45 but test results can be impacted by 398 at least three situations: (1) a subset of subjects with a positive 399 result from molecular genetic assays for SARS-CoV-2 infection 400 are seronegative due to the lag in antibody production following 401 infection, (2) the subjects may be seropositive yet negative for 402 molecular genetic assay results reflecting clearance of an earlier, 403 milder infection, and (3) limitation in sensitivity and specificity of 404 the assays. keywords: antibodies; assays; coronavirus; cov-2; covid-19; detection; infection; rna; sars; test; testing cache: cord-292347-d7xq7x5g.txt plain text: cord-292347-d7xq7x5g.txt item: #501 of 973 id: cord-292364-jhiimglg author: Hayakawa, Jun title: Genetic and Antigenic Characterization and Retrospective Surveillance of Bovine Influenza D Viruses Identified in Hokkaido, Japan from 2018 to 2020 date: 2020-08-11 words: 4380 flesch: 42 summary: The biology of influenza viruses The glycoprotein of influenza C virus is the haemagglutinin, esterase and fusion factor Structure and function of the hef glycoprotein of influenza c virus Hemagglutinin-esterase-fusion (HEF) protein of influenza C virus Novel influenza D virus: Epidemiology, pathology, evolution and biological characteristics An Open Receptor-Binding Cavity of Hemagglutinin-Esterase-Fusion Glycoprotein from Newly-Identified Influenza D Virus: Basis for Its Broad Cell Tropism Isolation of a Novel Swine Influenza Virus from Oklahoma in 2011 Which Is Distantly Related to Human Influenza C Viruses Characterization of a novel influenza virus in cattle and swine: Proposal for a new genus in the Orthomyxoviridae family Cocirculation of Two Distinct Genetic and Antigenic Lineages of Proposed Influenza D Virus in Cattle Pathogenesis of Influenza D Virus in Cattle An inactivated influenza D virus vaccine partially protects cattle from respiratory disease caused by homologous challenge A Metagenomics and Case-Control Study To Identify Viruses Associated with Bovine Respiratory Disease Metagenomic characterization of the virome associated with bovine respiratory disease in feedlot cattle identified novel viruses and suggests an etiologic role for influenza D virus Serological evidence for the presence of influenza D virus in small ruminants Serologic evidence for influenza c and d virus among ruminants and Camelids Serological evidence for the co-circulation of two lineages of influenza D viruses in equine populations of the Midwest United States Serologic evidence of exposure to influenza D virus among persons with occupational contact with cattle Influenza D virus: Serological evidence in the Italian population from Identification of a potential novel type of influenza virus in Bovine in China Influenza d virus in cattle Influenza D virus infection in Mississippi beef cattle Detection of influenza D virus among swine and cattle Nationwide distribution of bovine influenza D virus infection in Japan Influenza d virus infection in herd of cattle Influenza D Virus in Cattle Influenza D virus circulation in cattle and swine Molecular epidemiological survey and phylogenetic analysis of bovine influenza D virus in Japan Pestiviruses isolated from pigs, cattle and sheep can be allocated into at least three genogroups using polymerase chain reaction and restriction endonuclease analysis Development of nested PCR assays for detection of bovine respiratory syncytial virus in clinical samples Experimental inoculation of adult dairy cows with bovine coronavirus and detection of coronavirus in feces by RT-PCR Development of a one-run real-time PCR detection system for pathogens associated with bovine respiratory disease complex Design of a multiplex quantitative reverse transcription-PCR system to simultaneously detect 16 pathogens associated with bovine respiratory and enteric diseases Detection and Antibiotic Susceptibility of Mycoplasma bovis and Other Respiratory Disease Pathogens from Pneumonic Lung Samples in a Calf Rearing Unit Prevalence of Mycoplasma bovis in Respiratory Tract of Cattle Slaughtered in Balochistan A simple method of estimating fifty per cent endpoints Molecular Evolutionary Genetics Analysis Across Computing Platforms Recommendations for the classification of group a rotaviruses using all 11 genomic RNA segments Full Genome-Based Classification of Rotaviruses Reveals a Common Origin between Human Wa-Like and Porcine Rotavirus Strains and Human DS-1-Like and Bovine Rotavirus Strains Genomic diversity and evolution of rotaviruses: An overview This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license We thank H. Takahashi, K. Uegaki, and K. Kobayashi for sample collection and technical assistance. Supplementary Materials: The following are available online at http://www.mdpi.com/1999-4915/12/8/877/s1, Figure S1 : Image of BIDV virus, which isolated from HRT-18G cell culture, by transmission electron microscopy observation. keywords: bidvs; bovine; brd; cattle; hokkaido; influenza; pcr; samples; virus; viruses cache: cord-292364-jhiimglg.txt plain text: cord-292364-jhiimglg.txt item: #502 of 973 id: cord-292575-vsswxwdi author: Hammou, Rahma Ait title: Chapter 7 Scientific Advances in the Diagnosis of Emerging and Reemerging Viral Human Pathogens date: 2020-12-31 words: 8502 flesch: 30 summary: These features make miRNAs, in single or in a combination (Peng et al., 2016) , ideally suited as biomarkers for disease diagnosis. The normal state is determined by the collected data and by creating baselines for a given area or community (Wang et al., 2005; Berger et al., 2006) . keywords: detection; diagnosis; disease; et al; human; identification; infection; influenza; laboratory; methods; mirnas; molecular; nucleic; pathogens; pcr; studies; systems; time; virus cache: cord-292575-vsswxwdi.txt plain text: cord-292575-vsswxwdi.txt item: #503 of 973 id: cord-292742-mio4przi author: McAloose, Denise title: From People to Panthera: Natural SARS-CoV-2 Infection in Tigers and Lions at the Bronx Zoo date: 2020-10-13 words: 6384 flesch: 38 summary: Among these, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and ebolaviruses have killed thousands; the human immunodeficiency virus (HIV) has killed millions. The current SARS-CoV-2 pandemic and outbreaks of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) before it raise awareness and concerns about zoonotic (animal-tohuman) diseases and cross-species transmission of coronaviruses (8) (9) (10) (11) . keywords: animals; cov-2; data; genome; human; infection; keepers; lions; pcr; positive; samples; sars; sequences; sequencing; tiger; transmission; virus cache: cord-292742-mio4przi.txt plain text: cord-292742-mio4przi.txt item: #504 of 973 id: cord-292772-xdic7rcy author: Petini, Matteo title: Nested–polymerase chain reaction detection of Pneumocystis carinii f. sp. canis in a suspected immunocompromised Cavalier King Charles spaniel with multiple infections date: 2019-04-26 words: 2471 flesch: 39 summary: 21 Pneumocystosis in dogs: metaanalysis of 43 published cases including clinical signs, diagnostic procedures, and treatment Pneumocystis carinii pneumonia in dogs-a diagnostic challenge Occurrence of Pneumocystis carinii in canine distemper Pneumocystis carinii pneumonia in two Cavalier King Charles Spaniels Common variable immunodeficiency in miniature dachshunds affected with Pneumonocystis carinii pneumonia Pneumocystis pneumonia in two Cavalier King Charles Spaniel littermates Common variable immune deficiency in a Pomeranian with Pneumocystis carinii pneumonia Pneumocystis carinii infection with severe pneumomediastinum and lymph node involvement in a Whippet mixedbreed dog Molecular diagnosis of pneumocystis pneumonia in dogs Improved detection of Pneumocystis jirovecii in upper and lower respiratory tract specimens from children with suspected pneumocystis pneumonia using real-time PCR: a prospective study Pneumocystis PCR: it is time to make PCR the test of choice ECIL guidelines for the diagnosis of Pneumocystis jirovecii pneumonia in patients with haematological malignancies and stem cell transplant recipients The unroot phylogenetic tree constructed using mtSSU rRNA sequences showed that Pneumocystis carinii f. sp. canis was distinct from Pneumocystis spp. keywords: carinii; dog; pcr; pneumocystis; pneumonia; reference; spp cache: cord-292772-xdic7rcy.txt plain text: cord-292772-xdic7rcy.txt item: #505 of 973 id: cord-292828-29jbf9ik author: Alsaleh, Asma N title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control date: 2014-01-09 words: 3920 flesch: 39 summary: Such studies do however have some logistical challenges, particularly concerning respiratory sample collection and transport. The EHV1 component was performed as an extraction and inhibitor control as described previously [24] , while ERV3 was used as a marker to evaluate the quality of nasal swab sample collection [25] . keywords: detection; erv3; human; mould; nasal; samples; study; swab; time; virus cache: cord-292828-29jbf9ik.txt plain text: cord-292828-29jbf9ik.txt item: #506 of 973 id: cord-292831-oihcay6w author: Choudhary, Manohar L. title: Development of a multiplex one step RT-PCR that detects eighteen respiratory viruses in clinical specimens and comparison with real time RT-PCR date: 2013-01-08 words: 3726 flesch: 44 summary: CDC protocol of real-time RTPCR for influenza A (H1N1) Comparative analysis of the multiple test methods for the detection of pandemic influenza A/H1N1 2009 virus Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene Simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested-PCR assays Nucleic acid amplification tests for detection of respiratory viruses Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Real time RT PCR detection of 12 respiratory viral infections in four triplex reactions Development and evaluation of a four-tube real time multiplex PCR assay covering fourteen respiratory viruses, and comparison to its corresponding single target counterparts Rapid detection and identification of 12 respiratory viruses using a dual priming oligonucleotide system-based multiplex PCR assay High-throughput, sensitive, and accurate multiplex PCR-microsphere flow cytometry system for large-scale comprehensive detection of respiratory viruses Comparison of a multiplex reverse transcription-PCR-enzyme hybridization assay with conventional viral culture and immunofluorescence techniques for the detection of seven viral respiratory pathogens Real-time reverse transcriptase PCR assay for detection of human metapneumoviruses from all known genetic lineages Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay Rapid detection of respiratory viruses by centrifugation enhanced cultures from children with acute lower respiratory tract infections Comparison of the Luminex xTAG Detection of nine respiratory RNA viruses using three multiplex RT PCR assays incorporating a novel RNA internal control transcript Development of three multiplex RT PCR assays for the detection of 12 respiratory RNA viruses Respiratory viral infections detected by multiplex PCR among pediatric patients with lower respiratory tract infections seen at an urban hospital in Delhi from Detection of influenza virus types A and B and type A subtypes (H1, H3, and H5) by multiplex polymerase chain reaction Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens-duration of symptoms significantly affects detection rate A prospective three-year cohort study of the epidemiology and virology of acute respiratory infections of children in rural India. keywords: detection; influenza; mrt; pcr; respiratory; viruses cache: cord-292831-oihcay6w.txt plain text: cord-292831-oihcay6w.txt item: #507 of 973 id: cord-292928-a4bn30ul author: Ghosh, Bipasha title: Review of bioaerosols in indoor environment with special reference to sampling, analysis and control mechanisms date: 2015-10-03 words: 16772 flesch: 27 summary: Among the six locations, all five sites revealed significantly smaller bioaerosol concentration in winter than in summer except the restroom in hospital lobby which may be due to the maintenance of almost similar indoor air conditions by air conditioning system artificially in both summer and winter (Lee et al., 2012) . A recently developed electrostatic precipitator had no charging unit in the inlet while the physical collection efficiency strongly depended on the precipitation voltage which eventually depended on the charge present on the airborne microbes naturally due to aerosolization (Kunkel, 1950; Flagan, 2001 ) thereby making collection possible by differentiating between the positively and negatively charged microorganisms by adding a signature to the bioaerosol particle sampled (Lee et al., 2004a; ; Lee et al., 2004b) . keywords: air; airborne; analysis; bacterial; bioaerosol; cells; collection; concentration; detection; dna; effects; efficiency; environments; et al; exposure; flow; fungal; fungi; health; identification; indoor; laser; methods; microorganisms; particles; pcr; sampler; sampling; sequencing; size; species; spores; studies; technique; temperature; time cache: cord-292928-a4bn30ul.txt plain text: cord-292928-a4bn30ul.txt item: #508 of 973 id: cord-292958-k5d5fo3i author: Sekhon, Simranjeet Singh title: Porcine epidemic diarrhea (PED) infection, diagnosis and vaccination: A mini review date: 2017-01-04 words: 7442 flesch: 31 summary: This sequence is particularly rich in arginine (Arg), serine (Ser) and asparagine (Asp) residues, and presents in PED virus N protein with no counterpart in the remainder of Coronaviruses. The encoded polypeptides range of PEDV N protein is from 377 to 455 amino acids and has the similar physical properties with the other members of the family Coronaviridae 60 . keywords: cell; coronavirus; detection; diarrhea; diarrhea virus; elisa; epidemic; epidemic diarrhea; infection; pcr; pedv; porcine; porcine epidemic; protein; samples; study; virus cache: cord-292958-k5d5fo3i.txt plain text: cord-292958-k5d5fo3i.txt item: #509 of 973 id: cord-293234-ouykx6g5 author: Puig-Barberà, J. title: Effectiveness of the 2010–2011 seasonal influenza vaccine in preventing confirmed influenza hospitalizations in adults: A case–case comparison, case-control study date: 2012-08-24 words: 4424 flesch: 38 summary: As a consequence of antigenic drift, influenza vaccines are to be a produced every year [3] . Information related to the administration of the 2009-2010 seasonal influenza vaccine, the A(H1N1) pandemic vaccine and previous 23-valent polysaccharide plain pneumococcal vaccinations was obtained from the Vaccine Information System. keywords: age; case; conditions; controls; effectiveness; influenza; pcr; risk; study; vaccine; years cache: cord-293234-ouykx6g5.txt plain text: cord-293234-ouykx6g5.txt item: #510 of 973 id: cord-293421-0ksn0fc7 author: Rodriguez, J. M. title: Detection of animal pathogens by using the polymerasechain reaction (PCR) date: 1997-05-31 words: 9107 flesch: 40 summary: Cohen et al., 1993; Way et al., 1993; Booster PCR methods for the genus-specific detection of salmonellas in equine and chicken faeces have been developed (Cohen et al., 1994a, b) with detection possible within 10-12h from the time of submission of samples. keywords: amplification; animals; bovine; cattle; chain; chain reaction; detection; diagnosis; disease; dna; et al; genes; identification; infected; infection; isolates; methods; pcr; polymerase; polymerase chain; reaction; samples; species; strains; technique; use; viral; virus cache: cord-293421-0ksn0fc7.txt plain text: cord-293421-0ksn0fc7.txt item: #511 of 973 id: cord-293590-0xn6mqh6 author: Peña, Andrea A title: An evaluation of potential reference genes for stability of expression in two salmonid cell lines after infection with either Piscirickettsia salmonis or IPNV date: 2010-04-14 words: 3732 flesch: 42 summary: Intracellular pathogens such as bacteria and viruses modulate key cellular processes which may involve changes in reference gene expression [25, 26] . Following this criteria, only the IPNV infection assay on RTS11 cell cultures might consider the inclusion of a UBQ and EF1A were the best ranked reference gene candidates, as they had the lowest sum p values (0.813 and 1.023, respectively) which represents the standard deviation (SD) of reference gene expression over all infections investigated (Table 2 ). keywords: cell; chse-214; expression; genes; infection; ipnv; pcr; reference; rts11; salmonis; time cache: cord-293590-0xn6mqh6.txt plain text: cord-293590-0xn6mqh6.txt item: #512 of 973 id: cord-293629-1cno01un author: Vila Estapé, Jordi title: Métodos moleculares de diagnóstico de infecciones respiratorias. ¿Ha cambiado el esquema diagnóstico? date: 2016-07-31 words: 5052 flesch: 25 summary: y hasta varias semanas (en el caso de cultivo de virus y hongos). Sin embargo, las técnicas moleculares también presentan una serie de inconvenientes: posibles inhibiciones; variabilidad de los virus que obliga a revisar periódicamente las dianas de cebadores y sondas; falsos positivos por la detección de virus que colonizan la mucosa respiratoria en personas asintomáticas, o virus no viables excretados de forma prolongada después de la resolución de la infección 23, 24 . keywords: amplificación; como; con; del; detección; detection; diagnóstico; entre; estas; han; identificación; infecciones; infección; las; los; moleculares; más; neumonía; pacientes; para; pcr; pneumonia; por; que; respiratorias; son; tiempo; tratamiento; técnicas; una; virus cache: cord-293629-1cno01un.txt plain text: cord-293629-1cno01un.txt item: #513 of 973 id: cord-293849-p3j2keyo author: Renaud, Christian title: Comparison of FilmArray Respiratory Panel and laboratory-developed real-time reverse transcription–polymerase chain reaction assays for respiratory virus detection date: 2012-12-31 words: 3294 flesch: 41 summary: These controls have been used for respiratory virus PCR for a long time in our clinical laboratory; they are well characterized and their expected results are in the low positive range (Ct value of~30). Respiratory virus detection is necessary in the clinical setting and has been used for many years to follow the epidemiology of respiratory tract infections and to elaborate pediatric patient care (Byington et al., 2002; Vega, 2005) . keywords: filmarray; pcr; samples; viruses cache: cord-293849-p3j2keyo.txt plain text: cord-293849-p3j2keyo.txt item: #514 of 973 id: cord-293966-5c466xvz author: Fehr, Anthony R. title: Bacterial Artificial Chromosome-Based Lambda Red Recombination with the I-SceI Homing Endonuclease for Genetic Alteration of MERS-CoV date: 2019-09-14 words: 3813 flesch: 58 summary: CoV BAC plasmids contain a CMV promoter 5 0 of the viral genome, allowing for transcription of the viral genome following transfection of BAC DNA into mammalian cells. We have tested the Xtra Midi Kit side by side with a BAC-prep kit and found little to no difference in CoV BAC DNA yield. keywords: bac; cells; cov; dna; mers; pcr; recombination; scei; sequence; virus cache: cord-293966-5c466xvz.txt plain text: cord-293966-5c466xvz.txt item: #515 of 973 id: cord-294138-h7sfd1wa author: McIver, David J. title: Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents date: 2020-06-01 words: 2787 flesch: 49 summary: The 1.4% prevalence of CoV RNA in rodents was much lower than what had been detected in bats in Laos; however, such observations have been made repeatedly, re-emphasizing the role of bats as a primary CoV source [5, [15] Studies in which CoV RNA was more frequently detected in rodents have used intestine or fecal matter for their studies, while we tested oral and rectal swab samples keywords: animals; bats; coronavirus; cov; covs; laos; rna; rodents; species; wildlife cache: cord-294138-h7sfd1wa.txt plain text: cord-294138-h7sfd1wa.txt item: #516 of 973 id: cord-294155-94skyx5f author: Terrosi, Chiara title: Human bocavirus detection in an atopic child affected by pneumonia associated with wheezing date: 2007-08-07 words: 1361 flesch: 45 summary: A panel of bacteria and respiratory viruses were searched in the nasopharyngeal swab, only human bocavirus was detected by PCR. CONCLUSIONS: Detection of HboV, as the only microbial agent, in samples from children with wheezing and acute respiratory diseases supports the assumption that this emerging virus could have an aetiologic role in the pathogenesis of respiratory diseases. keywords: hbov; human cache: cord-294155-94skyx5f.txt plain text: cord-294155-94skyx5f.txt item: #517 of 973 id: cord-294335-qnu19ru5 author: Yousaf, Anna R title: A prospective cohort study in non-hospitalized household contacts with SARS-CoV-2 infection: symptom profiles and symptom change over time date: 2020-07-28 words: 3232 flesch: 41 summary: For symptoms experienced throughout the illness, the percent of household contacts reporting neurologic symptoms increased to 94% (n=44), predominated by headache (n=41, 87%), followed by upper respiratory symptoms (n=42, 89%). Among the different age groups, the most common symptoms were as follows: upper respiratory symptoms in children <18 years (n=10, 71%), neurologic symptoms in adults 18-49 years (n=14, 70%), and upper respiratory symptoms in adults 50 years or older (n=11, 85%). keywords: contacts; covid-19; day; household; pcr; symptoms; years cache: cord-294335-qnu19ru5.txt plain text: cord-294335-qnu19ru5.txt item: #518 of 973 id: cord-294454-uzfsv2df author: Bellau-Pujol, S. title: Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses date: 2005-02-24 words: 6070 flesch: 40 summary: Retrospective study Evaluation of the Prodesse Hexaplex multiplex PCR assay for direct detection of seven respiratory viruses in clinical specimens Persistence of rhinovirus and enterovirus RNA after acute respiratory illness in children Rapid detection of parainfluenza virus type 3 RNA in respiratory specimens: use of reverse transcription-PCR-enzyme immunoassay Evaluation of the Hexaplex assay for detection of respiratory viruses in children Parainfluenza virus type 4 infections in pediatric patients Comparison of a multiplex reverse transcription-PCR-enzyme hybridization assay with conventional viral culture and immunofluorescence techniques for the detection of seven viral respiratory pathogens Epidemiology of viral and mycoplasmal agents associated with childhood lower respiratory illness in a civilian population Influenza C virus infection in France A simultaneous outbreak of respiratory syncytial virus and parainfluenza virus type 3 in a newborn nursery Studies on dental selfcuring resins. Detection and identification of human parainfluenza viruses 1, 2, 3, and 4 in clinical samples of pediatric patients by multiplex reverse transcription-PCR Human metapneumovirus infections in hospitalized children Viral co-infections in immunocompetent infants with bronchiolitis: prospective epidemiologic study Respiratory syncytial virus heterogeneity during an epidemic: analysis by limited nucleotide sequencing (SH gene) and restriction mapping (N gene) Lack of sensitivity of rapid antigen tests for the diagnosis of respiratory syncytial virus infection in adults Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-PCR assay Simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested-PCR assays Stable and noncompetitive RNA internal control for routine clinical diagnostic reverse transcription-PCR Detection of influenza A and B in respiratory secretions with the polymerase chain reaction Simultaneous detection and identification of human parainfluenza viruses 1, 2, and 3 from clinical samples by multiplex PCR Multiplex PCR: optimization and application in diagnostic virology Detection of respiratory syncytial virus A and B and parainfluenza virus 3 sequences in respiratory tracts of infants by a single PCR with primers targeted to the L-polymerase gene and differential hybridization Rapid simultaneous diagnosis of infections with respiratory syncytial viruses A and B, influenza viruses A and B, and human parainfluenza virus types 1, 2, and 3 by multiplex quantitative reverse transcription-polymerase chain reaction-enzyme hybridization assay (Hexaplex) Viruses responsible for respiratory infections in pediatrics. keywords: et al; influenza; methods; multiplex; pcr; respiratory; viruses cache: cord-294454-uzfsv2df.txt plain text: cord-294454-uzfsv2df.txt item: #519 of 973 id: cord-294546-0otd1heg author: Prendki, V. title: Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study date: 2019-01-12 words: 3023 flesch: 36 summary: Infectious Diseases Society of America/American Thoracic Society consensus guidelines on the management of community-acquired pneumonia in adults BTS guidelines for the management of community acquired pneumonia in adults: update Guidelines for the management of adult lower respiratory tract infectionsdfull version Evolving understanding of the causes of pneumonia in adults, with special attention to the role of Pneumococcus Impact of microbiological samples in the hospital management of community-acquired, nursing home-acquired and hospital-acquired pneumonia in older patients Comprehensive molecular testing for respiratory pathogens in community-acquired pneumonia Impact of rapid detection of viral and atypical bacterial pathogens by real-time polymerase chain reaction for patients with lower respiratory tract infection Routine molecular point-of-care testing for respiratory viruses in adults presenting to hospital with acute respiratory illness (ResPOC): a pragmatic, open-label, randomised controlled trial A comparison of nasopharyngeal and oropharyngeal swabbing for the detection of influenza virus by real-time PCR Low-dose computed tomography for the diagnosis of pneumonia in elderly patients: a prospective, interventional cohort study Diagnosis and management of community and hospital acquired pneumonia in adults: summary of NICE guidance Pneumonia in the very old Lower respiratory tract virus findings in mechanically ventilated patients with severe community-acquired pneumonia Viral infection in patients with severe pneumonia requiring intensive care unit admission Viruses detected by systematic multiplex polymerase chain reaction in adults with suspected community-acquired pneumonia attending emergency departments in France Viral pneumonia in older adults Respiratory syncytial virus and other respiratory viral infections in older adults with moderate to severe influenza-like illness Human metapneumovirus: review of an important respiratory pathogen Radiographic and CT features of viral pneumonia CT findings in viral lower respiratory tract infections caused by parainfluenza virus, influenza virus and respiratory syncytial virus Rhinovirusdnot just the common cold Community-acquired pneumonia requiring hospitalization among US adults Heterogeneous and dynamic prevalence of asymptomatic influenza virus infections Respiratory syncytial virus evaluation among asymptomatic and symptomatic subjects in a university hospital in Sao Paulo, Brazil in the period of Viral shedding and transmission potential of asymptomatic and paucisymptomatic influenza virus infections in the community The impact of the 13-valent pneumococcal conjugate vaccine on pneumococcal carriage in the Community Acquired Pneumonia Immunization Trial in Adults (CAPiTA) Study Early chest computed tomography scan to assist diagnosis and guide treatment decision for suspected community-acquired pneumonia key: cord-294546-0otd1heg authors: Prendki, V.; Huttner, B.; Marti, C.; Mamin, A.; Fubini, P.E.; Meynet, M.P.; Scheffler, M.; Montet, X.; Janssens, J.P.; Reny, J.L.; Kaiser, L.; Garin, N.; Stirnemann, J. title: Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study date: 2019-01-12 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2018.12.037 sha: doc_id: 294546 cord_uid: 0otd1heg OBJECTIVES: keywords: comprehensive; patients; pcr; pneumonia; results; study; testing cache: cord-294546-0otd1heg.txt plain text: cord-294546-0otd1heg.txt item: #520 of 973 id: cord-294798-ji3p0l4j author: White, Sarah K. title: Detection and phylogenetic characterization of arbovirus dual-infections among persons during a chikungunya fever outbreak, Haiti 2014 date: 2018-05-31 words: 4796 flesch: 41 summary: As part of ongoing screening of schoolchildren presenting with acute undifferentiated febrile illness in rural Haiti, we used RT-PCR to identify CHIKV infections in 82 of 100 children with this diagnosis during May—August 2014. The acute symptoms of CHIKV infection are similar to those of infection with other arbovirus species, including Dengue virus (DENV), Zika virus (ZIKV), and Mayaro virus (MAYV), each presenting with a constellation of symptoms including fever, headache, and myalgias/arthralgias. keywords: chikungunya; chikv; clade; haiti; infection; mayv; pcr; rtrt; specimens; strains; virus; zikv cache: cord-294798-ji3p0l4j.txt plain text: cord-294798-ji3p0l4j.txt item: #521 of 973 id: cord-294947-g4ntyddb author: Zhu, Yu title: Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus date: 2016-06-10 words: 2856 flesch: 48 summary: Industry, veterinarians trying to contain PED virus, new to the US Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the US Receptor usage and cell entry of porcine epidemic diarrhea coronavirus Binding characterization of determinants in porcine aminopeptidase N, the cellular receptor for transmissible gastroenteritis virus Severe acute respiratory syndrome-associated coronavirus 3a protein forms an ion channel and modulates virus release Characterisation of a recent virulent transmissible gastroenteritis virus from Britain with a deleted ORF 3a Differentiation of a Vero cell adapted porcine epidemic diarrhea virus from Korean field strains by restriction fragment length polymorphism analysis of ORF 3 PEDV ORF3 encodes an ion channel protein and regulates virus production Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field isolates in Korea Isolation and serial propagation of porcine epidemic diarrhea virus in cell cultures and partial characterization of the isolate Rapid and sensitive detection of porcine epidemic diarrhea virus by reverse transcription loop-mediated isothermal amplification combined with a vertical flow visualization strip Evaluation of two real-time polymerase chain reaction assays for Porcine epidemic diarrhea virus (PEDV) to assess PEDV transmission in growing pigs Effect of temperature on the detection of porcine epidemic diarrhea virus and transmissible gastroenteritis virus in fecal samples by reverse transcription-polymerase chain reaction NanoPCR observation: different levels of DNA replication fidelity in nanoparticle-enhanced polymerase chain reactions Porcine epidemic diarrhea virus infection: Etiology, epidemiology, pathogenesis and immunoprophylaxis Molecular epidemiology of porcine epidemic diarrhea virus in China Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in south China A nanoparticleassisted PCR assay to improve the sensitivity for rapid detection and differentiation of wild-type pseudorabies virus and genedeleted vaccine strains A new nanoPCR molecular assay for detection of porcine bocavirus Development of a nanoparticle-assisted PCR assay for detection of porcine epidemic diarrhea virus Acknowledgements Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic and lethal virus. keywords: assay; nanoparticle; pcr; pedv; strains cache: cord-294947-g4ntyddb.txt plain text: cord-294947-g4ntyddb.txt item: #522 of 973 id: cord-295296-jtjx1vgd author: Tiwari, Shashi Kant title: `In-silico primer designing and PCR for detection of novel coronavirus-19 date: 2020-10-23 words: 574 flesch: 59 summary: quality control for PCR primers Higher binding capacity of primers in MFE primer tool showed higher specificity against virus [5] . keywords: pcr; primers cache: cord-295296-jtjx1vgd.txt plain text: cord-295296-jtjx1vgd.txt item: #523 of 973 id: cord-295401-3p6q92x4 author: Gueudin, M title: Quantitation of respiratory syncytial virus RNA in nasal aspirates of children by real-time RT-PCR assay date: 2003-02-18 words: 3980 flesch: 54 summary: The mean number of RSV RNA copies was higher in the severe disease group than in the non-severe group 4.05×10(7) vs 9.1×10(6) (P=0.055). However, the mean ratio of RSV RNA copies to GAPDH mRNA copies was 42.8 in the severe group, and 22.2 in non-severe group (P=NS). keywords: assay; disease; pcr; rna; rsv; time; time rt cache: cord-295401-3p6q92x4.txt plain text: cord-295401-3p6q92x4.txt item: #524 of 973 id: cord-295445-f4p00yaw author: Wang, Hao title: Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments date: 2018-02-01 words: 6892 flesch: 40 summary: Water Sa Evaluation of positively charged alumina nanofibre cartridge filters for the primary concentration of noroviruses, adenoviruses and male-specific coliphages from seawater Diarrhea and enteric emerging viruses in HIVinfected patients Detection of pathogenic viruses in sewage provided early warnings of hepatitis A virus and norovirus outbreaks Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein New method using a positively charged microporous filter and ultrafiltration for concentration of viruses from tap water Mechanism of ozone inactivation of bacteriophage f2 Application of ozone for enhancing the microbiological safety and quality of foods: a review Disinfection of wastewater with peracetic acid: a review Environmental persistence and transfer of enteric viruses Mucosal and cutaneous human papillomaviruses detected in raw sewages Previously unknown evolutionary groups dominate the ssDNA gokushoviruses in oxic and anoxic waters of a coastal marine environment Quantitative RT-PCR for the enumeration of noroviruses (Norwalk-like viruses) in water and sewage Profile and fate of bacterial pathogens in sewage treatment plants revealed by high-Throughput metagenomic approach Presence of noroviruses and other enteric viruses in sewage and surface waters in The Netherlands Pathogenic enteric viruses and microbial indicators during secondary treatment of municipal wastewater Tracing of norovirus outbreak strains in mussels collected near sewage effluents Diversity of viruses associated with acute gastroenteritis in children hospitalized with diarrhea in Ho Chi Minh City, Vietnam Disinfection and oxidation of sewage effluent water using ozone and UV technologies Removal of viruses, parasitic protozoa and microbial indicators in conventional and membrane processes in a wastewater pilot plant Removal of noro-and enteroviruses, Giardia cysts, Cryptosporidium oocysts, and fecal indicators at four secondary wastewater treatment plants in Sweden Removal of noro-and enteroviruses Giardia cysts, Cryptosporidium oocysts, and fecal indicators at four secondary wastewater treatment plants in Sweden Visualizing phylogenetic trees using TreeView Effect of disinfection of drinking-Water with ozone or chlorine dioxide on survival of cryptosporidium-parvum oocysts Acute diarrhea in West African children: diverse enteric viruses and a novel parvovirus genus The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin Wastewater disinfection with ozone -process control and operating results Uses of Ozone in Drinking Water Treatment Standard and new faecal indicators and pathogens in sewage treatment plants, microbiological parameters for improving the control of reclaimed water Reproducible (1)H NMRbased metabolomic responses in fish exposed to different sewage effluents in two separate studies Science and technology for water purification in the coming decades Tyrrell et al., 1995) , but knowledge regarding its effect for reducing human enteric viruses is relatively scarce. keywords: adenovirus; et al; human; min; ozone; pcr; samples; sewage; treatment; viruses; wastewater; water cache: cord-295445-f4p00yaw.txt plain text: cord-295445-f4p00yaw.txt item: #525 of 973 id: cord-296109-kco85lqn author: Vanuytsel, Kim title: Rapid Implementation of a SARS-CoV-2 Diagnostic qRT-PCR Test with Emergency Use Authorization at a Large Academic Safety-Net Hospital date: 2020-05-19 words: 2506 flesch: 35 summary: Subsequently, we implemented a quantitative, real-time reverse transcriptase polymerase chain reaction (qRT-PCR)-based assay to detect viral SARS-CoV-2 RNA from nasopharyngeal swabs, based on guidelines from the Centers for Disease Control and Prevention (CDC) and the FDA for use with in-house testing of BMC patient samples ( Figure 1 ) (CDC, 2020; Wang et al., 2020a). Given that our hospital takes care of a large portion of Boston's homeless and housing unstable patients, rapid testing is vital in order to mitigate community spread in an already vulnerable population living in low resource settings in which social distancing is not possible. keywords: cov-2; covid-19; health; laboratory; patient; pcr; sars; testing cache: cord-296109-kco85lqn.txt plain text: cord-296109-kco85lqn.txt item: #526 of 973 id: cord-296197-ohfhnpma author: Deborggraeve, Stijn title: A Simplified and Standardized Polymerase Chain Reaction Format for the Diagnosis of Leishmaniasis date: 2008-11-15 words: 4238 flesch: 43 summary: We describe here the development of a simple and rapid test for the detection of polymerase chain reaction-amplified Leishmania DNA. The lower detection limits of the assay are 10 fg of Leishmania DNA and 1 parasite in 180 µL of blood. keywords: blood; control; detection; diagnosis; dna; leishmania; leishmaniasis; patients; pcr; samples; test cache: cord-296197-ohfhnpma.txt plain text: cord-296197-ohfhnpma.txt item: #527 of 973 id: cord-296309-i1mpov7k author: Houldcroft, Charlotte J. title: Clinical and biological insights from viral genome sequencing date: 2017-01-16 words: 9059 flesch: 23 summary: The concentration of virus particles (see the Zika virus example above 72 ), depletion of host material and/or sequencing to high read depth can increase the amount of virus sequence, but all of these methods add to the cost. This is particularly relevant for rapid responses to emerging threats, such as Zika virus 81 . keywords: dna; drug; enrichment; example; genome; hiv; methods; pcr; resistance; rna; sequence; sequencing; target; variants; virus; viruses; wgs; zika cache: cord-296309-i1mpov7k.txt plain text: cord-296309-i1mpov7k.txt item: #528 of 973 id: cord-296364-7rp60d2m author: Youn, Soonjeon title: In vitro assembled, recombinant infectious bronchitis viruses demonstrate that the 5a open reading frame is not essential for replication date: 2005-02-05 words: 5114 flesch: 50 summary: The transcripts from the full-length cDNA (along with the N transcript alone), total cellular RNA from IBV infected Vero cells (positive control), and PBS (negative control) were electroporated into non-permissive BHK-21 cells, which were then cultured with Vero cells. The entire IBV N ORF, including the 3V UTR, was amplified by RT-PCR from total cellular RNA extracted from IBV infected Vero cells, and the RT-PCR product was cloned into a transcription vector, pGEM-3Zf(+) (Promega, Madison, WI). keywords: cells; coronavirus; egfp; gibv; ibv; orf; pcr; rna; virus cache: cord-296364-7rp60d2m.txt plain text: cord-296364-7rp60d2m.txt item: #529 of 973 id: cord-296392-2u9mz6d3 author: Sarıgül, Figen title: Investigation of compatibility of severe acute respiratory syndrome coronavirus 2 reverse transcriptase-PCR kits containing different gene targets during coronavirus disease 2019 pandemic date: 2020-08-26 words: 3900 flesch: 47 summary: We have observed high correlation between different PCR kits, however, using different PCR kits during the pandemic may provide a more accurate diagnosis of SARS-CoV-2, since despite correlation there are a number of patients showing contradicting diagnosis. Our results suggest, in the light of clinic symptoms of COVID-19 using different PCR kits that target different genes concurrently during the pandemic may provide a more accurate diagnosis. keywords: correlation; diagnosis; diagnovital; gene; kits; pcr; rdrp cache: cord-296392-2u9mz6d3.txt plain text: cord-296392-2u9mz6d3.txt item: #530 of 973 id: cord-296593-ox6x53vj author: Sonoo, M. title: Correlation between PCR Examination Rate among the Population and the Containment of Pandemic of COVID-19 date: 2020-05-16 words: 1084 flesch: 53 summary: Close inspection of individual countries suggested that the social distancing is the largest factor to achieve containment, and the contribution of broad PCR tests is smaller. Close inspection of individual countries suggested that the social distancing is the largest factor to achieve containment, and the contribution of broad PCR tests is smaller. keywords: countries; preprint cache: cord-296593-ox6x53vj.txt plain text: cord-296593-ox6x53vj.txt item: #531 of 973 id: cord-296736-jsm6o5pq author: Chidlow, Glenys R. title: An Economical Tandem Multiplex Real-Time PCR Technique for the Detection of a Comprehensive Range of Respiratory Pathogens date: 2009-06-08 words: 4138 flesch: 37 summary: The prevalence of potential pathogenic bacteria in nasopharyngeal samples from healthy children and adults Detection of 11 common viral and bacterial pathogens causing community-acquired pneumonia or sepsis in asymptomatic patients by using a multiplex reverse transcription-PCR assay with manual (enzyme hybridization) or automated (electronic microarray) detection Microbial interactions during upper respiratory tract infections Presence of the newly discovered human polyomaviruses KI and WU in Australian patients with acute respiratory tract infection No evidence for an association between infections with WU and KI polyomaviruses and respiratory disease Rapid multiplex nested PCR for detection of respiratory viruses Detection and typing by molecular techniques of respiratory viruses in children hospitalized for acute respiratory infection in Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis Association of rhinovirus infection with increased disease severity in acute bronchiolitis Differential detection of rhinoviruses and enteroviruses RNA sequences associated with classical immunofluorescence assay detection of respiratory virus antigens in nasopharyngeal swabs from infants with bronchiolitis Highly effective detection of human papillomavirus 16 and 18 DNA by a testing algorithm combining broad-spectrum and typespecific PCR Rapid identification of nine microorganisms causing acute respiratory tract infections by single-tube multiplex reverse transcription-PCR: Feasibility study Simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested-PCR assays RespiFinder: a new multiparameter test to differentially identify fifteen respiratory viruses High-throughput, sensitive, and accurate multiplex PCR-Microsphere flow cytometry system for large-scale comprehensive detection of respiratory viruses Multiplex real-time PCR assay for detection of Influenza and human respiratory syncytial viruses Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illnesses in infants Utility of a multiplex PCR assay for detecting herpesvirus DNA in clinical samples Enhanced reverse transcription-PCR assay for detection of norovirus genogroup I A 5'-nuclease real-time reverse transcriptase-polymerase chain reaction assay for the detection of a broad range of influenza A subtypes, including H5N1 Improved detection of rhinoviruses in nasal and throat swabs by seminested RT-PCR Polymerase chain reaction for human picornaviruses Multiple extracts from each sample have been required to set up a comprehensive range of PCR assays for respiratory pathogens, and the sample volume available may be insufficient for all of the required tests. keywords: assay; detection; human; multiplex; pathogens; pcr; samples; tandem; time cache: cord-296736-jsm6o5pq.txt plain text: cord-296736-jsm6o5pq.txt item: #532 of 973 id: cord-296819-gztmidn2 author: Sambri, Vittorio title: Diagnosis of West Nile Virus Human Infections: Overview and Proposal of Diagnostic Protocols Considering the Results of External Quality Assessment Studies date: 2013-09-25 words: 6733 flesch: 36 summary: West nile virus: Characteristics of an african virus adapting to the third millennium world West Nile virus West Nile virus: Immunity and pathogenesis West nile virus (Kunjin subtype) disease in the northern territory of Australia-A case of encephalitis and review of all reported cases Human case of autochthonous West Nile virus lineage 2 infection in Italy West Nile virus lineage 2 from blood donor Detection of West Nile virus lineage 2 in mosquitoes during a human outbreak in Greece Outbreak of West Nile virus infection in humans Novel flavivirus or new lineage of West Nile virus, central Nile virus isolates from India: evidence for a distinct genetic lineage Putative new lineage of west nile virus Rebel-Bauder, B.; Nowotny, N. Emergence of Usutu virus, an African mosquito-borne flavivirus of the Japanese encephalitis virus group West Nile virus: Dengue virus infection in a traveller returning from Croatia to Germany Isolation of usutu virus in Germany Simultaneous detection and quantitation of Chikungunya, dengue and West Nile viruses by multiplex RT-PCR assays and dengue virus typing using high resolution melting Fast duplex one-step reverse transcriptase PCR for rapid differential detection of West Nile and Japanese encephalitis viruses Detection of West Nile virus in formalin-fixed, paraffin-embedded human tissues by RT-PCR: a useful adjunct to conventional tissue-based diagnostic methods Pathologic and immunohistochemical findings in naturally occuring West Nile virus infection in horses Detection of West Nile Virus infection in birds in the United States by blocking ELISA and immunohistochemistry keywords: detection; diagnosis; encephalitis; human; igm; infection; methods; nile; nile virus; pcr; virus; west; west nile; wnv cache: cord-296819-gztmidn2.txt plain text: cord-296819-gztmidn2.txt item: #533 of 973 id: cord-296979-8r851j4t author: Zhong, Ying title: Host genes regulate transcription of sperm-introduced hepatitis B virus genes in embryo date: 2017-10-31 words: 6777 flesch: 44 summary: Finally, we silenced the target genes and a control gene by RNA interference (RNAi) to detect effects of the silencing of these genes on transcriptional level of HBV genes to determine whether host genes participate in regulation of HBV gene transcription. The transcription levels of HBV genes between the test and control groups are significantly different (P < 0.05), which suggested that in the test group the target genes have been silenced by RNAi and participated in transcriptional regulation of HBV genes, causing the change of HBV gene transcription levels. keywords: cell; control; embryos; expression; genes; group; hbv; hepatitis; human; pcr; sperm; target; test; transcription; virus cache: cord-296979-8r851j4t.txt plain text: cord-296979-8r851j4t.txt item: #534 of 973 id: cord-297160-tqw9vx2b author: Geerligs, H.J. title: The use of RT-PCR for determination of separate end-points for the strains IB H120 and IB D274 in titration of the combination vaccine Poulvac IB(®) primer date: 2013-07-01 words: 2863 flesch: 51 summary: The vials were lyophilized according to routine procedures and subsequently stored in the dark at 5 ± 3 • C. Titrations of IB virus were performed according to standard procedures as described by Doherty (1967) . Allantoic fluids from the eggs were investigated for the presence of IB virus by reverse transcriptase PCR with strains specific reverse transcriptase PCR primers for IB H120 and IB D274. keywords: d274; eggs; h120; pcr; strains; virus cache: cord-297160-tqw9vx2b.txt plain text: cord-297160-tqw9vx2b.txt item: #535 of 973 id: cord-297396-r1p7xn3a author: Ng, Ming-Yen title: Development and Validation of Risk Prediction Models for COVID-19 Positivity in a Hospital Setting date: 2020-09-15 words: 3254 flesch: 47 summary: Reverse transcription polymerase chain reaction (RT-PCR) is regarded as a vital tool in identifying the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and quarantining COVID-19 patients to prevent further spread of the disease 4 . As yet, the data which supports these strategies are predominantly based on data of COVID-19 patients 12, 13 but without comparisons to patients with other conditions and symptoms overlapping with COVID-19 (eg. fever, shortness of breath, cough). keywords: contact; covid-19; cxr; model; nomograms; patients; points; step cache: cord-297396-r1p7xn3a.txt plain text: cord-297396-r1p7xn3a.txt item: #536 of 973 id: cord-297432-2edncbgn author: Helleberg, Marie title: Persistent COVID-19 in an Immunocompromised Patient Temporarily Responsive to Two Courses of Remdesivir Therapy date: 2020-07-23 words: 2399 flesch: 43 summary: This pattern was repeated during and after a second course of remdesivir treatment. The role of ongoing viral infection versus a secondary hyperreactive immune response in the aftermath of viral replication for the development of severe COVID-19 is not completely understood [6] . keywords: covid-19; day; infection; patients; remdesivir; sars; treatment cache: cord-297432-2edncbgn.txt plain text: cord-297432-2edncbgn.txt item: #537 of 973 id: cord-297646-49l6k5h2 author: Yu, Zhongjia title: Prevalence of intestinal parasites in companion dogs with diarrhea in Beijing, China, and genetic characteristics of Giardia and Cryptosporidium species date: 2017-11-18 words: 4601 flesch: 41 summary: key: cord-297646-49l6k5h2 authors: Yu, Zhongjia; Ruan, Yang; Zhou, Mengjie; Chen, Siyuan; Zhang, Yinxin; Wang, Liya; Zhu, Guan; Yu, Yonglan title: Prevalence of intestinal parasites in companion dogs with diarrhea in Beijing, China, and genetic characteristics of Giardia and Cryptosporidium species date: 2017-11-18 journal: Collectively, this study indicates that parasites are a significant group of pathogens in companion dogs in Beijing, and companion dogs may potentially transmit certain zoonotic parasites to humans, particularly those with weak or weakened immunity. keywords: companion; cryptosporidium; dogs; duodenalis; giardia; parasites; pcr; specimens cache: cord-297646-49l6k5h2.txt plain text: cord-297646-49l6k5h2.txt item: #538 of 973 id: cord-298002-jvnwivrg author: Wang, Jian title: COVID-19 confirmed patients with negative antibodies results date: 2020-09-22 words: 1505 flesch: 55 summary: In summary, this work presents two typical cases of COVID-19 patients without producing IgM/ IgG and comprehensively characterizes their initial symptoms, chest CT results, medication, and laboratory test results, hoping to draw more attentions to this type of patients. From January 30 to March 15, 310 of COVID-19 patients who were positive for SARS-CoV-2 real time reverse-transcription PCR (RT-PCR) testing and received IgM and IgG detection at Wuhan Union Hospital (Wuhan, China) were enrolled. keywords: covid-19; igg; patients; results cache: cord-298002-jvnwivrg.txt plain text: cord-298002-jvnwivrg.txt item: #539 of 973 id: cord-298049-gabjdkx9 author: Gomez, D.E. title: Detection of Bovine Coronavirus in Healthy and Diarrheic Dairy Calves date: 2017-09-15 words: 4543 flesch: 55 summary: The results of this study demonstrated a positive association between BCoV and diarrhea in dairy calves as detection rates of this agent were higher in diarrheic calves than in farm-, season-, aged-matched nondiarrheic calves. 3 Common etiologic agents involved in calf diarrhea include Escherichia coli, Cryptosporidium spp, bovine rotavirus (BRoV), and bovine coronavirus (BCoV). keywords: assay; bcov; calves; detection; diarrhea; pcr; samples; study cache: cord-298049-gabjdkx9.txt plain text: cord-298049-gabjdkx9.txt item: #540 of 973 id: cord-298051-ej8qxkce author: Louten, Jennifer title: Detection and Diagnosis of Viral Infections date: 2016-05-06 words: 11215 flesch: 55 summary: Sequencing also allows us to track the genetic differences between related subtypes and strains of viruses, and it assists scientists in identifying novel viruses by comparing genome sequences with those of known viruses. Consequently, the first efforts to identify specific viruses relied upon serology, the analysis of the protein antibodies found in blood that the immune system synthesizes against pathogens. keywords: antibodies; antibody; antigen; beads; blood; cells; dna; enzyme; fig; patient; pcr; sample; test; virus; viruses cache: cord-298051-ej8qxkce.txt plain text: cord-298051-ej8qxkce.txt item: #541 of 973 id: cord-298076-rujylmib author: Chen, Zhiyong title: Comparison of reverse transcription loop-mediated isothermal amplification, conventional PCR and real-time PCR assays for Japanese encephalitis virus date: 2010-11-30 words: 2953 flesch: 44 summary: [14] reported the application of RT-LAMP assay to detect JEV in the cerebrospinal fluid samples from patients with clinical diagnosis of acute encephalitis, which the sensitivity of JEV detection was comparable to conventional RT-PCR. The solution turned green in the presence of LAMP amplification products, while it retained orange in the absence of the amplicon. keywords: assay; detection; jev; lamp; pcr; time cache: cord-298076-rujylmib.txt plain text: cord-298076-rujylmib.txt item: #542 of 973 id: cord-298401-4szmu1dh author: Lyoo, Kwang-Soo title: Development of rapid immunochromatographic strip test for the detection of porcine epidemic diarrhoea virus date: 2017-12-02 words: 3508 flesch: 46 summary: Based on extensive phylogenetic analysis using obtained sequences, PEDV strains are classified into two major categories: the classical PEDV strain showing lower pathogenicity and highly virulent PEDV strain that emerged in 2010. Moreover, the emergence of PEDV has been reported in western, central and eastern Europe, and the genome sequences were found to be closely related to PEDV strains from the USA, showing a sequence identity of more than 99 per cent. keywords: cent; ica; kit; pcr; pedv; porcine; protein; test; time; virus cache: cord-298401-4szmu1dh.txt plain text: cord-298401-4szmu1dh.txt item: #543 of 973 id: cord-298462-xpx3orvs author: Lin, Feng title: Quantification of human bocavirus in lower respiratory tract infections in China date: 2007-01-31 words: 1456 flesch: 43 summary: The main clinical symptom of patients who were positive for HBoV DNA was a pneumonia-like syndrome represented by high fever and cough. To date, there have been no studies reporting the detection of HBoV DNA in children with LRTI from China. keywords: children; hbov; human; pcr; tract cache: cord-298462-xpx3orvs.txt plain text: cord-298462-xpx3orvs.txt item: #544 of 973 id: cord-298600-cnolne6k author: Majeed, Talal title: The Role of the Computed Tomography (CT) Thorax in the Diagnosis of COVID-19 for Patients Presenting with Acute Surgical Emergencies. A Single Institute Experience date: 2020-10-20 words: 3223 flesch: 43 summary: Standard reporting for COVID-19 infection for CT chest based on guidelines from British Society of Thoracic Imaging (BSTI) and Radiological Society of North America (RSNA) was used. Our aim was to determine the diagnostic accuracy in terms of sensitivity and specificity of CT chest in diagnosing and confirming COVID-19 infection in patients presenting with acute surgical and medical pathologies. keywords: covid-19; diagnosis; infection; patients; pcr; test cache: cord-298600-cnolne6k.txt plain text: cord-298600-cnolne6k.txt item: #545 of 973 id: cord-298697-v1qdizwx author: Chang, Jia Jin Marc title: Takeaways from Mobile DNA Barcoding with BentoLab and MinION date: 2020-09-24 words: 7224 flesch: 49 summary: We sought to investigate if the basecalling model had an impact on MinION barcodes generated from an error correction pipeline like miniBarcoder. We then performed MinION barcode calling using the miniBarcoder pipeline [35] . keywords: barcodes; barcoding; basecalling; bentolab; dataset; dna; field; flow; laboratory; minion; model; nanopore; pcr; reads; samples; sequencing; species; time cache: cord-298697-v1qdizwx.txt plain text: cord-298697-v1qdizwx.txt item: #546 of 973 id: cord-298805-ntpm68cg author: Otašević, S. title: Non-culture based assays for the detection of fungal pathogens date: 2018-03-29 words: 9288 flesch: 30 summary: Until today, various samples have been used for PCR detection of P. jirovecii pneumonia. This method is characterized by minimal invasiveness and includes PCR detection of cell-free DNA, fragments of DNA which are present extra cellular in different body fluids, in serum samples [90] . keywords: aspergillosis; aspergillus; assay; blood; candida; detection; diagnosis; fungal; identification; infections; jirovecii; methods; patients; pcr; pneumocystis; pneumonia; samples; species; time cache: cord-298805-ntpm68cg.txt plain text: cord-298805-ntpm68cg.txt item: #547 of 973 id: cord-298991-5qae0ege author: Aiello, Francesco title: Coronavirus disease 2019 (SARS-CoV-2) and colonization of ocular tissues and secretions: a systematic review date: 2020-05-18 words: 3152 flesch: 45 summary: Origin and evolution of pathogenic coronaviruses SARS-associated coronavirus Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People's Republic of China Identification of a novel coronavirus in patients with severe acute respiratory syndrome Koch's postulates fulfilled for SARS virus A novel coronavirus associated with severe acute respiratory syndrome Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the coronavirus study group Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Clinical features of patients infected with 2019 novel coronavirus in Wuhan Clinical characteristics of coronavirus disease 2019 in China Note from the editors: World Health Organization declares novel coronavirus (2019-nCoV) sixth public health emergency of international concern Novel Coronavirus (2019-nCoV) Situation Report-22 Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. Novel coronavirus (COVID-19) situation Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus Enteric involvement of coronaviruses: is faecal-oral transmission of SARS-CoV-2 possible? Concentration and detection of SARS coronavirus in sewage from Xiao Tang Shan hospital and the 309th Hospital of the Chinese People's Liberation Army Identification of a new human coronavirus Human coronavirus NL63, France The severe acute respiratory syndrome coronavirus in tears keywords: conjunctival; conjunctivitis; coronavirus; cov-2; covid-19; patients; pcr; sars cache: cord-298991-5qae0ege.txt plain text: cord-298991-5qae0ege.txt item: #548 of 973 id: cord-298998-n5rhhzc9 author: Vashee, Sanjay title: Cloning, Assembly, and Modification of the Primary Human Cytomegalovirus Isolate Toledo by Yeast-Based Transformation-Associated Recombination date: 2017-10-04 words: 9360 flesch: 42 summary: Passage 7 of HCMV Toledo contains both wild-type and mutated ULb' regions. Next-generation sequence analysis of an early passage of HCMV Toledo. keywords: assembly; bac; cells; cloning; cytomegalovirus; dna; fragments; genomes; hcmv; human; pcr; sequence; tar; toledo; ul128; yeast cache: cord-298998-n5rhhzc9.txt plain text: cord-298998-n5rhhzc9.txt item: #549 of 973 id: cord-299537-lbx1plqx author: Wang, Wei title: Molecular monitoring of causative viruses in child acute respiratory infection in endemo-epidemic situations in Shanghai date: 2010-09-19 words: 4012 flesch: 45 summary: Bronchiolitis-associated hospitalizations among US children Trends in infectious disease mortality in the United States during the 20th century Human rhinoviruses: the cold wars resume Human bocavirus and acute wheezing in children Human bocavirus: a novel parvovirus epidemiologically associated with pneumonia requiring hospitalization in Thailand Serodiagnosis of human bocavirus infection Correlation between bocavirus infection and humoral response, and co-infection with other respiratory viruses in children with acute respiratory infection Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses Direct screening of clinical specimens for multiple respiratory pathogens using the Genaco Respiratory Panels 1 and 2 Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Evidence from multiplex molecular assays for complex multipathogen interactions in acute respiratory infections Simultaneous detection of respiratory viruses in children with acute respiratory infection using two different multiplex reverse transcription-PCR assays Human (non-severe acute respiratory syndrome) coronavirus infections in hospitalised children in France Cloning of a human parvovirus by molecular screening of respiratory tract samples Molecular identification of adenoviruses in clinical samples by analyzing a partial hexon genomic region A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium Human metapneumovirus infection in hospitalized children with acute respiratory disease in Korea Detection and characterization of new influenza B virus variants in 2002 Cocirculation and evolution of two lineages of influenza B viruses in europe and Israel in the 2001-2002 season A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illnesses in infants Genetic clustering of all 102 human rhinovirus prototype strains: serotype 87 is close to human enterovirus 70 Acute respiratory disease associated with adenovirus serotype 14-four states Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C) Multiplex MassTag-PCR for respiratory pathogens in pediatric nasopharyngeal washes negative by conventional diagnostic testing shows a high prevalence of viruses belonging to a newly recognized rhinovirus clade Evidence of recombination and genetic diversity in human rhinoviruses in children with acute respiratory infection A newly discovered human pneumovirus isolated from young children with respiratory tract disease Human metapneumovirus: a newly emerging respiratory pathogen Antigenic and genetic variability of human metapneumoviruses Genetic variability of human metapneumovirus infection: evidence of a shift in viral genotype without a change in illness The role of human metapneumovirus in upper respiratory tract infections in children: a 20-year experience Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia Identification of a new human coronavirus Human bocavirus Detection of human bocavirus in hospitalised children Human bocavirus infections in hospitalized children and adults High incidence of human bocavirus infection in children in Spain Respiratory syncytial virus, human bocavirus and rhinovirus bronchiolitis in infants Multipathogen infections in hospitalized children with acute respiratory infections Sole pathogen in acute bronchiolitis: is there a role for other organisms apart from respiratory syncytial virus? Diagnostic system for rapid and sensitive differential detection of pathogens A metagenomic survey of microbes in honey bee colony collapse disorder A new arenavirus in a cluster of fatal transplant-associated diseases The study was supported by the Li Ka-Shing Foundation (RESPARI network) for discovery of new emerging viruses, the French Agency for the Development for Surveillance and Investigation of Epidemic Situations in Southeast Asia (SISEA project), the National Science and Technology Major Project (2009ZX10004-105) of the Chinese Ministry of Health for the establishment of pathogen and immuno-response detection platforms for respiratory and central nervous system viral infections, the AREVA Foundation which supports the salary of Dr. Wei Wang. The diagnosis of respiratory viruses mainly relies on molecular techniques. keywords: children; hcov; hrv; human; infection; patients; pcr; strains; study; viruses cache: cord-299537-lbx1plqx.txt plain text: cord-299537-lbx1plqx.txt item: #550 of 973 id: cord-299585-fkg8d6ym author: Wang, Leyi title: Development of a triplex real-time RT-PCR assay for detection and differentiation of three US genotypes of porcine hemagglutinating encephalomyelitis virus date: 2019-04-05 words: 2740 flesch: 47 summary: In contrast to conventional singleplex real time RT-PCR, the triplex real time RT-PCR that we have developed in this present study can be used to monitor PHEV genotypes and potentially to identify new variants if test results cannot be explained as expected. The sensitivity of the triplex rRT-PCR was determined through 10fold serial dilutions of RNAs of known PHEV genotypes (15SW1362 for G123 and G13, and 15SW25049 for G3) and plasmids pCR 2.1-15SW1582-N for G123, pCR 2.1-15SW1362-NS2 for G13, and pCR 2.1-15SW25049-NS2 for G3 in duplicate. keywords: genotype; ns2; pcr; phev; porcine; virus cache: cord-299585-fkg8d6ym.txt plain text: cord-299585-fkg8d6ym.txt item: #551 of 973 id: cord-299672-dq1y1gkc author: Leung, Ting Fan title: Multiplex Molecular Detection of Respiratory Pathogens in Children With Asthma Exacerbation date: 2010-02-28 words: 3647 flesch: 46 summary: The objectives of this study were: (1) to investigate the importance of different respiratory patho gens in childhood asthma exacerbation, and (2) to delineate the epidemiology of respiratory pathogens causing asthma exacerbation in Hong Kong children. key: cord-299672-dq1y1gkc authors: Leung, Ting Fan; To, Man Yin; Yeung, Apple C.M.; Wong, Yun Sze; Wong, Gary W.K.; Chan, Paul K.S. title: Multiplex Molecular Detection of Respiratory Pathogens in Children With Asthma Exacerbation date: 2010-02-28 journal: Chest DOI: 10.1378/chest.09-1250 sha: doc_id: 299672 cord_uid: dq1y1gkc Background Up to 80% of asthma exacerbations in white children are associated with viral upper respiratory infections. keywords: asthma; children; exacerbation; group; hrv; pathogens; patients; pcr; study cache: cord-299672-dq1y1gkc.txt plain text: cord-299672-dq1y1gkc.txt item: #552 of 973 id: cord-299737-r34d0rx7 author: Grant, Paul R title: Extraction-free COVID-19 (SARS-CoV-2) diagnosis by RT-PCR to increase capacity for national testing programmes during a pandemic date: 2020-04-08 words: 1385 flesch: 54 summary: Capacity can be significantly increased without the extraction step but is dependent on the number of safety cabinets for swab processing and number of real time PCR thermal cyclers. We recommend this method is explored further by other medical laboratories using alternative PCR reagents to improve the resilience and capacity of virology laboratories during the pandemic. keywords: extraction; pcr; rna cache: cord-299737-r34d0rx7.txt plain text: cord-299737-r34d0rx7.txt item: #553 of 973 id: cord-299943-wzkh04dv author: Santhanam, Manikandan title: DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment date: 2020-08-18 words: 7358 flesch: 37 summary: In electrochemical DNA sensors, nucleic acid hybridization is coupled with the electrochemical reaction for selective detection of target DNA [13, 14] . To simplify DNA detection for point-of-care testing, other alternative approaches are being developed, namely, colorimetric keywords: amplification; approach; capture; detection; dna; electrochemical; electrode; hybridization; probe; reporter; rna; signal; surface; target; target dna cache: cord-299943-wzkh04dv.txt plain text: cord-299943-wzkh04dv.txt item: #554 of 973 id: cord-299944-1e44usl6 author: Gardner, Shea N. title: Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes date: 2014-08-03 words: 4148 flesch: 48 summary: JCVI has an automated degenerate PCR primer design system called JCVI Primer Designer, which is similar to run tiled primers in that it designs degenerate primers to tile across viral genomes [4] . By staggering the primer sets into different multiplex reactions, the amplification of overlapping primer regions created by the reverse primer from one set with the forward primer of the overlapping, adjacent primer set was eliminated. keywords: amplicons; genome; multiplex; pcr; primers; regions; sets; tiled cache: cord-299944-1e44usl6.txt plain text: cord-299944-1e44usl6.txt item: #555 of 973 id: cord-300243-5q67tnx4 author: Priya, A. Kokila title: Prevalence of enteropathogens and their antibiotic sensitivity pattern in puppies with hemorrhagic gastroenteritis date: 2017-08-04 words: 2997 flesch: 46 summary: C. difficile is identified to be a common enteropathogen in diarrheic as well as healthy puppies, yet its role in pathogenesis is not clearly understood. A variety of 20 species of bacteria and 10 species of fungi were isolated from the rectal swabs taken from healthy dogs [25] . keywords: canine; coli; dogs; pcr; puppies; toxin cache: cord-300243-5q67tnx4.txt plain text: cord-300243-5q67tnx4.txt item: #556 of 973 id: cord-300285-su2fueox author: Gajurel, Kiran title: Persistently positive severe acute respiratory syndrome coronavirus 2 (SARS‐COV2) nasopharyngeal PCR in a kidney transplant recipient date: 2020-07-27 words: 385 flesch: 46 summary: This is particularly relevant in transplant recipients who carry a significant mortality and morbidity associated with SARS COV2 infection. She had no fever or respiratory symptoms, and NP PCR was repeated to document clearance of the virus so that she could come back for follow-up clinic visits (two consecutive negative PCRs were required). keywords: covid-19; pcr cache: cord-300285-su2fueox.txt plain text: cord-300285-su2fueox.txt item: #557 of 973 id: cord-300313-w8njg569 author: Clifford, S. title: Strategies to reduce the risk of SARS-CoV-2 re-introduction from international travellers date: 2020-07-24 words: 7283 flesch: 45 summary: We consider the effectiveness of each strategy in reducing the number of infectious travellers who enter into the community and their remaining infectious duration. This effect is more pronounced when comparing a two-test scenario to a one-test scenario of equivalent duration ( Figure S1A , The additional impact of pre-flight testing on the number of infectious travellers entering the community was small, and was most effective if implemented the day prior to departure in scenarios with no post-flight testing ( Figure S2 ). . keywords: day; infectious; license; number; preprint; quarantine; test; testing; travellers cache: cord-300313-w8njg569.txt plain text: cord-300313-w8njg569.txt item: #558 of 973 id: cord-300316-r54ksiy3 author: Moesker, F.M. title: Diagnostic performance of influenza viruses and RSV rapid antigen detection tests in children in tertiary care date: 2016-03-25 words: 3353 flesch: 53 summary: Community-acquired pneumonia requiring hospitalization among U.S children Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: a systematic review and meta-analysis Global burden of respiratory infections due to seasonal influenza in young children: a systematic review and meta-analysis Diagnostic assays for respiratory syncytial virus disease Antigen-based assays for the identification of influenza virus and respiratory syncytial virus: why and how to use them in pediatric practice Update on influenza diagnostics: lessons from the novel H1N1 influenza A pandemic Accuracy of rapid influenza diagnostic tests: a meta-analysis WHO Recommendations on the Use of Rapid Testing for Influenza Diagnosis, World Health Organization Evaluation of five rapid diagnostic kits for influenza A/B virus Diagnostic performance of the BinaxNow Influenza A&B rapid antigen test in ED patients Performance of six influenza rapid tests in detecting human influenza in clinical specimens Low sensitivity of rapid diagnostic test for influenza Incidence of viral respiratory pathogens causing exacerbations in adult cystic fibrosis patients, Scand Development of a quantitative TaqMan RT-PCR for respiratory syncytial virus Rapid diagnosis of infections caused by respiratory syncytial virus Rapid viral diagnosis for acute febrile respiratory illness in children in the Emergency Department Impact of the availability of an influenza virus rapid antigen test on diagnostic decision making in a pediatric emergency department Impact of rapid influenza diagnostic test on physician estimation of viral infection probability in paediatric emergency department during epidemic period Performance of a rapid antigen test (Binax NOW ® RSV) for diagnosis of respiratory syncytial virus compared with real-time polymerase chain reaction in a pediatric population Host and viral factors affecting clinical performance of a rapid diagnostic test for respiratory syncytial virus in hospitalized children The influenza virus: disease, diagnostics, and treatment Evaluation of novel second-generation RSV and influenza rapid tests at the point of care Evaluation of a rapid antigen detection point-of-care test for respiratory syncytial virus and influenza in a pediatric hospitalized population in the Netherlands Identification of respiratory viruses with a novel point-of-care multianalyte antigen detection test in children with acute respiratory tract infection Performance of the Alere i influenza A&B assay and mariPOC test for the rapid detection of influenza A and B viruses Diagnostic performance of near-patient testing for influenza Prospective and retrospective evaluation of the Cepheid Xpert ® Flu/RSV XC assay for rapid detection of influenza A, influenza B, and respiratory syncytial virus key: cord-300316-r54ksiy3 authors: Moesker, F.M.; van Kampen, J.J.A.; Aron, G.; Schutten, M.; van de Vijver, D.A.M.C.; Koopmans, M.P.G.; Osterhaus, A.D.M.E.; Fraaij, P.L.A. title: Diagnostic performance of influenza viruses and RSV rapid antigen detection tests in children in tertiary care date: 2016-03-25 journal: J Clin Virol DOI: 10.1016/j.jcv.2016.03.022 sha: doc_id: 300316 cord_uid: r54ksiy3 BACKGROUND: keywords: bni; bnr; influenza; pcr; rsv; virus cache: cord-300316-r54ksiy3.txt plain text: cord-300316-r54ksiy3.txt item: #559 of 973 id: cord-300338-duhyb754 author: Urashima, Mitsuyoshi title: BCG Vaccination and Mortality of COVID-19 across 173 Countries: An Ecological Study date: 2020-08-03 words: 5682 flesch: 39 summary: An ecological study was conducted by obtaining data of 61 factors in 173 countries, including BCG vaccine coverage (%), using morbidity and mortality as outcomes, obtained from open resources. Only countries that had data of both total deaths and BCG vaccine coverage were included for analyses in this study. keywords: bcg; countries; covid-19; morbidity; mortality; pcr; population; tests; vaccine cache: cord-300338-duhyb754.txt plain text: cord-300338-duhyb754.txt item: #560 of 973 id: cord-300399-21xozruq author: Jayamohan, Harikrishnan title: SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations date: 2020-10-18 words: 13021 flesch: 38 summary: Recent studies on four different commercial antigen tests demonstrated a wide range of sensitivities from 16.7 to 85% (with 100% specificity) in COVID-19 clinical samples [113] . Such methods have been extensively reviewed [44, 163, 164] and will need to be validated with COVID-19 clinical samples. keywords: amplification; antibody; antigen; assay; collection; coronavirus; cov-2; covid-19; crispr; detection; diagnostic; novel; pandemic; patients; pcr; rna; samples; sars; sensitivity; sequencing; swabs; testing; tests cache: cord-300399-21xozruq.txt plain text: cord-300399-21xozruq.txt item: #561 of 973 id: cord-300508-po2zolo8 author: Inoue, Gen title: Experience of an Orthopaedic Surgery Department Early During the COVID-19 Outbreak in Japan Including Real-Time Polymerase Chain Reaction Assay Results for SARS-CoV-2 date: 2020-10-24 words: 3949 flesch: 43 summary: The incidence of abnormal values, which are commonly noted in COVID-19 patients, were eosinopaenia 37.5%; lymphopaenia 18.8%; thrombocytopaenia 8.3%; and elevated prothrombin time 10.4%. In COVID-19 patients with pneumonia and abnormal findings on chest computed tomography, the reported signs/symptoms at onset included fever (98%), cough (76%), myalgia or fatigue (44%), sputum production (28%), headache (8%), haemoptysis (5%), and diarrhoea (3%); and after a median time of eight days from the onset of illness, dyspnoea developed in 55% of 41 patients [17] . keywords: cases; covid-19; number; patients; pcr; sars; surgery cache: cord-300508-po2zolo8.txt plain text: cord-300508-po2zolo8.txt item: #562 of 973 id: cord-300685-bcjnujlj author: Poon, Leo L M title: Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) date: 2003-06-01 words: 2432 flesch: 50 summary: The disease is highly infectious, and attach rates Ͼ56% have been reported in healthcare workers caring for SARS patients (2 ) . Recently, we identified a novel virus in the family Coronaviridae in SARS patients (4 ) . keywords: assay; patients; pcr; rna; sars; virus cache: cord-300685-bcjnujlj.txt plain text: cord-300685-bcjnujlj.txt item: #563 of 973 id: cord-300999-20c17smt author: Xiao, Yong title: Exploration of turn-positive RT-PCR results and factors related to treatment outcome in COVID-19: A retrospective cohort study date: 2020-09-13 words: 3386 flesch: 48 summary: Notably, CT test results seem to be more convincing to explain the so-called recurrence. Levels of CD3, CD4, CD8, CD19, IgM, C3 complement, C4 complement and CT results were significantly correlated with the outcome of COVID-19. keywords: covid-19; group; negative; patients; pcr; results cache: cord-300999-20c17smt.txt plain text: cord-300999-20c17smt.txt item: #564 of 973 id: cord-301066-62qe4fb0 author: Chiu, Susan S. title: Human Coronavirus NL63 Infection and Other Coronavirus Infections in Children Hospitalized with Acute Respiratory Disease in Hong Kong, China date: 2005-06-15 words: 3958 flesch: 51 summary: A infection is an important cause of febrile seizures Cost-effectiveness of rapid diagnosis of viral respiratory tract infections in pediatric patients Evaluation of the Directigen FluA+B test for rapid diagnosis of influenza virus type A and B infections Rapid diagnosis of a coronavirus associated with severe acute respiratory syndrome (SARS) Identification of a novel coronavirus in patients with severe acute respiratory syndrome Detection of rhinovirus in sinus brushings of patients with acute community-acquired sinusitis by reverse transcription-PCR Frequent detection of human coronaviruses in clinical specimens from patients with respiratory tract infection by use of a novel real-time reverse-transcriptase polymerase chain reaction Coronavirus infection in acute lower respiratory tract disease of infants Epidemiology of coronavirus respiratory infections An outbreak of coronavirus OC43 respiratory infection in Normandy, France Performance of virus isolation and Directigen Flu A to detect influenza A virus in experimental human infection Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Coronavirus infections in military recruits: three-year study with coronavirus strains OC43 and 229E The association of viral and bacterial respiratory infections with exacerbations of wheezing in young asthmatic children We thank Bonnie Wong and Chiu Mei Pang, for technical support, and Wilfred H. S. Wong, for statistical analysis. All children admitted to Queen Mary Hospital with signs and symptoms of respiratory infection on one fixed day each week (Tuesday) were included in the study. keywords: children; coronavirus; hcov; infection; nl63; oc43; patients; pcr cache: cord-301066-62qe4fb0.txt plain text: cord-301066-62qe4fb0.txt item: #565 of 973 id: cord-301102-jbjysyqm author: Priestnall, Simon L. title: Quantification of mRNA encoding cytokines and chemokines and assessment of ciliary function in canine tracheal epithelium during infection with canine respiratory coronavirus (CRCoV) date: 2009-01-15 words: 6031 flesch: 40 summary: The development of an accurate method for the quantification of CRCoV in tissue samples enabled nucleocapsid gene RNA to be quantified in cDNA from canine tracheal cultures inoculated with CRCoV. The mean CRCoV nucleocapsid gene copy number within tracheal cultures from different dogs at 24-96 h post-inoculation was determined (Fig. 4) . Production of plasmid standards for real-time quantitative RT-PCR The following cytokines were selected for mRNA quantification in canine tracheal cultures; TNF-a, IL-6 and IL-8. keywords: canine; cells; crcov; cultures; cytokine; inoculation; levels; mrna; respiratory; tracheal cache: cord-301102-jbjysyqm.txt plain text: cord-301102-jbjysyqm.txt item: #566 of 973 id: cord-301167-101lnq4f author: Liu, Quanjun title: Microarray-in-a-Tube for Detection of Multiple Viruses date: 2007-02-01 words: 3256 flesch: 40 summary: Microarray detection is a good method, but requires complex procedures for multiple virus detection. Methods: We developed a novel PCR assay, the microarray-in-a-tube system, which integrates multiple PCR processes and DNA microarrays for multiple virus detection. keywords: detection; hybridization; microarray; pcr; probes; sars; system; tube; virus cache: cord-301167-101lnq4f.txt plain text: cord-301167-101lnq4f.txt item: #567 of 973 id: cord-301254-093yih5n author: Brittain-Long, Robin title: Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens—Duration of symptoms significantly affects detection rate date: 2010-01-18 words: 2860 flesch: 40 summary: Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses Development and implementation of a molecular diagnostic platform for daily rapid detection of 15 respiratory viruses Practical experience of high throughput real time PCR in the routine diagnostic virology setting Respiratory viruses and severe lower respiratory tract complications in hospitalized patients Enhanced identification of viral and atypical bacterial pathogens in lower respiratory tract samples with nucleic acid amplification tests Impact of rapid detection of viral and atypical bacterial pathogens by real-time polymerase chain reaction for patients with lower respiratory tract infection Surveillance of respiratory virus infections in adult hospital admissions using rapid methods High prevalence of respiratory viral infections in patients hospitalized in an intensive care unit for acute respiratory infections as detected by nucleic acid-based assays Detection of respiratory viruses by molecular methods A recently identified rhinovirus genotype is associated with severe respiratory-tract infection in children in Germany Rhinovirus associated with severe lower respiratory tract infections in children Rapid multiplex nested PCR for detection of respiratory viruses Influenza diagnosis: from dark isolation into the molecular light West of Scotland Respiratory Virus Study Group Multiplex real-time PCR for detection of respiratory tract infections Duration of influenza A virus shedding in hospitalized patients and implications for infection control Aetiological role of viral and bacterial infections in acute adult lower respiratory tract infection (LRTI) in primary care Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay Viral etiology of common cold in children Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Human picornavirus and coronavirus RNA in nasopharynx of children without concurrent respiratory symptoms Predominance of rhinovirus in the nose of symptomatic and asymptomatic infants Persistence of rhinovirus and enterovirus RNA after acute respiratory illness in children Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 Respiratory viral infections in transplant recipients Respiratory virus infection among hematopoietic cell transplant recipients: evidence for asymptomatic parainfluenza virus infection Correlation of viral load as determined by real-time RT-PCR and clinical characteristics of respiratory syncytial virus lower respiratory tract infections in early infancy Human respiratory syncytial virus (hRSV) RNA quantification in nasopharyngeal secretions identifies the hRSV etiologic role in acute respiratory tract infections of hospitalized infants Respiratory picornavirus infections in Korean children with lower respiratory tract infections Detection and typing by molecular techniques of respiratory viruses in children hospitalized for acute respiratory infection in Rome, Italy Multiple simultaneous viral infections in infants with acute respiratory tract infections in Spain Real-time polymerase chain reaction (PCR) techniques are gaining increasing acceptance for diagnosis of viral respiratory tract infections (RTI). keywords: detection; infections; patients; pcr; respiratory; symptoms cache: cord-301254-093yih5n.txt plain text: cord-301254-093yih5n.txt item: #568 of 973 id: cord-301430-gzou8b9k author: Beier, D. title: Establishment of a new bovine leukosis virus producing cell line date: 2004-08-17 words: 4098 flesch: 52 summary: Furthermore, it is possible to use a wide range of passages of cell line PO714 for BLV antigen production: there were no Table 2 Analysis of BLV antigen prepared from cell line PO714 after the 23rd and 69th subculture by means of AGID using gp51-and p24-specific reference sera Antigens presented in the table were prepared after the second (23rd subculture) and fourth (69th subculture) harvest of cell culture supernatant, respectively. Although many attempts have been made either to improve the antigen-producing properties of existing permanent bovine leukosis virus (BLV) expressing cell lines or to generate corresponding new lines (Graves and Ferrer, 1976; Mamoun et al., 1981; Altaner et al., 1985; Altanerova et al., 1989; Wagner et al., 1995) , the cell line FLK/BLV still is the one that is used mainly for BLV antigen production for commercial diagnostic test kits. keywords: antigen; blv; bovine; cell; culture; line; pcr; po714; sera; virus cache: cord-301430-gzou8b9k.txt plain text: cord-301430-gzou8b9k.txt item: #569 of 973 id: cord-301695-zl7cjs1k author: Wang, Ji title: Identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge, Guyana date: 2019-12-31 words: 3071 flesch: 47 summary: Tissue samples from the two deceased subjects (No. 1 and No. 2) were cut into 5 mm 3 pieces, then put into freeze-storage tubes containing 500 μL sterile phosphate-buffered saline and repeatedly homogenized using an electric tissue grinder for 30 s with 1 min intervals until the tissues were completely dispersed. The presenting clinical symptoms of the patients and the mortality rate (10%-20%) were in accordance with those expected for Histoplasma infection [17, 18] . keywords: disease; histoplasma; ngs; patient; pcr; sequencing; time; tissue; virus cache: cord-301695-zl7cjs1k.txt plain text: cord-301695-zl7cjs1k.txt item: #570 of 973 id: cord-301720-majpfxqn author: Saadat, Yousef title: Molecular characterization of infectious bronchitis viruses isolated from broiler flocks in Bushehr province, Iran: 2014 - 2015 date: 2017-09-15 words: 2841 flesch: 45 summary: Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran Detection and identification of infectious bronchitis virusby RT-PCR in Iran Detection of the Italy 02 strain of infectious bronchitis virus in the UK Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods Molecular analysis of the 793/B serotype of IBV in Great Britain Relationship between sequence variation in the S1 spike protein of infectious bronchitis virus and the extent of cross-protection in vivo Molecular studies on infectious bronchitis virus isolated in Poland Factors influencing the outcome of infectious bronchitis vaccination and challenge experiments Genotypes of infectious bronchitis viruses circulating in the Middle East between Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus indicates the emergence of a new genotype in the Middle East Genotyping of infectious bronchitis viruses from broiler farmsin Iraq during 2014-2015 Emergence of a novel genotype of avian infectious bronchitis virus in Egypt Al saad S. Presence of infectious bronchitis virus strain CK/CH/LDL/97I in the Middle East Presence of IS/1494/06 genotype-related infectious bronchitis virus in breeder and broiler flocks in Turkey Detection and molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 Detection of variant infectious bronchitis viruses in broiler flocks in Libya Identification of a novel nephropathogenic infectious bronchitis virus in Israel Phylogenetic study of Iranian infectious bronchitis virus isolates during 2010 -2011 using glycoprotein S1 gene A survey of the prevalence of infectious bronchitis virus type 4/91 in Iran Investigation and molecular characterization of avian infectious bronchitis virus in suspected broiler farms in Slemani Governorate The results emphasize the need for new control strategies and re-arrangement of preventative measure of IBV in Bushehr, Iran. One of a series of the Veterinary medicine-large animal clinical sciences department, Florida cooperative extension service Avian infectious bronchitis virus Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand Severe acute respiratory syndrome vaccine development experiences of vaccination against avian infectious bronchitis coronavirus Coronaviruses: Structure and genome expression Cloning and sequencing of genes encoding structural proteins of avian infectious bronchitis virus Structural characterization of the spike protein The coronavirus surface glycoprotein Amino acids within hypervariable region 1 of avian coronavirus IBV (Massachusetts serotype) spike glycoprotein are associated with neutralization epitopes Antigenic domains on the peplomer protein of avian infectious bronchitis virus: correlation with biological functions Identification of amino acids involved in a serotype and neutralization specific epitope within the S1 subunit of avian infectious bronchitis virus Structural polypeptides of coronavirus IBV Coronavirus proteins: Structure and function of the oligosaccharides of the avian infectious bronchitis virus glycoproteins Molecular Biology and Pathogenesis of Coronaviruses Monoclonal antibodies to the S1 spike and membrane proteins of avian infectious bronchitis virus coronavirus strain Massachusetts M41 Coronavirus IBV: keywords: bronchitis; flocks; ibv; iran; pcr; virus; viruses cache: cord-301720-majpfxqn.txt plain text: cord-301720-majpfxqn.txt item: #571 of 973 id: cord-301823-fbeb1nw1 author: Sridhar, Sushmita title: A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities date: 2020-10-21 words: 6124 flesch: 46 summary: key: cord-301823-fbeb1nw1 authors: Sridhar, Sushmita; Forrest, Sally; Kean, Iain; Young, Jamie; Bartholdson Scott, Josefin; Maes, Mailis; Pereira-Dias, Joana; Parmar, Surendra; Routledge, Matthew; Sparkes, Dominic; Rivett, Lucy; Dougan, Gordon; Weekes, Michael; Curran, Martin; Goodfellow, Ian; Baker, Stephen title: A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities date: 2020-10-21 journal: Eurosurveillance Editorial Team: Updated rapid risk assessment from ECDC on the novel coronavirus disease 2019 (COVID-19) pandemic: increased transmission in the EU/EEA and the UK Challenges for NHS hospitals during covid-19 epidemic COVID-19: towards controlling of a pandemic PubMed Abstract | Publisher Full Text | Free Full Text The Laboratory Diagnosis of COVID-19: Current Issues and Challenges Virological assessment of hospitalized patients with COVID-2019 RT-qPCR detection of SARS-COV-2 RNA from patient nasopharyngeal swab using qiagen rneasy kits or directly via omission of an rna extraction step Rapid and simple method for purification of nucleic acids The use of control charts in the clinical laboratory Performance characteristics of rules for internal quality control: probabilities for false rejection and error detection countries: COVID-19 and risks to the supply and quality of tests, drugs, and vaccines PubMed Abstract | Publisher Full Text | Free Full Text A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities: extended data We wish to acknowledge all involved from the onset in giving their time, effort, and knowledge in getting this going. keywords: assay; cov2; covid-19; data; hospital; laboratory; pcr; plate; samples; sars; staff cache: cord-301823-fbeb1nw1.txt plain text: cord-301823-fbeb1nw1.txt item: #572 of 973 id: cord-302024-zz7mt6be author: Hakhverdyan, Mikhayil title: Evaluation of a single-tube fluorogenic RT-PCR assay for detection of bovine respiratory syncytial virus in clinical samples date: 2004-11-17 words: 3713 flesch: 47 summary: Vaccine Bovine respiratory syncytial virus Local and systemic antibody response to bovine respiratory syncytial virus infection and reinfection in calves with and without maternal antibodies Diagnosis of enzootic pneumonia in Danish cattle: reverse transcription-polymerase chain reaction assay for detection of bovine respiratory syncytial virus in naturally and experimentally infected cattle Identifying bovine respiratory syncytial virus by reverse transcription-polymerase chain reaction and oligonucleotide hybridizations Detection of all seven serotypes of foot-andmouth disease virus by real-time, fluorogenic reverse transcription polymerase chain reaction assay A survey of virus infections of the respiratory tract of cattle and their association with disease An experimental infection model for reproduction of calf pneumonia with bovine respiratory syncytial virus (BRSV) based on one combined exposure of calves Viral aetiology of enzootic pneumonia in Danish dairy herds: diagnostic tools and epidemiology Evaluation of a nested reverse transcription-PCR assay based on the nucleoprotein gene for diagnosis of spontaneous and experimental bovine respiratory syncytial virus infections Evolution of bovine respiratory syncytial virus Development of nested PCR assays for detection of bovine respiratory syncytial virus in clinical samples Sites of replication of bovine respiratory syncytial virus in naturally infected calves as determined by in situ hybridization Cytokine responses of bovine dendritic cells and T cells following exposure to live or inactivated bovine respiratory syncytial virus A comparison of diagnostic methods for the detection of bovine respiratory syncytial virus in experimental clinical specimens BRSV nested PCR results from analyses on the same RNA templates as described in Fig. keywords: assay; brsv; detection; frt; pcr; samples; virus cache: cord-302024-zz7mt6be.txt plain text: cord-302024-zz7mt6be.txt item: #573 of 973 id: cord-302189-3xab3yxc author: Tillmann, Ramona Liza title: Sensitive Commercial NASBA Assay for the Detection of Respiratory Syncytial Virus in Clinical Specimen date: 2007-12-26 words: 1778 flesch: 35 summary: Hospitalized children with respiratory syncytial virus infection and neuromuscular impairment face an increased risk of a complicated course Human metapneumovirus infections cause similar symptoms and clinical severity as respiratory syncytial virus infections Viral etiology of acute respiratory tract infections in children presenting to hospital: role of polymerase chain reaction and demonstration of multiple infections Bronchiolitis: assessment and evidence-based management Community-acquired pneumonia in children Selected populations at increased risk from respiratory syncytial virus infection Respiratory syncytial virus infections in the pediatric intensive care unit: clinical characteristics and risk factors for adverse outcomes Palivizumab prophylaxis reduces hospitalization due to respiratory syncytial virus in young children with hemodynamically significant congenital heart disease Prospective population-based study of viral lower respiratory tract infections in children under 3 years of age (the PRI.DE study) Therefore, the FDA cleared CE marked NOW® RSV ELISA, the NucliSENS® EasyQ RSV A+B NASBA, and a literature based inhouse RT-PCR protocol were compared for their relative sensitivities. keywords: elisa; pcr; rsv cache: cord-302189-3xab3yxc.txt plain text: cord-302189-3xab3yxc.txt item: #574 of 973 id: cord-302207-ljpfgih2 author: Lichtmannsperger, Katharina title: Molecular characterization of Giardia intestinalis and Cryptosporidium parvum from calves with diarrhoea in Austria and evaluation of point-of-care tests date: 2019-07-12 words: 4497 flesch: 45 summary: Tpi negative Giardia samples were further analysed amplifying a fragment of the small subunit rRNA (SSU rRNA) using nested PCR [41, 42] . IFA results were used as a reference for the calculation of performance criteria of the FASTest ® Giardia and PCM results for the validation of FASTest ® Crypto. keywords: assemblage; calves; cryptosporidium; giardia; pcr; samples; subtype; weeks cache: cord-302207-ljpfgih2.txt plain text: cord-302207-ljpfgih2.txt item: #575 of 973 id: cord-302296-7ge92p69 author: Lilleeng, Einar title: Comparison of intestinal gene expression in Atlantic cod (Gadus morhua) fed standard fish meal or soybean meal by means of suppression subtractive hybridization and real-time PCR date: 2007-07-03 words: 6493 flesch: 47 summary: In the present study we used molecular tools like suppression subtractive hybridization (SSH) and realtime PCR to gain information on possible changes in intestinal gene expression in Atlantic cod fed SBM compared to Atlantic cod fed FM. key: cord-302296-7ge92p69 authors: Lilleeng, Einar; Frøystad, Marianne K.; Vekterud, Kristin; Valen, Elin C.; Krogdahl, Åshild title: Comparison of intestinal gene expression in Atlantic cod (Gadus morhua) fed standard fish meal or soybean meal by means of suppression subtractive hybridization and real-time PCR date: 2007-07-03 journal: Aquaculture DOI: 10.1016/j.aquaculture.2007.01.048 sha: doc_id: 302296 cord_uid: 7ge92p69 Gene expression was studied in Atlantic cod fed two different diets, fish meal (FM) and dehulled and extracted soybean meal (SBM). keywords: acid; atlantic; cdna; clone; cod; et al; expression; fed; fish; gh4a; pcr; protein; sbm cache: cord-302296-7ge92p69.txt plain text: cord-302296-7ge92p69.txt item: #576 of 973 id: cord-302459-grs2x26l author: Matin, Farhana title: A Plasma Biomarker Panel of Four MicroRNAs for the Diagnosis of Prostate Cancer date: 2018-04-27 words: 8323 flesch: 39 summary: The translational potential of microRNAs as biofluid markers of urological tumours Phase 2 study of circulating microRNA biomarkers in castration-resistant prostate cancer Human seminal fluid as a source of prostate cancer-specific microRNA biomarkers Discovery of circulating microRNAs associated with human prostate cancer using a mouse model of disease Circulating microRNAs predict biochemical recurrence in prostate cancer patients MicroRNA Theranostics in Prostate Cancer Precision Medicine miRNet -dissecting miRNA-target interactions and functional associations through network-based visual analysis Circulating microRNA profiling identifies a subset of metastatic prostate cancer patients with evidence of cancerassociated hypoxia Plasma miRNAs as biomarkers to identify patients with castration-resistant metastatic prostate cancer Effects of pooling samples on the performance of classification algorithms: a comparative study Next Generation Sequencing of Pooled Samples: Guideline for Variants' Filtering Operating characteristics of prostate-specific antigen in men with an initial PSA level of 3.0 ng/ml or lower Prostate-specific antigen and prostate cancer: prediction, detection and monitoring Diagnostic, prognostic and predictive value of cell-free miRNAs in prostate cancer: a systematic review A circulating miRNA assay as a first-line test for prostate cancer screening PSA testing for men at average risk of prostate cancer Prostate-Specific Antigen (PSA)-Based Population Screening for Prostate Cancer: An Evidence-Based Analysis Phase of care prevalence for prostate cancer in New South Wales, Australia: A population-based modelling study Prostate cancer screening in Australia: Position statement Screening for prostate cancer: U.S. Preventive Services Task Force recommendation statement The relationship between amniotic fluid miRNAs and congenital obstructive nephropathy A Computational Approach for Predicting Role of Human MicroRNAs in MERS-CoV Genome Novel diagnostic and prognostic classifiers for prostate cancer identified by genome-wide microRNA profiling A novel microRNAs expression signature for hepatocellular carcinoma diagnosis and prognosis MicroRNA-98 Suppress Warburg Effect by Targeting HK2 in Colon Cancer Cells miR-98 inhibits expression of TWIST to prevent progression of non-small cell lung cancers MicroRNA-98-5p inhibits cell proliferation and induces cell apoptosis in hepatocellular carcinoma via targeting IGF2BP1 Meta-analysis of miRNA expression profiles for prostate cancer recurrence following radical prostatectomy miR-152 controls migration and invasive potential by targeting TGFalpha in prostate cancer cell lines MicroRNA profiling of novel African American and Caucasian Prostate Cancer cell lines reveals a reciprocal regulatory relationship of miR-152 and DNA methyltranferase 1 Clinical significance of miRNA host gene promoter methylation in prostate cancer Evaluation of Plasma miR-21 and miR-152 as Diagnostic Biomarkers for Common Types of Human Cancers Extracellular vesicle transfer of cancer pathogenic components Exosomal tumor microRNA modulates premetastatic organ cells MicroRNAs and metastasis: small RNAs play big roles Exosomes in diagnosis and therapy of prostate cancer Plasma Exosomal miRNAs in Persons with and without Alzheimer Disease: key: cord-302459-grs2x26l authors: Matin, Farhana; Jeet, Varinder; Moya, Leire; Selth, Luke A.; Chambers, Suzanne; Clements, Judith A.; Batra, Jyotsna title: A Plasma Biomarker Panel of Four MicroRNAs for the Diagnosis of Prostate Cancer date: 2018-04-27 journal: Sci Rep DOI: 10.1038/s41598-018-24424-w sha: doc_id: 302459 cord_uid: grs2x26l Prostate cancer is diagnosed in over 1 million men every year globally, yet current diagnostic modalities are inadequate for identification of significant cancer and more reliable early diagnostic biomarkers are necessary for improved clinical management of prostate cancer patients. keywords: analysis; cancer; cell; cohort; data; discovery; expression; mir-152; mirna; patients; plasma; prostate; prostate cancer; samples; study; validation cache: cord-302459-grs2x26l.txt plain text: cord-302459-grs2x26l.txt item: #577 of 973 id: cord-302486-z36hcvrx author: Cobo, Fernando title: Diagnostic approaches for viruses and prions in stem cell banks date: 2006-03-30 words: 7277 flesch: 32 summary: However, viral contamination of cell cultures and feeder cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus detection and the potential to cause serious disease in recipients of these cell products (Cobo et al., 2005) . Viral and prion contamination of cell cultures and “feeder” cells, which is a common risk in all biotechnological products derived from the cell lines, is the most challenging and potentially serious outcome to address, due to the difficulty involved in virus and prion detection and the potential to cause serious disease in recipients of these cell products. keywords: cell; culture; detection; et al; human; lines; method; microscopy; pcr; prion; products; protein; prp; stem; tests; viruses cache: cord-302486-z36hcvrx.txt plain text: cord-302486-z36hcvrx.txt item: #578 of 973 id: cord-302503-7s9f8wje author: Fu, Yuguang title: Rapid and efficient detection methods of pathogenic swine enteric coronaviruses date: 2020-05-19 words: 6360 flesch: 33 summary: Multiplex nested RT-PCR for the detection of porcine enteric viruses SARS-CoV and emergent coronaviruses: viral determinants of interspecies transmission Field validation of a commercial blocking ELISA to differentiate antibody to transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus and to identify TGEV-infected swine herds Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification Interspecies transmission and emergence of novel viruses: lessons from bats and birds Complete genome sequence of a variant porcine epidemic diarrhea virus strain isolated in China Full-length genome characterization of Chinese porcine deltacoronavirus strain CH/ SXD1/2015 Molecular epidemiology of porcine epidemic diarrhea virus in China Pathogenicity and pathogenesis of a United States porcine deltacoronavirus cell culture isolate in 5-day-old neonatal piglets Detection and characterization of group C rotaviruses in asymptomatic piglets in Ireland Development of a multiplex RT-PCR for the detection of major diarrhoeal viruses in pig herds in China Transmissible gastroenteritis virus infection induces NF-kappaB activation through RLR-mediated signaling Porcine deltacoronavirus in mainland China A transmissible gastroenteritis in pigs Transmissible gastroenteritis: demonstration of the virus from field specimens by means of cell culture and pig inoculation SYBR Green real-time reverse transcription-polymerase chain reaction assay for the generic detection of coronaviruses Transmissible gastroenteritis Epidemiological survey of porcine epidemic diarrhea virus in swine farms in A new bat-HKU2-like coronavirus in swine Serological evidence of infection with a coronavirus related to transmissible gastroenteritis virus and porcine epidemic diarrhea virus Establishment and application of a multiplex RT-PCR to differentiate wild-type and vaccine strains of porcine epidemic diarrhea virus Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan Development of a one-step RT-PCR assay for detection of pancoronaviruses (alpha-, beta-, gamma-, and delta-coronaviruses) using newly designed degenerate primers for porcine and avian`fecal samples A TaqManprobe-based multiplex real-time RT-qPCR for simultaneous detection of porcine enteric coronaviruses Porcine deltacoronavirus infection: etiology, cell culture for virus isolation and propagation, molecular epidemiology and pathogenesis Porcine epidemic diarrhea virus infection: etiology, epidemiology, pathogenesis and immunoprophylaxis Viral load quantitation of SARS-coronavirus RNA using a one-step real-time RT-PCR Development of a reverse transcription-nested polymerase chain reaction assay for differential diagnosis of transmissible gastroenteritis virus and porcine respiratory coronavirus from feces and nasal swabs of infected pigs Multiplex real-time RT-PCR for the simultaneous detection and quantification of transmissible gastroenteritis virus and porcine epidemic diarrhea virus Differential detection of transmissible gastroenteritis virus and porcine epidemic diarrhea virus by duplex RT-PCR Isolation and serial propagation of porcine epidemic diarrhea virus in cell cultures and partial characterization of the isolate Porcine respiratory coronavirus: molecular features and virus-host interactions Detection and characterization of distinct alphacoronaviruses in five different bat species in Denmark Genetic differentiation of the nucleocapsid protein of Korean isolates of porcine epidemic diarrhoea virus by RT-PCR based restriction fragment length polymorphism analysis Complete genome characterization of Korean porcine deltacoronavirus strain KOR/KNU14-04 Full-length genome sequence of porcine deltacoronavirus strain USA/IA/2014/8734 New variants of porcine epidemic diarrhea virus, China Detection and differentiation of five diarrhea related pig viruses utilizing a multiplex PCR assay A TaqMan probe-based real-time PCR to differentiate porcine epidemic diarrhea virus virulent strains from attenuated vaccine strains Reverse transcription-PCR assays for the differentiation of various US porcine epidemic diarrhea virus strains Origin, evolution, and virulence of porcine deltacoronaviruses in the United States Rapid detection, complete genome sequencing, and phylogenetic analysis of porcine deltacoronavirus A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium The first case of porcine epidemic diarrhea in Canada Discovery of a novel swine enteric alphacoronavirus (SeACoV) in southern China Cloning and further sequence analysis of the ORF3 gene of wild-and attenuated-type porcine epidemic diarrhea viruses Detection of transmissible gastroenteritis virus by RT-PCR and differentiation from porcine respiratory coronavirus Isolation of a porcine respiratory, non-enteric coronavirus related to transmissible gastroenteritis A new coronavirus-like particle associated with diarrhea in swine Complete genome sequence of transmissible gastroenteritis coronavirus PUR46-MAD clone and evolution of the purdue virus cluster Development of reverse transcription loop-mediated isothermal amplification for rapid detection of porcine epidemic diarrhea virus Rapid detection of swine transmissible gastroenteritis virus by nested polymerase chain reaction Comparative pathogenesis of enteric viral infections of swine Isolation of porcine epidemic diarrhea virus in porcine cell cultures and experimental infection of pigs of different ages Development and optimization of a sensitive TaqMan(R) real-time PCR with synthetic homologous extrinsic control for quantitation of Human cytomegalovirus viral load Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: identification, prevalence and full-length genome sequence analysis Differentiation of a Vero cell adapted porcine epidemic diarrhea virus from Korean field strains by restriction fragment length polymorphism analysis of ORF 3 Emergence of porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences A novel duplex TaqMan probebased real-time RT-qPCR for detecting and differentiating classical and variant porcine epidemic diarrhea viruses An immunohistochemical investigation of porcine epidemic diarrhoea Epidemiology and vaccine of porcine epidemic diarrhea virus in China: a mini-review Outbreak of porcine epidemic diarrhea in suckling piglets An outbreak of swine diarrhea of a new-type associated with coronavirus-like particles in Japan Development of a TaqMan MGB RT-PCR for the rapid detection of H3 subtype avian influenza virus circulating in China Evidence of recombinant strains of porcine epidemic diarrhea virus Solid phase immune electron microscopy for diagnosis of transmissible gastroenteritis in pigs A real-time TaqMan RT-PCR assay with an internal amplification control for rapid detection of transmissible gastroenteritis virus in swine fecal samples A pancoronavirus RT-PCR assay for detection of all known coronaviruses Reverse transcription cross-priming amplificationnucleic acid test strip for rapid detection of porcine epidemic diarrhea virus Rapid detection of transmissible gastroenteritis virus in swine small intestine samples using real-time reverse transcription recombinase polymerase amplification Detection and genetic characterization of deltacoronavirus in pigs Development and evaluation of a duplex real-time RT-PCR for detection and differentiation of virulent and variant strains of porcine epidemic diarrhea viruses from the United States Simultaneous detection of five pig viruses associated with enteric disease in pigs using EvaGreen real-time PCR combined with melting curve analysis Evidence for a porcine respiratory coronavirus, antigenically similar to transmissible gastroenteritis virus, in the United States Coronavirus genomics and bioinformatics analysis Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus Ultrasensitive detection of porcine epidemic diarrhea virus from fecal samples using functionalized nanoparticles Whole-genome analysis of porcine epidemic diarrhea virus (PEDV) from eastern China Genetic variation analysis of reemerging porcine epidemic diarrhea virus prevailing in central China from Development of a nanoparticle-assisted PCR assay for detection of porcine epidemic diarrhea virus Porcine deltacoronavirus: overview of infection dynamics, diagnostic methods, prevalence and genetic evolution Evaluation of two singleplex reverse transcription-Insulated isothermal PCR tests and a duplex real-time RT-PCR test for the detection of porcine epidemic diarrhea virus and porcine deltacoronavirus A multiplex RT-PCR assay for rapid and differential diagnosis of four porcine diarrhea associated viruses in field samples from pig farms in East China from 2010 to 2012 Development of a multiplex TaqMan probe-based real-time PCR for discrimination of variant and classical porcine epidemic diarrhea virus Development of a TaqMan-based real-time RT-PCR assay for the detection of SADS-CoV associated with severe diarrhea disease in pigs Comparison and evaluation of conventional RT-PCR, SYBR green I and TaqMan real-time RT-PCR assays for the detection of porcine epidemic diarrhea virus Development of TaqMan real-time reverse transcription-polymerase chain reaction for the detection and quantitation of porcine kobuvirus A sensitive duplex nanoparticle-assisted PCR assay for identifying porcine epidemic diarrhea virus and porcine transmissible gastroenteritis virus from clinical specimens Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations In October 2010, a severe PED outbreak caused by a highly virulent PEDV variant emerged in southern China with high mortality ranging from 70 to 100%; the result was devastating damage to the pig farm industry and tremendous economic losses, and later, the PEDV variant spreads to other countries, e.g., USA, Canada, and Mexico ( For the early and rapid detection of PEDV, different types of PCR methods have been developed. keywords: assay; detection; diarrhea; et al; gene; pcr; pedv; porcine; time; virus cache: cord-302503-7s9f8wje.txt plain text: cord-302503-7s9f8wje.txt item: #579 of 973 id: cord-302713-h3aoag4y author: Jauréguiberry, Stéphane title: Clinical and Microbiological Evaluation of Travel‐Associated Respiratory Tract Infections in Travelers Returning From Countries Affected by Pandemic A(H1N1) 2009 Influenza date: 2011-12-08 words: 3014 flesch: 45 summary: The main etiological agents were influenza A(H1N1) 2009 (18%), influenza viruses (14%), and rhinovirus (20%). 3 Seroconversion for influenza virus was confirmed in 12% of 211 febrile Swiss travelers compared with 2.8% for all Swiss travelers surveyed; the incidence was estimated to be around one influenza-associated event per 100 person-months abroad. keywords: a(h1n1; influenza; patients; rti; travelers; virus; viruses cache: cord-302713-h3aoag4y.txt plain text: cord-302713-h3aoag4y.txt item: #580 of 973 id: cord-302819-oj33i2ma author: Pasick, J title: Investigation into the Role of Potentially Contaminated Feed as a Source of the First-Detected Outbreaks of Porcine Epidemic Diarrhea in Canada date: 2014-08-07 words: 7964 flesch: 48 summary: Because the negative control group from this bioassay was co-mingled with the experimental groups, negative control piglets were not available for microscopic examination. Thus, negative control piglets from the second bioassay experiment euthanized at 12 dpi were used for the histopathology and immunohistochemistry observations. keywords: animals; contact; control; diarrhea; dpi; feed; gene; group; pcr; pedv; piglets; porcine; samples; sdpp; virus cache: cord-302819-oj33i2ma.txt plain text: cord-302819-oj33i2ma.txt item: #581 of 973 id: cord-302829-1o1jo8uk author: Chen, Hao-tai title: Rapid detection of porcine circovirus type 2 by loop-mediated isothermal amplification date: 2008-03-19 words: 2822 flesch: 38 summary: The detection rate of PCV2 LAMP for 86 clinical samples was 96.5% and appeared greater than that of the PCR method. Overall, the detection rate of PCV2 LAMP for 86 clinical tissue samples was 96.5% and appeared better than that for the PCR method. keywords: detection; lamp; pcr; pcv2; porcine; syndrome cache: cord-302829-1o1jo8uk.txt plain text: cord-302829-1o1jo8uk.txt item: #582 of 973 id: cord-302871-x3mjov5l author: Ribeiro, Juliane title: Extra-intestinal detection of canine kobuvirus in a puppy from Southern Brazil date: 2016-11-25 words: 2593 flesch: 39 summary: key: cord-302871-x3mjov5l authors: Ribeiro, Juliane; Headley, Selwyn Arlington; Diniz, Jaqueline Assumpção; Pereira, Alfredo Hajime Tanaka; Lorenzetti, Elis; Alfieri, Amauri Alcindo; Alfieri, Alice Fernandes title: Extra-intestinal detection of canine kobuvirus in a puppy from Southern Brazil date: 2016-11-25 journal: This study presents the pathological, immunohistochemical, and molecular findings associated with the extra-intestinal detection of canine kobuvirus (CaKV) in a 5-month-old Chihuahua puppy, that had a clinical history of bloody-tinged feces. keywords: cakv; canine; cdv; kobuvirus; pcr; puppy; tissues cache: cord-302871-x3mjov5l.txt plain text: cord-302871-x3mjov5l.txt item: #583 of 973 id: cord-303289-qoukiqr7 author: Hemida, M. G. title: Coronavirus infections in horses in Saudi Arabia and Oman date: 2017-03-13 words: 2821 flesch: 44 summary: Presence of antibodies but no evidence for circulation of MERS-CoV in dromedaries on the Canary Islands Characterization of a coronavirus isolated from a diarrheic foal Seroepidemiology of Middle East respiratory syndrome (MERS) coronavirus in Saudi Arabia (1993) and Australia (2014) and characterisation of assay specificity Middle East Respiratory Syndrome (MERS) coronavirus seroprevalence in domestic livestock in Saudi Arabia Development of an equine coronavirus-specific enzyme-linked immunosorbent assay to determine serologic responses in naturally infected horses Human infection with MERS coronavirus after exposure to infected camels Serologic assessment of possibility for MERS-CoV infection in equids Absence of middle east respiratory syndrome coronavirus in camelids First detection of equine coronavirus (ECoV) in Europe Epidemic of equine coronavirus at Obihiro Racecourse, Hokkaido, Japan in 2012 Kinetics of serologic responses to MERS coronavirus infection in humans Seroepidemiology for MERS coronavirus using microneutralisation and pseudoparticle virus neutralisation assays reveal a high prevalence of antibody in dromedary camels in Egypt Prevalence of equine coronavirus in nasal secretions from horses with fever and upper respiratory tract infection Geographic distribution of MERS coronavirus among dromedary camels Middle East respiratory syndrome coronavirus (MERS-CoV) Isolation and characterization of dromedary camel coronavirus UAE-HKU23 from dromedaries of the middle east: Minimal serological cross-reactivity between MERS coronavirus and dromedary camel coronavirus UAE-HKU23 Novel betacoronavirus in dromedaries of the Middle East SUPPORTING INFORMATION There were twenty-four sera with undetectable antibody to BCoV with detectable ECoV antibody titres ranging from 20 to 640. keywords: bcov; coronavirus; ecov; hku23; horses; mers cache: cord-303289-qoukiqr7.txt plain text: cord-303289-qoukiqr7.txt item: #584 of 973 id: cord-303588-bwllypvq author: Ababneh, Mustafa title: High-resolution melting curve analysis for infectious bronchitis virus strain differentiation date: 2020-03-03 words: 3150 flesch: 54 summary: Viral RNA of these samples and IBV vaccine strains were extracted, then went through cDNA synthesis, and then nested PCR amplification of a spike 1 gene fragment. IBV strains can be classified into six genotypes that together comprise 32 distinct viral lineages, the majority of which belong to genotype 1 keywords: cluster; field; gene; hrm; ibv; pcr; strains cache: cord-303588-bwllypvq.txt plain text: cord-303588-bwllypvq.txt item: #585 of 973 id: cord-303665-l57e54hu author: Lahrich, S. title: Review on the contamination of wastewater by COVID-19 virus: Impact and treatment date: 2020-09-10 words: 5853 flesch: 35 summary: It enables rapid virus detection (virus detection using lab-on-a-chip methods takes 7 to 16 minutes)  Some of these methods have been modified by: i) concentration (ELISA tests, PCR and NASBA reactions, application of microarrays) (Li et al., 2002; Alhamlan et al., 2013; Kittigul et al., 2000) , ii) combination of different methods (PCR reaction combined with plate-forming tests, atomic force microscopy combined with protein microarray technology) (Straub et al., 1995; Haab et al., 2001; Zhu et al., 2001) , iii) change in the pore size of the filter (epifluorescence microscopy) (Weinbauer and Suttle, 1997) , iv) dilution of the sample (flow cytometry) keywords: coronavirus; cov-2; covid-19; detection; environment; et al; health; methods; pcr; sars; sewage; treatment; viruses; wastewater cache: cord-303665-l57e54hu.txt plain text: cord-303665-l57e54hu.txt item: #586 of 973 id: cord-303697-oj05bstn author: YOSHIMURA, Kuniko title: Detection of Sirtuin-1 protein expression in peripheral blood leukocytes in dogs date: 2018-05-11 words: 3783 flesch: 44 summary: Thus SIRT1 expression was evaluated by measuring mRNA transcription, tissue SIRT1 protein expression or plasma SIRT1 concentration in association with nutritional conditions or diseases [10, 21, 23, 24, 29, 35, 36, 38, 49] . SIRT1 regulates circadian clock gene expression through PER2 deacetylation A low dose of dietary resveratrol partially mimics caloric restriction and retards aging parameters in mice SIRT1 mediates central circadian control in the SCN by a mechanism that decays with aging Increase in activity during calorie restriction requires Sirt1 Tumor suppressor HIC1 directly regulates SIRT1 to modulate Calorie restriction on insulin resistance and expression of SIRT1 and SIRT4 in rats Calorie restriction promotes mammalian cell survival by inducing the SIRT1 deacetylase Caloric restriction delays disease onset and mortality in rhesus monkeys Analysis of mutation in human cells by using an Epstein-Barr virus shuttle system The effect of Ramadan fasting on sirtuin and visfatin levels Sirtuins, a promising target in slowing down the ageing process Characteristics of a human cell line transformed by DNA from human adenovirus type 5 Mammalian sirtuins: biological insights and disease relevance Small molecule SIRT1 activators for the treatment of aging and age-related diseases Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase Ten years of NAD-dependent SIR2 family deacetylases: implications for metabolic diseases Change in mRNA expression of sirtuin 1 and sirtuin 3 in cats fed on high fat diet Sirtuin 1 suppresses nuclear factor κB induced transactivation and pro-inflammatory cytokine expression in cat fibroblast cells Obesity is associated with low NAD(+)/SIRT pathway expression in adipose tissue of BMI-discordant monozygotic twins The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms Regulation of SIRT1 protein levels by nutrient availability A remarkable age-related increase in SIRT1 protein expression against oxidative stress in elderly: SIRT1 gene variants and longevity in human Fatty liver is associated with reduced SIRT3 activity and mitochondrial protein hyperacetylation Visceral adiposity is associated with SIRT1 expression in peripheral blood mononuclear cells: a pilot study Aging-Related Correlation between Serum Sirtuin 1 Activities and Basal Metabolic Rate in Women, but not in Men Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiae SIRT1 undergoes alternative splicing in a novel auto-regulatory loop with p53 Established kidney cell lines of normal adult bovine and ovine origin Serum concentrations and gene expression of sirtuin 1 in healthy and slightly overweight subjects after caloric restriction or resveratrol supplementation: A randomized trial Involvement of FOXO transcription factors, TRAIL-FasL/Fas, and sirtuin proteins family in canine coronavirus type II-induced apoptosis A multicancer-like syndrome in a dog characterized by p53 and cell cycle-checkpoint kinase 2 (CHK2) mutations and sirtuin gene (SIRT1) downregulation Plasma levels of SIRT1 associate with non-alcoholic fatty liver disease in obese patients Circulating SIRT1 increases after intragastric balloon fat loss in obese patients Age-associated changes in oxidative stress and NAD+ metabolism in human tissue SIRT1 promotes endothelium-dependent vascular relaxation by activating endothelial nitric oxide synthase Rugby-specific small-sided games training is an effective alternative to stationary cycling at reducing clinical risk factors associated with the development of type 2 diabetes: a randomized Seven sirtuins for seven deadly diseases of aging. keywords: antibody; canine; cells; dogs; expression; human; pcr; protein; sirt1; variants cache: cord-303697-oj05bstn.txt plain text: cord-303697-oj05bstn.txt item: #587 of 973 id: cord-303818-z3js3mr4 author: Chen, Huixin title: Development and Evaluation of a SYBR Green–Based Real-Time Multiplex RT-PCR Assay for Simultaneous Detection and Serotyping of Dengue and Chikungunya Viruses date: 2015-10-11 words: 3849 flesch: 43 summary: I. Infection enhancement by non-neutralizing antibody Enhancement of dengue virus infection in monocytes by flavivirus antisera Dengue typing assay based on real-time PCR using SYBR Green I Standardization of immunoglobulin M capture enzymelinked immunosorbent assays for routine diagnosis of arboviral infections Development of group-and serotype-specific one-step SYBR green I-based real-time reverse transcription-PCR assay for dengue virus Development of real-time reverse transcriptase PCR assays to detect and serotype dengue viruses The pair of DEst1 and CHK1 (Figure 2 ) (the specific Tm of CHIKV PCR amplicon was 88.28 C, with coefficient of variation of 0.46%) was selected because not only was it able to detect DENV and CHIKV but also it had a similar annealing temperature and low tendency of forming heterodimers. keywords: assay; chikv; dengue; denv; detection; pcr; rna; time; virus cache: cord-303818-z3js3mr4.txt plain text: cord-303818-z3js3mr4.txt item: #588 of 973 id: cord-303978-z3888e3g author: Hong, Ka Lok title: Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications date: 2015-06-23 words: 15737 flesch: 39 summary: After the retrieval of target bound ssDNA molecules for each round of selection, a small-scale PCR can be carried out to determine the cycles of PCR needed to successfully amplify the library. It then summarizes advancements in the identification and biosensing application of ssDNA aptamers specific for bacteria, viruses, their associated molecules, and selected chemical toxins. keywords: affinity; aptamers; assay; bacteria; binding; candidate; cell; detection; et al; fluorescence; gold; immobilized; library; lod; molecules; mre; mres; ochratoxin; range; reported; rounds; selection; selex; specific; specificity; ssdna; ssdna mre; target cache: cord-303978-z3888e3g.txt plain text: cord-303978-z3888e3g.txt item: #589 of 973 id: cord-303986-9g24xg9x author: Huang, W. title: A CRISPR-Cas12a-based specific enhancer for more sensitive detection of SARS-CoV-2 infection date: 2020-06-05 words: 5025 flesch: 46 summary: Totally 295 clinic samples 172 or specimens (mainly pharyngeal swabs) collected from 282 individuals were tested by rRT-PCR 173 followed by SENA detection (Table S3) . Except for asymptomatic carriers, all the cases of 174 uncertain analytic and false positive or negative readouts of rRT-PCR diagnosis were encountered 175 and finally confirmed or corrected by SENA detection. keywords: detection; figure; license; medrxiv; negative; pcr; preprint; rrt; sena cache: cord-303986-9g24xg9x.txt plain text: cord-303986-9g24xg9x.txt item: #590 of 973 id: cord-304044-i1ikf96b author: Wu, Yue title: Inhibition of white spot syndrome virus in Litopenaeus vannamei shrimp by sequence-specific siRNA date: 2007-10-03 words: 4744 flesch: 47 summary: Moreover, the suppression effect of WSSV gene expression was low at 48 h p.i. To detect the corresponding mRNA expression of WSSV genes in shrimp, 2 μg of RNA extract was used as template for RT-PCR amplification with the one-step RT-PCR system (Invitrogen, USA). keywords: et al; expression; genes; replication; sequence; shrimp; sirna; target; virus; wssv cache: cord-304044-i1ikf96b.txt plain text: cord-304044-i1ikf96b.txt item: #591 of 973 id: cord-304058-i8cywew0 author: Pfefferle, Susanne title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date: 2009-08-24 words: 9581 flesch: 50 summary: The characterization of virus proteins can be unreliable if only the protein of interest is studied on its own. In CaCo-2 and HUH7 cells, but not in Vero cells, the variant carrying the ORF 7b deletion had a replicative advantage against the parental virus (4- and 6-fold increase of virus RNA in supernatant, respectively). keywords: cdna; cells; coronavirus; cov; deletion; figure; fragment; frankfurt-1; genome; infection; interferon; orf; pcr; protein; replication; rna; sars; syndrome; virus cache: cord-304058-i8cywew0.txt plain text: cord-304058-i8cywew0.txt item: #592 of 973 id: cord-304457-8g36h1bz author: Idelsis, E.-M. title: Effect and safety of combination of interferon alpha-2b and gamma or interferon alpha-2b for negativization of SARS-CoV-2 viral RNA. Preliminary results of a randomized controlled clinical trial. date: 2020-08-01 words: 5864 flesch: 40 summary: Negativization for HeberFERON treated patients was related to a significant increase in lymphocytes counts and an also significant reduction in CRP as early as 7 days after commencing the therapeutic schedule. Earlier increase in lymphocytes percentage was observed only for HeberFERON treated patients (p=0.0141) with a marked trend for increment in lymphocytes concentrations. keywords: clinical; cov-2; covid-19; group; heberferon; ifn; medrxiv; patients; preprint; sars; treatment; trial cache: cord-304457-8g36h1bz.txt plain text: cord-304457-8g36h1bz.txt item: #593 of 973 id: cord-304610-6o3hydg6 author: Odeyemi, Festus Ayotunde title: Gauging the laboratory responses to coronavirus disease (COVID‐19) in Africa date: 2020-08-27 words: 2320 flesch: 41 summary: The critical roles of laboratory testing cannot be overemphasised in the prevention and management of infectious diseases outbreak (Bedford et al., 2020) . NCDC also developed a framework for incorporation of up to high throughput HIV molecular testing laboratories, which are capable of raising national capacity to a minimum of 5,000 tests per day (NCDC, 2020a) . keywords: africa; coronavirus; covid-19; disease; laboratory; south; testing cache: cord-304610-6o3hydg6.txt plain text: cord-304610-6o3hydg6.txt item: #594 of 973 id: cord-304656-v0fyb161 author: Balayla, J. title: Prevalence Threshold and Temporal Interpretation of Screening Tests: The Example of the SARS-CoV-2 (COVID-19) Pandemic date: 2020-05-22 words: 2131 flesch: 48 summary: Herein, we use differential 71 equations to assess the geometry of screening curves and aim to describe the prevalence 72 threshold point beyond which the PPV of various COVID-19 screening tests declines 73 most acutely. In other 133 words, we would expect a sharp increase in the number of false positive screening tests, 134 in turn falsely increasing the estimated prevalence of disease. keywords: covid-19; disease; preprint; prevalence; screening cache: cord-304656-v0fyb161.txt plain text: cord-304656-v0fyb161.txt item: #595 of 973 id: cord-304720-0lgup7yj author: Robbins, R.C. title: Swine Diseases and Disorders date: 2014-08-21 words: 12875 flesch: 41 summary: A postmortem examination, or necropsy, of affected pigs should occur last. Bacteriologic isolation of a β-hemolytic strain of E. coli from affected pigs with meningoencephalitis is not sufficient for a diagnosis. keywords: age; causes; control; diagnosis; diarrhea; disease; herd; infection; lesions; morbidity; mortality; pcr; piglets; pigs; porcine; prevention; production; result; signs; suis; swine; treatment; vaccination; vaccines; virus cache: cord-304720-0lgup7yj.txt plain text: cord-304720-0lgup7yj.txt item: #596 of 973 id: cord-304913-qb9zeazk author: Thibivilliers, Sandra title: Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection date: 2009-04-27 words: 6690 flesch: 47 summary: Plant gene expression was similar for both race 41 and 49 during the first 48 hours of the infection process but varied significantly at the later time points (72–96 hours after inoculation) mainly due to the presence of the Avr4 gene in the race 49 leading to a hypersensitive response in the bean plants. Among these 10,581 unisequences, 10,221 were annotated as bean genes and 360 were annotated as fungal genes based on best Blast hits to the database These 360 fungal unisequences included 62 singletons and 298 contigs (Table 1) . keywords: appendiculatus; bean; cdna; ests; expression; fungal; genes; infection; library; pcr; plant; race; resistance; rust; sequences cache: cord-304913-qb9zeazk.txt plain text: cord-304913-qb9zeazk.txt item: #597 of 973 id: cord-305008-8gl9d79i author: Sousa, T. C. M. d. title: Socioeconomic Vulnerabilities and the Intensity of RT-PCR SARS-CoV-2 Testing Efforts in the Public Health System in Sao Paulo State date: 2020-11-03 words: 4530 flesch: 44 summary: The findings provide evidence that a key component of surveillance capacity, laboratory testing, was underperformed during the pandemic and might have contributed to the emergency's poor handling even in Brazil's richest and most well-endowed state. In this study, we developed a new index to measure and evaluate the intensity effort of RT-PCR testing within the public health system based on the best-recommended guidelines in testing effort, especially those issued recommendations issued by the World Health Organization (WHO) (4) (5) (6) keywords: health; medrxiv; paulo; pcr; preprint; public; state; testing cache: cord-305008-8gl9d79i.txt plain text: cord-305008-8gl9d79i.txt item: #598 of 973 id: cord-305025-pqye1ebh author: Sharifi, Majid title: Rapid diagnostics of coronavirus disease 2019 in early stages using nanobiosensors: challenges and opportunities date: 2020-09-28 words: 3594 flesch: 17 summary: In conclusion, it can be deduced that as rapid COVID-19 detection infection can play a vital role in disease control and treatment, this review may be of great help for controlling the COVID-19 outbreak by providing some necessary information for the development of portable, accurate, selectable and simple nanobiosensors. press2009 Molecular diagnosis of influenza Sensitive 650 in situ hybridization with catalyzed reporter deposition, streptavidin-Nanogold, and silver 651 acetate autometallography: detection of single-copy human papillomavirus electrochemical DNA biosensor for detecting hepatitis A virus A versatile DNA detection scheme based on the 657 quenching of fluorescent silver nanoclusters by MoS 2 nanosheets: application to aptamer-658 based determination of hepatitis B virus and of dopamine The field effect transistor DNA biosensor based on ITO nanowires in label-661 free hepatitis B virus detecting compatible with CMOS technology chitosan and MWCNT for the determination of daclatasvir: a hepatitis C 665 antiviral drug A smart nanosensor for the detection of human immunodeficiency virus and associated 668 cardiovascular and arthritis diseases using functionalized graphene-based transistors Two types of nanoparticle-based bio-barcode amplification assays to detect HIV-1 p24 672 antigen Copper sulfide nanoplates as nanosensors for fast, 674 sensitive and selective detection of DNA A novel electrochemical DNA biosensor for Ebola virus detection Field-678 effect transistor biosensor for rapid detection of Ebola antigen Colorimetric detection of influenza A (H1N1) virus by a peptide-functionalized 681 polydiacetylene (PEP-PDA) nanosensor Electrophoresis-enhanced detection of 683 deoxyribonucleic acids on a membrane-based lateral flow strip using avian influenza H5 684 genetic sequence as the model Novel magnetic 686 relaxation nanosensors: an unparalleled spin on influenza diagnosis Direct acoustic profiling of 689 DNA hybridisation using HSV type 1 viral sequences Multiplexed colorimetric detection of 691 Kaposi's sarcoma associated herpesvirus and Bartonella DNA using gold and silver 692 nanoparticles Portable bioactive 694 paper based genosensor incorporated with Zn-Ag nanoblooms for herpes detection at the 695 point-of-care Reactive carbon nano-onion modified glassy 697 carbon surfaces as DNA sensors for human papillomavirus oncogene detection with enhanced 698 sensitivity Impedimetic biosensor for the DNA of the human papilloma virus based on the use of gold 701 nanosheets An ultrasensitive label free 703 human papilloma virus DNA biosensor using gold nanotubes based on nanoporous 704 polycarbonate in electrical alignment Plasmonic and chiroplasmonic nanobiosensors based on gold 708 nanoparticles Cancer diagnosis using nanomaterials based electrochemical 711 nanobiosensors Chapter 4 -Nanobiosensors for virus detection in the environment Development of point-of-care 716 nanobiosensors for breast cancers diagnosis Nanobiosensor: Current Trends and Applications Electrochemical virus detections with nanobiosensors Nanosensors for Smart Cities Recent trends in rapid detection of influenza infections by bio and nanobiosensor An alternative medical diagnosis method: 726 Biosensors for virus detection Coronavirus disease 2019 (COVID-19): situation report Covid-19 in Critically Ill Patients in the 730 Seattle Region-Case Series Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China, The 733 lancet Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia 736 in Wuhan, China: a descriptive study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-739 infected pneumonia in Wuhan, China Clinical 741 course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: 742 a single-centered, retrospective, observational study Analysis of CT 747 features of 15 children with 2019 novel coronavirus infection, Zhonghua er ke za zhi= 748 Cancer patients in SARS-CoV-2 infection: a nationwide analysis in China coronavirus disease 2019 (COVID-19) in China: a report of 754 1014 cases Clinical characteristics of 2019 novel coronavirus infection in China Clinical 759 characteristics of 25 death cases infected with COVID-19 pneumonia: a retrospective review 760 of medical records in a single medical center A 762 tool to early predict severe 2019-novel coronavirus pneumonia (COVID-19): a multicenter 763 study using the risk nomogram in Wuhan and Guangdong Laboratory Parameters in COVID-19 detection Patients with Positive 766 COVID-19: A systematic review and meta-analysis, Travel medicine and infectious disease Diagnosis, treatment, and prevention of 2019 novel coronavirus infection in children: experts' 775 consensus statement Population-scale COVID-19 diagnostics using a compressed 778 barcode space Al-alawneh, COVID-19 Infection Diagnosis: Potential Impact of 780 Isothermal Amplification Technology to Reduce Community Transmission of SARS-CoV-2 Evaluation of COVID-19 RT-qPCR test in 784 multi-sample pools TaqMan probes to increase the sensitivity of 1-step quantitative reverse transcription-PCR: 787 application to the detection of SARS coronavirus RNA as a control for multiplex real-time reverse transcription-PCR detection of influenza 790 virus and severe acute respiratory syndrome coronavirus Detection of 2019 novel coronavirus (2019-nCoV) by 794 real-time RT-PCR Early transmission dynamics in Wuhan, China, of novel coronavirus-infected 797 pneumonia Improved molecular diagnosis of COVID-19 800 by the novel, highly sensitive and specific COVID-19-RdRp/Hel real-time reverse 801 transcription-PCR assay validated in vitro and with clinical specimens Novel coronavirus strain 2019-ncov Co-diagnostics Inc designs test for new coronavirus using coprimer 806 platform Bgi develops real-time fluorescent rt-pcr kit for detecting the 2019 novel 809 coronavirus Altona diagnostics is developing a rt-pcr kit for detection of novel 812 novel coronavirus disease (COVID-19): 815 paving the road for rapid detection and point-of-care diagnostics Rapid Detection of SARS-CoV-2 Using Reverse transcription RT-LAMP method Overcoming the 821 bottleneck to widespread testing: A rapid review of nucleic acid testing approaches for COVID-19 detection Detection of Middle East respiratory syndrome coronavirus using reverse 825 loop-mediated isothermal amplification (RT-LAMP) Development and evaluation of a novel loop-mediated isothermal amplification 829 method for rapid detection of severe acute respiratory syndrome coronavirus Development of Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) keywords: coronavirus; cov-2; covid-19; detection; diagnosis; methods; nanobiosensors; novel; pcr; sars cache: cord-305025-pqye1ebh.txt plain text: cord-305025-pqye1ebh.txt item: #599 of 973 id: cord-305059-8z54lw2d author: Qu, Jie-Ming title: Chapter 4 Diagnosis of COVID-19 date: 2021-12-31 words: 5057 flesch: 43 summary: At present, the problems encountered in virus nucleic acid detection may come from the following: (1) Timing and location malfunction of specimen collection. Currently, there are four recommended assays, including virus isolation and culture, serum-specific antibody detection, virus antigen detection, and nucleic acid detection. keywords: acid; cases; cov-2; covid-19; detection; diagnosis; patients; pneumonia; sars; virus cache: cord-305059-8z54lw2d.txt plain text: cord-305059-8z54lw2d.txt item: #600 of 973 id: cord-305336-wxiazglk author: Li, Ji Lian title: Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date: 2014-01-21 words: 6929 flesch: 43 summary: RNA viruses have extremely high mutation rates and thus represent a significant source of these infectious diseases. Among major pathogen groups, RNA viruses have the highest rate of mutation, because the virus-encoded RNA polymerases lack 3=¡5= exonuclease proofreading activity (29) . keywords: analysis; bee; colonies; honeybees; host; infection; mites; pcr; plant; pollen; rna; study; tissues; trsv; varroa; viral; virus; viruses cache: cord-305336-wxiazglk.txt plain text: cord-305336-wxiazglk.txt item: #601 of 973 id: cord-305399-98sqovwb author: Li, Hao title: Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of porcine pegivirus date: 2019-04-22 words: 2859 flesch: 47 summary: In the past decade, loop-mediated isothermal amplification (LAMP) has become an effective technique, which exhibits high sensitivity and specificity for diagnosing important pathogens in medicine and veterinary medicine (Notomi et al., 2015) . LAMP is a nucleic acid amplification-based method that generally requires a group of four specific external and internal primers (Notomi et al., 2000) . keywords: assay; lamp; pcr; ppgv cache: cord-305399-98sqovwb.txt plain text: cord-305399-98sqovwb.txt item: #602 of 973 id: cord-305462-2wz1f6k6 author: Beckham, J. David title: Respiratory viral infections in patients with chronic, obstructive pulmonary disease date: 2004-09-22 words: 3218 flesch: 34 summary: Deaths: final data for 1999 Deaths: final data for Effect of exacerbation on quality of life in patients with chronic obstructive pulmonary disease Severe exacerbations of COPD patients: the role of pulmonary infections Interactions between viruses and bacteria in patients with chronic bronchitis Impact of respiratory virus infection in patients with chronic chest disease Chronic airway disease: the infection connection Respiratory viral infections in adults with and without chronic obstructive pulmonary disease Respiratory viruses, symptoms, and inflammatory markers in acute exacerbations and stable chronic obstructive pulmonary disease Impact of respiratory virus infections on persons with chronic underlying conditions Role of viruses in exacerbations of chronic obstructive pulmonary disease Community study of role of viral infections in exacerbations of asthma in 9-11 year old children Respiratory tract viral infections in inner-city asthmatic adults Standards for the diagnosis and care of patients with chronic obstructive pulmonary disease (COPD) and asthma. 8 Respiratory viral infections were identified in 19% of COPD subjects with acute respiratory illness. Reverse-transcription polymerase chain reaction (RT-PCR) assays can identify respiratory virus infection missed by cell culture. keywords: copd; infections; patients; pcr; study; virus cache: cord-305462-2wz1f6k6.txt plain text: cord-305462-2wz1f6k6.txt item: #603 of 973 id: cord-305473-w30hsr4m author: Jiang, Lili title: Detection of viral respiratory pathogens in mild and severe acute respiratory infections in Singapore date: 2017-02-20 words: 4976 flesch: 35 summary: Decision analysis of empirical antiviral treatment of influenza virus infection versus treatment based on rapid test results Summer influenza outbreak in a home for the elderly: application of preventive measures Oseltamivir Ring Prophylaxis for Containment of 2009 H1N1 Influenza Outbreaks Influenza in the acute hospital setting Better Tests, Better Care: Improved Diagnostics for Infectious Diseases Performance of case definitions for influenza surveillance Clinical symptoms cannot predict influenza infection during the 2013 influenza season in Bavaria Molecular diagnosis of respiratory virus infections Advances in diagnosis of respiratory virus infections Influenza and other respiratory virus infections in outpatients with medically attended acute respiratory infection during the 2011-12 influenza season Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Performance of diagnostic tests to detect respiratory viruses in older adults Pathogen chip for respiratory tract infections Detection of influenza virus infection using two PCR methods Viral load dynamics in adult patients with A(H1N1)pdm09 influenza Association of the CT values of real-time PCR of viral upper respiratory tract infection with clinical severity, Kenya Correlation of pandemic (H1N1) 2009 viral load with disease severity and prolonged viral shedding in children Virus shedding after human rhinovirus infection in children, adults and patients with hypogammaglobulinaemia Comparison of severely ill patients with influenza A(H1N1)pdm09 infection during the pandemic and post-pandemic periods in Singapore Use of healthcare worker sickness absenteeism surveillance as a potential early warning system for influenza epidemics in acute care hospitals Seasonal trends of viral respiratory tract infections in the tropics Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes Evaluation of PCR testing of ethanol-fixed nasal swab specimens as an augmented surveillance strategy for influenza virus and adenovirus identification Detection by PCR declined with days post-onset for influenza virus; decrease was faster for community-ARI than for inpatient-ARI. keywords: ari; case; community; definitions; episodes; influenza; inpatient; pcr; viruses cache: cord-305473-w30hsr4m.txt plain text: cord-305473-w30hsr4m.txt item: #604 of 973 id: cord-305475-lhi0hcki author: Risku, Minna title: Human bocavirus types 1, 2 and 3 in acute gastroenteritis of childhood date: 2012-05-24 words: 3585 flesch: 52 summary: Cloning of a human parvovirus by molecular screening of respiratory tract samples Human bocavirus and acute wheezing in children Human bocavirus infection in children with respiratory tract disease Human bocavirus in children: mono-detection, high viral load and viraemia are associated with respiratory tract infection Serodiagnosis of human bocavirus infection Human bocavirus infections in hospitalized children and adults Clinical and epidemiologic characteristics of human bocavirus in danish infants: results from a prospective birth cohort study Frequent and prolonged shedding of bocavirus in young children attending daycare Human bocavirus infection in children with acute gastroenteritis in Japan and Thailand Human bocavirus, a respiratory and enteric virus Human bocavirus infection in children hospitalized with acute gastroenteritis in China Detection of human bocavirus in children hospitalized because of acute gastroenteritis Human bocavirus in children hospitalized for acute gastroenteritis: a case-control study A novel bocavirus associated with acute gastroenteritis in Australian children A newly identified bocavirus species in human stool Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent in enteric infections Development of a real-time PCR assay for detecting and quantifying human bocavirus 2 Detection of human bocavirus-2 in children with acute gastroenteritis in South Korea Real-time quantitative PCR detection of four human bocaviruses High prevalence of human bocavirus 2 and its role in childhood acute gastroenteritis in China Detection of human bocavirus 3 in China Again, co-infections with known human gastroenteritis viruses have commonly been found (18, 20) as well as shedding in stools of asymptomatic children (20) . keywords: age; cases; children; gastroenteritis; hbov2; human cache: cord-305475-lhi0hcki.txt plain text: cord-305475-lhi0hcki.txt item: #605 of 973 id: cord-305657-ayqxesiv author: Kalra, Mannudeep K. title: Chest CT practice and protocols for COVID-19 from radiation dose management perspective date: 2020-07-03 words: 3965 flesch: 45 summary: CEBM Laboratory Diagnosis of COVID-19: Current Issues and Challenges Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Fast, portable tests come online to curb coronavirus pandemic Chest CT findings in coronavirus disease-19 (COVID-19): relationship to duration of infection The Clinical and Chest CT Features Associated With Severe and Critical COVID-19 Pneumonia Chest CT severity score: an imaging tool for assessing severe COVID-19 CT image visual quantitative evaluation and clinical classification of coronavirus disease (COVID-19) Relation between chest CT findings and clinical conditions of coronavirus disease (COVID-19) pneumonia: a multicenter study Performance of radiologists in differentiating COVID-19 from viral pneumonia on chest CT Chest CT for typical 2019-nCoV pneumonia: relationship to negative RT-PCR testing Coronavirus disease 2019: initial detection on chest CT in a retrospective multicenter study of 103 Chinese subjects Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases Sensitivity of chest CT for COVID-19: comparison to RT-PCR Chest CT and RT-PCR: radiologists' experience in the diagnosis of COVID-19 in China Frequency and distribution of chest radiographic findings in COVID-19 positive patients Can lung US help critical care clinicians in the early diagnosis of novel coronavirus (COVID-19) pneumonia? Yet, chest CT is often used in patients with known or suspected COVID-19 due to regional preferences, lack of availability of PCR assays, and false-negative PCR assays, as well as for monitoring of disease progression, complications, and treatment response. keywords: chest; covid-19; dose; patients; pcr; pneumonia; use cache: cord-305657-ayqxesiv.txt plain text: cord-305657-ayqxesiv.txt item: #606 of 973 id: cord-305694-qzf425lw author: Andrés-Lasheras, Sara title: Preliminary studies on isolates of Clostridium difficile from dogs and exotic pets date: 2018-03-09 words: 4546 flesch: 43 summary: There is limited information about antimicrobial susceptibilities of C. difficile strains obtained from dogs or exotic animal species [7, 15] . Overall, these results suggest that antimicrobial susceptibility surveillance programs should be implemented in C. difficile strains isolated from dogs since they could be a possible source of metronidazole-resistant and MDR C. difficile. keywords: animals; clostridium; difficile; dogs; isolates; metronidazole; resistance; samples; strains cache: cord-305694-qzf425lw.txt plain text: cord-305694-qzf425lw.txt item: #607 of 973 id: cord-305872-66vij492 author: Caasi, Donna Ria J. title: A multi-target, non-infectious and clonable artificial positive control for routine PCR-based assays date: 2013-09-05 words: 4835 flesch: 39 summary: APCs will streamline and standardize routine PCR, improve reliability and biosafety, and create opportunities for development and commercialization of new synthetic positive control sequences. An array of APC priming sequences from different organisms and/or previously tested primers can be accommodated in a large and flexible number of positive control targets. keywords: apc; apcs; controls; dna; et al; inserts; pcr; plant; primer; sequences cache: cord-305872-66vij492.txt plain text: cord-305872-66vij492.txt item: #608 of 973 id: cord-306135-pt4jsr6d author: Chan, Kamfai title: A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics date: 2016-02-12 words: 6327 flesch: 52 summary: While others have reported fast PCR reactions using various approaches, seldom were the systems challenged with PCR reactions containing low numbers of template per PCR reaction. Speeding up PCR reactions when polypropylene tubes are used While polypropylene plastic tubes are commonly used in most commercial thermal cycles, they are not ideal for achieving a fast PCR reaction time because of the slow heat transfer between the plastic and the heating element. keywords: cycles; min; pcr; reaction; rna; temperature; thermal; time; ttc; tubes; ° c cache: cord-306135-pt4jsr6d.txt plain text: cord-306135-pt4jsr6d.txt item: #609 of 973 id: cord-306175-p5rtp31m author: Weissbrich, Benedikt title: Frequent detection of bocavirus DNA in German children with respiratory tract infections date: 2006-07-11 words: 3232 flesch: 52 summary: Respiratory tract infections are a major cause of human morbidity and are caused by a broad spectrum of microbial agents. Viruses account for the largest number of respiratory tract infections. keywords: children; dna; hbov; infections; samples; tract cache: cord-306175-p5rtp31m.txt plain text: cord-306175-p5rtp31m.txt item: #610 of 973 id: cord-306278-c4q4la5c author: Esposito, Susanna title: Epidemiology and Clinical Characteristics of Respiratory Infections Due to Adenovirus in Children Living in Milan, Italy, during 2013 and 2014 date: 2016-04-05 words: 4662 flesch: 43 summary: Overall, little data on HAdV circulation have been collected in Europe and no recent data regarding the epidemiology, molecular characterization, and clinical features of respiratory HAdV infections in children have been collected in Italy. [22, 23] , where this virus was the predominant type for respiratory HAdV infection from 1981 to 2002. keywords: adenovirus; cases; children; hadv; infection; load; pcr; species; study; time cache: cord-306278-c4q4la5c.txt plain text: cord-306278-c4q4la5c.txt item: #611 of 973 id: cord-306396-wci56l0c author: Kim, Jayoung title: Evaluation of an Immunochromatographic Assay for the Rapid and Simultaneous Detection of Rotavirus and Adenovirus in Stool Samples date: 2014-04-08 words: 2743 flesch: 41 summary: However, interpretation of adenovirus positive/negative result should be cautious because of different detectability for adenovirus subtypes among adenovirus detection methods. The overall agreement among the 4 methods for adenovirus detection was 85.5%. keywords: adenovirus; agreement; detection; ica; pcr; rotavirus cache: cord-306396-wci56l0c.txt plain text: cord-306396-wci56l0c.txt item: #612 of 973 id: cord-306502-jkqg1qal author: Dee, Scott title: An evaluation of contaminated complete feed as a vehicle for porcine epidemic diarrhea virus infection of naïve pigs following consumption via natural feeding behavior: proof of concept date: 2014-08-05 words: 3754 flesch: 50 summary: However, upon inspection of the bin lumen it was observed that clusters of feed material (feed particles and feed dust) were adhered to the interior walls. For the preparation of challenge for the Treatment group, 30 grams of feed material from the PCR-positive bin samples from Farms A, B and C was pooled and diluted in 30 mL of sterile phosphate buffered saline. keywords: control; diarrhea; farm; feed; group; material; pedv; positive; risk; study cache: cord-306502-jkqg1qal.txt plain text: cord-306502-jkqg1qal.txt item: #613 of 973 id: cord-306605-mnafslqw author: Gibson, CS title: Fetal exposure to herpesviruses may be associated with pregnancy‐induced hypertensive disorders and preterm birth in a Caucasian population date: 2008-02-06 words: 4774 flesch: 44 summary: No significant association was observed between SGA or APH and exposure to viral infection. However, it is postulated that viral infection of extravillous trophoblast cells may alter the process of placental invasion and predispose the mother and fetus to adverse reproductive outcomes that result from placental dysfunction. keywords: exposure; infection; pcr; pihd; pregnancy; ptb; sga; study; viruses cache: cord-306605-mnafslqw.txt plain text: cord-306605-mnafslqw.txt item: #614 of 973 id: cord-306656-cbtf2y2f author: Giuliano, A. title: Idiopathic sterile pyogranuloma in three domestic cats date: 2018-05-15 words: 2541 flesch: 37 summary: Disseminated Mycobacterium avium infection in young cats: overrepresentation of Abyssinian cats Evidence of Bartonella henselae infection in cats and dogs in the United Kingdom Study into sterile neutrophilic-macrophagic lymphadenitis in the English springer spaniel Epidemiology, diagnosis, and treatment of blastomycosis in dogs and cats Cutaneous pyogranuloma in a cat caused by virulent Rhodococcus equi containing an 87 kb type I plasmid Idiopathic sterile pyogranulomatous lymphadenitis in a nine-month-old springer spaniel Molecular characterization of a novel fastidious mycobacterium causing lepromatous lesions of the skin, subcutis, cornea, and conjunctiva of cats living in Victoria Determination of the aetiology of presumptive feline leprosy by 16S rRNA gene analysis PCR studies of feline leprosy cases Morphologic features and development of granulomatous vasculitis in feline infectious peritonitis Development and clinical application of a panfungal PCR assay to detect and identify fungal DNA in tissue specimens Cryptococcosis in cats: clinical and mycological assessment of 29 cases and evaluation of treatment using orally administered fluconazole Diagnosis and treatment of pyogranulomatous panniculitis due to mycobacterium smegmatis in cats Infection of the subcutis and skin of cats with rapidly growing mycobacteria: a review of microbiological and clinical findings Nocardia infections in cats: a retrospective multi-institutional study of 17 cases Campylobacter species and neutrophilic inflammatory bowel disease in cats Pyogranulomatous skin disease and cellulitis in a cat caused by Rhodococcus equi General categories of Cytologic interpretation Detection and identification of mycobacteria in fixed stained smears and formalin-fixed paraffin-embedded tissues using PCR Cutaneous sterile granulomas/pyogranulomas, leishmaniasis and mycobacterial infections Idiopathic sterile granulomatous and pyogranulomatous dermatitis in cats Intra-abdominal actinomycetoma in a cat Immunohistochemical demonstration of feline infectious peritonitis virus antigen in paraffin-embedded tissues using feline ascites or murine monoclonal antibodies Laser capture microdissection of feline Streptomyces spp pyogranulomatous dermatitis and cellulitis Localized cutaneous infection with Francisella tularensis resembling ulceroglandular tularemia in a cat Identification of Bartonella henselae in 2 cats with pyogranulomatous myocarditis and diaphragmatic myositis Pathogenesis of feline infetious peritonitis: pathologic changes and immunofluorescence Idiopathic sterile pyogranulomatous dermatitis has also been described in cats (Scott et al. 1990 ). keywords: cats; feline; mass; negative cache: cord-306656-cbtf2y2f.txt plain text: cord-306656-cbtf2y2f.txt item: #615 of 973 id: cord-306682-01q775up author: Vijgen, Leen title: Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13)() date: 2004-06-22 words: 2971 flesch: 47 summary: This region is encoded by the major part of APN exon 3, whole exon 4 and a small part of APN exon 5 (nt 802-1083, hAPN mRNA, GenBank accession number X13276). An 871 bp fragment, encompassing APN exon 3, intron 3 and exon 4 was PCR-amplified and sequenced, and was submitted to GenBank under accession number AF527789. keywords: apn; exon; gene; human; intron; receptor; variations cache: cord-306682-01q775up.txt plain text: cord-306682-01q775up.txt item: #616 of 973 id: cord-306780-9xelf8oh author: Dale, Timothy D. title: Enhancement of wildlife disease surveillance using multiplex quantitative PCR: development of qPCR assays for major pathogens in UK squirrel populations date: 2016-07-28 words: 6936 flesch: 40 summary: When viral loads were calculated as RQ values, the correlation coefficients for comparison of uniplex and multiplex assays were r = 1.00 and 1.00 (n = 8) for grey squirrel SQPV and SADV assays and r = 0.85 and 1.00 (n = 8) for red squirrel SQPV and SADV assays, respectively. (2010) SYBR® green assay, showing good qualitative agreement; k value (agreement) of 0.75 (n = 7) and 1.00 (n = 12) for grey and red squirrel assays, respectively. keywords: assays; dna; et al; grey; infection; red; sadv; samples; sqpv; squirrels cache: cord-306780-9xelf8oh.txt plain text: cord-306780-9xelf8oh.txt item: #617 of 973 id: cord-306829-88nihy7q author: Sharif, Saeed title: Diagnostic Methods for Feline Coronavirus: A Review date: 2010-07-28 words: 3832 flesch: 44 summary: Evolutionary insights into the ecology of coronaviruses Coronaviridae An enteric coronavirus infection of cats and its relationship to feline infectious peritonitis Two related strains of feline infectious peritonitis virus coronavirus Feline infectious peritonitis viruses arise by mutation from endemic feline enteric coronaviruses The molecular genetics of feline coronaviruses: comparative sequence analysis of the ORF7a/7b transcription unit of different biotypes A review of feline infectious peritonitis virus infection Genetics and pathogenesis of feline infectious peritonitis virus Field strain feline coronaviruses with small deletions in ORF7b associated with both enteric infection and feline infectious peritonitis Detection of feline coronavirus RNA in feces, tissues, and body fluids of naturally infected cats by reverse transcriptase PCR Detection of feline coronavirus using RT-PCR: basis for the study of the pathogenesis of feline infectious peritonitis (FIP) Detection of feline coronaviruses by culture and reverse transcriptase-polymerase chain reaction of blood samples from healthy cats and cats with clinical feline infectious peritonitis Intrinsic resistance of feline peritoneal macrophages to coronavirus infection correlates with in vivo virulence An overview of feline enteric coronavirus and infectious peritonitis virus infections Feline infectious peritonitis A comparison of the genomes of FECVs and FIPVs and what they tell us about the relationships between feline coronaviruses and their evolution Molecular cloning and sequence determination of the peplomer protein gene of feline infectious peritonitis virus type I Prevalence of feline coronavirus types I and II in cats with histopathologically verified feline infectious peritonitis A study of naturally occurring feline coronavirus infections in kittens Persistence and evolution of feline coronavirus in a closed cat-breeding colony Clustering of feline coronaviruses in multicat households Common virus infections in cats, before and after being placed in shelters, with emphasis on feline enteric coronavirus Serological survey of catteries for cats infected with feline coronavirus Prevalence of antibodies against feline coronavirus and Chlamydophila felis in Swedish cats Prevalence of feline coronavirus in two cat populations in Malaysia Pathogenesis of feline enteric coronavirus infection Feline coronavirus infection Review of companion animal viral diseases and immunoprophylaxis Feline infectious peritonitis Incetious diseases Small Animal Radiology and Ultrasonography; A Diagnostic Atlas and Text Laboratory changes consistent with feline infectious peritonitis in cats from multicat environments Infectious Diseases of the Dog and Cat Protein electrophoresis on effusions from cats as a diagnostic test for feline infectious peritonitis Feline infectious peritonitis: a review of clinicopathological changes in 65 cases, and a critical assessment of their diagnostic value An appraisal of the value of laboratory tests in the diagnosis of feline infectious peritonitis Comparison of different tests to diagnose feline infectious peritonitis Feline coronavirus infections, in Infectious Diseases of the Dog and Cat Value of α1-acid glycoprotein in the diagnosis of feline infectious peritonitis Critical assessment of the diagnostic value of feline alpha1-acid glycoprotein for feline infectious peritonitis using the likelihood ratios approach Association between faecal shedding of feline coronavirus and serum α1-acid glycoprotein sialylation Evaluation of an in-practice test for feline coronavirus antibodies Evaluation of antibodies against feline coronavirus 7b protein for diagnosis of feline infectious peritonitis in cats Virion polypeptide specificity of immune complexes and antibodies in cats inoculated with feline infectious peritonitis virus Feline coronavirus type II trains 79-1683 and 79-1146 originate from a double recombination between feline coronavirus type I and canine coronavirus SYBR Green real-time reverse transcription-polymerase chain reaction assay for the generic detection of coronaviruses Evaluation of real-time RT-PCR for the quantification of FCoV shedding in the faeces of domestic cats One-tube fluorogenic reverse transcription-polymerase chain reaction for the quantitation of feline coronaviruses Preliminary studies on feline coronavirus distribution in naturally and experimentally infected cats Detection of feline coronavirus RNA in feces, tissues, and body fluids of naturally infected cats by reverse transcriptase PCR Detection of feline coronavirus (FCoV) using reverse transcriptase polymerase chain reaction (RT-PCR) Genetic diversity and phylogenetic analysis of Feline Coronavirus sequences from Portugal One-step SYBR green-based real-time reverse transcriptase polymerase chain reaction assay for detection of feline coronavirus Persistence and transmission of natural type I feline coronavirus infection Phylogenetic analysis of feline coronavirus isolates from healthy cats in Malaysia Descriptive distribution and phylogenetic analysis of feline infectious peritonitis virus isolates of Malaysia A mRNA PCR for the diagnosis of feline infectious peritonitis Feline infectious peritonitis: typical findings and a new PCR test The detection of feline coronaviruses in blood samples from cats by mRNA RT-PCR Development of a nested PCR assay for detection of feline infectious peritonitis virus in clinical specimens Detection of feline coronaviruses in cell cultures and in fresh and fixed feline tissues using polymerase chain reaction Feline infectious peritonitis The authors wish to thank Dr. Diane Addie (www.catvirus.com) for providing the photograph and proofreading the paper. Two biological types of FCoVs are known: feline infectious peritonitis virus (FIPV) and feline enteric coronavirus (FECV). keywords: cats; coronavirus; detection; fcov; feline; fip; pcr; peritonitis cache: cord-306829-88nihy7q.txt plain text: cord-306829-88nihy7q.txt item: #618 of 973 id: cord-307068-360qs3ov author: Hagiwara, Masanori title: Loop‐mediated isothermal amplification method for detection of human papillomavirus type 6, 11, 16, and 18 date: 2007-03-26 words: 3334 flesch: 52 summary: In order to evaluate the reliability of HPV type‐specific LAMP detecting HPV DNA from clinical samples, tissue specimens were obtained from 27 patients with external genital polypoid lesions. HPV DNA was not detected in the seborrheic keratoses, epidermolytic acanthoma, and hairy nymphae. keywords: detection; dna; hpv; lamp; pcr; type cache: cord-307068-360qs3ov.txt plain text: cord-307068-360qs3ov.txt item: #619 of 973 id: cord-307070-tqxvu3pu author: Iqbal, Phool title: Should We Rely on Screening Tests for Further Management Alone in Polymerase Chain Reaction Negative COVID-19 Patients? A Case Series date: 2020-09-20 words: 2764 flesch: 47 summary: Herein, we report our experience with COVID-19 patients who were tested multiple times using this system but were negative for the SARS-CoV-2 virus. The dilemma of a diagnosis based on less sensitive and specific tests or atypical presentations may cause complications due to delay in the management of COVID-19 patients. keywords: cov-2; covid-19; disease; infection; patients; pcr; test cache: cord-307070-tqxvu3pu.txt plain text: cord-307070-tqxvu3pu.txt item: #620 of 973 id: cord-307261-0a3iztns author: Hayden, Randall T. title: Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children date: 2012-01-30 words: 4054 flesch: 43 summary: Instrumentation for the FilmArray process was provided by Idaho Technology, Inc. Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses Multiplex real-time PCR assay for detection of influenza and human respiratory syncytial viruses Use of a multiplex real-time PCR to study the incidence of human metapneumovirus and human respiratory syncytial virus infections during two winter seasons in a Belgian paediatric hospital Multiplex real-time PCR for detection of respiratory tract infections Evaluation of the Prodesse Hexaplex multiplex PCR assay for direct detection of seven respiratory viruses in clinical specimens Evaluation of the Hexaplex assay for detection of respiratory viruses in children Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza a and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay MultiCode-PLx system for multiplexed detection of seventeen respiratory viruses Multiplex PCR and emerging technologies for the detection of respiratory pathogens Detection of respiratory viruses by molecular methods Nucleic acid amplification-based diagnosis of respiratory virus infections Cloning of a human parvovirus by molecular screening of respiratory tract samples Human metapneumovirus infections in young and elderly adults Metapneumovirus and acute wheezing in children Human metapneumovirus: a newly emerging respiratory pathogen A newly discovered human pneumovirus isolated from young children with respiratory tract disease Identification of a new human coronavirus Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia A novel multiplex real-time RT-PCR assay with FRET hybridization probes for the detection and quantitation of 13 respiratory viruses Evaluation of commercial ResPlex II v2.0, MultiCode-PLx, and xTAG respiratory viral panels for the diagnosis of respiratory viral infections in adults Immunofluorescence versus xTAG multiplex PCR for the detection of respiratory picornavirus infections in children Viral and atypical bacterial detection in acute respiratory infection in children under five years Comparison of the Eragen multi-code respiratory virus panel with conventional viral testing and real-time multiplex PCR assays for detection of respiratory viruses Clinical evaluation of multiplex real-time PCR panels for rapid detection of respiratory viral infections Rhinovirus and acute respiratory infections in hospitalized children retrospective study Multiple simultaneous viral infections in infants with acute respiratory tract infections in Spain Dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis Comparison of two multiplex methods for detection of respiratory viruses: FilmArray RP and xTAG keywords: detection; filmarray; pcr; respiratory; resplex; samples; time; viral; viruses cache: cord-307261-0a3iztns.txt plain text: cord-307261-0a3iztns.txt item: #621 of 973 id: cord-307338-4nta9b6w author: Slomka, Marek J. title: Original Article: Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs date: 2010-08-17 words: 8001 flesch: 52 summary: The first variant ('perfect match' M gene RRT PCR) included modification of the AIV reverse primer used by Spackman et al. 38 to provide a perfect match primer (reverse modified, i.e. 'Rev-mod') with the corresponding region in the M gene of H1N1v isolates ( The second variant ('combo' M gene RRT PCR) included an equimolar mix of the original AIV reverse primer plus the above Rev-mod primer, with each included at 0AE2 lm final concentration. These were designed to investigate any UK clinical specimens that may be positive by M gene RRT PCR but negative by 'H1-118' RRT PCR and negative by VI. keywords: gene; h1n1v; influenza; match; pcr; pigs; rrt; rrt pcr; swine; table cache: cord-307338-4nta9b6w.txt plain text: cord-307338-4nta9b6w.txt item: #622 of 973 id: cord-307602-2cmgu7rf author: McErlean, P. title: Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis date: 2007-05-07 words: 3272 flesch: 42 summary: Many of these strains may represent novel HRV serotypes. Most PCR-based HRV studies have targeted the 5 -UTR region for nucleotide sequencing of these variants but this region's use as a discriminator of serotype is hindered by the paucity of complete UTR sequences available both from known serotypes and HRV variants. keywords: hrv; hrvs; pcr; qpm; rhinovirus; sequence; vp1 cache: cord-307602-2cmgu7rf.txt plain text: cord-307602-2cmgu7rf.txt item: #623 of 973 id: cord-307702-n74wvika author: Durant, Thomas J S title: Impact of COVID-19 Pandemic on Laboratory Utilization date: 2020-07-14 words: 2818 flesch: 35 summary: We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. We performed a retrospective assessment of laboratory test order and specimen container utilization at a single, urban tertiary care medical center. keywords: covid-19; laboratory; pandemic; pcr; testing; tests; utilization; volume cache: cord-307702-n74wvika.txt plain text: cord-307702-n74wvika.txt item: #624 of 973 id: cord-307758-a4sgt66g author: Hong, Ching-Ye title: Acute respiratory symptoms in adults in general practice date: 2004-06-17 words: 3928 flesch: 52 summary: key: cord-307758-a4sgt66g authors: Hong, Ching-Ye; Lin, Raymond TP; Tan, Elaine SL; Chong, Phui-Nah; Tan, Yvette SL; Lew, Yii-Jen; Loo, Liat-Hui title: Acute respiratory symptoms in adults in general practice date: 2004-06-17 journal: The purpose of this study was to determine the infective aetiology in patients who presented to primary care doctors with acute respiratory symptoms. keywords: culture; group; infections; pathogens; patients; pcr; study; symptoms; virus cache: cord-307758-a4sgt66g.txt plain text: cord-307758-a4sgt66g.txt item: #625 of 973 id: cord-307768-xx46w6dc author: Ding, Yun title: From single-molecule detection to next-generation sequencing: microfluidic droplets for high-throughput nucleic acid analysis date: 2017-03-10 words: 9495 flesch: 32 summary: Common actuating sources for such purposes include pneumatic pressure (Unger et al. 2000; Willaime et al. 2006; Zeng et al. 2009 ), mechanical forces , electrical fields (Link et al. 2006) , magnetic fields (Vekselman et al. 2015) , acoustic waves (Collins et al. 2013) , optical traps (Lorenz et al. 2006 ) and thermal gradients (Baroud et al. 2007) . Droplet surface area is nearly minimised by producing spherical ends (Baroud et al. 2010) keywords: amplification; analysis; cell; chip; control; detection; dna; droplet; emulsion; et al; example; fig; flow; generation; methods; microfluidics; pcr; reaction; sequencing; systems; throughput; use cache: cord-307768-xx46w6dc.txt plain text: cord-307768-xx46w6dc.txt item: #626 of 973 id: cord-307874-0obomty2 author: Pardon, Bart title: Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis? date: 2020-05-23 words: 7063 flesch: 37 summary: Mosby International Limited Rapid identification of mycoplasma bovis from bovine bronchoalveolar lavage fluid with MALDI-TOF MS after enrichment procedure Matrix-assisted laser desorption ionizationtime of flight mass spectrometry is a superior diagnostic tool for the identification and differentiation of Mycoplasmas isolated from animals Rapid identification of respiratory bacterial pathogens from bronchoalveolar lavage fluid in cattle by MALDI-TOF MS Rapid detection of tetracycline resistance in bovine Pasteurella multocida isolates by MALDI Biotyper antibiotic susceptibility test rapid assay Analysis of culture-dependent versus culture-independent techniques for identification of bacteria in clinically obtained bronchoalveolar lavage fluid Patterns of detection of respiratory viruses in nasal swabs from calves in Ireland: a retrospective study Pathogen-specific risk factors in acute outbreaks of respiratory disease in calves Bayesian estimation of pneumonia etiology: epidemiologic considerations and applications to the pneumonia etiology research for child health study Metagenomic characterization of the virome associated with bovine respiratory disease in feedlot cattle identified novel viruses and suggests an etiologic role for influenza D virus Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis Respiratory bacterial microbiota in cattle: from development to modulation to enhance respiratory health Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection Mycoplasma bovis infections in cattle Transmission dynamics of Mycoplasma bovis in newly received beef bulls at fattening operations Detection by real-time RT-PCR of a bovine respiratory syncytial virus vaccine in calves vaccinated intranasally Characterization of Mannheimia haemolytica isolated from feedlot cattle that were healthy or treated for bovine respiratory disease Colonization and infection Variability in acquired resistance of Pasteurella and Mannheimia isolates from the nasopharynx of calves, with particular reference to different herd types Bacterial pathogens of the bovine respiratory disease complex Bioaerosols play a major role in the nasopharyngeal microbiota content in agricultural environment Effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of recently weaned beef cattle Quantitative bacterial cultures and cytological examination of bronchoalveolar lavage specimens in dogs Differential expression of sheep betadefensin-1 and -2 and interleukin 8 during acute Mannheimia haemolytica pneumonia Comparison of bronchoalveolar lavage fluid bacteriology and cytology in calves classified based on combined clinical scoring and lung ultrasonography Clinicopathological features of 11 suspected outbreaks of bovine adenovirus infection and development of a real-time quantitative PCR to detect bovine adenovirus type 10 Prevalence of respiratory pathogens in diseased, non-vaccinated, routinely medicated veal calves Bovine adenovirus type 3 pneumonia in dexamethasone-treated calves Apoptosis in calf pneumonia induced by endobronchial inoculation with bovine adenovirus type 3 (BAV-3) Structured literature review of responses of cattle to viral and bacterial pathogens causing bovine respiratory disease complex What is the evidence that bovine coronavirus is a biologically significant respiratory pathogen in cattle? A deep nasopharyngeal swab versus nonendoscopic bronchoalveolar lavage for isolation of bacterial pathogens from preweaned calves with respiratory disease Transmission dynamics of Mannheimia haemolytica in newly-received beef bulls at fattening operations A sequential broncho-alveolar washing in non-anaesthetized normal bovines: method and preliminary results Comparison of the nasopharyngeal bacterial microbiota of beef calves raised without the use of antimicrobials between healthy calves and those diagnosed with bovine respiratory disease Distinct bacterial metacommunities inhabit the upper and lower respiratory tracts of healthy feedlot cattle and those diagnosed with bronchopneumonia Use of deep nasopharyngeal swabs as a predictive diagnostic method for natural respiratory infections in calves The microbial flora of the respiratory tract in feedlot calves: associations between nasopharyngeal and bronchoalveolar lavage cultures Agreement among 4 sampling methods to identify respiratory pathogens in dairy calves with acute bovine respiratory disease Sample collection for diagnostics of bovine respiratory diseases Respiratory disease in calves: microbiological investigations on trans-tracheally aspirated bronchoalveolar fluid and acute phase protein response Collection and interpretation of tracheal wash and bronchoalveolar lavage for diagnosis of infectious and non-infectious lower airway disorders Factors associated with lung cytology as obtained by non-endoscopic broncho-alveolar lavage in grouphoused calves Effect of sedation on the intrapulmonary position of a bronchoalveolar lavage catheter in calves Influence of tilmicosin on quantified pulmonary concentrations of three bacterial pathogens in calves with naturallyoccurring bovine respiratory disease Mini-BAL, Blinded Bronchial Sampling, Blinded Protected Specimen Brush] to investigate for pulmonary infections, inflammation, and cellular and molecular markers: a narrative review Comparison of deep nasopharyngeal swab, bronchoalveolar lavage and transtracheal wash for the diagnosis of infectious bronchopneumonia in calves: which one is most animal friendly? keywords: animals; bovine; calves; cattle; culture; disease; pathogens; primary; results; sample; sampling; test; tract; use cache: cord-307874-0obomty2.txt plain text: cord-307874-0obomty2.txt item: #627 of 973 id: cord-308315-g6udfu2a author: Decaro, Nicola title: Characterisation of bubaline coronavirus strains associated with gastroenteritis in water buffalo (Bubalus bubalis) calves date: 2010-10-26 words: 3721 flesch: 37 summary: The 5 0 end of the S gene of the four prototype BuCoV strains was PCR-amplified and sequenced as previously described (Decaro et al., 2008d) and the obtained sequences were compared to reference BuCoV strain 179/07-11 and BCoV strains Mebus (old strain) and 339/ 06 (recently isolated in Italy, Decaro et al., 2008c) . We have already shown that more than one BCoV strain or ancestor virus was likely involved in the origin of CRCoV, thus leading to the emergence of different canine strains (Lorusso et al., 2009) . keywords: bcov; bovine; buffalo; calves; coronavirus; decaro; et al; pcr; strains cache: cord-308315-g6udfu2a.txt plain text: cord-308315-g6udfu2a.txt item: #628 of 973 id: cord-308344-ao9z00t7 author: Diep, Nguyen Van title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation date: 2017-01-17 words: 4211 flesch: 47 summary: (DOCX) Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines An apparently new syndrome of porcine epidemic diarrhoea A new coronavirus-like particle associated with diarrhea in swine Porcine epidemic diarrhea virus infection: Etiology, epidemiology, pathogenesis and immunoprophylaxis Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea Porcine epidemic diarrhea virus variants with high pathogenicity New variants of porcine epidemic diarrhea virus, China Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences Distinct characteristics and complex evolution of PEDV strains Comparison of porcine epidemic diarrhea viruses from Germany and the United States Complete genome sequence of a porcine epidemic diarrhea s gene indel strain isolated in france in Complete genome sequence of a porcine epidemic diarrhea virus from a novel outbreak in belgium PubMed Central Outbreak-related porcine epidemic diarrhea virus strains similar to US strains, South Korea US-like strain of porcine epidemic diarrhea virus outbreaks in Taiwan US-like isolates of porcine epidemic diarrhea virus from Japanese outbreaks between New variant of porcine epidemic diarrhea virus, United States Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene Novel porcine epidemic diarrhea virus variant with large genomic deletion New porcine epidemic diarrhoea virus variant with a large deletion in the spike gene identified in domestic pigs Detection and molecular diversity of spike gene of porcine epidemic diarrhea virus in China Cloning and further sequence analysis of the spike gene of attenuated porcine epidemic diarrhea virus DR13 Porcine epidemic diarrhea virus: An emerging and re-emerging epizootic swine virus Genetic diversity of ORF3 and spike genes of porcine epidemic diarrhea virus in Thailand Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) samples from field cases in Fujian Differentiation of a Vero cell adapted porcine epidemic diarrhea virus from Korean field strains by restriction fragment length polymorphism analysis of ORF 3 PEDV ORF3 encodes an ion channel protein and regulates virus production Molecular epidemiology of porcine epidemic diarrhea virus in China Isolation and serial propagation of porcine epidemic diarrhea virus in cell cultures and partial characterization of the isolate An immunohistochemical investigation of porcine epidemic diarrhoea Porcine epidemic diarrhea: its diagnosis and control Molecular characterization of pig epidemic diarrhoea viruses isolated in Japan from Differential detection of transmissible gastroenteritis virus and porcine epidemic diarrhea virus by duplex RT-PCR Sequence determination of the nucleocapsid protein gene of the porcine epidemic diarrhoea virus confirms that this virus is a coronavirus related to human coronavirus 229E and porcine transmissible gastroenteritis virus MEGA6: Molecular Evolutionary Genetics Analysis version 6.0 Coronavirus spike proteins in viral entry and pathogenesis Identification of the epitope region capable of inducing neutralizing antibodies against the porcine epidemic diarrhea virus Identification of two novel B cell epitopes on porcine epidemic diarrhea virus spike protein The GPRLQPY motif located at the carboxy-terminal of the spike protein induces antibodies that neutralize Porcine epidemic diarrhea virus Mutations in the spike gene of porcine epidemic diarrhea virus associated with growth adaptation in vitro and attenuation of virulence in vivo Genetic variation analysis of reemerging porcine epidemic diarrhea virus prevailing in central China from Defective viral particles and viral disease processes Defective interfering viruses and their potential as antiviral agents Evolution, antigenicity and pathogenicity of global porcine epidemic diarrhea virus strains Cellular entry of the porcine epidemic diarrhea virus Establishment of feline intestinal epithelial cell cultures for the propagation and study of feline enteric coronaviruses Manipulation of the porcine epidemic diarrhea virus genome using targeted RNA recombination Genetic evolution and tropism of transmissible gastroenteritis coronaviruses Diseases of Swine, Tenth Ed The work was conducted with funding from the University of Miyazaki (grant number 2014-70). keywords: diarrhea; epidemic; gene; pedv; porcine; strains; variants; virus cache: cord-308344-ao9z00t7.txt plain text: cord-308344-ao9z00t7.txt item: #629 of 973 id: cord-308422-ueyaw8pd author: Wong, Christopher W title: Optimization and clinical validation of a pathogen detection microarray date: 2007-05-28 words: 6500 flesch: 39 summary: With various metrics to assess annealing potential and sequence specificity, microarray probes have traditionally been designed to ensure maximal specific hybridization (to a known target) with minimal cross-hybridization (to nonspecific sequences). The SARS sample hybridized well to the SARS tiling probes, with all 3,805 SARS-specific probes displaying fluorescent (Cy3) signal well above the detection threshold (determined by probe signal intensities >2 standard deviations (SD) above the mean array signal intensity; Figure 1a ). keywords: amplification; data; detection; hybridization; microarray; pathogen; pcr; primer; probes; rsv; sequence; signal; signatures cache: cord-308422-ueyaw8pd.txt plain text: cord-308422-ueyaw8pd.txt item: #630 of 973 id: cord-308655-zntwwqod author: Dabisch-Ruthe, Mareike title: Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay date: 2012-07-24 words: 5803 flesch: 45 summary: Furthermore, this is the first screening study determining the incidence of infections with respiratory pathogens in a mechanically ventilated patient cohort developing an atypical pneumonia during post-operative monitoring using multiplex PCR assays. Analysis of clinical samples showed a high concordance of detected viruses by the RespiFinder-19 compared to monoplex tests. keywords: assay; detection; pcr; respifinder-19; rvp; samples; time; viruses cache: cord-308655-zntwwqod.txt plain text: cord-308655-zntwwqod.txt item: #631 of 973 id: cord-308867-mrtf8l4f author: Heaney, Jude title: Chapter 6 Low-Density TaqMan® Array Cards for the Detection of Pathogens date: 2015-12-31 words: 5607 flesch: 31 summary: Although each assay had previously been extensively validated, the changes required for transformation to TAC assays necessitated re-optimisation and validation. The TaqMan ® Fast Virus 1-Step mastermix (Life Technologies) is our preferred chemistry for TAC assays; therefore, initial development work must ensure all existing primer and probe sets perform adequately using this chemistry and fast ramping and cycling times. keywords: array; assays; card; detection; development; diagnosis; figure; pathogens; pcr; sensitivity; tac; time cache: cord-308867-mrtf8l4f.txt plain text: cord-308867-mrtf8l4f.txt item: #632 of 973 id: cord-308945-i2agpvhk author: Phipps, William S title: SARS-CoV-2 Antibody Responses Do Not Predict COVID-19 Disease Severity date: 2020-07-15 words: 3176 flesch: 43 summary: We compared IgG levels from all SARS-CoV-2 PCR-positive patients who had a mild/moderate disease course to those who had severe disease (admitted to the intensive care unit [ICU]), and there was no difference in IgG antibody levels between the 2 groups ❚Figure 3A❚. IgG levels and seroconversion based on the calculated index (S/C) were tracked over time. keywords: cov-2; days; igg; igm; patients; samples; sars cache: cord-308945-i2agpvhk.txt plain text: cord-308945-i2agpvhk.txt item: #633 of 973 id: cord-308979-qhlvd2mt author: Sumino, Kaharu C. title: Detection of Severe Human Metapneumovirus Infection by Real-Time Polymerase Chain Reaction and Histopathological Assessment date: 2005-09-15 words: 4301 flesch: 35 summary: Moreover, the prevalence and other characteristics of hMPV infection in the clinical setting of patients undergoing bronchoscopy for respiratory tract infections still need to be defined. In the present study, we add several critical pieces to the diagnostic and clinical matrix for hMPV infection: (1) we detected hMPV at a frequency similar to that of other respiratory tract viruses in patients who underwent bronchoscopy for suspected respiratory tract infection; (2) we quantitatively detected hMPV by real-time PCR in bronchoscopy samples from patients with severe respiratory tract illness but not in those without symptoms or signs of respiratory tract infection; (3) we used a viral culture system to develop a specific antisense probe for hMPV and then demonstrated hMPV mRNA in the lung tissue samples; and (4) we found organizing and acute lung injury and the prominent formation of smudge cells in the lung tissue samples of these patients, thereby suggesting that this pattern may be characteristic of hMPV infection. keywords: cells; hmpv; illness; infection; lung; patients; samples; tract; virus cache: cord-308979-qhlvd2mt.txt plain text: cord-308979-qhlvd2mt.txt item: #634 of 973 id: cord-309083-ew9cwiw0 author: Su, Hang title: Cyprinid viral diseases and vaccine development date: 2018-09-07 words: 11170 flesch: 39 summary: In the late 1990s, the commercialization of fish vaccines developed rapidly and as a result, there are 38 global approvals in 2003, over 100 in 2006, and over 140 in 2012 according to incomplete statistics [7] . In the following decades, many researchers make extensive explorations of the preparation of fish vaccines to prevent the sudden emergence of fish diseases that are difficult to control with drugs. keywords: aquaculture; carp; carp virus; cyprinid; detection; development; disease; dna; fish; gcrv; gene; goldfish; grass; grass carp; herpesvirus; immune; infection; khv; koi; necrosis; pcr; spring; svcv; vaccine; virus cache: cord-309083-ew9cwiw0.txt plain text: cord-309083-ew9cwiw0.txt item: #635 of 973 id: cord-309107-2xzam3x9 author: Emmler, Laura title: Feline coronavirus with and without spike gene mutations detected by real-time RT-PCRs in cats with feline infectious peritonitis date: 2019-11-15 words: 4625 flesch: 48 summary: Interestingly, although S gene mutation RT-PCR was negative despite a high virus load in one sample, FCoV with S gene mutation or mixed FCoV (both FCoVs with and without S gene mutations) were detected in at least one different tissue or fluid in all of the four cats. This study investigated the presence of FCoV with and without S gene mutations in cats with FIP using two different real-time RT-PCRs on different samples obtained under clinical conditions. keywords: cats; fcov; feline; gene; mutated; mutations; pcr cache: cord-309107-2xzam3x9.txt plain text: cord-309107-2xzam3x9.txt item: #636 of 973 id: cord-309540-4pk5tq5w author: Brandsma, E. title: Rapid, sensitive and specific SARS coronavirus-2 detection: a multi-center comparison between standard qRT-PCR and CRISPR based DETECTR. date: 2020-07-29 words: 4299 flesch: 46 summary: Hence, DETECTR results were consistent with qRT-PCR, and provided a clear-cut positive (n=2) or negative (n=2) test result for the samples with NI qRT-PCR results. DETECTR results with gRNA1, gRNA2 and combined gRNA1/gRNA2 yielded similar results ( Figure 1I ). keywords: cov-2; detection; detectr; figure; lamp; pcr; preprint; samples; sars cache: cord-309540-4pk5tq5w.txt plain text: cord-309540-4pk5tq5w.txt item: #637 of 973 id: cord-309565-8syjr6k8 author: KANNO, Toru title: A long-term animal experiment indicating persistent infection of bovine coronavirus in cattle date: 2018-05-18 words: 2490 flesch: 50 summary: Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses Bovine coronavirus Shedding of enteric coronavirus in adult cattle Monoclonal antibody capture enzyme-linked immunosorbent assay for detection of bovine enteric coronavirus Severe outbreak of bovine coronavirus infection in dairy cattle during the warmer season Isolation of bovine respiratory coronaviruses from feedlot cattle and comparison of their biological and antigenic properties with bovine enteric coronaviruses A longitudinal study of bovine coronavirus enteric and respiratory infections in dairy calves in two herds in Ohio Coronavirus-like particles in the feces of normal cats Hemagglutination with Nebraska calf diarrhea virus Molecular analysis of the S glycoprotein gene of bovine coronaviruses isolated in Japan from 1999 to Phylogenetic studies of bovine coronaviruses isolated in Japan Association between infection of the respiratory tract attributable to bovine coronavirus and health and growth performance of cattle in feedlots Detection and characterization of bovine coronaviruses in fecal specimens of adult cattle with diarrhea during the warmer seasons Bovine respiratory coronavirus Experimentally induced coronavirus infections in calves: viral replication in the respiratory and intestinal tracts Coronavirus isolation from nasal swab samples in cattle with signs of respiratory tract disease after shipping Morbidity in Swedish dairy calves from birth to 90 days of age and individual calf-level risk factors for infectious diseases Risk factors for calf mortality in large Swedish dairy herds Experimental reproduction of winter dysentery in lactating cows using BCV -comparison with BCV infection in milk-fed calves Experimental inoculation of adult dairy cows with bovine coronavirus and detection of coronavirus in feces by RT-PCR Recovery of transmissible gastroenteritis virus from chronically infected experimental pigs Astrovirus-like, coronavirus-like, and parvovirus-like particles detected in the diarrheal stools of beagle pups ACKNOWLEDGMENTS. Often, calf diarrhea caused by BCoV repeatedly occurs at the same farm every year. keywords: calf; cattle; coronavirus; dpi; feces; pcr; virus cache: cord-309565-8syjr6k8.txt plain text: cord-309565-8syjr6k8.txt item: #638 of 973 id: cord-309644-cujlpm4i author: Sola, Augusto title: COVID-19 perinatal en América Latina date: 2020-07-31 words: 3059 flesch: 48 summary: Son preocupantes la falta de acompañamiento materno, la baja tasa de lactancia y la frecuente separación de la díada madre-hijo. Hoy más que nunca resulta imperioso sostener recomendaciones específicas para asignar los recursos sanitarios de una manera justa, lo que incluye maximizar los beneficios de las prácticas que se saben efectivas, cuidar la salud de los trabajadores, aplicar la evidencia y colaborar con su construcción a través del reporte de datos, y siempre aplicar los mismos principios éticos para el cuidado de los niños y las madres con COVID-19 20 y sin ella. keywords: casos; con; cov-2; covid-19; del; embarazadas; fue; las; los; madre; para; pcr; perinatal; por; que; sars cache: cord-309644-cujlpm4i.txt plain text: cord-309644-cujlpm4i.txt item: #639 of 973 id: cord-309763-8eywr57j author: Kuypers, Jane title: Detection and quantification of human metapneumovirus in pediatric specimens by real-time RT-PCR date: 2005-02-11 words: 3883 flesch: 43 summary: Children aged 7-12 months had a significantly higher prevalence of hMPV positive specimens (12.4%) than did children younger than 7 months (4.7%) Among the 15% of hMPV positive specimens that were co-infected with another respiratory virus as determined by FA, RSV, and influenza were the most common co-infections, similar to findings reported by others (Viazov et al., 2003; Boivin et al., 2003) . keywords: assay; children; copies; et al; hmpv; pcr; specimens cache: cord-309763-8eywr57j.txt plain text: cord-309763-8eywr57j.txt item: #640 of 973 id: cord-310064-p8u424ch author: Katz, Andrew P. title: False‐positive reverse transcriptase polymerase chain reaction screening for SARS‐CoV‐2 in the setting of urgent head and neck surgery and otolaryngologic emergencies during the pandemic: Clinical implications date: 2020-06-12 words: 4510 flesch: 44 summary: We sparked conversation with infectious disease physicians, pulmonologists, and particularly infectious disease specialists who were now specializing in the care of COVID-19 positive patients to seek expert opinions. While COVID-specific units are appropriate and necessary for the safe treatment of COVID-positive patients, the misplacement of false positive patients in these units exposes the patients to SARS-CoV-2 at an unnecessarily high rate. keywords: cov-2; covid-19; patients; pcr; sars; surgery; testing; tests cache: cord-310064-p8u424ch.txt plain text: cord-310064-p8u424ch.txt item: #641 of 973 id: cord-310095-1pxki8y8 author: Huang, Huanhuan title: Detection and clinical characteristics analysis of respiratory viruses in hospitalized children with acute respiratory tract infections by a GeXP‐based multiplex‐PCR assay date: 2019-11-27 words: 2144 flesch: 40 summary: Huanhuan Huang https://orcid.org/0000-0002-7226-588X Yongbin Zeng https://orcid.org/0000-0002-4355-0710 Bin Wu https://orcid.org/0000-0001-8247-6843 Altered respiratory virome and serum cytokine profile associated with recurrent respiratory tract infections in children Aetiological role of common respiratory viruses in acute lower respiratory infections in children under five years: a systematic review and meta-analysis Respiratory viral infections in infants: causes, clinical symptoms, virology, and immunology Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy Rapid detection of respiratory organisms with the FilmArray respiratory panel in a large children's hospital in China Nucleic acid amplification-based diagnosis of respiratory virus infections Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City Beijing: People's Medical Publishing House Simultaneous differentiation of the N1 to N9 neuraminidase subtypes of avian influenza virus by a GeXP analyzer-based multiplex reverse transcription PCR assay Comparing the yield of oropharyngeal swabs and sputum for detection of 11 common pathogens in hospitalized children with lower respiratory tract infection A comparison study between GeXPbased multiplex-PCR and serology assay for Mycoplasma pneumoniae detection in children with community acquired pneumonia Evaluation of viral co-infections in hospitalized and non-hospitalized children with respiratory infections using microarrays Use of multiple imputation to estimate the proportion of respiratory virus detections among patients hospitalized with community-acquired pneumonia The spectrum of viral pathogens in children with severe acute lower respiratory tract infection: a 3-year prospective study in the pediatric intensive care unit Epidemiology and clinical characteristics of acute respiratory tract infections among hospitalized infants and young children in Epidemiology and burden of influenza in healthy children aged 6 to 35 months: analysis of data from the placebo arm of a phase III efficacy trial Global role and burden of influenza in pediatric respiratory hospitalizations, 1982-2012: a systematic analysis 8, 14, 15 Many studies documented that respiratory viral infection was characterized by seasonal distributions, with their peaks lasting from winter to early spring. keywords: children; detection; pcr; respiratory; study cache: cord-310095-1pxki8y8.txt plain text: cord-310095-1pxki8y8.txt item: #642 of 973 id: cord-310096-a242g5kg author: Yokota, I. title: Mass screening of asymptomatic persons for SARS-CoV-2 using saliva date: 2020-08-14 words: 1957 flesch: 36 summary: In this study, we confirmed this in a large population of asymptomatic persons using saliva samples; there were no samples that were We declare no competing interests. [9] [10] [11] [12] , the utility of saliva in detecting the virus in asymptomatic persons remains to be elucidated. keywords: asymptomatic; nps; pcr; saliva; sars cache: cord-310096-a242g5kg.txt plain text: cord-310096-a242g5kg.txt item: #643 of 973 id: cord-310140-h7uwl0pb author: Templeton, K.E. title: A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses date: 2005-07-12 words: 4187 flesch: 43 summary: Respiratory virus proficiency panels were produced from diluted stocks of respiratory viruses provided and tested by four reference laboratories. Respiratory virus detection by culture has limitations owing to the sensitivities of cell lines to clinical isolates, this is particularly apparent with hRV and hCoV. Although reference strains can be used to check sensitivity of a particular cell line this does not necessarily mean that it will detect all clinical isolates. keywords: detection; panel; participants; pcr; positive; results; viruses cache: cord-310140-h7uwl0pb.txt plain text: cord-310140-h7uwl0pb.txt item: #644 of 973 id: cord-310501-ro55cqxw author: de Castro, Alessandra MMG title: Detection of porcine circovirus genotypes 2a and 2b in aborted foetuses from infected swine herds in the State of São Paulo, Brazil date: 2012-05-03 words: 2213 flesch: 53 summary: The findings indicate that the frequency of PCV2 infections in aborted porcine foetuses from the State of São Paulo is rather low (10.7%) and that co-infection with other pathogens is common and may be involved in PCV2 associated reproductive failure. A number of studies have reported co-infections with PCV2 and PPV, and PPV has been established as an important virus involved in PCV2 associated reproductive failure [17, 18] . keywords: failure; pcr; pcv2; porcine; ppv; samples; spp cache: cord-310501-ro55cqxw.txt plain text: cord-310501-ro55cqxw.txt item: #645 of 973 id: cord-310748-ao29zx1u author: Banner, Lisa R. title: Random nature of coronavirus RNA recombination in the absence of selection pressure date: 1991-11-30 words: 2860 flesch: 49 summary: Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. These results suggest that RNA recombination is common and random in nature, but only certain recombinants can be selected. keywords: crossover; pcr; recombinant; recombination; rna; viruses cache: cord-310748-ao29zx1u.txt plain text: cord-310748-ao29zx1u.txt item: #646 of 973 id: cord-310771-tnwfp1je author: Revilla-Fernández, Sandra title: The use of endogenous and exogenous reference RNAs for qualitative and quantitative detection of PRRSV in porcine semen date: 2005-02-23 words: 5961 flesch: 40 summary: A method was developed for qualitative and quantitative detection of the seminal cell-associated PRRSV RNA in relation to endogenous and exogenous reference RNAs. Particularly for the analysis of persistent infections associated with low copy numbers of PRRSV RNA, UBE2D2 mRNA is an ideal control due to its low expression in seminal cells and its detection in all samples analysed (n = 36). keywords: assays; boars; detection; expression; mrna; pcr; porcine; prrsv; reference; rna; semen; time; ube2d2; viral; virus cache: cord-310771-tnwfp1je.txt plain text: cord-310771-tnwfp1je.txt item: #647 of 973 id: cord-310946-rjwyirld author: Wiseman, Jessica title: False negative SARS-CoV-2 PCR - A case report and literature review date: 2020-07-06 words: 1693 flesch: 49 summary: The authors suggested that antibody response can provide better sensitivity than PCR testing alone [8] . This case highlights multiple negative nasopharyngeal SARS-CoV-2 PCR swabs in a patient with high clinical suspicion for SARS-CoV-2, who ultimately tested positive when deep sputum was sent for PCR nine days into his admission (10 days after respiratory symptoms started). keywords: covid-19; day; nasopharyngeal; pcr; sars cache: cord-310946-rjwyirld.txt plain text: cord-310946-rjwyirld.txt item: #648 of 973 id: cord-311204-fc12f845 author: Zhou, Ling title: Full-length genomic characterization and molecular evolution of canine parvovirus in China date: 2016-04-02 words: 2237 flesch: 62 summary: To further examine CPV-2 isolates, we used a larger dataset composed only of VP2 protein sequences. In this study, molecular phylogenetic analysis of CPV-NY-14 and other CPV-2 isolates in GenBank revealed that CPV-NY-14 is closely related to isolates s5, SC02-11, LZ1, LZ2, and nj01-06, especially isolate LZ2. keywords: china; dogs; genome; pcr; samples; test cache: cord-311204-fc12f845.txt plain text: cord-311204-fc12f845.txt item: #649 of 973 id: cord-311410-lgqup9ug author: Ayers, M. title: A single tube RT-PCR assay for the detection of mosquito-borne flaviviruses date: 2006-05-02 words: 3108 flesch: 43 summary: The assay was validated using RNA from the yellow fever virus vaccine strain and from representative strains of dengue viruses 1, 2, 3 and 4, West Nile virus, Kunjin virus (a clade of West Nile virus), and St. Louis encephalitis virus. Measures to prevent West Nile virus transmission through cells, tissues and organs for transplantation and assisted reproduction First Isolation of West Nile virus from a patient with encephalitis in the United States Comprehensive PCRbased assay for detection and species identification of human herpesviruses Japanese encephalitis in India: an overview Laboratory diagnosis of dengue virus infection: current and future perspectives in clinical diagnosis and public health Update: West Nile virus screening of blood donations and transfusion-associated transmission Universal diagnostic RT-PCR protocol for arboviruses Phylogeny of the genus Flavivirus Rapid detection of west nile virus from human clinical specimens, field-collected mosquitoes, and avian samples by a TaqMan reverse transcriptase-PCR assay Flaviviridae: the viruses and their replication Emerging flaviviruses: the spread and resurgence of Japanese encephalitis, West Nile and dengue viruses Flavivirus infection, fatal, Argentina (Cordoba) (03): St Louis encephalitis Japanese encephalitis, India (Uttar Pradesh) (06) Comparison of flavivirus universal primer pairs and development of a rapid, highly sensitive heminested reverse transcription-PCR assay for detection of flaviviruses targeted to a conserved region of the NS5 gene sequences The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Yellow fever: the recurring plague TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment High levels of plasma dengue viral load during defervescence in patients with dengue hemorrhagic fever: implications for pathogenesis Comparison of assays for the detection of West Nile virus antibodies in chicken serum Emergence of Usutu virus, an African mosquitoborne flavivirus of the Japanese encephalitis virus group Transcripts from a single full-length cDNA clone of hepatitis C virus are infectious when directly transfected into the liver of a chimpanzee This work was supported by the Department of Paediatric Laboratory Medicine, Hospital for Sick Children. keywords: dengue; encephalitis; et al; flaviviruses; pcr; virus; viruses cache: cord-311410-lgqup9ug.txt plain text: cord-311410-lgqup9ug.txt item: #650 of 973 id: cord-311439-y9jwu38r author: Bao, Changjun title: Possible Spread of adenovirus type 3 from poultry to humans: indirect evidence from an outbreak in China date: 2007-09-30 words: 4304 flesch: 47 summary: Case-control study Significant factors for illness included contact with other cases, contact with poultry, and sharing towels among the members of a family. The results indicated that contact with poultry was still a significant risk factor despite removing the effect of contact with other cases. keywords: acute; adenovirus; cases; infection; outbreak; poultry; respiratory; specimens; township; type cache: cord-311439-y9jwu38r.txt plain text: cord-311439-y9jwu38r.txt item: #651 of 973 id: cord-311506-fb8c3ix0 author: Shen, C. title: Combining PCR and CT testing for COVID date: 2020-05-29 words: 3085 flesch: 59 summary: The incubation period used in the model [13] because of false negative PCR tests), here we set it to be 5% for Figs. 1 and 2, and perform a sensitivity analysis by varying the percentage. Moreover, PCR test results typically take several days. keywords: cases; contact; pcr; scan cache: cord-311506-fb8c3ix0.txt plain text: cord-311506-fb8c3ix0.txt item: #652 of 973 id: cord-311639-zij2wbzs author: Kim, Hyun Soo title: Evaluation of the SD Bioline Norovirus rapid immunochromatography test using fecal specimens from Korean gastroenteritis patients date: 2012-08-30 words: 3678 flesch: 40 summary: Very few studies have measured the detection limit of norovirus antigen test kits. In this study, the ICG test had inferior analytical sensitivity (i.e., a higher detection limit) than real time PCR tests. keywords: et al; kit; norovirus; pcr; samples; test; time cache: cord-311639-zij2wbzs.txt plain text: cord-311639-zij2wbzs.txt item: #653 of 973 id: cord-311748-yr2ep7uf author: Kahyaoglu, L. N. title: 11 New approaches in microbial pathogen detection date: 2013-12-31 words: 8026 flesch: 37 summary: Several molecular methods using nucleic acid amplifi cation have been developed for virus detection in food (Jean et al. , 2003) . In recent years, polymerase chain reaction (PCR)-based methods in particular, have become the gold standard for virus detection in food due to their high sensitivity, specifi city and potential to detect even a single virus particle (Bosch et al. , 2011; Martinez-Martinez et al. , 2011; Richards et al. , 2003; Cook and Rzezutka, 2006) . keywords: amplifi; assay; cation; detection; et al; food; foodborne; hav; havs; hepatitis; methods; pcr; samples; sensitivity; specifi; taqman; time; viruses cache: cord-311748-yr2ep7uf.txt plain text: cord-311748-yr2ep7uf.txt item: #654 of 973 id: cord-311801-m2otfdjw author: Wang, Pei title: Combination of Serological Total Antibody and RT-PCR Test for Detection of SARS-CoV-2 Infections date: 2020-06-15 words: 2727 flesch: 56 summary: The aim of this study was to evaluate the performance of total antibody test by using CMIA, the RT-PCR, and explore the feasibility of the combination, serological total antibody tests and RT-PCR, as a possible diagnostic tool for detection of SARS-CoV-2. The results indicated that diagnostic sensitivity and specificity were 95.7% and 98.7%, 92.2% and 100% by total antibody tests and RT-PCR, respectively. keywords: antibody; cov-2; patients; pcr; sars cache: cord-311801-m2otfdjw.txt plain text: cord-311801-m2otfdjw.txt item: #655 of 973 id: cord-311982-wkg56xeq author: Dye, Charlotte title: Genomic RNA sequence of feline coronavirus strain FCoV C1Je date: 2007-06-17 words: 5243 flesch: 46 summary: key: cord-311982-wkg56xeq authors: Dye, Charlotte; Siddell, Stuart G. title: Genomic RNA sequence of feline coronavirus strain FCoV C1Je date: 2007-06-17 journal: J Feline Med Surg DOI: 10.1016/j.jfms.2006.12.002 sha: doc_id: 311982 cord_uid: wkg56xeq Comparison of the FCoV C1Je genomic RNA sequence with that of the laboratory strain FCoV FIP virus (FIPV) 79-1146 showed that both viruses have a similar genome organisation and predictions made for the open reading frames and cis-acting elements of the FIPV 79-1146 genome hold true for FCoV C1Je. keywords: c1je; coronavirus; fcov; feline; fipv; genomic; rna; sequence; strain cache: cord-311982-wkg56xeq.txt plain text: cord-311982-wkg56xeq.txt item: #656 of 973 id: cord-312024-qdgqif5j author: Talbot, H. Keipp title: The Diagnosis of Viral Respiratory Disease in Older Adults date: 2010-02-01 words: 3426 flesch: 35 summary: The increasing availability of new rapid and sensitive molecular diagnostics such as polymerase chain reaction testing, should provide more accurate and timely diagnoses of viral respiratory infections in older adults in the near future. Because viral respiratory infections in older adults represent reinfection, a single serum sample to detect viral specific immunoglobulin G is not useful for diagnosis. keywords: adults; culture; diagnosis; infection; influenza; pcr; virus cache: cord-312024-qdgqif5j.txt plain text: cord-312024-qdgqif5j.txt item: #657 of 973 id: cord-312139-g1hczx54 author: Liu, Wei title: Non-specific Primers Reveal False-negative Risk in Detection of COVID-19 Infections date: 2020-04-11 words: 3350 flesch: 54 summary: PCR primers for SARS developed by WHO network laboratories 12 Primer-BLAST (https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi) was applied to determine whether specific primers for SARS-CoV-2 virus show significant matches with human . keywords: covid-19; license; pcr; preprint; primers cache: cord-312139-g1hczx54.txt plain text: cord-312139-g1hczx54.txt item: #658 of 973 id: cord-312161-egwo19oc author: Aw, Tiong Gim title: Detection of pathogens in water: from phylochips to qPCR to pyrosequencing date: 2011-12-05 words: 4554 flesch: 22 summary: It is clear that the field of environmental pathogen detection is and will remain highly dynamic with tremendous potential for development of new tools and continuous improvement of existing concepts. High-density microarrays, quantitative real-time PCR (qPCR) and pyrosequencing which are considered to be breakthrough technologies borne out of the ‘molecular revolution’ are at present emerging rapidly as tools of pathogen detection and discovery. keywords: detection; dna; pathogens; pcr; pyrosequencing; samples; sequencing; time; viruses; water; waterborne cache: cord-312161-egwo19oc.txt plain text: cord-312161-egwo19oc.txt item: #659 of 973 id: cord-312197-d5d8amk7 author: Edmond, Karen title: New Approaches to Preventing, Diagnosing, and Treating Neonatal Sepsis date: 2010-03-09 words: 5228 flesch: 35 summary: key: cord-312197-d5d8amk7 authors: Edmond, Karen; Zaidi, Anita title: New Approaches to Preventing, Diagnosing, and Treating Neonatal Sepsis date: 2010-03-09 journal: PLoS Med DOI: 10.1371/journal.pmed.1000213 sha: doc_id: 312197 cord_uid: d5d8amk7 Karen Edmond and Anita Zaidi highlight new approaches that could reduce the burden of neonatal sepsis worldwide. Neonatal sepsis or septicaemia is a clinical syndrome characterized by systemic signs of circulatory compromise (e.g., poor peripheral perfusion, pallor, hypotonia, poor responsiveness) caused by invasion of the bloodstream by bacteria in the first month of life. keywords: blood; care; countries; health; income; infants; infections; mortality; neonatal; neonates; rates; sepsis; studies cache: cord-312197-d5d8amk7.txt plain text: cord-312197-d5d8amk7.txt item: #660 of 973 id: cord-312206-0pkbbb99 author: SUNAGA, Fujiko title: Development of a one-run real-time PCR detection system for pathogens associated with porcine respiratory diseases date: 2019-12-23 words: 3219 flesch: 40 summary: A total of 30 samples of porcine lung tissue submitted in 2016-2018 to Azabu University for diagnosis of porcine respiratory pathogens were used to test. The extracted nucleic acids were evaluated in triplicated by targeting respiratory disease complex pathogens in a single run of Dempo-PCR. keywords: assay; dempo; detection; pathogens; pcr; porcine; time; virus cache: cord-312206-0pkbbb99.txt plain text: cord-312206-0pkbbb99.txt item: #661 of 973 id: cord-312222-aw5849rc author: Österdahl, Marc F. title: Detecting SARS-CoV-2 at point of care: preliminary data comparing loop-mediated isothermal amplification (LAMP) to polymerase chain reaction (PCR) date: 2020-10-20 words: 3959 flesch: 48 summary: However, as the pandemic has progressed, it has become apparent that there is no true gold standard for COVID-19 testing with highly-anticipated antibody testing not always proving helpful; even in mild disease, antibodies in PCR positive patients may not be detected [22] . Low temperatures (< 36°C were detected in a minority of COVID PCR positive patients ( Table 3 ). keywords: care; covid-19; day; lamp; patients; pcr; sars; testing cache: cord-312222-aw5849rc.txt plain text: cord-312222-aw5849rc.txt item: #662 of 973 id: cord-312223-qgwzgazd author: Shafagati, Nazly title: The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus date: 2013-07-04 words: 8854 flesch: 55 summary: Viral inactivation was assayed by plaque assays (C) and viral RNA was extracted from the particles with Ambion's MagMax 96-well Viral RNA extraction kit and quantitated by qRT-PCR (D Comparison of capture efficacy of NanoTrap particles and commercially available beads for RVFV capture NanoTrap particles have unique properties not demonstrated in other beads that are used for protein purification and albumin exclusion such as dye baits that make them an ideal candidate in virus capture. Characterization of RVFV NanoTrap particle capture. keywords: assays; capture; minutes; nanotrap; nanotrap particles; nt53; particles; pcr; plaque; qrt; rna; rvfv; samples; virus cache: cord-312223-qgwzgazd.txt plain text: cord-312223-qgwzgazd.txt item: #663 of 973 id: cord-312240-0k8y86pf author: Schlaberg, Robert title: Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology date: 2017-05-01 words: 4842 flesch: 41 summary: We cannot exclude that highly diverse viruses without homology to known human viral pathogens may have caused CAP in some of the children. Although both RNA-seq and PVG PCR provide broadrange detection of respiratory viruses, each method has potential advantages and disadvantages. keywords: cap; children; control; patients; pcr; pvg; rna; seq; subjects; viruses cache: cord-312240-0k8y86pf.txt plain text: cord-312240-0k8y86pf.txt item: #664 of 973 id: cord-312456-6lxc2rj2 author: Soltan, Mohamed A. title: Comparison of electron microscopy, ELISA, real time RT-PCR and insulated isothermal RT-PCR for the detection of Rotavirus group A (RVA) in feces of different animal species date: 2016-05-11 words: 4217 flesch: 45 summary: The lyophilized Premix was rehydrated before reaction in 50 l Premix Buffer B and 5 l of sample RNA were added to the mixture. The aim of this investigation was to evaluate a commercially available RT-iiPCR assay for RVA detection in feces from different animal species. keywords: assay; detection; iipcr; pcr; rotavirus; rtrt; rva; samples cache: cord-312456-6lxc2rj2.txt plain text: cord-312456-6lxc2rj2.txt item: #665 of 973 id: cord-312477-2y88gzji author: Mlcochova, P. title: Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. date: 2020-06-18 words: 4922 flesch: 46 summary: Rapid combined tests have the potential to transform our management of COVID-19, including inflammatory manifestations where nucleic acid test results are negative. Rapid combined tests have the potential to transform our management of COVID-19, including inflammatory manifestations where nucleic acid test results are negative. keywords: acid; antibody; cov-2; covid-19; igg; license; medrxiv; preprint; sars; test cache: cord-312477-2y88gzji.txt plain text: cord-312477-2y88gzji.txt item: #666 of 973 id: cord-312996-qzu8pkyt author: Iles, R. K. title: A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work. date: 2020-08-22 words: 6852 flesch: 41 summary: Viral envelope protein peak intensities were clearly elevated in the spiked samples ( Figure 5 ). Viral envelope proteins (VEPs) became more prevalent in live virus culture and Ig light chains and IgA heavy chain were additional peaks found in gargle/saliva samples. keywords: covid-19; envelope; gargle; levels; maldi; mass; pcr; preprint; proteins; saliva; samples; sars; spectrometry; tof; virus cache: cord-312996-qzu8pkyt.txt plain text: cord-312996-qzu8pkyt.txt item: #667 of 973 id: cord-313000-as507p4t author: Dare, Ryan K. title: Human Coronavirus Infections in Rural Thailand: A Comprehensive Study Using Real-Time Reverse-Transcription Polymerase Chain Reaction Assays date: 2007-11-01 words: 4130 flesch: 41 summary: Given the year-to-year variation in the prevalence of HCoV infections, only a multiyear study may be able to definitively assess whether an association between HCoV infection and severe illness exists. HCoV infections were detected throughout both study years; 93.6% of OC43 infections in the first year occurred from January through March. keywords: coronavirus; hcov; human; infections; oc43; patients; pneumonia; study; year cache: cord-313000-as507p4t.txt plain text: cord-313000-as507p4t.txt item: #668 of 973 id: cord-313004-gdnaiodj author: Wang, Yong title: Simultaneous detection of duck circovirus and novel goose parvovirus via SYBR green I-based duplex real-time polymerase chain reaction analysis date: 2020-08-14 words: 2290 flesch: 48 summary: The results of our duplex real-time 218 PCR assay were in 100% agreement with singular real-time PCR. Other non-target duck viruses that were tested did not show melting peaks. keywords: assay; duplex; ngpv; pcr; time cache: cord-313004-gdnaiodj.txt plain text: cord-313004-gdnaiodj.txt item: #669 of 973 id: cord-313107-6cfenpxm author: Singh, Anirudh K. title: Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study date: 2020-09-22 words: 2891 flesch: 45 summary: In a recent study Hogan and co-workers made a similar observation while assessing the utility of pooled sample testing strategy to detect community transmission of SARS-CoV-2 in San Francisco Bay Area, CA, USA. At the reported point prevalence of 4.8% among the individuals tested in this study, the NPV of pooled sample strategy was around 96%; thereby suggesting the possibility of missing infected cases and risking community transmission from undiagnosed individuals. keywords: covid-19; pcr; pools; samples; strategy; study; testing cache: cord-313107-6cfenpxm.txt plain text: cord-313107-6cfenpxm.txt item: #670 of 973 id: cord-313375-rs3jjiuj author: Panning, Marcus title: Singleplex real-time RT-PCR for detection of influenza A virus and simultaneous differentiation of A/H1N1v and evaluation of the RealStar influenza kit date: 2010-11-13 words: 2310 flesch: 50 summary: After validation of the in-house version the commercial RealStar kit was used to assess the clinical performance and specificity on a panel of influenza viruses including A/H1N1v, A/H1N1, swine A/H1N1, A/H3N2, avian A/H5N1 as well as patient specimens. After validation of the in-house version the commercial RealStar kit was used to assess the clinical performance and specificity on a panel of influenza viruses including A/H1N1v, A/H1N1, swine A/H1N1, A/H3N2, avian A/H5N1 as well as patient specimens. keywords: assay; h1n1v; influenza; pcr; virus cache: cord-313375-rs3jjiuj.txt plain text: cord-313375-rs3jjiuj.txt item: #671 of 973 id: cord-313439-cadyykks author: Felten, Sandra title: Diagnosis of Feline Infectious Peritonitis: A Review of the Current Literature date: 2019-11-15 words: 12473 flesch: 40 summary: Pathogenesis of feline enteric coronavirus infection Common virus infections in cats, before and after being placed in shelters, with emphasis on feline enteric coronavirus Pathogenic characteristics of persistent feline enteric coronavirus infection in cats Feline infectious peritonitis viruses arise by mutation from endemic feline enteric coronaviruses Infection studies in kittens, using feline infectious peritonitis virus propagated in cell culture An enteric coronavirus infection of cats and its relationship to feline infectious peritonitis Clinical and laboratory features of cats with feline infectious peritonitis-a retrospective study of 231 confirmed cases (2000-2010) Prevalence of feline infectious peritonitis in specific cat breeds Epidemiology of feline infectious peritonitis among cats examined at veterinary medical teaching hospitals The inheritance of susceptibility to feline infectious peritonitis in purebred catteries Performances of different diagnostic tests for feline infectious peritonitis in challenging clinical cases A review of feline infectious peritonitis virus infection: 1963-2008 Feline infectious peritonitis: Still an enigma? Immunologic phenomena in the effusive form of feline infectious peritonitis Levels of feline infectious peritonitis virus in blood, effusions, and various tissues and the role of lymphopenia in disease outcome following experimental infection Experimental feline enteric coronavirus infection reveals an aberrant infection pattern and shedding of mutants with impaired infectivity in enterocyte cultures Cats inoculated with feline infectious peritonitis virus exhibit a biphasic acute phase plasma protein response Serologic studies of naturally occurring feline infectious peritonitis Feline coronavirus antibodies in cats Utility of feline coronavirus antibody tests Seroepidemiology of feline infectious peritonitis virus infections using transmissible gastroenteritis virus as antigen Feline infectious peritonitis: A worldwide serosurvey Feline coronavirus serotypes 1 and 2: Seroprevalence and association with disease in switzerland Evaluation of an in-practice test for feline coronavirus antibodies Comparison of serologic techniques for the detection of antibodies against feline coronaviruses The history and interpretation of feline coronavirus serology A. Cats and coronaviruses Long-term impact on a closed household of pet cats of natural infection with feline coronavirus, feline leukaemia virus and feline immunodeficiency virus A study of naturally occurring feline coronavirus infections in kittens Risk of feline infectious peritonitis in cats naturally infected with feline coronavirus Coronavirus serology in healthy pedigree cats keywords: cats; coronavirus; detection; diagnosis; effusion; fcov; feline; fip; gene; mutations; pcr; peritonitis; samples; study cache: cord-313439-cadyykks.txt plain text: cord-313439-cadyykks.txt item: #672 of 973 id: cord-313506-6bb4q7nv author: Sano, Akiko title: Physiological Level Production of Antigen-Specific Human Immunoglobulin in Cloned Transchromosomic Cattle date: 2013-10-24 words: 6718 flesch: 46 summary: In order to improve the functional interactions between the hIgM and bIgα/ Igβ proteins in the pre-BCR, as well as the overall functionality of hIgM in Tc bovine B cells, we constructed a gene-targeting vector to bovinize the CH2-TM2 domain of hIgM that is involved in interacting with bIgα/Igβ [18] . To detect surface hIgG on Tc bovine B cells, goat anti-hIgG (Life Technologies, Grand Island, NY) directly labeled with AF 488 was used. keywords: bovine; cattle; cell; clone; dt40; figure; fragment; gene; genomic; higg; hpabs; human; locus; pcr; site cache: cord-313506-6bb4q7nv.txt plain text: cord-313506-6bb4q7nv.txt item: #673 of 973 id: cord-313676-6rebpe57 author: De la Torre, David I. title: Enteric Virus Diversity Examined by Molecular Methods in Brazilian Poultry Flocks date: 2018-03-29 words: 5876 flesch: 44 summary: Detection of rotaviruses and intestinal lesions in broiler chicks from flocks with runting and stunting syndrome (RSS) Investigation into the aetiology of runting and stunting syndrome in chickens A metagenomic comparison of endemic viruses from broiler chickens with runting stunting syndrome and from normal birds Detection of enteric viruses in pancreas and spleen of broilers with runting-stunting syndrome A retrospective study on poult enteritis syndrome in Minnesota Epidemiological study of enteric viruses in broiler chickens: Comparison of tissue culture and direct electron microscopy Simultaneous detection of astrovirus, rotavirus, reovirus and adenovirus type I in broiler chicken flocks Enteric viruses in Brazilian turkey flocks: turkeys A Multiplex RT-PCR test for the differential identification of turkey astrovirus type 1, turkey astrovirus type 2, chicken astrovirus, avian nephritis virus, and avian rotavirus Enteric viruses detected by molecular methods in commercial chicken and turkey flocks in the United States between Partial genome sequence analysis of parvoviruses associated with enteric disease in poultry Isolation of high-molecular-weight DNA using organic solvents Single-step method of RNA isolation by acid guanidinium extraction Development of a polymerase chain reaction procedure for detection of chicken and turkey parvoviruses Detection and molecular characterization of chicken astrovirus associated with chicks that have an unusual condition known as white chicks in Brazil The neighbor-joining method: A new method for reconstructing phylogenetic trees Confidence limits on phylogenies: An approach using the bootstrap Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees Molecular survey of enteric viruses in commercial chicken farms in Korea with a history of enteritis Chicken parvovirus-Induced runting-stunting syndrome in young broilers Detection and molecular characterization of enteric viruses in breeder turkeys Naturally occurring parvoviral infection in Hungarian broiler flocks Molecular characterization of avian astroviruses Chicken parvovirus viral loads in cloacal swabs from malabsorption syndrome-affected and healthy broilers Molecular characterization and typing of chicken and turkey astroviruses circulating in the United States: Implications for diagnostics Epidemiological investigation of outbreaks of fowl adenovirus infections in commercial chickens in China Chicken anemia virus and fowl adenoviruses: Association to induce the inclusion body hepatitis/hydropericardium syndrome Viral agents related to enteric disease in commercial chicken flocks, with special reference to Latin America Multisystemic adenovirus infection in broiler chicks with hypoglycemia and spiking mortality Characterization of fowl adenoviruses isolated in Ontario and Quebec Detection and quantitation of fowl adenovirus genome by a real-time PCR assay Complete genome sequence of a non-pathogenic strain of Fowl Adenovirus serotype 11: Minimal genomic differences between pathogenic and non-pathogenic viruses Lesions of the Avian Pancreas Parvovirus-associated cerebellar hypoplasia and hydrocephalus in day old broiler chickens Molecular detection of chicken parvovirus in broilers with enteric disorders presenting curving of duodenal loop, pancreatic atrophy, and mesenteritis Sequence analyses of the representative chinese-prevalent strain of avian nephritis virus in healthy chicken flocks Sciences, A. Detection and partial genetic characterisation of a novel variant of avian nephritis virus in Indian poultry flocks showing diverse clinical signs High-resolution melt curve analysis to confirm the presence of co-circulating isolates of avian nephritis virus in commercial chicken flocks Comparative dynamic distribution of avian infectious bronchitis virus M41, H120, and SAIBK strains by quantitative real-time RT-PCR in SPF chickens Comparative analysis of the intestinal bacterial and RNA viral communities from sentinel birds placed on selected broiler chicken farms A primary epidemic of inclusion body hepatitis in broilers Characterization of fowl adenoviruses from outbreaks of inclusion body hepatitis/hydropericardium syndrome in Chile Identification and virulence characterization of fowl adenoviruses in the Republic of Korea Inclusion body hepatitis associated with an outbreak of fowl adenovirus type 2 and type 8b in broiler flocks in South Africa Phylogenetic and geographic analysis of fowl adenovirus field strains isolated from poultry in Poland Genetic characterization of parvoviruses circulating in turkey and chicken flocks in Poland Genetic characterization of three novel chicken parvovirus strains based on analysis of their coding sequences Detection of avian nephritis virus in Australian chicken flocks Enteric viruses in turkey enteritis Genome sequences of rotavirus A strains Ty-1 and Ty-3, isolated from turkeys in Ireland in 1979 Molecular epidemiology of avian rotaviruses group A and D shed by different bird species in Nigeria keywords: broilers; chicken; enteric; infections; min; pcr; samples; table; viruses cache: cord-313676-6rebpe57.txt plain text: cord-313676-6rebpe57.txt item: #674 of 973 id: cord-313749-f2ct57em author: Brittain-Long, Robin title: Multiplex real-time PCR for detection of respiratory tract infections date: 2007-12-26 words: 1568 flesch: 40 summary: Diagnosis of viral respiratory tract infections using viral culture, antigen detection or serology is either too slow or too insensitive to be applicable in clinical practice (Gunson et al., 2005) . Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses Aetiological role of viral and bacterial infections in acute adult lower respiratory tract infection (LRTI) in primary care Etiology of community-acquired pneumonia in hospitalized patients in Chile: the increasing prevalence of respiratory viruses among classic pathogens Practical implementation of a multiplex PCR for acute respiratory tract infections in children Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Pring-Akerblom P. Rapid and quantitative detection of human adenovirus DNA by real-time PCR Comparison of real-time PCR assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children Simultaneous detection and high-throughput identification of a panel of RNA viruses causing respiratory tract infections Comparison of a multiplex reverse transcription-PCR-enzyme hybridization assay with conventional viral culture and immunofluorescence techniques for the detection of seven viral respiratory pathogens Antibiotic prescribing in outpatients: a 1-week diagnosis-prescribing study in 5 counties in Sweden Evaluation of a multiplex reverse transcriptase PCR ELISA for the detection of nine respiratory tract pathogens Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 Design and performance testing of quantitative real-time PCR assays for influenza A and B viral load measurement Real-time quantitative PCR assays for detection and monitoring of pathogenic human viruses in immunosuppressed pediatric patients We are grateful to Dr Lars Nielsen, Copenhagen, for sharing experience, oligonucleotide sequences and samples. keywords: infections; pcr; time cache: cord-313749-f2ct57em.txt plain text: cord-313749-f2ct57em.txt item: #675 of 973 id: cord-313994-l15qa9tr author: Pabbaraju, Kanti title: Detection of enteroviruses and parechoviruses by a multiplex real-time RT-PCR assay date: 2015-02-11 words: 3674 flesch: 42 summary: The sensitivity of NASBA methodology is comparable to realtime RT-PCR for molecular-based diagnostic procedures for RNA viruses; in addition specimens tested for EV detection by the NASBA assay were readily available in our laboratory and were thus used for the validation. Different EV types are associated with certain clinical manifestations such as coxsackievirus A16 (CV-A16), enterovirus 71 (EV-A71), and CV-A6 have strong associations with outbreaks of hand, foot, and mouth disease and CV-A24 and EV-D70 with hemorrhagic conjunctivitis. keywords: assay; detection; enterovirus; evs; pcr cache: cord-313994-l15qa9tr.txt plain text: cord-313994-l15qa9tr.txt item: #676 of 973 id: cord-314051-dr27bsvt author: Lother, Sylvain A. title: Preoperative SARS-CoV-2 screening: Can it really rule out COVID-19? date: 2020-06-23 words: 3125 flesch: 46 summary: 2 Avant que l'ARN viral n'atteigne des seuils détectables, les patients pourraient apparaître en bonne santé avant une chirurgie non urgente malgré avoir été exposés au SARS-CoV-2 au cours des 14 jours précédents. Si la présence virale n'est pas dépistée par un test, les patients peuvent aller de l'avant avec leur chirurgie non urgente, à la suite de laquelle les signes et symptômes d'une atteinte au coronavirus (COVID-19) pourraient survenir en période postopératoire, entraînant des devenirs défavorables. keywords: cov-2; des; les; patients; sars; surgery; test cache: cord-314051-dr27bsvt.txt plain text: cord-314051-dr27bsvt.txt item: #677 of 973 id: cord-314069-8dxzf2ip author: Dongliu, Yuan title: Outbreak of acute febrile respiratory illness caused by human adenovirus B P14H11F14 in a military training camp in Shandong China date: 2016-06-28 words: 4291 flesch: 48 summary: Some earlier statistical analyses have shown that marching training and firing training are significantly associated with the onset of pneumonia and FRI, especially in HAdV outbreaks To investigate the genetic relationships between isolate SD77001 and other HAdV strains, phylogenetic trees were constructed by the maximum-likelihood method with 1000 bootstrap pseudoreplicates using the MEGA 5 program [18] . keywords: adenovirus; gene; hadv; military; outbreak; patients; pcr; sequence; strains; virus cache: cord-314069-8dxzf2ip.txt plain text: cord-314069-8dxzf2ip.txt item: #678 of 973 id: cord-314201-6njwigco author: Maher-Sturgess, Sheryl L title: Universal primers that amplify RNA from all three flavivirus subgroups date: 2008-01-24 words: 4628 flesch: 50 summary: The amplification of cDNA was followed by restriction enzyme digestion to identify a range of virus species [7] . Flavivirus detection and taxonomy has recently become more difficult with the determination of the nucleotide sequence of Tamana bat virus (TABV), and Cell fusing agent virus (CFAV) keywords: cdna; flavivirus; gene; human; pcr; primers; regions; rna; sequence; species; virus; viruses cache: cord-314201-6njwigco.txt plain text: cord-314201-6njwigco.txt item: #679 of 973 id: cord-314386-cxq9v218 author: Nitsche, Andreas title: SARS Coronavirus Detection date: 2004-07-17 words: 1905 flesch: 43 summary: Case definition for surveillance of severe acute respiratory syndrome SARS Rapid diagnosis of a coronavirus associated with severe acute respiratory syndrome (SARS) Variation of the sequence in the gene encoding for transmembrane protein M of canine coronavirus (CCV) Sequence comparison of porcine respiratory coronavirus isolates reveals heterogeneity in the S, 3, and 3-1 genes Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection The viruses and their replication Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China People's daily edited by ProMED-mail Wood L, questions about comparative genomics of SARS coronavirus isolates A guideline to reference gene selection for quantitative real-time PCR Canadian officials watch SARS-like mystery bug We thank Sabrina Wendt for excellent technical assistance, Ian M. Mackay for critically reading the manuscript, and Artus (Artus GmbH, Hamburg, Germany) for kindly providing the Real-Art HPA-Coronavirus LC RT PCR Reagents Kit. These patients were seropositive and are regarded as confirmed SARS patients. keywords: assays; cov; pcr; sars; time cache: cord-314386-cxq9v218.txt plain text: cord-314386-cxq9v218.txt item: #680 of 973 id: cord-314404-tkhupnko author: Ashokka, Balakrishnan title: Care of the Pregnant Woman with COVID-19 in Labor and Delivery: Anesthesia, Emergency cesarean delivery, Differential diagnosis in the acutely ill parturient, Care of the newborn, and Protection of the healthcare personnel date: 2020-04-10 words: 2126 flesch: 47 summary: key: cord-314404-tkhupnko authors: Ashokka, Balakrishnan; Loh, May-Han; Tan, Cher Heng; SU, Lin Lin; Young, Barnaby Edward; Lye, David Chien; Biswas, Arijit; E Illanes, Sebastian; Choolani, Mahesh title: Care of the Pregnant Woman with COVID-19 in Labor and Delivery: Anesthesia, Emergency cesarean delivery, Differential diagnosis in the acutely ill parturient, Care of the newborn, and Protection of the healthcare personnel date: 2020-04-10 journal: Am J Obstet Gynecol DOI: 10.1016/j.ajog.2020.04.005 sha: doc_id: 314404 cord_uid: tkhupnko COVID-19 in pregnancy can cause severe maternal morbidity in up to 9% of affected gravidae. When a COVID-19 parturient with desaturation (oxygen saturation decreases to ≤93%) presents 256 for emergency cesarean delivery, general anesthesia needs to be administered. keywords: care; covid-19; delivery; oxygen; parturient; patient cache: cord-314404-tkhupnko.txt plain text: cord-314404-tkhupnko.txt item: #681 of 973 id: cord-314937-jrxu65bl author: Kuwelker, K. title: High attack rates of SARS-CoV-2 infection through household-transmission: a prospective study date: 2020-11-04 words: 5882 flesch: 50 summary: key: cord-314937-jrxu65bl authors: Kuwelker, K.; Zhou, F.; Blomberg, B.; Lartey, S.; Brokstad, K. A.; Trieu, M. C.; Madsen, A.; Krammer, F.; Mohn, K. G. I.; Toendel, C.; Linchausen, D. W.; Cox, R. J.; Langeland, N. title: High attack rates of SARS-CoV-2 infection through household-transmission: a prospective study date: 2020-11-04 journal: nan DOI: 10.1101/2020.11.02.20224485 sha: doc_id: 314937 cord_uid: jrxu65bl Background: Household attack rates of SARS-CoV-2 ranging from 7% to 38% have been reported, using reverse transcription polymerase chain reaction (RT-PCR) of respiratory samples. Currently, there are only two other studies that have estimated household attack rates based on seropositivity, 37·4% in Spain (7) and 35% in Brazil (22). keywords: attack; cases; cov-2; household; medrxiv; members; pcr; preprint; sars cache: cord-314937-jrxu65bl.txt plain text: cord-314937-jrxu65bl.txt item: #682 of 973 id: cord-314986-uhpe69k0 author: Cai, Quan title: A model based on CT radiomic features for predicting RT-PCR becoming negative in coronavirus disease 2019 (COVID-19) patients date: 2020-10-20 words: 3755 flesch: 44 summary: We collected the clinical data and chest CT features of mild COVID-19 patients in Fangcang Shelter Hospital in Wuhan, Hubei, aiming to establish a predictive model for RT-PCR becoming negative during the recovery period. key: cord-314986-uhpe69k0 authors: Cai, Quan; Du, Si-Yao; Gao, Si; Huang, Guo-Liang; Zhang, Zheng; Li, Shu; Wang, Xin; Li, Pei-Ling; Lv, Peng; Hou, Gang; Zhang, Li-Na title: A model based on CT radiomic features for predicting RT-PCR becoming negative in coronavirus disease 2019 (COVID-19) patients date: 2020-10-20 journal: BMC Med Imaging DOI: 10.1186/s12880-020-00521-z sha: doc_id: 314986 cord_uid: uhpe69k0 BACKGROUND: Coronavirus disease 2019 (COVID-19) has emerged as a global pandemic. keywords: chest; covid-19; features; model; patients; pcr; study cache: cord-314986-uhpe69k0.txt plain text: cord-314986-uhpe69k0.txt item: #683 of 973 id: cord-315037-lmur80te author: Lin, Chien-Yu title: Increased Detection of Viruses in Children with Respiratory Tract Infection Using PCR date: 2020-01-15 words: 4192 flesch: 37 summary: Systematic review and meta-analysis The clinical significance of filmarray respiratory panel in diagnosing community-acquired pneumonia Comparison of real-time pcr assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children Rapid and sensitive method using multiplex real-time pcr for diagnosis of infections by influenza a and influenza b viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 Public health responses to reemergence of animal rabies Frequent detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction An economical tandem multiplex real-time pcr technique for the detection of a comprehensive range of respiratory pathogens Real-time reverse transcriptase pcr assay for detection of human metapneumoviruses from all known genetic lineages Design and performance testing of quantitative real time pcr assays for influenza a and b viral load measurement Simultaneous detection of influenza a, influenza b, and respiratory syncytial viruses and subtyping of influenza a h3n2 virus and h1n1 (2009) virus by multiplex real-time pcr Rapid testing for respiratory syncytial virus in a paediatric emergency department: Benefits for infection control and bed management Viral respiratory tract infections in allogeneic hematopoietic stem cell transplantation recipients in the era of molecular testing The use of antimicrobial agents after diagnosis of viral respiratory tract infections in hospitalized adults: Antibiotics or anxiolytics? Antimicrobial drug prescription in ambulatory care settings, united states Antibiotics for bronchiolitis in children Reducing unnecessary chest x-rays, antibiotics and bronchodilators through implementation of the nice bronchiolitis guideline Viral etiology of acute lower respiratory tract infections in hospitalized young children in northern Taiwan Respiratory viral infections detected by multiplex pcr among pediatric patients with lower respiratory tract infections seen at an urban hospital in delhi from Etiologic spectrum and occurrence of coinfections in children hospitalized with community-acquired pneumonia Respiratory virus of severe pneumonia in south korea: Prevalence and clinical implications Differential risk of hospitalization among single virus infections causing influenza like illnesses Epidemiological study of hospitalization associated with respiratory syncytial virus infection in Taiwanese children between Prolonged seasonality of respiratory syncytial virus infection among preterm infants in a subtropical climate Global respiratory syncytial virus-associated mortality in young children (rsv gold): A retrospective case series Epidemiology and clinical characteristics of community-acquired pneumonia in hospitalized children Etiology and impact of coinfections in children hospitalized with community-acquired pneumonia Table S2 A newly discovered human pneumovirus isolated from young children with respiratory tract disease Identification of a new human coronavirus Community-acquired pneumonia requiring hospitalization among US Children Viral pneumonia Community-acquired pneumonia requiring hospitalization among US Respiratory viral infections during the first 28 days after transplantation in pediatric hematopoietic stem cell transplant recipients Unrecognized viral respiratory tract infections in premature infants during their birth hospitalization: A prospective surveillance study in two neonatal intensive care units Implementation of rapid diagnostics with antimicrobial stewardship The role of multiplex pcr in respiratory tract infections in children Early diagnosis of lower respiratory tract infections (point-of-care tests) Etiological diagnosis reduces the use of antibiotics in infants with bronchiolitis Casas, I. Spectrum of respiratory viruses in children with community-acquired pneumonia Resisting the use of antibiotics for viral infections Diagnostic value of respiratory virus detection in symptomatic children using real-time pcr Are we ready for novel detection methods to treat respiratory pathogens in hospital-acquired pneumonia? Multiplex pcr system for the rapid diagnosis of respiratory virus infection: keywords: children; detection; infection; pcr; rsv; specimens; tests; viruses cache: cord-315037-lmur80te.txt plain text: cord-315037-lmur80te.txt item: #684 of 973 id: cord-315094-pzixgqcy author: Benetka, Viviane title: Prevalence of feline coronavirus types I and II in cats with histopathologically verified feline infectious peritonitis date: 2004-03-26 words: 5539 flesch: 48 summary: CCV exhibits an identity to FCoV-1 KU-2 of 72%; its much closer relationship to FCoV type II than to FCoV type I can nicely be observed by the similarity of several nucleotide changes of FCoV type II and CCV. These findings demonstrate that in FIP cases FCoV type I predominates, too, nonetheless, in 14% of the cases FCoV type II was detected, suggesting its causative involvement in cases of FIP. keywords: cats; et al; fcov; feline; fip; pcr; samples; type cache: cord-315094-pzixgqcy.txt plain text: cord-315094-pzixgqcy.txt item: #685 of 973 id: cord-315167-ph15z424 author: Goka, E. A. title: Pan-human coronavirus and human bocavirus SYBR Green and TaqMan PCR assays; use in studying influenza A viruses co-infection and risk of hospitalization date: 2014-12-05 words: 3313 flesch: 44 summary: [12] showed that, since 2005, over 40 studies conducted globally identified human bocavirus in children with acute respiratory virus infections; and that most of these prevalence studies found hBoV occurring mainly together with other viruses. The Genome sequence of the SARS-associated coronavirus Major genetic marker of nidoviruses encodes a replicative endoribonuclease Simple absolute quantification method correcting for quantitative PCR efficiency variations for microbial community samples SYBR Green real-time reverse transcriptionpolymerase chain reaction assay for the generic detection of coronaviruses A pancoronavirus RT-PCR assay for detection of all known coronaviruses Comprehensive detection and identification of human coronaviruses, including the SARS-associated coronavirus, with a single RT-PCR assay Real-time PCR for diagnosis of human bocavirus infections and phylogenetic analysis Real-time PCR assays for detection of bocavirus in human specimens World Health Organisation (WHO): H1N1 in post-pandemic period Coronavirus as a possible cause of severe acute respiratory syndrome Molecular epidemiology of the novel coronavirus that causes severe acute respiratory syndrome Clinical characteristics and outcomes in hospitalized patients with respiratory viral co-infection during the 2009 H1N1 influenza pandemic Viral etiology of influenza-like illnesses in Antananarivo Community-acquired respiratory viruses and co-infection among patients of Ontario sentinel practices Influenza A, viruses dual and multiple infections with other respiratory viruses and risk of hospitalisation and mortality. keywords: assay; coronavirus; hbov; hcov; human; infections; influenza; pcr; viruses cache: cord-315167-ph15z424.txt plain text: cord-315167-ph15z424.txt item: #686 of 973 id: cord-315476-7rdiesav author: Peret, Teresa C. T. title: Characterization of Human Metapneumoviruses Isolated from Patients in North America date: 2002-06-01 words: 1961 flesch: 49 summary: Data from that report suggest that HMPV is similar to respiratory syncytial virus (RSV), in that infection usually occurs during winter months and is common during childhood (most children have serologic evidence of infection by age 5 years). key: cord-315476-7rdiesav authors: Peret, Teresa C. T.; Boivin, Guy; Li, Yan; Couillard, Michel; Humphrey, Charles; Osterhaus, Albert D. M. E.; Erdman, Dean D.; Anderson, Larry J. title: Characterization of Human Metapneumoviruses Isolated from Patients in North America date: 2002-06-01 journal: J Infect Dis DOI: 10.1086/340518 sha: doc_id: 315476 cord_uid: 7rdiesav Human metapneumovirus (HMPV) was recently identified in The Netherlands and was linked to acute respiratory tract illness. keywords: hmpv; human; isolates; patients; sequences; tract cache: cord-315476-7rdiesav.txt plain text: cord-315476-7rdiesav.txt item: #687 of 973 id: cord-315541-tirod4t6 author: Henriques, Ana Margarida title: Development and validation of a real-time PCR for the detection and quantification of porcine circovirus type 2 date: 2018-07-17 words: 3567 flesch: 42 summary: The specificity was also evaluated by testing 13 samples positive for other swine diseases viruses, namely African swine fever virus (ASFV), classical swine fever virus (CSFV), European and American strains of porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), wild-type and gE deleted strains of pseudorabies virus (PRV), swine vesicular disease virus (SVDV), foot-and-mouth disease virus (FMDV), porcine parvovirus (PPV), swine influenza virus (SIV), swine coronavirus and swine rotavirus. Effect of vaccination against sub-clinical porcine circovirus type 2 infection in a high-health finishing pig herd: a randomised clinical field trial Multiplex PCR for detection and typing of porcine circoviruses Porcine circovirus type 2 (PCV2) infections: clinical signs, pathology and laboratory diagnosis Studying the effect of single mismatches in primer and probe binding regions on amplification curves and quantification in real-time PCR How good is a PCR efficiency estimate: recommendations for precise and robust qPCR efficiency assessments Development of isothermal recombinase polymerase amplification assay for rapid detection of porcine circovirus type 2 Detection of PCV2 DNA by SYBR Green I-based quantitative PCR Calibration curve obtained by the representation of the Ct values as a function of the logarithm of the plasmid copies number Rapid detection of porcine circovirus type 2 by TaqManbased real-time polymerase chain reaction assays Rapid detection of porcine circovirus type 2 using a TaqMan-based realtime PCR Loop-mediated isothermal amplification for detection of porcine circovirus type 2 Development and validation of a real-time PCR for the detection and quantification of… 361 Acknowledgements keywords: detection; dna; pcr; pcv2; porcine; samples; virus cache: cord-315541-tirod4t6.txt plain text: cord-315541-tirod4t6.txt item: #688 of 973 id: cord-315598-qwh72inx author: Mendoza, Jose Luis Accini title: ACTUALIZACION DE LA DECLARACIÓN DE CONSENSO EN MEDICINA CRITICA PARA LA ATENCIÓN MULTIDISCIPLINARIA DEL PACIENTE CON SOSPECHA O CONFIRMACIÓN DIAGNÓSTICA DE COVID-19 date: 2020-10-06 words: 69660 flesch: 31 summary: y los que tienen menos probabilidades de beneficiarse (él «demasiado enfermo»), no prestan suficiente atención a las diferencias entre grupos en términos de la duración de los cuidados intensivos necesarios para lograr resultados. Se recomienda aplicar la escala SOFA al menos cada 48 horas sumado al criterio de fragilidad y años de vida saludables salvados estos criterios podrían ser válidos en pacientes con fallo terapéutico a las medidas óptimas y orientar decisiones de deescalamiento de medidas y de nivel de complejidad de atención cuando la demanda potencial supera la oferta (capacidad y capacidades), estas decisiones deben ser tomadas idealmente en junta médica. keywords: 2019; 2020; acuerdo con; acute; además de; aguda; alto; amci; analysis; análisis de; asociado con; aumento de; bajo; calidad de; care; casos de; clinical; clínica; clínica de; clínicos; comité de; como el; como la; como los; como se; como una; compromiso; con covid-19; con el; con enfermedad; con hipoxemia; con infección; con la; con los; con mayor; con neumonía; con que; con sars; con sdra; con sospecha; con su; con un; condiciones de; considerar la; contar con; contra; control; coronavirus; cov-2; criterios de; crítico con; cual se; cuando se; cuenta la; de acuerdo; de aerosoles; de alta; de amci; de atención; de baja; de cada; de contaminación; de coronavirus; de covid-19; de cuidados; de de; de dificultad; de enfermedad; de esta; de estos; de estudios; de falla; de forma; de hcq; de hipoxemia; de il-6; de infección; de ingreso; de intubación; de la; de los; de manera; de marzo; de menor; de oxígeno; de pacientes; de protección; de salud; de ser; de soporte; de su; de tórax; de un; de ventilación; de vida; deben; del; del virus; dentro; desde el; después de; diagnóstico de; disease; disminución de; disminuir el; disponibilidad de; distress; donde; dosis; dosis de; duración de; durante la; días; días de; el consentimiento; el cual; el de; el diagnóstico; el día; el estudio; el grupo; el inicio; el manejo; el momento; el más; el nivel; el número; el paciente; el pronóstico; el riesgo; el sars; el tiempo; el traslado; el uso; elevación de; embargo; en china; en contra; en cuenta; en el; en este; en la; en los; en salud; en su; en uci; en un; entre el; entre la; entre los; es una; estado de; este; estrategia de; está; evidencia de; evitar la; fin de; final de; fue de; fuera de; fueron; grupo de; hasta el; horas; infección por; inicio de; intensive; la administración; la capacidad; la cual; la decisión; la disponibilidad; la enfermedad; la evidencia; la falla; la hcq; la hipoxemia; la infección; la intubación; la mortalidad; la oxigenación; la pandemia; la presencia; la presión; la relación; la respuesta; la salud; la seguridad; la terapia; la toma; la uci; la utilización; la valoración; la vida; la vía; las; los casos; los cuales; los días; los estudios; los síntomas; luego de; manejo de; mayor; mayoría de; mecánica; medición de; medidas de; mejorar la; mejoría; menor; más de; necesidad de; nivel de; niveles; número de; o por; o se; objetivo de; otros; pacientes con; pacientes covid-19; pacientes críticos; pacientes que; pacientes y; para el; para la; para los; para pacientes; para que; para sars; para su; parte de; patients; pcr; pero; personal de; plasma; por covid-19; por el; por la; por los; por sars; por un; posibilidad de; presión; protocolo de; pueden; pulmonar; punto de; que; que el; que la; que los; que puede; que se; que una; realización de; realizar; recomendación se; recomienda la; recomienda que; reducción de; renal; respiratoria; resultados; retiro de; review; riesgo de; salud y; sars; se debe; se han; se puede; se recomienda; según la; ser; severa; severidad de; shock; si el; si la; si se; sin; sobre el; sobre la; son de; sospecha de; syndrome; síndrome de; tasa de; tener; tener en; teniendo en; tiempo de; tipo de; todos los; tormenta de; trabajadores de; tratamiento de; treatment; uci y; un estudio; un paciente; una; unidad de; uso de; utilizar; ventilation; viral; y al; y cols; y como; y con; y de; y el; y en; y es; y la; y los; y para; y por; y puede; y que; y se; y su; y una cache: cord-315598-qwh72inx.txt plain text: cord-315598-qwh72inx.txt item: #689 of 973 id: cord-315780-uhi66unn author: Paton, David title: Detection of transmissible gastroenteritis virus by RT-PCR and differentiation from porcine respiratory coronavirus date: 1997-07-31 words: 2908 flesch: 45 summary: A comparative examination using CF, PLA and NPLA assays The multiplication of transmissible gastroenteritis viruses in several cell lines originated from porcine kidney and effects of trypsin on the growth of the viruses Molecular differentiation of transmissible gastroenteritis virus and porcine respiratory coronavirus strains Classical transmissible gastroenteritis returns Porcine respiratory coronavirus: molecular features and virus-host interactions Pathogenicity of experimental infection with pneumotropic porcine coronavirus Transmissible gastroenteritis Diagnosis of transmissible gastroenteritis in pigs by means of immunofluorescence Isolation of a porcine respiratory, non-enteric coronavirus related to transmissible gastroenteritis Development of a detection system for woody plants based on PCR analysis of immobilized virions Transmissible gastroenteritis coronavirus, but not the related porcine respiratory coronavirus, has a sialic acid (N-glycolylneuramic acid) binding activity In situ hybridization technique for the detection of swine enteric and respiratory coronaviruses, transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus (PRCV), in formalin-fixed paraffin-embedded tissues Region-specific initiation of mouse mammary tumour virus RNA synthesis by endogenous RNA polymerase II in preparations of cell nuclei The sensitivity of the RT-PCR for virus detection in culture fluids was compared with cell culture virus isolation. keywords: cell; gastroenteritis; pcr; porcine; tgev; transmissible; virus cache: cord-315780-uhi66unn.txt plain text: cord-315780-uhi66unn.txt item: #690 of 973 id: cord-315949-7id5mitl author: Sentilhes, Anne‐Charlotte title: Respiratory virus infections in hospitalized children and adults in Lao PDR date: 2013-06-25 words: 4099 flesch: 42 summary: Epidemiology and etiology of childhood pneumonia Estimates of world-wide distribution of child deaths from acute respiratory infections Lung infection-a public health priority Emerging infectious diseases in southeast Asia: regional challenges to control Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses Use of a multiplex PCR/RT-PCR approach to assess the viral causes of influenza-like illnesses in Cambodia during three consecutive dry seasons Simultaneous detection of respiratory viruses in children with acute respiratory infection using two different multiplex reverse transcription-PCR assays The role of respiratory viral infections among children hospitalized for community-acquired pneumonia in a developing country Pneumonia research to reduce childhood mortality in the developing world Pocket Book of Hospital Care for Children: Guidelines for the Management of Common Illnesses with Limited Resources Highly pathogenic influenza A(H5N1) virus survival in complex artificial aquatic biotopes The association of newly identified respiratory viruses with lower respiratory tract infections in Korean children Information for Laboratory Diagnosis of Pandemic (H1N1) Pandemic A(H1N1)2009 influenza virus detection by real time RT-PCR: is viral quantification useful? Viral pathogens associated with acute respiratory infections in central Vietnamese children Molecular monitoring of causative viruses in child acute respiratory infection in endemo-epidemic situations in Shanghai Viral etiologies of acute respiratory infections among hospitalized Vietnamese children in Ho Chi Minh City Incidence of respiratory pathogens in persons hospitalized with pneumonia in two provinces in Thailand Viral and atypical bacterial detection in acute respiratory infection in children under five years Rhinovirus and the lower respiratory tract Rhinovirus-associated hospitalizations in young children Rhinovirus associated with severe lower respiratory tract infections in children Human rhinovirus infections in rural Thailand: epidemiological evidence for rhinovirus as both pathogen and bystander Viral respiratory infections in hospitalized and community control children in Alaska The burden of hospitalized lower respiratory tract infection due to respiratory syncytial virus in rural Thailand The burden of respiratory syncytial virus infection in young children Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: a systematic review and meta-analysis Two distinct subtypes of human respiratory syncytial virus Genetic variability of group A human respiratory syncytial virus strains circulating in Germany from 1998 to Seroprevalence of anti-RSV IgG in Thai children aged 6 months to 5 years A study of the genetic variability of human respiratory syncytial virus (HRSV) in Cambodia reveals the existence of a new HRSV group B genotype An early report from newly established laboratory-based influenza surveillance in Lao PDR Parainfluenza virus type 3: seasonality and risk of infection and reinfection in young children Specific viruses detected in Nigerian children in association with acute respiratory disease Progress in the development of human parainfluenza virus vaccines Parainfluenza virus type 4 infections in pediatric patients Human parainfluenza virus type 4 infection in Chinese children with lower respiratory tract infections: a comparison study Detection and identification of human parainfluenza viruses 1, 2, 3, and 4 in clinical samples of pediatric patients by multiplex reverse transcription-PCR Contribution of human metapneumovirus to influenza-like infections in North Greece Population-based incidence of human metapneumovirus infection among hospitalized children Human metapneumovirus in infants and young children in Thailand with lower respiratory tract infections; molecular characteristics and clinical presentations Human bocavirus: a novel parvovirus epidemiologically associated with pneumonia requiring hospitalization in Thailand Evidence of human coronavirus HKU1 and human bocavirus in Australian children Detection of nine respiratory RNA viruses using three multiplex RT-PCR assays incorporating a novel RNA internal control transcript Detection and typing by molecular techniques of respiratory viruses in children hospitalized for acute respiratory infection in Rome, Italy Single versus dual respiratory virus infections in hospitalized infants Respiratory viral infections detected by multiplex PCR among pediatric patients with lower respiratory tract infections seen at an urban hospital in Delhi from Impact of human metapneumovirus and respiratory syncytial virus co-infection in severe bronchiolitis Viral infections of the lower respiratory tract: old viruses, new viruses, and the role of diagnosis Respiratory syncytial virus and human rhinoviruses are the major causes of severe lower respiratory tract infections in Kuwait Role of rhinovirus in hospitalized infants with respiratory tract infections in Spain Vientiane climate guide to the average weather & temperatures This study was supported by Surveillance and Investigation of Epidemic Situations in South-East Asia (SISEA) project, a grant from the French Agency for Development (AFD). key: cord-315949-7id5mitl authors: Sentilhes, Anne‐Charlotte; Choumlivong, Khamla; Celhay, Olivier; Sisouk, Thongchanh; Phonekeo, Darouny; Vongphrachanh, Phengta; Brey, Paul; Buchy, Philippe title: Respiratory virus infections in hospitalized children and adults in Lao PDR date: 2013-06-25 journal: keywords: children; infections; influenza; patients; respiratory; study; viruses; years cache: cord-315949-7id5mitl.txt plain text: cord-315949-7id5mitl.txt item: #691 of 973 id: cord-316173-ocdlh310 author: LIU, Dafei title: One-step triplex PCR/RT-PCR to detect canine distemper virus, canine parvovirus and canine kobuvirus date: 2018-01-23 words: 999 flesch: 24 summary: For one sample, the CPV was positive tested by CPV Ag Test Kit, but negative by the Isolation and immunisation studies of a canine parco-like virus from dogs with haemorrhagic enteritis High genetic diversity of the VP2 gene of a canine parvovirus strain detected in a domestic cat Phylogenetic analysis of astrovirus and kobuvirus in Korean dogs Canine kobuviruses in diarrhoeic dogs in Italy Detection of canine distemper virus in dogs by real-time RT-PCR Simultaneous detection of canine respiratory disease associated viruses by a multiplex reverse transcription-polymerase chain reaction assay Diagnostic performance of a rapid in-clinic test for the detection of Canine Parvovirus under different storage conditions and vaccination status Characterization of a canine homolog of human Aichivirus Molecular characterization of new described kobuvirus in dogs with diarrhea in China Prevalence and phylogenetic analysis of canine kobuviruses in diarrhoetic dogs in northeast Viruses in diarrhoeic dogs include novel kobuviruses and sapoviruses Physical chemical characteristics and biological test of attenuated virus strains of canine distemper virus, feline parvovirus and canine adenovirus Establishment of the duplex PCR for the detection of canine distemper virus and canine parvovirus Establishment of reverse transcription loop-mediated isothermal amplification for rapid detection and differentiation of canine distemper virus infected and vaccinated animals Mechanism of reduction of virus release and cell-cell fusion in persistent canine distemper virus infection Studies on canine distemper virus persistence in the central nervous system Canine kobuvirus infections in Korean dogs Molecular characterization of canine kobuvirus in wild carnivores and the domestic dog in Africa Establishment of multiplex RT-PCR for the detection of five zoonosis viruses Demyelination in canine distemper virus infection: a review Pathology and RT-PCR employed in the identification of canine distemper virus infection in Taiwan key: cord-316173-ocdlh310 authors: LIU, Dafei; LIU, Fei; GUO, Dongchun; HU, Xiaoliang; LI, Zhijie; LI, Zhigang; MA, Jianzhang; LIU, Chunguo title: One-step triplex PCR/RT-PCR to detect canine distemper virus, canine parvovirus and canine kobuvirus date: 2018-01-23 journal: J Vet Med Sci DOI: 10.1292/jvms.17-0442 sha: doc_id: 316173 cord_uid: ocdlh310 keywords: canine; cpv; pcr cache: cord-316173-ocdlh310.txt plain text: cord-316173-ocdlh310.txt item: #692 of 973 id: cord-316250-w0nl88jz author: Yang, Falong title: Selection of reference genes for quantitative real-time PCR analysis in chicken embryo fibroblasts infected with avian leukosis virus subgroup J date: 2013-10-07 words: 2191 flesch: 45 summary: [7] compared the expression of 10 candidate reference genes in cell lines infected with 6 human viruses: cytomegalovirus, human herpesvirus-6, camelpox virus, SARS coronavirus or yellow fever virus, and found that a commonly used gene ACTB, is unsuitable as reference gene, whereas TATA-Box binding protein (TBP) and peptidyl-prolyl-isomerase A (PPI) were stable genes for use as reference genes in expression studies in virus infected cells. Candidate genes with the lowest M values have the most expression stability and thus should preferentially be used as reference genes for gene expression and normalization of other genes. keywords: expression; genes; infected; pcr; reference; time; virus cache: cord-316250-w0nl88jz.txt plain text: cord-316250-w0nl88jz.txt item: #693 of 973 id: cord-316295-x636ux34 author: Roth, Bernhard title: Isolation of influenza viruses in MDCK 33016PF cells and clearance of contaminating respiratory viruses date: 2012-01-11 words: 4143 flesch: 39 summary: Collaborative studies have been initiated to investigate the growth and yield of influenza viruses in different cell lines, the efficiency and fidelity of influenza virus isolation, and the suitability for vaccine manufacture of different cell substrates key: cord-316295-x636ux34 authors: Roth, Bernhard; Mohr, Hannah; Enders, Martin; Garten, Wolfgang; Gregersen, Jens-Peter title: Isolation of influenza viruses in MDCK 33016PF cells and clearance of contaminating respiratory viruses date: 2012-01-11 journal: Vaccine DOI: 10.1016/j.vaccine.2011.11.063 sha: doc_id: 316295 cord_uid: x636ux34 keywords: cells; growth; influenza; mdck; pcr; results; samples; virus; viruses cache: cord-316295-x636ux34.txt plain text: cord-316295-x636ux34.txt item: #694 of 973 id: cord-316309-8xe7cg8q author: Lee, Wah Heng title: LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens date: 2008-09-10 words: 5902 flesch: 50 summary: Recently, we have published a pathogen detection approach using microarrays based on random primer amplification [14] . As it is not cost-effective to design specific primers for all the pathogens on the chip and quite impossible to design specific primers for yet to be known pathogens, random primer amplification is preferred over primer-specific amplification. keywords: aes; amplification; detection; genome; pcr; primer; probes; target cache: cord-316309-8xe7cg8q.txt plain text: cord-316309-8xe7cg8q.txt item: #695 of 973 id: cord-316343-u1uup5da author: Luo, Yun title: Longitudinal Surveillance of Betacoronaviruses in Fruit Bats in Yunnan Province, China During 2009–2016 date: 2018-02-01 words: 3511 flesch: 52 summary: immunopathology Middle east respiratory syndrome coronavirus (MERS-CoV): announcement of the coronavirus study group Identification of a novel coronavirus in patients with severe acute respiratory syndrome Xi River virus, a new bat reovirus isolated in southern China Metagenomic analysis of viruses from bat fecal samples reveals many novel viruses in insectivorous bats in China Filovirus RNA in fruit bats Bat origin of human coronaviruses A bat-derived putative cross-family recombinant coronavirus with a reovirus gene The nature of flight-the molecules and mechanics of flight in animals Seroprevalence of rabies virus antibodies in bats from southern China Coexistence of different genotypes in the same bat and serological characterization of Rousettus bat coronavirus HKU9 belonging to a novel Betacoronavirus subgroup Bats are natural reservoirs of SARS-like coronaviruses Antibodies to Nipah or Nipah-like viruses in bats Characterization and pathogenicity of a novel mammalian orthoreovirus from wild short-nosed fruit bats Generic detection of coronaviruses and differentiation at the prototype strain level by reverse transcription-PCR and nonfluorescent low-density microarray Bats as bushmeat: a global review Emerging infectious diseases associated with bat viruses Bartonella, bats and bugs: a review Novel bat adenoviruses with low G?C content shed new light on the evolution of adenoviruses Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features Genetically diverse filoviruses in Rousettus and Eonycteris spp. These fruit bats feed on fruits and flowers and have frequent contact with peoples and farms, thus increasing the risk of spillover of bat viruses to domestic animals and humans. keywords: batcov; bats; gccdc1; hku9; sequences; species; viruses cache: cord-316343-u1uup5da.txt plain text: cord-316343-u1uup5da.txt item: #696 of 973 id: cord-316376-76beuk0c author: Medeiros, Augusto Kreling title: Higher frequency of hepatic steatosis at CT among COVID-19-positive patients date: 2020-07-18 words: 4132 flesch: 36 summary: Major strengths include the fact that this is the first study to compare steatosis on CT between positive and negative COVID-19 patients; the sample size, which has allowed statistical power to identify the higher frequency of liver steatosis among SARS-CoV2 positive patients; finally, as CT studies were performed on the same scanner (to avoid exposure of patients without flu syndrome), with a variable protocol according to their body habitus, inter-scanner variability that could have affected measurements did not compromise the results, allowing uniformity. These findings are in accordance with other recent studies linking obesity and COVID-19 infection, as there is an intricate relationship between liver steatosis, metabolic syndrome and obesity. keywords: covid-19; disease; group; liver; obesity; patients; steatosis; study cache: cord-316376-76beuk0c.txt plain text: cord-316376-76beuk0c.txt item: #697 of 973 id: cord-316500-vik30moa author: Cardillo, Lorena title: Lifestyle as Risk Factor for Infectious Causes of Death in Young Dogs: A Retrospective Study in Southern Italy (2015–2017) date: 2020-06-05 words: 5528 flesch: 43 summary: key: cord-316500-vik30moa authors: Cardillo, Lorena; Piegari, Giuseppe; Iovane, Valentina; Viscardi, Maurizio; Alfano, Flora; Cerrone, Anna; Pagnini, Ugo; Montagnaro, Serena; Galiero, Giorgio; Pisanelli, Giuseppe; Fusco, Giovanna title: Lifestyle as Risk Factor for Infectious Causes of Death in Young Dogs: A Retrospective Study in Southern Italy (2015–2017) date: 2020-06-05 journal: Vet Med Int DOI: 10.1155/2020/6207297 sha: doc_id: 316500 cord_uid: vik30moa Infectious diseases are a common cause of death in young dogs. Several factors are thought to predispose young dogs to microbiological infections. keywords: age; canine; cases; cpv; death; dogs; infections; lesions; ownerless; pcr; study; time cache: cord-316500-vik30moa.txt plain text: cord-316500-vik30moa.txt item: #698 of 973 id: cord-316537-f5rto51t author: Loens, Katherine title: Mycoplasma pneumoniae: Current Knowledge on Nucleic Acid Amplification Techniques and Serological Diagnostics date: 2016-03-31 words: 4210 flesch: 26 summary: Curr Detection of Mycoplasma pneumoniae by two polymerase chain reactions and role of M. pneumoniae in acute respiratory tract infections in pediatric patients Community-acquired pneumonia requiring hospitalization among U.S. children Singlenucleotide polymorphism PCR for the detection of Mycoplasma pneumoniae and determination of macrolide resistance in respiratory samples Clinical significance of different bacterial load of Mycoplasma pneumoniae in patients with Mycoplasma pneumoniae pneumonia Genetic point-of-care diagnosis of Mycoplasma pneumoniae infection using LAMP assay Eaton agent and other non-bacterial pneumonias Rapid diagnosis of Mycoplasma pneumoniae in children with pneumonia by an immunochromatographic antigen assay Rapid detection of Mycoplasma pneumoniae and its macrolide-resistance mutation by Cycleave PCR Acute respiratory infection due to Mycoplasma pneumoniae: current status of diagnostic methods A multicenter pilot external quality assessment programme to assess the quality of molecular detection of Chlamydophila pneumoniae and Mycoplasma pneumoniae Molecular diagnosis of Mycoplasma pneumoniae respiratory tract infections Optimal sampling sites and methods for detection of pathogens possibly causing community-acquired lower respiratory tract infections Performance of different mono-and multiplex nucleic acid amplification tests on a multipathogen external quality assessment panel Mycoplasma pneumoniae as a causative agent of communityacquired pneumonia in children: clinical features and laboratory diagnosis Diagnostic sensitivity of a rapid antigen test for the detection of Mycoplasma pneumoniae: comparison with real-time PCR Evaluation of eight commercial tests for Mycoplasma pneumoniae antibodies in the absence of acute infection World health organization international standard to harmonize assays for detection of mycoplasma DNA Development of a multiplex real-time PCR assay for detection of Mycoplasma pneumoniae, Chlamydia pneumoniae and mutations associated with macrolide resistance in Mycoplasma pneumoniae from respiratory clinical specimens Comparative evaluation of six commercialized multiplex PCR kits for the diagnosis of respiratory infections FilmArray, an automated nested multiplex PCR system for multipathogen detection: development and application to respiratory tract infection Validation of a multiplex reverse transcriptase PCR ELISA for the detection of 19 respiratory tract pathogens Comparison of the illumigene Mycoplasma DNA amplification assay and culture for detection of Mycoplasma pneumoniae Real-time PCR detection of Mycoplasma pneumoniae in respiratory specimens Limited utility of culture for Mycoplasma pneumoniae and Chlamydophila pneumoniae for diagnosis of respiratory tract infections Association of targeted multiplex PCR with resequencing microarray for the detection of multiple respiratory pathogens Pathogen chip for respiratory tract infections Carriage of Mycoplasma pneumoniae in the upper respiratory tract of symptomatic and asymptomatic children: an observational study Analysis of eight commercial enzyme immunoassay tests for detection of antibodies to Mycoplasma pneumoniae in human serum New insights into the pathogenesis and detection of Mycoplasma pneumoniae infections Mycoplasma pneumoniae and its role as a human pathogen Field evaluation of TaqMan Array Card (TAC) for the simultaneous detection of multiple respiratory viruses in children with acute respiratory infection PCR versus serology for diagnosing Mycoplasma pneumoniae infection: a systematic review & meta-analysis Evaluation of a new real-time PCR assay for detection of Mycoplasma pneumoniae in clinical specimens Cultureindependent detection and genotyping of Mycoplasma pneumoniae in clinical specimens from Beijing The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Correct and rapid diagnosis and/or management of M. pneumoniae infections is, however, critical to initiate appropriate antibiotic treatment and is nowadays usually done by PCR and/or serology. keywords: detection; igm; infection; mycoplasma; pcr; pneumoniae; time cache: cord-316537-f5rto51t.txt plain text: cord-316537-f5rto51t.txt item: #699 of 973 id: cord-316719-uej7d5zf author: Witkowski, Peter T. title: Molekulare Identifikation von Hantaviren in neuen Wirten date: 2015-08-27 words: 1322 flesch: 45 summary: Zu den klassischen Phylogruppen der Viren, die von echten Mäusen (Gruppe I), Wühlmäusen (Gruppe IIa) und Neuweltmäusen (Gruppe IIb) beherbergt werden, sind nun zwei neue Gruppen gekommen, die eine große Zahl neuer, bisher meist nur molekular nachgewiesener Viren umfassen, die von Spitzmäusen, Fledermäusen und Maulwürfen getragen werden. Die PCR wurde zum ersten Mal in den 1970er-Jahren erwähnt [ Hantaviren bilden ein Genus innerhalb der Familie der Bunyaviren. keywords: als; das; den; der; die; für; hantaviren; mit; pcr; sind; und; virus; von; werden cache: cord-316719-uej7d5zf.txt plain text: cord-316719-uej7d5zf.txt item: #700 of 973 id: cord-316932-fia1w9jt author: Ireland, D. C. title: Improved detection of rhinoviruses in nasal and throat swabs by seminested RT‐PCR date: 2005-12-07 words: 4104 flesch: 57 summary: Restriction enzyme analysis of HRV PCR products [Torgersen et al., 19891 should enable us to determine whether or not the virus found in convalescent nasal and throat swabs is identical to that found in the corresponding acute specimens. HRVs could be differentiated from other PVs by this method: PCR products were 530 bp for HRVs and 650 bp for polioviruses, coxsackieviruses, and echoviruses. keywords: cell; hrv; hrvs; pcr; products; reaction; swabs cache: cord-316932-fia1w9jt.txt plain text: cord-316932-fia1w9jt.txt item: #701 of 973 id: cord-317000-bfc51e0m author: Visci, G. title: Serologic SARS-CoV-2 testing in healthcare workers with positive RT-PCR test or Covid-19 related symptoms date: 2020-10-27 words: 2667 flesch: 43 summary: The copyright holder for this preprint this version posted October 27, 2020. ; https://doi.org/10.1101/2020.10.25.20219113 doi: medRxiv preprint In this population of HCWs with positive RT-PCR test for SARS-CoV-2 infection from three institutions in Bologna, Italy, the sensitivity of serologic LFIA test was 75.2% and that of CLIA test, based on smaller number of tests, was 90.6%. Based on the results reported in Table 2 , and sensitivity of LFIA test equal to 75.2%, we estimated that 73.4% of HCWs with Covid-19 related symptoms, who were not tested with RT-PCR, were not infected with SARS-CoV-2. keywords: cov-2; covid-19; hcws; infection; sars; test cache: cord-317000-bfc51e0m.txt plain text: cord-317000-bfc51e0m.txt item: #702 of 973 id: cord-317042-dll3qt4g author: Lv, Jun title: Detection of SARS-CoV-2 RNA residue on object surfaces in nucleic acid testing laboratory using droplet digital PCR date: 2020-06-19 words: 2713 flesch: 44 summary: The SARS-CoV-2 test results of object surface samples from nucleic acid detection laboratory were shown in Table 1 . In this study, all objects in nucleic acid detection laboratory that tested positive for SARS-CoV-2 were directly or indirectly contacted by the operator's gloved hands. keywords: acid; copies; cov-2; detection; laboratory; samples; sars cache: cord-317042-dll3qt4g.txt plain text: cord-317042-dll3qt4g.txt item: #703 of 973 id: cord-317049-q3bvmkf7 author: Forde, Justin J. title: Yield and Implications of Pre-Procedural COVID-19 PCR Testing on Routine Endoscopic Practice date: 2020-05-25 words: 1142 flesch: 37 summary: Patients were also informed of the need for PCR testing at the time of the screening phone call. Those with negative verbal screening questionnaires were permitted to proceed with PCR testing. keywords: covid-19; pcr; procedure; testing cache: cord-317049-q3bvmkf7.txt plain text: cord-317049-q3bvmkf7.txt item: #704 of 973 id: cord-317129-wa1j2f6b author: Zhang, Jia title: De Novo synthesis of PCR templates for the development of SARS diagnostic assay date: 2003 words: 2320 flesch: 52 summary: By using a set of partially overlapping oligonucleotides, specific templates were quickly obtained by sequential primer extension. Two types of sequential primer extension were performed: single-step sequential primer extension and consecutive-step sequential primer extension. keywords: extension; pcr; primer; sequential cache: cord-317129-wa1j2f6b.txt plain text: cord-317129-wa1j2f6b.txt item: #705 of 973 id: cord-317244-4su5on6s author: Maganga, Gael D. title: Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date: 2014-12-31 words: 3483 flesch: 45 summary: A new mouse paramyxovirus (J virus) Isolation and molecular characterization of a novel cytopathogenic paramyxovirus from tree shrews Complete genome sequence of a novel paramyxovirus, Tailam virus, discovered in Sikkim rats Identification and phylogenetic comparison of Salem virus, a novel paramyxovirus of horses Reproduction and nutritional stress are risk factors for Hendra virus infection in little red flying foxes Bats host major mammalian paramyxoviruses Encephalitis caused by a lyssavirus in fruit bats in Australia Airborne transmission of lyssaviruses Rabies in nonhematophagous bats Guidelines of the American Society of Mammalogists for the use of wild mammals in research Ecological and behavioral methods for the study of bats Sensitive and broadly reactive reverse transcription-PCR assays to detect novel paramyxoviruses Marburg virus infection detected in a common African bat Newly discovered ebola virus associated with hemorrhagic Fever outbreak in Uganda Basic local alignment search tool MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance and Maximum Parsimony Methods MRBAYES: Bayesian inference of phylogenetic trees Isolation of Genetically Diverse Marburg Viruses from Egyptian Fruit Bats Studies of Reservoir Hosts for Marburg Virus Genomic characterizations of bat coronaviruses (1A, 1B and HKU8) and evidence for co-infections in Miniopterus bats Isolation of Hendra virus from pteropid bats: a natural reservoir of Hendra virus Bats are natural reservoirs of SARS-like coronaviruses Bats: important reservoir hosts of emerging viruses Novel astroviruses in insectivorous bats Bat white-nose syndrome: an emerging fungal pathogen? Inoculation of bats with European Geomyces destructans supports the novel pathogen hypothesis for the origin of white-nose syndrome Pathogenesis studies with Australian bat lyssavirus in grey-headed flying foxes (Pteropus poliocephalus) Bats and Lyssaviruses Discovery of an Ebolavirus-Like Filovirus in Europe Nipah virus infection in bats (Order Chiroptera) in Peninsular Malaysia Fruit bats as reservoirs of Ebola virus Is Marburg Virus Enzootic in Gabon? Bats as a continuing source of emerging infections in humans Risk factor for Nipah virus encephalitis in Bangladesh Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats Paramyxovirus and Pneumovirus diseases of animals and birds: comparatives aspects and diagnosis Dionisia bunoi n. g. n. sp., Haemoproteidae parasite du microchiroptè re Hipposideros cyclops au Gabon The chiropteran haemosporidian Polychromophilus melanipherus: A worldwide species complex restricted to the family Many authors suggested that persistence in the absence of pathology or disease appears to be a common characteristic of bat viruses in their natural host population [28, 29] . keywords: afra; bats; belpv; host; paramyxovirus; pcr; rna; species; virus; viruses cache: cord-317244-4su5on6s.txt plain text: cord-317244-4su5on6s.txt item: #706 of 973 id: cord-317948-svgguadm author: Xiao, Ai Tang title: Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients date: 2020-04-19 words: 1292 flesch: 52 summary: Our study attempted to explore the correlation between clinical characteristics and viral shedding in COVID-19 patients. Prolonged observation period is necessary for older patients. keywords: patients; pcr; sars cache: cord-317948-svgguadm.txt plain text: cord-317948-svgguadm.txt item: #707 of 973 id: cord-318013-5om35tu8 author: Marie, Tré-Hardy title: The role of serology for COVID-19 control: Population, kinetics and test performance do matter date: 2020-05-15 words: 944 flesch: 34 summary: (1-4) The authors of these reports or correspondence highlighted the added value of serological testing, which, if captured within the correct timeframe after disease onset, can detect both active and past infections.(1) (6) In the near future, serological testing will be required to assess the effectiveness of vaccine candidates and finally, they are also useful to identify individuals who developed a strong immunological response to the virus and whose antibody isolates can be used to treat patients via plasma therapy. keywords: cut; igg; sensitivity cache: cord-318013-5om35tu8.txt plain text: cord-318013-5om35tu8.txt item: #708 of 973 id: cord-318120-vfznyyz6 author: Dauner, Allison L. title: Development of a pan-serotype reverse transcription loop-mediated isothermal amplification assay for the detection of dengue virus date: 2015-05-15 words: 5272 flesch: 39 summary: Wallingford: CAB International Dengue and dengue hemorrhagic fever Development of simple and rapid assay to detect viral RNA of tick-borne encephalitis virus by reverse transcription-loop-mediated isothermal amplification Rapid identification of dengue virus isolates by using monoclonal antibodies in an indirect immunofluorescence assay Development and evaluation of a novel loop-mediated isothermal amplification method for rapid detection of severe acute respiratory syndrome coronavirus Highly sensitive detection of malaria parasitemia in a malaria-endemic setting: performance of a new loop-mediated isothermal amplification kit in a remote clinic in Uganda Loop-mediated isothermal amplification for direct detection of Mycobacterium tuberculosis complex, M. avium, and M. intracellulare in sputum samples Rapid detection of dengue viral RNA in mosquitoes by nucleic acid-sequence based amplification (NASBA) Tolerance of loop-mediated isothermal amplification to a culture medium and biological substances Laboratory diagnosis of dengue virus infection: current and future perspectives in clinical diagnosis and public health Comparison of methods for extraction of nucleic acid from hemolytic serum for PCR amplification of hepatitis B virus DNA sequences A real-time reverse transcription loop-mediated isothermal amplification assay for the rapid detection of yellow fever virus A simple, inexpensive device for nucleic acid amplification without electricity-toward instrument-free molecular diagnostics in low-resource settings Simultaneous detection and differentiation of dengue virus serotypes 1-4, Japanese encephalitis virus, and West Nile virus by a combined reverse-transcription loop-mediated isothermal amplification assay Rapid identification of dengue virus by reverse transcription-polymerase chain reaction using field-deployable instrumentation The Direct Boil-LAMP method: a simple and rapid diagnostic method for cutaneous leishmaniasis Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation Real-time turbidimetry of LAMP reaction for quantifying template DNA Loop-mediated isothermal amplification reaction using a nondenatured template Accelerated reaction by loop-mediated isothermal amplification using loop primers Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Loopmediated isothermal amplification of DNA Real-time reverse transcription loopmediated isothermal amplification for rapid detection of West Nile virus Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loopmediated isothermal amplification assay Development and evaluation of reverse transcription-loop-mediated isothermal amplification assay for rapid and real-time detection of Japanese encephalitis virus Rapid and sensitive detection of Macrobrachium rosenbergii nodavirus in giant freshwater prawns by reverse transcription loop-mediated isothermal amplification combined with a lateral flow dipstick Microevolution and virulence of dengue viruses Loop-mediated isothermal amplification assay for rapid diagnosis of malaria infections in an area of endemicity in Thailand Current advances in dengue diagnosis Simultaneous multiple target detection in real-time loop-mediated isothermal amplification Trends in dengue diagnosis Detection of dengue viruses using reverse transcription-loop-mediated isothermal amplification Rapid detection and quantification of Japanese encephalitis virus by real-time reverse transcription loop-mediated isothermal amplification The molecular epidemiology of Dengue viruses, genetic variation and microevolution The molecular epidemiology of dengue viruses, genetic variation and microevolution Dengue viremia titer, antibody response pattern, and virus serotype correlate with disease severity This work would not have been possible without the generous support of the Ministry of Health Peru, Direccion General de Epidemiologia and DIRESA Piura, Tumbes, Madre de Dios, and Iquitos. In conclusion, this work adds to the growing body of isothermal amplification assays available to detect DENV. keywords: amplification; assay; dengue; denv; detection; isothermal; lamp; loop; pcr; reaction; virus cache: cord-318120-vfznyyz6.txt plain text: cord-318120-vfznyyz6.txt item: #709 of 973 id: cord-318341-0827d8to author: Kaushik, Sulochana title: In-vitro and in silico activity of Cyamopsis tetragonoloba (Gaur) L. supercritical extract against the dengue-2 virus date: 2020-08-31 words: 3864 flesch: 45 summary: The material was stored in a shade and dry place at room temperature and minced after dry. Preparation of supercritical fluid extraction of C. tetragonoloba C. tetragonoloba extract was prepared by using Supercritical Fluid Extraction Machine (Applied Separation Inc. U.S.). The 100 ll of viral suspension of DENV-2 (100 copies/wells) was treated with an equal volume of the non-toxic dose (31.25 lg/ml) of C. tetragonoloba plant extract was inoculated in 96 well plates. keywords: anti; cell; dengue; extract; pcr; plant; study; tetragonoloba; virus cache: cord-318341-0827d8to.txt plain text: cord-318341-0827d8to.txt item: #710 of 973 id: cord-318392-r9bbomvk author: Woo, Patrick CY title: Coronavirus HKU15 in respiratory tract of pigs and first discovery of coronavirus quasispecies in 5′-untranslated region date: 2017-06-21 words: 3781 flesch: 45 summary: The presence of the virus in respiratory samples provides an alternative clinical sample to confirm the diagnosis of Coronavirus HKU15 infection. Third, the presence of the virus in respiratory samples provides an alternative clinical sample to confirm the diagnosis of Coronavirus HKU15 infection. keywords: coronavirus; coronavirus hku15; genome; hku15; nasopharyngeal; pcr; pigs; samples; sequence; strains cache: cord-318392-r9bbomvk.txt plain text: cord-318392-r9bbomvk.txt item: #711 of 973 id: cord-318614-518giv0m author: Tsai, Jih-Jin title: A fully automated sample-to-answer PCR system for easy and sensitive detection of dengue virus in human serum and mosquitos date: 2019-07-10 words: 4829 flesch: 42 summary: The semi-automated POCKIT combo system includes an automated taco mini for nucleic acid extraction and a POCKIT device for PCR detection. Sample info and test results of mosquito samples with pan-DENV RT-iiPCR on fully automated POCKIT Central system and semi-automated POCKIT combo system. keywords: dengue; denv; detection; extraction; iipcr; pan; pcr; pockit; system; virus cache: cord-318614-518giv0m.txt plain text: cord-318614-518giv0m.txt item: #712 of 973 id: cord-318991-tw7wgpsi author: Nair, A. title: A British Society of Thoracic Imaging statement: considerations in designing local imaging diagnostic algorithms for the COVID-19 pandemic date: 2020-05-31 words: 2953 flesch: 38 summary: 18 17 Conversely, CT thorax has a very low specificity, approximately 25%, for COVID-19 5 . Assuming it becomes necessary to elevate CT thorax to this position in the diagnostic work-up, the role of CT thorax in guiding management would be to triage patients into the categories discussed earlier (self-isolation at home with repeat testing as necessary, admission and isolation, or evaluation for alternative diagnoses and potentially aiding triage of unwell patients). keywords: cases; covid-19; diagnosis; patients; pcr cache: cord-318991-tw7wgpsi.txt plain text: cord-318991-tw7wgpsi.txt item: #713 of 973 id: cord-319253-8bssrn9o author: OKINO, Cintia Hiromi title: Rapid detection and differentiation of avian infectious bronchitis virus: an application of Mass genotype by melting temperature analysis in RT-qPCR using SYBR Green I date: 2018-02-27 words: 2507 flesch: 29 summary: A duplex SYBR Green I-based real-time RT-PCR assay for the simultaneous detection and differentiation of Massachusetts and non-Massachusetts serotypes of infectious bronchitis virus Rapid differentiation of avian infectious bronchitis virus isolates by sample to residual ratio quantitation using real-time reverse transcriptase-polymerase chain reaction Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens Dengue typing assay based on real-time PCR using SYBR Green I LNA probe-based real-time RT-PCR for the detection of infectious bronchitis virus from the oviduct of unvaccinated and vaccinated laying hens The long view: 40 years of infectious bronchitis research Assessment of cross-immunity dm chickens to strains of avian infectious bronchitis virus using tracheal organ cultures Infectious bronchitis virus variants: a review of the history, current situation and control measures Increased level of protection of respiratory tract and kidney by combining different infectious bronchitis virus vaccines against challenge with nephropathogenic Brazilian genotype subcluster 4 strains Characterization of infectious bronchitis viruses isolated from outbreaks of disease in commercial flocks in Brazil SYBR Green real-time reverse transcription-polymerase chain reaction assay for the generic detection of coronaviruses Nephritis associated with S1 variant brazilian isolate of infectious bronchitis virus and vaccine protection test in experimentally infected chickens A Real-Time Reverse-Transcription Polymerase Chain Reaction for Differentiation of Massachusetts Vaccine and Brazilian Field Genotypes of Avian Infectious Bronchitis Virus Vaccine efficacy against Ontario isolates of infectious bronchitis virus Rapid detection and non-subjective characterisation of infectious bronchitis virus isolates using high-resolution melt curve analysis and a mathematical model The genotyping of infectious bronchitis virus in Taiwan by a multiplex amplification refractory mutation system reverse transcription polymerase chain reaction Detection of infectious bronchitis virus by real-time reverse transcriptase-polymerase chain reaction and identification of a quasispecies in the Beaudette strain Review of infectious bronchitis virus around the world Serotype identification of avian infectious bronchitis virus by RT-PCR of the peplomer (S-1) gene Development of SYBR green I based one-step real-time RT-PCR assay for the detection and differentiation of very virulent and classical strains of infectious bursal disease virus Differentiation of infectious bronchitis virus serotypes using polymerase chain reaction and restriction fragment length polymorphism analysis A new typing method for the avian infectious bronchitis virus using polymerase chain reaction and restriction enzyme fragment length polymorphism Development of RT-qPCR assays for the specific identification of two major genotypes of avian infectious bronchitis virus Development of a real-time TaqMan RT-PCR assay for the detection of infectious bronchitis virus in chickens, and comparison of RT-PCR and virus isolation Molecular epidemiology and evolution of avian infectious bronchitis virus Genetic grouping of avian infectious bronchitis virus isolated in Brazil, based on RT-PCR/RFLP analysis of the S1 gene Inflammatory and cell-mediated immune responses in the respiratory tract of chickens to infection with avian infectious bronchitis virus Detection of viral antigen following exposure of one-day-old chicken to the Holland-52 strain of IBV Rapid detection and differentiation of Newcastle disease virus by real-time PCR with melting-curve analysis Cluster analysis method for grouping means in the analysis of variance Detection and differentiation of velogenic and lentogenic Newcastle disease viruses using SYBR I real-time PCR with nucleocapsid gene-specific primers Real-time RT-PCR and SYBR Green I melting curve analysis for the identification of Plum pox virus strains C, EA, and W: effect of amplicon size, melt rate, and dye translocation Genetic grouping for the isolates of avian infectious bronchitis virus in Taiwan Massachusetts live vaccination protects against a novel infectious bronchitis virus S1 genotype DMV/5642/06 Antigenic and immunogenic characterization of infectious bronchitis virus strains isolated in China between ACKNOWLEDGMENTS. keywords: bronchitis; ibv; qpcr; strains; time; virus cache: cord-319253-8bssrn9o.txt plain text: cord-319253-8bssrn9o.txt item: #714 of 973 id: cord-319324-zdpbrprg author: Jinks, Maggie R. title: Causes of endogenous uveitis in cats presented to referral clinics in North Carolina date: 2015-11-12 words: 5271 flesch: 47 summary: The seropositivity specifically in cats with uveitis has been documented to be between 74 and 78%, which is considerably higher than the seroprevalence in healthy cats in those same areas at 42.9% and 49.4%. This is consistent with more recent studies, in which 18.3% of cats with uveitis were seropositive in a nation-wide study performed in 2010, 21 and 34% of healthy cats were found to be seropositive in a nearby geographic area of this present study in Randolph County, North Carolina. keywords: bartonella; cases; cats; feline; gondii; spp; study; uveitis cache: cord-319324-zdpbrprg.txt plain text: cord-319324-zdpbrprg.txt item: #715 of 973 id: cord-319392-zg7gkf0j author: Yi, Li title: Development of a combined canine distemper virus specific RT-PCR protocol for the differentiation of infected and vaccinated animals (DIVA) and genetic characterization of the hemagglutinin gene of seven Chinese strains demonstrated in dogs date: 2011-11-18 words: 3497 flesch: 52 summary: Sensitivity of RT-PCRs to detect CDV vaccine by primers P1/P2 and CDV wildtype strain by primers P3/P4. Asia-1 CDV strains have also been detected in Japan (Mochizuki et al., 1999) , Taiwan (Chan et al., 2009; Lee et al., 2010) , and Korea . keywords: canine; cdv; pcr; strains; type; vaccine cache: cord-319392-zg7gkf0j.txt plain text: cord-319392-zg7gkf0j.txt item: #716 of 973 id: cord-319460-n4ezxnjc author: Bertasio, Cristina title: Porcine Epidemic Diarrhea Virus Shedding and Antibody Response in Swine Farms: A Longitudinal Study date: 2016-12-15 words: 5929 flesch: 47 summary: QPCR and clinical data were useful in understanding the dynamics of PEDV infections and, therefore, in implementing appropriate control measures. None of the farms had reported PEDV infections prior to this study, and thus, we can surmise that the sows had been recently infected at the time of their enrollment in the study, while piglets were infected after birth, through contact with infected sows. keywords: animals; diarrhea; epidemic; farms; pedv; piglets; porcine; sows; study; table; virus cache: cord-319460-n4ezxnjc.txt plain text: cord-319460-n4ezxnjc.txt item: #717 of 973 id: cord-319685-dw0qsl4s author: Porter, Emily title: Amino acid changes in the spike protein of feline coronavirus correlate with systemic spread of virus from the intestine and not with feline infectious peritonitis date: 2014-04-25 words: 5692 flesch: 52 summary: Overall, a leucine codon was found in the majority (39/43; 91%) of FIP tissue samples, but a significant number had a methionine codon (4/43; 9%). Second, a significant number (9%) of FIP tissue samples had a methionine codon at this position. keywords: cats; codon; faecal; fcov; feline; fip; pcr; position; protein; samples; tissue cache: cord-319685-dw0qsl4s.txt plain text: cord-319685-dw0qsl4s.txt item: #718 of 973 id: cord-319845-oob2ktnz author: Proença-Modena, José Luiz title: Detection of Human Bocavirus mRNA in Respiratory Secretions Correlates with High Viral Load and Concurrent Diarrhea date: 2011-06-20 words: 5862 flesch: 43 summary: The most frequent clinical diagnoses associated with respiratory HBoV are general upper respiratory tract infections (URTI), bronchiolitis, pneumonia, bronchitis and exacerbation of asthma [2] . A comparison of clinical features between HBoV patients with and without shedding of VP1 mRNA revealed an association of active viral replication with diarrhea (OR = 6.00; 95% CI = 1.15-34.14; p = 0.04) and a clinical diagnosis of URTI (OR = 19.33; 95% CI = 1.82-294.96; p = 0.01). keywords: ari; bocavirus; detection; hbov; human; infections; patients; pcr; samples; study; viruses cache: cord-319845-oob2ktnz.txt plain text: cord-319845-oob2ktnz.txt item: #719 of 973 id: cord-319921-uxtydu60 author: Meli, Marina L. title: Feline Leukemia Virus and Other Pathogens as Important Threats to the Survival of the Critically Endangered Iberian Lynx (Lynx pardinus) date: 2009-03-09 words: 5513 flesch: 42 summary: With the exception of feline immunodeficiency virus (FIV), evidence of infection by all tested feline pathogens was found in Iberian lynxes. Iberian lynxes are confined to two isolated populations in southern Spain in the Doñ ana and Sierra Morena areas, and only 40-50 and 150-200, respectively, are estimated to remain [5, 6, 7] . keywords: animals; cats; feline; felv; iberian; infection; leukemia; lynx; lynxes; pcr; provirus; samples; sequences; virus cache: cord-319921-uxtydu60.txt plain text: cord-319921-uxtydu60.txt item: #720 of 973 id: cord-319970-1gu0a6cb author: Edin, Alicia title: Development and Laboratory Evaluation of a Real-Time PCR Assay for Detecting Viruses and Bacteria of Relevance for Community-Acquired Pneumonia date: 2015-03-13 words: 5056 flesch: 32 summary: 9e12 Nevertheless, few studies have aimed to develop combined molecular detection assays for viruses and bacteria with relevance to CAP. The performance of the assay was evaluated with spiked samples and clinical respiratory specimens. keywords: assay; detection; influenza; pcr; pneumoniae; specimens; sputum; standard; time; viruses cache: cord-319970-1gu0a6cb.txt plain text: cord-319970-1gu0a6cb.txt item: #721 of 973 id: cord-320002-25ivll3q author: Mathew, Joseph L. title: Etiology of community acquired pneumonia among children in India: prospective, cohort study date: 2015-10-21 words: 4153 flesch: 41 summary: Global burden of childhood pneumonia and diarrhoea Epidemiology and etiology of childhood pneumonia in 2010: estimates of incidence, severe morbidity, mortality, underlying risk factors and causative pathogens for 192 countries Global and regional burden of hospital admissions for severe acute lower respiratory infections in young children in 2010: a systematic analysis Global, regional, and national causes of child mortality in 2000-13, with projections to inform post-2015 priorities: an updated systematic analysis Acute respiratory infection and pneumonia in India: a systematic review of literature for advocacy and action: UNICEF-PHFI series on newborn and child health World Health Organization. key: cord-320002-25ivll3q authors: Mathew, Joseph L.; Singhi, Sunit; Ray, Pallab; Hagel, Eva; Saghafian–Hedengren, Shanie; Bansal, Arun; Ygberg, Sofia; Sodhi, Kushaljit Singh; Kumar, B V Ravi; Nilsson, Anna title: Etiology of community acquired pneumonia among children in India: prospective, cohort study date: 2015-10-21 journal: Journal of global health DOI: 10.7189/jogh.05.020418 sha: doc_id: 320002 cord_uid: 25ivll3q BACKGROUND: Childhood community acquired pneumonia (CAP) is a significant problem in developing countries, and confirmation of microbial etiology is important for individual, as well as public health. keywords: cap; childhood; children; data; etiology; pathogens; pcr; pneumonia; study cache: cord-320002-25ivll3q.txt plain text: cord-320002-25ivll3q.txt item: #722 of 973 id: cord-320085-n9i54wzh author: Pfefferle, Susanne title: Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system date: 2020-03-05 words: 2040 flesch: 43 summary: Limit of detection of the SARS-CoV-2 UCT was determined by analysing each of eight replicates of a dilution series containing IVT RNA diluted in E-swab medium (Copan, Brescia, Italy; modified liquid Amies medium) and Roche cobas PCR medium (1:1) at 10,000, 1,000, 500, 250 and 125 copies/mL and eight negative samples. Samples were mixed 1:1 with Roche cobas PCR media (≤ 40% guanidine hydrochloride in Tris-HCL buffer) and incubated for 30 min before loading onto the cobas 6800 system. keywords: assay; cobas; cov-2; detection; pcr; sars cache: cord-320085-n9i54wzh.txt plain text: cord-320085-n9i54wzh.txt item: #723 of 973 id: cord-320547-law20pmw author: Luchsinger, Vivian title: Comparison of Luminex xTAG® RVP fast assay and real time RT‐PCR for the detection of respiratory viruses in adults with community‐acquired pneumonia date: 2016-02-02 words: 3945 flesch: 54 summary: respiratory viral panel fast in a clinical laboratory setting Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays XTAG TM RVP assay: Analytical and clinical performance Enhanced identification of viral and atypical bacterial pathogens in lower respiratory tract samples with nucleic acid amplification tests High prevalence of respiratory viral infections in patients hospitalized in an intensive care unit for acute respiratory infections as detected by nucleic acid based assays Identification of respiratory viruses in adults: Nasopharyngeal versus oropharyngeal sampling Comparison of a multiplex reverse transcription-PCR-enzyme hybridization assay with conventional viral culture and immunofluorescence techniques for the detection of seven viral respiratory pathogens Advances in diagnosis of respiratory virus infection The clinical relevance in the detection of viruses and atypical bacteria Development of a respiratory virus panel test for detection of twenty respiratory viruses by use of multiplex PCR and The type of sample can affect the diagnostic technique performance and a variety of different respiratory sampling methods (nasal, oro, or nasopharyngeal, wash, swab, aspirate) have been applied for respiratory viruses detection with discrepant results keywords: detection; et al; pcr; rvp; viruses; xtag cache: cord-320547-law20pmw.txt plain text: cord-320547-law20pmw.txt item: #724 of 973 id: cord-320617-ucm7wx8b author: B’Krong, Nguyen Thi Thuy Chinh title: Enterovirus serotypes in patients with central nervous system and respiratory infections in Viet Nam 1997–2010 date: 2018-04-12 words: 3960 flesch: 45 summary: Similarly, in patients with respiratory infection, the clinical significance of EV infection should be interpreted with caution because of the high rate of co-infection with more common respiratory viruses [39] . EV infections are often asymptomatic, but may also result in a diverse spectrum of clinical illness, varying from mild febrile illnesses to severe disease of the cutaneous, gastrointestinal, respiratory, cardiovascular, and central nervous system (CNS) keywords: children; clinical; cns; enterovirus; infection; patients; pcr; study cache: cord-320617-ucm7wx8b.txt plain text: cord-320617-ucm7wx8b.txt item: #725 of 973 id: cord-320769-qcpua9ck author: Park, Su-Jin title: Molecular epidemiology of bovine toroviruses circulating in South Korea date: 2008-01-25 words: 2808 flesch: 46 summary: The primer sets and RT-PCR and nested PCR conditions used for the detection of the BToV, BCoV, BRV A-C, becovirus, BNoV, and BVDV are described elsewhere (Cho et al., 2001; Park et al., 2006, in pressa,b) . (Asakura et al., 1998; Park et al., in press-a,b; Soulsby, 1982; Timoney et al., 1988) . keywords: bovine; btov; et al; pcr cache: cord-320769-qcpua9ck.txt plain text: cord-320769-qcpua9ck.txt item: #726 of 973 id: cord-320787-dwyyjq6o author: La Rosa, Giuseppina title: First detection of SARS-CoV-2 in untreated wastewaters in Italy date: 2020-05-23 words: 2753 flesch: 43 summary: Moreover, the environmental surveillance will be extended to the collection of wastewater samples available in the Department of Environment and Health of the Italian National Health Institute, that were collected throughout Italy in the framework of different projects on enteric viruses. A synthetic DNA (Biofab Research, Italy) including the PCR target region, was used to set up PCR conditions before experiments with study samples, but was not amplified along with samples to avoid risks of PCR contamination. keywords: cov-2; pcr; samples; sars; wastewater cache: cord-320787-dwyyjq6o.txt plain text: cord-320787-dwyyjq6o.txt item: #727 of 973 id: cord-320854-ybah03kr author: Kongprajug, Akechai title: Suppression of PmRab11 inhibits YHV infection in Penaeus monodon date: 2017-05-17 words: 6792 flesch: 50 summary: In order to investigate YHV protein levels in hemocytes and supernatant of the complete PmRab11 knockdown shrimp, shrimps were injected with dsRNA-PmRab11 at 1.8 mg/g shrimp by intramuscular injection. The results revealed that YHV protein level cannot be observed in both fractions of all experimental groups at 24 h post-dsRNA injection (Fig. 6 ). keywords: dsrna; expression; fig; head; hemocytes; infection; knockdown; membrane; pmrab11; post; protein; shrimp; supernatant; virus; yhv cache: cord-320854-ybah03kr.txt plain text: cord-320854-ybah03kr.txt item: #728 of 973 id: cord-320938-f526k9q1 author: Chen, Hongjun title: Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses date: 2012-09-28 words: 8653 flesch: 51 summary: key: cord-320938-f526k9q1 authors: Chen, Hongjun; Ye, Jianqiang; Xu, Kemin; Angel, Matthew; Shao, Hongxia; Ferrero, Andrea; Sutton, Troy; Perez, Daniel R. title: Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses date: 2012-09-28 journal: PLoS One DOI: 10.1371/journal.pone.0046378 sha: doc_id: 320938 cord_uid: f526k9q1 Since 1999, plasmid-based reverse genetics (RG) systems have revolutionized the way influenza viruses are studied. In addition, influenza viruses were recovered from a full set of Flu PCR amplicons without the use of plasmids. keywords: amplicons; cells; fig; influenza; lane; pcr; pcr amplicons; pdm; plasmid; pol1; pr8; primer; virus; viruses cache: cord-320938-f526k9q1.txt plain text: cord-320938-f526k9q1.txt item: #729 of 973 id: cord-321074-7jfy8cn6 author: Caruso, Damiano title: Quantitative Chest CT analysis in discriminating COVID-19 from non-COVID-19 patients date: 2020-10-12 words: 2924 flesch: 40 summary: CT quantification of ground-glass opacities and fibrotic alterations is able to identify COVID-19 patients with moderate accuracy and may help radiologists to overcome low specificity of Chest CT. Future application might also include COVID-19 CT follow-up with a quantitative assessment of lung impairment as expression of worsening, stability or healing of lung parenchyma. keywords: analysis; chest; covid-19; patients; results cache: cord-321074-7jfy8cn6.txt plain text: cord-321074-7jfy8cn6.txt item: #730 of 973 id: cord-321076-kont2sff author: Yeo, Wee Song title: Cohort PCR Testing: A Strategic Method for Rapid SARS-CoV-2 Screening date: 2020-05-30 words: 810 flesch: 41 summary: key: cord-321076-kont2sff authors: Yeo, Wee Song; Ng, Qin Xiang; Tan, Kuan Yang title: Cohort PCR Testing: A Strategic Method for Rapid SARS-CoV-2 Screening date: 2020-05-30 journal: Am J Clin Pathol DOI: 10.1093/ajcp/aqaa092 sha: doc_id: 321076 cord_uid: kont2sff nan The world is currently facing an unprecedented outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes viral pneumonias and the coronavirus disease 2019 (COVID-19) in humans. If cohort PCR is used to test a family or living unit where one member has confirmed SARS-CoV-2 infection, then there would be a very high likelihood that the pool would be positive (increasing probability with pool size). keywords: cohort; cov-2; pcr cache: cord-321076-kont2sff.txt plain text: cord-321076-kont2sff.txt item: #731 of 973 id: cord-321181-bqdsfgdc author: Garitano, Ignacio title: Estimando el número de casos de COVID-19 mediante una herramienta web: resultados de la primera semana del proyecto "Covid-19 Trends" en Euskadi date: 2020-05-21 words: 3193 flesch: 49 summary: El director general de la OMS, en la reunión del 30 de enero de 2020 del Comité de Emergencias del Reglamento Sanitario Internacional, (aprobado en 2005), declaró el brote de SARS-CoV-2 como una Emergencia de Salud Publica de Importancia Internacional (ESPII) España notificó su primer caso el 31 de enero de 2020 en un turista en la isla de La Gomera keywords: 2020; casos; como; con; covid-19; cuestionario; datos; del; este; euskadi; las; los; marzo; para; pcr; por; que; una cache: cord-321181-bqdsfgdc.txt plain text: cord-321181-bqdsfgdc.txt item: #732 of 973 id: cord-321284-0y69n1ea author: El Kholy, A. A. title: The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season date: 2016-06-10 words: 3346 flesch: 42 summary: The underrecognized burden of influenza in young children Respiratory syncytial virus and parainfluenza virus Progress in the development of respiratory syncytial virus and parainfluenza virus vaccines Practical implementation of a multiplex PCR for acute respiratory tract infections in children Influenza and other respiratory virus infections in outpatients with medically attended acute respiratory infection during the 2011-12 influenza season Performance of a novel microarray multiplex PCR for the detection of 23 respiratory pathogens (SYMP-ARI study) Does respiratory virus coinfection increases the clinical severity of acute respiratory infection among children infected with respiratory syncytial virus? Human bocavirus and acute wheezing in children Frequent detection of respiratory viruses without symptoms: toward defining clinically relevant cutoff values A case-control study of acute respiratory tract infection in general practice patients in the Netherlands Respiratory pathogens in children with and without respiratory symptoms Human bocavirus: a novel parvovirus epidemiologically associated with pneumonia requiring hospitalization in Thailand Detection of bocavirus in children suffering from acute respiratory tract infections in Saudi Arabia Antiviral strategies against human coronaviruses Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Predominance of rhinovirus in the nose of symptomatic and asymptomatic infants Viruses and bacteria in the etiology of the common cold Rhinovirus illnesses during infancy predict subsequent childhood wheezing Role of respiratory viruses in acute upper and lower respiratory tract illness in the first year of life: a birth cohort study Highly frequent infections with human rhinovirus in healthy young children: a longitudinal cohort study The burden of respiratory syncytial virus infection in young children Influenza A and B virus infections in children Viral etiology of severe pneumonia among Kenyan infants and children Nucleic acids of respiratory viruses causing SARI were detected in 159/177 (89.9 %) patients enrolled in the study. keywords: children; detection; infection; patients; pcr; study; viruses cache: cord-321284-0y69n1ea.txt plain text: cord-321284-0y69n1ea.txt item: #733 of 973 id: cord-321361-6bkrt49b author: Chang, De title: Reply to Suri et al.: COVID-19 Real-Time RT-PCR: Does Positivity on Follow-up RT-PCR Always Imply Infectivity? date: 2020-07-01 words: 200 flesch: 22 summary: The trial evaluated both the value of aortic pulse wave velocity (aPWV) to predict all-cause mortality (ACM) in this population and Time kinetics of viral clearance and resolution of symptoms in novel coronavirus infection Novel Coronavirus Outbreak Research Team. COVID-19 Real-Time RT-PCR: Does Positivity on Follow-up RT-PCR Always Imply Infectivity? date: 2020-07-01 journal: Am J Respir Crit Care Med DOI: 10.1164/rccm.202004-1458le sha: doc_id: 321361 cord_uid: 6bkrt49b nan To the Editor: We read with keen interest the results of the SUMMIT (Study to Understand Mortality and Morbidity in COPD) randomized controlled trial of fluticasone furoate/vilanterol in patients with moderate chronic obstructive pulmonary disease (COPD) with a history of cardiovascular disease or at increased cardiovascular risk (1) . keywords: mortality cache: cord-321361-6bkrt49b.txt plain text: cord-321361-6bkrt49b.txt item: #734 of 973 id: cord-321432-qi2knswx author: Gardner, Shea N title: A microbial detection array (MDA) for viral and bacterial detection date: 2010-11-25 words: 8432 flesch: 45 summary: This occurs because detection array probes are designed for high sensitivity to low target concentrations, so that probe intensities approach the saturation level whenever a probe has significant similarity to a target in the sample. Consequently, in v.2 of the chip design, we imposed an entropy filter as described in the methods, and additionally designed more probe sequences at the expense of the number of replicates per probe. keywords: analysis; array; design; detection; family; mda; number; organisms; presence; present; probes; samples; sequences; species; target; viral; viruses cache: cord-321432-qi2knswx.txt plain text: cord-321432-qi2knswx.txt item: #735 of 973 id: cord-321443-89o13sox author: Umazume, Takeshi title: Survey on the use of personal protective equipment and COVID‐19 testing of pregnant women in Japan date: 2020-08-10 words: 2031 flesch: 50 summary: The number of annual deliveries at the General Perinatal Maternal and Child Care Center was determined to be higher than that of the Regional Perinatal Maternal and Child Care Center or other facilities (P < 0.01). Pregnant women were tested for COVID-19 not only in perinatal medical centers and university hospitals, but also other facilities, at a rate of 9-17% (Table S2) . keywords: covid-19; facilities; ppe; women cache: cord-321443-89o13sox.txt plain text: cord-321443-89o13sox.txt item: #736 of 973 id: cord-321514-knyw023l author: Bénet, Thomas title: Severity of Pneumonia in Under 5-Year-Old Children from Developing Countries: A Multicenter, Prospective, Observational Study date: 2017-07-12 words: 4449 flesch: 39 summary: Pocket Book of Hospital Care for Children Refining clinical diagnosis with likelihood ratios Epidemiology of hypoxaemia in children with acute lower respiratory infection Viral pneumonia Differentiation of bacterial and viral pneumonia in children Global burden of acute lower respiratory infections due to respiratory syncytial virus in young PNEUMONIA SEVERITY IN CHILDREN FROM DEVELOPING COUNTRIES children: a systematic review and meta-analysis Viral etiology of severe pneumonia among Kenyan infants and children Association of respiratory viruses with outcomes of severe childhood pneumonia in Botswana Human metapneumovirus: review of an important respiratory pathogen Hypoxaemia in children with severe pneumonia in Papua New Guinea Global burden of childhood pneumonia and diarrhoea Colonisation by Streptococcus pneumoniae and Staphylococcus aureus in healthy children The present study selectively comprised sites with better quality data on oxygen saturation (SO 2 ) at admission, mortality among pneumonia cases, and documented recording of patient follow-up during hospitalization. keywords: admission; blood; children; countries; death; hypoxemia; patients; pneumonia; study cache: cord-321514-knyw023l.txt plain text: cord-321514-knyw023l.txt item: #737 of 973 id: cord-321739-dnuu6jok author: Bowman, Andrew S title: Investigating the introduction of porcine epidemic diarrhea virus into an Ohio swine operation date: 2015-02-15 words: 4728 flesch: 50 summary: At the same time, the CN7 east barn housed PEDV negative pigs weighing approximately 50 lbs. In addition, feed pellets collected from unopened bags at the affected sites tested positive for PEDV using RT-PCR. keywords: feed; flow; operation; pcr; pedv; pellets; pigs; swine; virus cache: cord-321739-dnuu6jok.txt plain text: cord-321739-dnuu6jok.txt item: #738 of 973 id: cord-321855-7b1c2xdh author: Alshami, Alanoud title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date: 2020-10-30 words: 3382 flesch: 53 summary: A recent study has shown that the viral load detected in asymptomatic patients was similar to the viral load of symptomatic patients suggesting that asymptomatic patients can also transmit the disease This regulation has helped us to better understand the prevalence of SARS-COV-2 infection in asymptomatic patients. keywords: asymptomatic; disease; patients; residents; study; symptoms cache: cord-321855-7b1c2xdh.txt plain text: cord-321855-7b1c2xdh.txt item: #739 of 973 id: cord-322184-kgv9f58a author: Sohn, Yujin title: Assessing Viral Shedding and Infectivity of Asymptomatic or Mildly Symptomatic Patients with COVID-19 in a Later Phase date: 2020-09-10 words: 3482 flesch: 51 summary: Viral culture studies using patient specimens to confirm the presence of infectious SARS-CoV-2 are still limited. SARS-CoV-2 infection is confirmed by the detection of viral RNA using reverse transcription polymerase chain reaction (RT-PCR). keywords: cov-2; patients; pcr; sars; specimens cache: cord-322184-kgv9f58a.txt plain text: cord-322184-kgv9f58a.txt item: #740 of 973 id: cord-322234-1zyy536y author: Lorusso, Alessio title: One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date: 2009-12-17 words: 4171 flesch: 40 summary: In that case, two consequences will be obvious: first, a reservoir of H1N1 virus in the swine population poses an elevated risk for human infection via aerosol transmission from clinically ill pigs, and second, dramatic economic losses for the pork industry due to direct disease related costs as well as indirect market losses. Although the 2009 H1N1 is related genetically to swine influenza viruses, human infection has not been connected to pig exposure. keywords: assay; h1n1; influenza; pandemic; pcr; pigs; rna; swine; virus; viruses cache: cord-322234-1zyy536y.txt plain text: cord-322234-1zyy536y.txt item: #741 of 973 id: cord-322389-rd93y7hu author: Ritzi-Lehnert, Marion title: On-chip analysis of respiratory viruses from nasopharyngeal samples date: 2011-05-21 words: 5589 flesch: 52 summary: Finally, the entire volume of eluted NA is pumped into PCR chamber 1 for rehydration of the dried amplification reagents. These pellets are based on the QuantiTect Virus Kit (QIAGEN) in PCR chamber 1 and the QuantiFast Probe PCR Kit (QIAGEN) in PCR chamber 2, supplemented with cryo-protectives and bulking agents (formulation and freeze-drying protocols undisclosed). keywords: cartridge; chamber; chip; heating; lysis; magnetic; pcr; sample; system; volume; ° c cache: cord-322389-rd93y7hu.txt plain text: cord-322389-rd93y7hu.txt item: #742 of 973 id: cord-322391-tumpiid5 author: Freymuth, François title: Detection of viral, Chlamydia pneumoniae and Mycoplasma pneumoniae infections in exacerbations of asthma in children date: 1999-08-31 words: 3825 flesch: 40 summary: RS virus infections were observed during the winter period, whereas rhinovirus infections were distributed all over the year (Freymuth et al., 1987) . The same authors documented RS virus infections in 4.1% of asthmatic exacerbations, which contrasted with a rate of 21.2% identified in our study. keywords: detection; pcr; pneumoniae; rhinovirus; virus cache: cord-322391-tumpiid5.txt plain text: cord-322391-tumpiid5.txt item: #743 of 973 id: cord-322448-s04e6po9 author: Gadsby, Naomi J. title: Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia date: 2016-04-01 words: 4378 flesch: 30 summary: Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. One limitation of our study was that it was restricted to CAP patients who could produce a sputum specimen. keywords: bacterial; cap; community; culture; detection; patients; pcr; pneumonia; specimens; time cache: cord-322448-s04e6po9.txt plain text: cord-322448-s04e6po9.txt item: #744 of 973 id: cord-322524-bq9ok8h1 author: Belongia, Edward A title: Clinical Features, Severity, and Incidence of RSV Illness During 12 Consecutive Seasons in a Community Cohort of Adults ≥60 Years Old date: 2018-11-27 words: 5191 flesch: 39 summary: Additional studies are needed in diverse populations to estimate the burden of adult RSV illness and the potential impact of future licensed vaccines. Samples collected from the 2004-2005 through 2009-2010 seasons were previously tested using the GenMark multiplex assay in a separate study of RSV illness in adults ≥50 years of age [19] . keywords: adults; enrollment; illness; influenza; patients; rsv; study; syncytial; virus; years cache: cord-322524-bq9ok8h1.txt plain text: cord-322524-bq9ok8h1.txt item: #745 of 973 id: cord-322566-ye27nqj2 author: Huang, Yuxiang title: Stable Internal Reference Genes for Normalizing Real-Time Quantitative PCR in Baphicacanthus cusia under Hormonal Stimuli and UV Irradiation, and in Different Plant Organs date: 2017-05-03 words: 5813 flesch: 40 summary: Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets Role of plant hormones in plant defence responses Selection of endogenous genes for gene expression studies in Eucalyptus under biotic (Puccinia psidii) and abiotic (acibenzolar-S-methyl) stresses using RT-qPCR Selection of candidate reference genes for realtime PCR studies in lettuce under abiotic stresses Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors Evaluation of coffee reference genes for relative expression studies by quantitative real-time RT-PCR Stable internal reference genes for normalization of real-time RT-PCR in tobacco (Nicotiana tabacum) during development and abiotic stress How to do successful gene expression analysis using real-time PCR Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process Intervention effects of QRZSLXF, a Chinese medicinal herb recipe, on the DORβ-arrestin1-Bcl2 signal transduction pathway in a rat model of ulcerative colitis Selection of reliable reference genes for quantitative real-time polymerase chain reaction studies in maize grains Selection and validation of reference genes for quantitative gene expression studies by real-time PCR in eggplant (Solanum melongena L) Selection and validation of reference genes for quantitative real-time PCR in Gentiana macrophylla Arsenic disulfide induced apoptosis and concurrently promoted erythroid differentiation in cytokine-dependent myelodysplastic syndrome-progressed leukemia cell line F-36p with complex karyotype including monosomy 7 Evaluation of meisoindigo, an indirubin derivative: in vitro antileukemic activity and in vivo pharmacokinetics Careful selection of reference genes is required for reliable performance of RT-qPCR in human normal and cancer cell lines Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR Identification of three shikimate kinase genes in rice: characterization of their differential expression during panicle development and of the enzymatic activities of the encoded proteins Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice Reference genes in real-time PCR RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome Selection of reliable reference genes for gene expression analysis under abiotic stresses in the desert biomass willow, Salix psammophila Chemical studies of strobilanthes cusia Suitable reference genes for accurate gene expression analysis in parsley (Petroselinum crispum) for abiotic stresses and hormone stimuli Validation of candidate reference genes for the accurate normalization of real-time quantitative RT-PCR data in rice during seed development Natura-alpha targets forkhead box m1 and inhibits androgen-dependent and -independent prostate cancer growth and invasion Comparison of refined and crude indigo naturalis ointment in treating psoriasis: randomized, observer-blind, controlled, intrapatient trial Validation of reference genes for gene expression studies in virus-infected Nicotiana benthamiana Using quantitative real-time An indirubin derivative, indirubin-3 ′ -monoxime suppresses oral cancer tumorigenesis through the downregulation of survivin Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses Pharmacopoeia of the People's Republic of China Vol 1 Quantification of mRNA using real-time RT-PCR A new mathematical model for relative quantification in real-time RT-PCR Reference gene selection for RT-qPCR analysis of flower development in Chrysanthemum morifolium and Chrysanthemum lavandulifolium An optimized grapevine RNA isolation procedure and statistical determination of reference Reference Genes Selection in B. cusia genes for real-time RT-PCR during berry development Primer3 on the WWW for general users and for biologist programmers Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data Analyses of Catharanthus roseus and Arabidopsis thaliana WRKY transcription factors reveal involvement in jasmonate signaling The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes Research progress of chemical constituents and pharmacological activities for Baphicacanthus cusia (Nees)bremek Therapeutic efficacy of the Qing Dai in patients with intractable ulcerative colitis Selection of suitable reference genes for qPCR normalization under abiotic stresses and hormone stimuli in carrot leaves Potential utilization of NAC transcription factors to enhance abiotic stress tolerance in plants by biotechnological approach Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Abscisic Acid and abiotic stress signaling Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Twenty-five years of quantitative PCR for gene expression analysis Cloning and expression of cDNAs encoding two enzymes of the MEP pathway in Catharanthus roseus Identification of reference genes for reverse transcription quantitative real-time PCR normalization in pepper (Capsicum annuum L.) Synergistic effects of ultraviolet-B and methyl jasmonate on tanshinone biosynthesis in Salvia miltiorrhiza hairy roots Evaluation and selection of appropriate reference genes for real-time quantitative pcr analysis of gene expression in Nile Tilapia (Oreochromis niloticus) during vaccination and infection RNA-Seq: a revolutionary tool for transcriptomics Characterization of anti-leukemia components from Indigo naturalis using comprehensive two-dimensional K562/cell membrane chromatography and in silico target identification Chemical studies of Baphicacanthus cusia (Nees)Bremek. keywords: cusia; different; expression; genes; pcr; reference; reference genes; samples; stress; time cache: cord-322566-ye27nqj2.txt plain text: cord-322566-ye27nqj2.txt item: #746 of 973 id: cord-322573-1fw1ehzd author: Vicente, Diego title: Human Bocavirus, a Respiratory and Enteric Virus date: 2007-04-17 words: 1297 flesch: 41 summary: To determine the prevalence and clinical characteristics of HBoV, we investigated the presence of this virus in children with respiratory tract infection in our region (Gipúzkoa, Basque Country, Spain). Human bocavirus is associated with respiratory tract infections, particularly in infants and young children. keywords: bocavirus; children; hbov; virus cache: cord-322573-1fw1ehzd.txt plain text: cord-322573-1fw1ehzd.txt item: #747 of 973 id: cord-322657-q4aeood2 author: Jartti, Tuomas title: Respiratory Picornaviruses and Respiratory Syncytial Virus as Causative Agents of Acute Expiratory Wheezing in Children date: 2004-06-17 words: 3171 flesch: 39 summary: Principle and practice Enzyme immunoassays for detection of IgG and IgM antibodies to parainfluenza types 1, 2 and 3 Purification of adenovirus hexon protein by high-performance liquid chromatography Immunoglobulin class-specific antibody response in respiratory syncytial virus infection measured by enzyme immunoassay Enterovirus infection as a risk factor for beta-cell autoimmunity in the prospective birth-cohort trial DIPP Picornaviridae: Rhinoviruses-common cold viruses Detection of enteroviruses and rhinoviruses in clinical specimens by PCR and liquid-phase hybridization Detection of rhinovirus, respiratory syncytial virus, and coronavirus infections in acute otitis media by reverse transcriptase polymerase chain reaction Human metapneumovirus and acute wheezing in children A collaborative study of the aetiology of acute respiratory infections in Britain 1961-4. A report of the Medical Research Council Working Party on acute respiratory virus infections Epidemiologic patterns of acute lower respiratory disease of children in a pediatric group practice Respiratory viral infection in children: a survey in general practice, Roehampton Viral infections in wheezy bronchitis and asthma in children The etiologic and epidemiologic spectrum of bronchitis in pediatric practice Respiratory viral infection and wheezy bronchitis in childhood Role of viruses and bacteria in acute wheezy bronchitis in childhood: a study of sputum Respiratory virus infections and aeroallergens and acute bronchial asthma The association of viruses with acute asthma Risk factors for acute wheezing in infants and children: viruses, passive smoke, and IgE antibodies to inhalant allergens Wheezing bronchitis in children. keywords: children; expiratory; pcr; rsv; study; virus; wheezing cache: cord-322657-q4aeood2.txt plain text: cord-322657-q4aeood2.txt item: #748 of 973 id: cord-322778-a411t2wg author: Skalidis, Ioannis title: Unenhanced computed tomography (CT) utility for triage at the emergency department during COVID-19 pandemic date: 2020-07-28 words: 4087 flesch: 44 summary: CT results modified the direction of 16 patients awaiting results of RT-PCR (which could take up to 24 hours). For patients with negative RT-PCR tests but positive CT results, follow-up RT-PCR analyses and/or CT images were tracked to further confirm the imaging diagnosis if available. keywords: chest; covid-19; hospital; patients; pcr; probability; results cache: cord-322778-a411t2wg.txt plain text: cord-322778-a411t2wg.txt item: #749 of 973 id: cord-322937-lakdi3x8 author: Kang, Xiao-ping title: A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus date: 2010-06-02 words: 2341 flesch: 49 summary: The assay could simultaneously detect H5N1 avian influenza virus and pandemic H1N1 influenza virus, which could be used for early diagnosis of influenza-like patients and for epidemiological surveillance. Compared with single real-time RT-PCR assay, the duplex real-time RT-PCR assay had the same sensitivity for pandemic H1N1 virus, and about 10-fold more sensitive for H5N1 virus (0.02 TCID 50 ) (Figure 1 ). keywords: duplex; h1n1; influenza; pcr; time; virus cache: cord-322937-lakdi3x8.txt plain text: cord-322937-lakdi3x8.txt item: #750 of 973 id: cord-322987-zv58s79r author: Zali, Alireza title: Correlation between Low-Dose Chest Computed Tomography and RT-PCR Results for the Diagnosis of COVID-19: A Report of 27824 Cases in Tehran, Iran date: 2020-09-21 words: 3236 flesch: 41 summary: Several initial studies reported a high sensitivity for chest CT, which was superior to that of reverse transcriptase-polymerase chain reaction (RT-PCR) 7, 8 ; however, RT-PCR remained the preferred test for confirmation of COVID-19 9, 10 . Figure 2 shows the trend of total patients who underwent chest CT due to high clinical suspicion and also the trend of cases with positive CT scan in each specific hospital during this three-month period. keywords: chest; covid-19; patients; pcr; study cache: cord-322987-zv58s79r.txt plain text: cord-322987-zv58s79r.txt item: #751 of 973 id: cord-323029-7hqp8xuq author: Bognár, Zsófia title: Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications date: 2020-08-11 words: 19355 flesch: 41 summary: In case of IgE aptamers, however, a salt induced aggregation can readily occur due to intermolecular hybridization of the AuNP modifying aptamer strands that was called hairpin aptamer sticky-end pairing effect by the authors. A method with wide applicability was published by He et al. where a mixture of fluorescentand quencher-labeled nucleic acid strands were able to hybridize to IgE aptamers in the absence of the target molecule bringing the labels in close proximity, which results in a very low fluorescence backgorund signal. keywords: acid; affinity; amplification; antibodies; antibody; aptamer; assay; binding; complex; concentration; detection; dna; figure; fluorescence; gold; human; ige; ige aptamer; ige binding; ige detection; igg; immunoglobulin; method; nanoparticles; protein; selection; signal; specific; surface; target cache: cord-323029-7hqp8xuq.txt plain text: cord-323029-7hqp8xuq.txt item: #752 of 973 id: cord-323397-5yop6clu author: Albalate, M. title: Alta prevalencia de covid19 asintomático en hemodiálisis. Aprendiendo dia a dia el primer mes de pandemia de covid19 date: 2020-04-30 words: 5233 flesch: 49 summary: Si el resultado era positivo se les avisaba telefónicamente y se les informaba de la obligatoriedad de aislamiento domiciliario, y de cómo acudir a la sesión de hemodiálisis. A partir del día 15 de marzo y con el objetivo de evitar sanciones por violar confinamiento, se entregó carta/certificado a los conductores, especificando el nombre del paciente sin especificar turno en previsión de posibles cambios. keywords: clínica; como; con; cov2; covid19; del; diálisis; día; han; hemodiálisis; hospital; las; los; marzo; momento; más; pacientes; para; patients; pcr; personal; por; que; sars; triaje; una; unidad cache: cord-323397-5yop6clu.txt plain text: cord-323397-5yop6clu.txt item: #753 of 973 id: cord-323473-e2pgjynr author: Cevey-Macherel, Manon title: Etiology of community-acquired pneumonia in hospitalized children based on WHO clinical guidelines date: 2009-02-24 words: 3447 flesch: 35 summary: Dehydration was the only clinical sign associated with bacterial pneumonia. Indeed, 47% of children with bacterial pneumonia, while only 24% in the mixed group and 6% in the viral pneumonia group (P=0.003), showed signs of dehydration, ( Table 2 ). keywords: cap; children; community; etiology; infection; patients; pcr; pneumonia; study cache: cord-323473-e2pgjynr.txt plain text: cord-323473-e2pgjynr.txt item: #754 of 973 id: cord-323700-5awng7h1 author: Goggin, Rachel K. title: Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites date: 2018-09-19 words: 3528 flesch: 35 summary: Prevalence of rhinovirus and respiratory syncytial virus among patients with chronic rhinosinusitis Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control Exploring the prevalence of ten polyomaviruses and two herpes viruses in breast cancer Newly identified human rhinoviruses: molecular methods heat up the cold viruses Adult chronic rhinosinusitis: definitions, diagnosis, epidemiology, and pathophysiology Latent sites of Epstein-Barr virus infection High rates of detection of respiratory viruses in the nasal washes and mucosae of patients with chronic rhinosinusitis The bacterial microbiome in chronic rhinosinusitis: richness, diversity, postoperative changes, and patient outcomes Chronic rhinosinusitis: potential role of microbial dysbiosis and recommendations for sampling sites Detection of herpesviruses 1-6 and community-acquired respiratory viruses in patients with chronic rhinosinusitis with nasal polyposis Human coronavirus infections in rural Thailand: a comprehensive study using real-time reverse-transcription polymerase chain reaction assays The nasal microbiome in asthma European position paper on rhinosinusitis and nasal polyps Community-acquired respiratory viruses Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Nasal swab versus nasopharyngeal aspirate for isolation of respiratory viruses Rapid and quantitative detection of human adenovirus DNA by real-time PCR Detection of rhinovirus in turbinate epithelial cells of chronic sinusitis Quantitative analysis of Epstein-Barr virus load by using a real-time PCR assay The etiology and pathogenesis of chronic rhinosinusitis: a review of current hypotheses Comparing nose-throat swabs and nasopharyngeal aspirates collected from children with symptoms for respiratory virus identification using real-time polymerase chain reaction Respiratory viral infection in the chronic persistent phase of chronic rhinosinusitis The seasonality of respiratory viruses in patients with chronic rhinosinusitis The healthy human microbiome Staging in rhinosinusitus Real-time reverse transcriptase PCR assay for detection of human metapneumoviruses from all known genetic lineages The human respiratory microbiome: implications and impact Comparative evaluation of Taqman real-time PCR and semi-nested VP1 PCR for detection of enteroviruses in clinical specimens Python for scientific computing Adenovirus and respiratory syncytial virus in chronic sinusitis using polymerase chain reaction Quantitative detection and differentiation of human herpesvirus 6 subtypes in bone marrow transplant patients by using a single real-time polymerase chain reaction assay Clinical practice guideline (update): adult sinusitis. keywords: detection; et al; nasal; patients; pcr; samples; sampling; viruses cache: cord-323700-5awng7h1.txt plain text: cord-323700-5awng7h1.txt item: #755 of 973 id: cord-323963-whv88ggl author: Fan, Xiaofeng title: Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples date: 2006-08-11 words: 5723 flesch: 47 summary: However, there has been limited success in applying this concept to the amplification of large RNA genomes that require the reverse transcription (RT) step prior to PCR amplification. Taken together, the quantitation of viral diversity, if present at a high level within a given sample, is largely underestimated and/or biased by current protocols for PCR amplification and cloning. keywords: amplification; cloning; dna; hcv; hepatitis; length; lrp; pcr; rna; virus cache: cord-323963-whv88ggl.txt plain text: cord-323963-whv88ggl.txt item: #756 of 973 id: cord-323973-wszo9s3d author: Zhu, Hanliang title: The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond date: 2020-07-20 words: 9786 flesch: 42 summary: This is an old technique that was used in the early days of PCR systems, with three baths with different temperatures and a laboratory technician or robot to move a basket with samples from bath to bath. There was another push to release PCR systems for POC applications and this has contributed to disease diagnosis during pandemics such as the 2014 Ebola outbreak. keywords: amplification; analysis; cartridge; chamber; chip; detection; dna; nucleic; pcr; poc; polymerase; preparation; reaction; rna; sample; system; temperature; test; time; viral; virus cache: cord-323973-wszo9s3d.txt plain text: cord-323973-wszo9s3d.txt item: #757 of 973 id: cord-323987-gh1m05gi author: Dziąbowska, Karolina title: Detection Methods of Human and Animal Influenza Virus—Current Trends date: 2018-10-18 words: 11146 flesch: 43 summary: Influenza Other Respir Bioassay Development for Ultrasensitive Detection of Influenza A Nucleoprotein Using Digital ELISA Highly sensitive colorimetric immunosensor for influenza virus H5N1 based on enzyme-encapsulated liposome A highly sensitive europium nanoparticle-based immunoassay for detection of influenza A/B virus antigen in clinical specimens Identification and subtyping of avian influenza viruses by reverse transcription-PCR Evaluation of saliva as diagnostic materials for influenza virus infection by PCR-based assays Nucleic acid dipstick test for molecular diagnosis of pandemic H1N1 Development and evaluation of a real-time nucleic acid sequence based amplification assay for rapid detection of influenza A Detection of human influenza A viruses by loop-mediated isothermal amplification Development and evaluation of reverse transcription loop-mediated isothermal amplification assay for rapid and real-time detection of the swine-origin influenza A H1N1 virus Comparison of Next-Generation Sequencing Systems A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing Electrochemical Sensors for Detections of Influenza Viruses: Fundamentals and Applications Novel Nano Biosensor Developed for Rapid Detection of Flu Virus Applying the miniaturization technologies for biosensor design Rapid detection for primary screening of influenza A virus: Microfluidic RT-PCR chip and electrochemical DNA sensor Use of semiconductor-based oligonucleotide microarrays for influenza a virus subtype identification and sequencing Detection of viruses with molecularly imprinted polymers integrated on a microfluidic biochip using contact-less dielectric microsensors Evaluation of a smartphone-based rapid fluorescent diagnostic system for H9N2 virus in specific-pathogen-free chickens A paper-based microfluidic Dot-ELISA system with smartphone for the detection of influenza A. Microfluid Electrochemical assay to detect influenza viruses and measure drug susceptibility The phenomenon of fluorescence in immunosensors Electrochemical Sensors and Biosensors for Influenza Detection-Literature Survey Direct and label-free influenza virus detection based on multisite binding to sialic acid receptors A rapid-response ultrasensitive biosensor for influenza virus detection using antibody modified boron-doped diamond A PCR-free point-of-care capacitive immunoassay for influenza A virus Electrochemical immunosensor for detection of antibodies against influenza A virus H5N1 in hen serum An amplified electrochemical immunosensor based on in situ-produced 1-naphthol as electroactive substance and graphene oxide and Pt nanoparticles functionalized CeO2 nanocomposites as signal enhancer Dual immunosensor based on methylene blue-electroadsorbed graphene oxide for rapid detection of the influenza A virus antigen Label-free Detection of Influenza Viruses using a Reduced Graphene Oxide-based Electrochemical Immunosensor Integrated with a Microfluidic Platform Highly sensitive detection of influenza virus by boron-doped diamond electrode terminated with sialic acid-mimic peptide Universal biosensor for detection of influenza virus Electrochemical Biosensing for the Diagnosis of Viral Infections and Tropical Diseases Electrochemical biosensing of influenza A subtype genome based on meso/macroporous cobalt (II) oxide nanoflakes-applied to human samples Role of metal and metal oxide nanoparticles as diagnostic and therapeutic tools for highly prevalent viral infections Amperometric bioaffinity sensing platform for avian influenza virus proteins with aptamer modified gold nanoparticles on carbon chips Carbon nanotag based visual detection of influenza A virus by a lateral flow immunoassay In situ self-assembly of gold nanoparticles on hydrophilic and hydrophobic substrates for influenza virus-sensing platform Highly Uniform Gold Nanobipyramids for Ultrasensitive Colorimetric Detection of Influenza Virus Hewlett, I. Sensitive detection of influenza viruses with Europium nanoparticles on an epoxy silica sol-gel functionalized polycarbonate-polydimethylsiloxane hybrid microchip Aptasensors for Detection of Avian Influenza Virus H5N1 Rapid detection of avian influenza virus H5N1 in chicken tracheal samples using an impedance aptasensor with gold nanoparticles for signal amplification Aptamer-based 'point-of-care testing Specific Recognition of Human Influenza Virus with PEDOT Bearing Sialic Acid-Terminated Trisaccharides Silver nanoparticles coated graphene electrochemical sensor for the ultrasensitive analysis of avian influenza virus H7 A nanohybrid of platinum nanoparticles-porous ZnO-hemin with electrocatalytic activity to construct an amplified immunosensor for detection of influenza LabVIEW-based impedance biosensing system for detection of avian influenza virus A multi-virus detectable microfluidic electrochemical immunosensor for simultaneous detection of H1N1, H5N1, and H7N9 virus using ZnO nanorods for sensitivity enhancement Label-free electrochemical detection of neuraminidase activity: A facile whole blood diagnostic probe for infectious diseases Ultrasensitive detection of influenza viruses with a glycan-based impedimetric biosensor Influenza A Virus-Host Protein Interactions Control Viral Pathogenesis Immunomodulatory Nonstructural Proteins of Influenza A Viruses Identification of Novel Influenza A Virus Proteins Translated from PA mRNA PA-X is a virulence factor in avian H9N2 influenza virus Direct electrochemical detection of PB1-F2 protein of influenza A virus in infected cells Extrinsic surface-enhanced Raman scattering detection of influenza A virus enhanced by two-dimensional gold@silver core-shell nanoparticle arrays Surface-enhanced Raman scattering based lateral flow immunochromatographic assay for sensitive influenza detection Fluorescent Neuraminidase Assay Based on Supramolecular Dye Capture After Enzymatic Cleavage A promising magnetic SERS immunosensor for sensitive detection of avian influenza virus Early Diagnosis of Influenza Virus A Using Surface-enhanced Raman Scattering-based Lateral Flow Assay Rapid detection of avian influenza A virus by immunochromatographic test using a novel fluorescent dye Enhanced catalytic activity of gold nanoparticle-carbon nanotube hybrids for influenza virus detection Detection of influenza virus using peroxidase-mimic of gold nanoparticles Upconversion luminescence resonance energy transfer (LRET)-based biosensor for rapid and ultrasensitive detection of avian influenza virus H7 subtype Detection and differentiation of influenza viruses with glycan-functionalized gold nanoparticles Neuraminidase Resistant Sialosides for the Detection of Influenza Viruses keywords: acid; amplification; analysis; antibodies; assay; authors; detection; diagnosis; gold; influenza; influenza virus; methods; pcr; rapid; results; sensitivity; sensor; surface; tests; time; virus; viruses cache: cord-323987-gh1m05gi.txt plain text: cord-323987-gh1m05gi.txt item: #758 of 973 id: cord-324012-q2ilk6gs author: Inui, Ken title: A field‐deployable insulated isothermal RT‐PCR assay for identification of influenza A (H7N9) shows good performance in the laboratory date: 2019-09-05 words: 1524 flesch: 47 summary: Novel technologies, such as the insulated isothermal PCR (iiRT-PCR), are portable PCR systems that can be applied under field conditions by the fast PCR reaction (in 42 minutes). While conventional PCR requires multiple cycles of heating and cooling, iiRT-PCR is performed through the creation of a temperature gradient in a capillary tube with a single heating source at the bottom of a capillary tube and establishment of thermal convection within the tube, mimicking the cycles of conventional real-time PCR. keywords: h7n9; iirt; pcr; virus cache: cord-324012-q2ilk6gs.txt plain text: cord-324012-q2ilk6gs.txt item: #759 of 973 id: cord-324094-23kzr8rq author: Parida, M. M. title: Rapid and real-time detection technologies for emerging viruses of biomedical importance date: 2008-11-01 words: 5710 flesch: 39 summary: LAMP amplifi cation can also be accomplished with the two outer (F3 and B3) and two internal primers (FIP and BIP) but by using the two loop primers (FLP and BLP), the amplifi cation is accelerated and thereby shortens amplifi cation time by one third to one half ( (Notomi et al 2000) . Designing of a highly sensitive and specifi c primer set is crucial for performing LAMP amplifi cation. keywords: amplifi; amplifi cation; assays; cation; detection; dna; lamp; loop; pcr; strand; time; virus cache: cord-324094-23kzr8rq.txt plain text: cord-324094-23kzr8rq.txt item: #760 of 973 id: cord-324213-3uqlimov author: Bolotin, S. title: Development of a novel real-time reverse-transcriptase PCR method for the detection of H275Y positive influenza A H1N1 isolates date: 2009-01-30 words: 4064 flesch: 42 summary: A (H1N1) viruses Oseltamivir resistance during treatment of influenza A (H5N1) infection Use of the Seeplex RV Detection kit for surveillance of respiratory viral outbreaks in A new and rapid genotypic assay for the detection of neuraminidase inhibitor resistant influenza A viruses of subtype H1N1, H3N2, and H5N1 Reduced sensitivity of influenza A (H5N1) to oseltamivir Clustal W and Clustal X version 2.0 Avian flu: isolation of drug-resistant H5N1 virus Antiviral resistance and the control of pandemic influenza Influenza antiviral susceptibility monitoring activities in relation to national antiviral stockpiles in Europe during the winter Oseltamivir resistance-disabling our influenza defenses A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing Rapid and highly informative diagnostic assay for H5N1 influenza viruses Comparison of the Seeplex reverse transcription PCR assay with the R-mix viral culture and immunofluorescence techniques for detection of eight respiratory viruses WHO Rapid Advice Guidelines for pharmacological management of sporadic human infection with avian influenza A (H5N1) virus Application of a fluorogenic PCR assay for typing and subtyping of influenza viruses in respiratory samples Surveillance for neuraminidase inhibitor resistance among human influenza A and B viruses circulating worldwide in Neuraminidase subtyping of human influenza a viruses by RT-PCR and its application to clinical isolates Short consensus probes with 3[prime]-minor groove binder of the immunoglobulin heavy-chain gene for real-time quantitative PCR in B-cell non-Hodgkin lymphomas WHO intercountry consultation. While both phenotypic and sequencing methods are effective in detecting resistance, they can be labour intensive, have a long turn-around-time and be quite expensive, suggesting the need for a rapid, high-throughput approach to influenza drug resistance testing. keywords: assay; h275y; influenza; isolates; oseltamivir; pcr; resistance cache: cord-324213-3uqlimov.txt plain text: cord-324213-3uqlimov.txt item: #761 of 973 id: cord-324321-y96x8x3h author: Cai, Yingyun title: Down-regulation of transcription of the proapoptotic gene BNip3 in cultured astrocytes by murine coronavirus infection date: 2003-11-10 words: 8540 flesch: 42 summary: These data thus unequivocally establish that MHV infection downregulated BNip3 gene expression in DBT cells. The mechanism by which MHV infection of DBT cells downregulates BNip3 gene expression is currently unknown. keywords: bnip3; cells; dbt; dna; expression; fig; gene; infection; luciferase; mhv; pcr; promoter; protein; regulation; virus cache: cord-324321-y96x8x3h.txt plain text: cord-324321-y96x8x3h.txt item: #762 of 973 id: cord-324531-lpoelp91 author: Artesi, Maria title: A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay date: 2020-09-22 words: 2887 flesch: 53 summary: Examination of viral genomes deposited on GISAID showed this mutation has arisen independently at least four times. Viral genomes marked by GISAID as complete (Ͼ29,000 bases) and high coverage (Ͻ1% Ns, Ͻ0.05% unique amino acid mutations, and no insertion/deletions unless verified by submitter) were selected, leaving 20,386 viral genomes. keywords: cov-2; gene; genomes; pcr; sars; viruses cache: cord-324531-lpoelp91.txt plain text: cord-324531-lpoelp91.txt item: #763 of 973 id: cord-324559-p92y5er2 author: None title: cord-324559-p92y5er2 date: None words: 14724 flesch: 44 summary: Increasing reports on human PRV infection cases in China have recently indicated that PRV poses a significant threat to public health in China, especially in people in close contact with sick pigs and/or related pork products/contaminants. 3 , 8 Here we explored a simple data-driven, Boltzmann functionbased approach for estimation only based on the daily cumulative number of confirmed cases of SARS-CoV-2 (Note: the rational for Boltzmann function-based regression analysis is presented in supporting information (SI) file). keywords: 2019; cases; china; colistin; control; data; disease; gene; health; human; infection; isolates; laboratory; novel; number; outbreak; patients; pcr; pertussis; pjp; pneumoniae; prv; resistance; table; time; treatment cache: cord-324559-p92y5er2.txt plain text: cord-324559-p92y5er2.txt item: #764 of 973 id: cord-324944-ixh3ykrc author: Mitsakakis, Konstantinos title: Diagnostic tools for tackling febrile illness and enhancing patient management date: 2018-12-05 words: 20813 flesch: 41 summary: This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. Nucleic acid amplification technologies (NAATs) are based on sequence-specific recognition and amplification of unique target regions in the genome of pathogens to be detected. keywords: acid; amplification; assay; blood; care; cartridge; detection; diagnosis; diseases; dna; e.g.; febrile; fever; fig; health; infections; malaria; management; nucleic; patients; pcr; platform; point; process; reaction; reagents; sample; specific; system; target; technologies; technology; test; time; tools; use; virus cache: cord-324944-ixh3ykrc.txt plain text: cord-324944-ixh3ykrc.txt item: #765 of 973 id: cord-325014-n7mnhk2v author: Gujski, Mariusz title: Prevalence of Current and Past SARS-CoV-2 Infections among Police Employees in Poland, June–July 2020 date: 2020-10-11 words: 4900 flesch: 43 summary: Participants aged ≥60 years had a higher odds of positive IgG index vs. those aged 20–29 years (OR: 3.309). Daily vaping also increased the odds of positive IgG index (OR: 2.058). keywords: cov-2; covid-19; employees; igg; igm+iga; index; participants; police; sars; study cache: cord-325014-n7mnhk2v.txt plain text: cord-325014-n7mnhk2v.txt item: #766 of 973 id: cord-325068-j1lfq60o author: Pene, Frédéric title: Coronavirus 229E-Related Pneumonia in Immunocompromised Patients date: 2003-10-01 words: 2586 flesch: 29 summary: Three-year study with coronavirus strains OC43 and 229E Viruses and bacteria in the etiology of the common cold An Outbreak of coronavirus OC43 respiratory infection in Normandy, France Coronavirus as a possible cause of severe acute respiratory syndrome Survival benefit of highdose therapy in poor-risk aggressive non-Hodgkin's lymphoma: final analysis of the prospective LNH87-2 protocol-a groupe d'Etude des lymphomes de l'Adulte study Detection of varicella-zoster virus DNA by polymerase chain reaction in the cerebrospinal fluid of patients suffering from neurological complications associated with chicken pox or herpes zoster Direct diagnosis of human respiratory coronaviruses 229E and OC43 by the polymerase chain reaction Cytomegalovirus: an unexpected cause of ventilator-associated pneumonia Coronavirusrelated nosocomial viral respiratory infections in a neonatal and paediatric intensive care unit: a prospective study Nosocomial adenovirus infection in a paediatric respiratory unit Electron microscopic studies of coronavirus Diagnosis of human coronavirus infection by immunofluorescence: method and application to respiratory disease in hospitalized children Detection of human coronavirus 229E in nasal washings using RNA:RNA hybridisation Occurrence and frequency of coronavirus infections in humans as determined by enzyme-linked immunosorbent assay Mouse hepatitis virus strain JHM infects a human hepatocellular carcinoma cell line Comparison of immunofluorescence with monoclonal antibodies and RT-PCR for the detection of human coronaviruses 229E and OC43 in cell culture Rhinovirus infections in myelosuppressed adult blood and marrow transplant recipients Impact of respiratory virus infections on persons with chronic underlying conditions Rhinovirus infections in hematopoietic stem cell transplant recipients with pneumonia Coronavirus pneumonia following autologous bone marrow transplantation for breast cancer The efficacy and tolerance of intranasal interferons: studies at the Common Cold Unit The role of gamma interferon in infection of susceptible mice with murine coronavirus, MHV-JHM Although chronic underlying conditions are major determinants of severe respiratory virus infections, few data about coronavirus-related pneumonia in immunocompromised patients are available. keywords: 229e; bal; coronavirus; fluid; pcr; pneumonia; specimens cache: cord-325068-j1lfq60o.txt plain text: cord-325068-j1lfq60o.txt item: #767 of 973 id: cord-325101-9qslo6qh author: Gizzi, Aline Baumann da Rocha title: Presence of infectious agents and co-infections in diarrheic dogs determined with a real-time polymerase chain reaction-based panel date: 2014-01-16 words: 5165 flesch: 44 summary: The detection of individual pathogens in the panel with real-time PCR (Table 3) showed that CPA was the most prevalent pathogen in the fecal samples, infecting 40/104 (38.5%) diarrheic dogs and 6/43 (14.0%) control dogs, and the difference between the groups was highly statistically significant (P = 0.006). Although Giardia spp. were detected in 14/104 (13.5%) diarrheic dogs and 2/43 (4.7%) control dogs, the difference was not significant (P = 0.151). keywords: control; diarrhea; dogs; infections; pcr; samples; spp; study; time cache: cord-325101-9qslo6qh.txt plain text: cord-325101-9qslo6qh.txt item: #768 of 973 id: cord-325113-sou8xyld author: Kuiper, Johannes W. P. title: Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date: 2020-11-02 words: 4980 flesch: 43 summary: A RNA-and DNA-reading heat-stable polymerase reverse transcribes and amplifies viral RNA Evidence of an acute SARS-CoV-2 infection depends on the detection of viral RNA species in patient samples, which necessitates reverse transcription of RNA followed by PCR amplification of the resulting DNA. When 5000 genome equivalents of the purified, in vitro transcribed viral RNA was used as a PCR template for a generic, heat-stable DNA-dependent DNA polymerase (Taq DNA polymerase) keywords: dna; fig; patient; pcr; polymerase; rna; samples; sars; temperature; volcano3 cache: cord-325113-sou8xyld.txt plain text: cord-325113-sou8xyld.txt item: #769 of 973 id: cord-325124-0hxan9rw author: Li, Chenyu title: Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing date: 2020-05-18 words: 6147 flesch: 47 summary: We designed a panel of 172 pairs of multiplex PCR primers in order to increase the sensitivity of detecting SARS-CoV-2 (Fig. 1B) . Finally, the purified cDNA was dissolved in 1X TE buffer and used per multiplex PCR reaction. keywords: copies; coronavirus; cov-2; fig; genome; human; mutations; pcr; reads; sars; sequencing cache: cord-325124-0hxan9rw.txt plain text: cord-325124-0hxan9rw.txt item: #770 of 973 id: cord-325137-6c6er06a author: Moser, Lindsey A. title: A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses date: 2016-06-07 words: 9977 flesch: 48 summary: In summary, we describe a rapid, universal standard operating procedure that generates high-quality NGS libraries free of infectious virus and infectious viral RNA. Applying NGS to sequencing RNA viruses represents an unparalleled capacity to generate large amounts of sequence data, which can be used to identify consensus sequences as well as minor sequence variants, or quasispecies, present in a viral population (25) . keywords: cells; cpe; data; fig; fmdv; genomic; hrv-16; infectivity; material; pcr; rna; samples; sequence; sequencing; sispa; sop; viral; virus; viruses cache: cord-325137-6c6er06a.txt plain text: cord-325137-6c6er06a.txt item: #771 of 973 id: cord-325349-57n1878d author: Thieux, M. title: Assessment of a Diagnostic Strategy Based on Chest Computed Tomography in Patients Hospitalized for COVID-19 Pneumonia: an observational study date: 2020-06-30 words: 3766 flesch: 52 summary: https://doi.org/10.1101/2020.06.29.20140129 doi: medRxiv preprint All 223 patients (except one) with COVID-19 CT compatible had ground-glass opacities (GGOs) and 64.1% had consolidation. To face this situation, there was a need for emergency physicians to act quickly and accurately in the care of COVID-19 patients, which necessitates to anticipate the use of hospital resources. keywords: covid-19; patients; pcr; preprint cache: cord-325349-57n1878d.txt plain text: cord-325349-57n1878d.txt item: #772 of 973 id: cord-325529-pid58g2r author: Ben-Ami, Roni title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date: 2020-06-23 words: 2830 flesch: 45 summary: Here we describe and demonstrate practical pooling solutions that save time and reagents by performing RNA extraction and RT-PCR on pooled samples. Alternatively, it is possible to dynamically adapt pooling sizes, when the measured rate of positive samples is different than expected. keywords: covid-19; pooling; rna; samples; sars; testing cache: cord-325529-pid58g2r.txt plain text: cord-325529-pid58g2r.txt item: #773 of 973 id: cord-325611-tu1bn4hu author: Pérez-Sautu, Unai title: Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology date: 2019-07-23 words: 5292 flesch: 35 summary: Identification of respiratory viruses by HTS was confirmed by contig-specific RT-PCR analysis. Deaths by cause, age, sex, by country and by region Epidemiology and etiology of childhood pneumonia in 2010: estimates of incidence, severe morbidity, mortality, underlying risk factors and causative pathogens for 192 countries Emerging advances in rapid diagnostics of respiratory infections Mortality due to gastroenteritis of unknown etiology in the United States Deaths due to unknown foodborne agents Viral encephalitis of unknown cause: current perspective and recent advances National Institutes of Health Consensus Development Conference on Infantile Apnea and Home Monitoring Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-PCR assay Simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested-PCR assays Infections and coinfections by respiratory human bocavirus during eight seasons in hospitalized children A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach Characterization of the nasopharyngeal viral microbiome from children with community-acquired pneumonia but negative for Luminex xTAG keywords: analysis; contigs; control; group; hts; human; infections; pathogens; reads; specimens; virus; viruses cache: cord-325611-tu1bn4hu.txt plain text: cord-325611-tu1bn4hu.txt item: #774 of 973 id: cord-325736-gs9d8y55 author: Marin, J title: Persistence of Viruses in Upper Respiratory Tract of Children with Asthma date: 2000-07-31 words: 1875 flesch: 50 summary: In addition to allergens, respiratory viruses have been proven to be important factors in provoking asthmatic attacks. Due to the high viral NAs detection rate in asthmatic children compared to the lower detection rate in the control group, we can speculate that the results could be related to the disease itself or to the glucocorticoid treatment, since there is data which suggests that glucocorticoid therapy increases the titre of respiratory viruses and prolongs viral shedding. keywords: asthma; children; dna; pcr; viruses cache: cord-325736-gs9d8y55.txt plain text: cord-325736-gs9d8y55.txt item: #775 of 973 id: cord-325969-9zhmmvdg author: To, Kelvin KW title: Additional molecular testing of saliva specimens improves the detection of respiratory viruses date: 2017-06-07 words: 4544 flesch: 43 summary: Although NPAs have high viral loads and remain the specimen of choice for most patients with respiratory virus infections, supplementary molecular testing of saliva can improve the clinical management of these patients. 17 However, in studies that have tested multiple specimen types, nasopharyngeal specimens have been found to be negative in some patients with respiratory virus infections. keywords: detection; influenza; npa; patients; pcr; respiratory; saliva; specimens; viruses cache: cord-325969-9zhmmvdg.txt plain text: cord-325969-9zhmmvdg.txt item: #776 of 973 id: cord-326017-qw4qynqv author: Laskar, Partha title: “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies date: 2020-08-06 words: 14817 flesch: 35 summary: Thus, early, rapid, and accurate diagnosis of COVID-19 patients is becoming very crucial to control the sources of infection and to prevent further community spread. Such tests have proven lung histology (lung damage or holes/honeycomb-like appearance) of COVID-19 patients [70] . keywords: 2019; amplification; antiviral; cases; coronavirus; cov-2; covid-19; data; detection; development; disease; drug; health; human; iii; infection; methods; number; pandemic; patients; pcr; pneumonia; research; rna; sars; time; treatment; use cache: cord-326017-qw4qynqv.txt plain text: cord-326017-qw4qynqv.txt item: #777 of 973 id: cord-326122-5m1727m1 author: Wishaupt, Jérôme O. title: PCR testing for Paediatric Acute Respiratory Tract Infections date: 2014-08-04 words: 4910 flesch: 36 summary: Diagnosis and management of bronchiolitis Bronchiolitis: recent evidence on diagnosis and management Bronchiolitis management before and after the AAP guidelines Manual of Childhood Infections, The Blue Book Additional diagnostic yield of adding serology to PCR in diagnosing viral acute respiratory infections in Kenyan patients 5 years of age and older Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Currently used nucleic acid amplification tests for the detection of viruses and atypicals in acute respiratory infections Evaluation of respiratory syncytial virus detection by rapid antigen tests in childhood Prospective evaluation of rapid antigen tests for diagnosis of respiratory syncytial virus and human metapneumovirus infections Comparison of BD Directigen EZ RSV and Binax NOW RSV tests for rapid detection of respiratory syncytial virus from nasopharyngeal aspirates in a pediatric population Clinical and financial benefits of rapid detection of respiratory viruses: an outcomes study A randomized, controlled trial of the impact of early and rapid diagnosis of viral infections in children brought to an emergency department with febrile respiratory tract illnesses Cost-effectiveness of rapid diagnosis of viral respiratory tract infections in pediatric patients New molecular virus detection methods and their clinical value in lower respiratory tract infections in children Clinical and economical impact of multiplex respiratory virus assays Impact of rapid detection of viral and atypical bacterial pathogens by real-time polymerase chain reaction for patients with lower respiratory tract infection Does real-time PCR for respiratory virusses change antibiotic use in children admitted at the pediatric intensive care unit with lower respiratory tract infection? Prospective multicenter study of viral etiology and hospital length of stay in children with severe bronchiolitis Frequent detection of respiratory viruses without symptoms: toward defining clinically relevant cutoff values Respiratory pathogens in children with and without respiratory symptoms Expanding roles for CD4(+) T cells in immunity to viruses Bordetella pertussis and mixed infections Infection with multiple viruses is not associated with increased disease severity in children with bronchiolitis Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children Viral respiratory co-infections in pediatric patients admitted for acute respiratory infection and their impact on clinical severity Clinical risk factors are more relevant than respiratory viruses in predicting bronchiolitis severity Multiple simultaneous viral infections in infants with acute respiratory tract infections in Spain Dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis Identification of a novel coronavirus in patients with severe acute respiratory syndrome A novel coronavirus associated with severe acute respiratory syndrome SARS virus: the beginning of the unraveling of a new coronavirus Coronavirus as a possible cause of severe acute respiratory syndrome Human Infection with a Novel Avian-Origin Influenza A (H7N9) Virus infection control, outbreak management Rapid testing for respiratory syncytial virus in a paediatric emergency department: benefits for infection control and bed management Co-infections in children hospitalised for bronchiolitis: role of roomsharing Empiric antibiotics are justified for infants with respiratory syncytial virus lower respiratory tract infection presenting with respiratory failure: a prospective study and evidence review Viral load drives disease in humans experimentally infected with respiratory syncytial virus Disease severity and viral load are correlated in infants with primary respiratory syncytial virus infection in the community Equal virulence of rhinovirus and respiratory syncytial virus in infants hospitalized for lower respiratory tract infection Respiratory syncytial virus infections in hospitalized infants: association between viral load, virus subgroup, and disease severity Correlation of viral load of respiratory pathogens and co-infections with disease severity in children hospitalized for lower respiratory tract infection Prospective study of human metapneumovirus infection: diagnosis, typing and virus quantification in nasopharyngeal secretions from pediatric patients Quantitation of respiratory viruses in relation to clinical course in children with acute respiratory tract infections Illness severity, viral shedding, and antibody responses in infants hospitalized with bronchiolitis caused by respiratory syncytial virus We thank P. Goswami, MD for critically reviewing the manuscript in the English language. keywords: ari; bronchiolitis; children; disease; infection; pcr; tract; virus; viruses cache: cord-326122-5m1727m1.txt plain text: cord-326122-5m1727m1.txt item: #778 of 973 id: cord-326130-wm3l1849 author: Van Pelt, Amelia title: Evaluation of COVID-19 Testing Strategies for Repopulating College and University Campuses: A Decision Tree Analysis date: 2020-11-03 words: 4769 flesch: 52 summary: Greater rates of asymptomatic disease in younger people [13e15] and low testing sensitivity early in infection may limit testing strategies for coronavirus infection. The number of RT-PCR tests needed per identified case is a useful metric to rank order strategies and to aid institutions in their decision-making on testing strategies for returning students. keywords: pcr; strategies; strategy; students; testing; tests cache: cord-326130-wm3l1849.txt plain text: cord-326130-wm3l1849.txt item: #779 of 973 id: cord-326497-458mnekj author: Schaible, Jan title: Sharp margin and geographic shape: systematic evaluation of two novel CT features in COVID-19 pneumonia date: 2020-07-08 words: 2799 flesch: 47 summary: All patients with reverse transcription polymerase chain reaction proven COVID-19 pneumonia and chest CT between March first and April 15, 2020 were retrospectively identified from two tertiary care hospitals in Germany. This morphology is otherwise not often seen in chest CT and would be strongly suggestive for COVID-19 pneumonia during the pandemic. keywords: covid-19; opacifications; patients; pneumonia; shape cache: cord-326497-458mnekj.txt plain text: cord-326497-458mnekj.txt item: #780 of 973 id: cord-326596-8ux1q9xw author: Chen, Yanyu title: Biological and phylogenetic characterization of a novel hemagglutination‐negative avian avulavirus 6 isolated from wild waterfowl in China date: 2018-09-08 words: 2667 flesch: 33 summary: Yin http://orcid.org/0000-0001-7431-2523 Newcastle disease and other avian paramyxoviruses Taxonomy of the order Mononegavirales: update 2017 Complete genome sequence of a novel avian paramyxovirus Characterization of a genetic and antigenic variant of avian paramyxovirus 6 isolated from a migratory wild bird, the red-necked stint (Calidris ruficollis) Evaluation of the replication and pathogenicity of a variant avian paramyxovirus serotype 6 in mice Development of an improved vaccine evaluation protocol to compare the efficacy of Newcastle disease vaccines Complete nucleotide sequence of avian paramyxovirus type 6 isolated from ducks Genetic diversity of avian paramyxovirus type 6 isolated from Wild Ducks in the Republic of Genetic diversity of avian paramyxovirus type 1: Proposal for a unified nomenclature and classification system of Newcastle disease virus genotypes A virological survey in migrating waders and other waterfowl in one of the most important resting sites of Germany Complete genome sequence of a novel avian paramyxovirus isolated from wild birds in South Korea Characterization of class I Newcastle disease virus isolates from Hong Kong live bird markets and detection using real-time reverse transcription-PCR The Molecular Biology of Paramyxoviruses MEGA X: Molecular evolutionary genetics analysis across computing platforms A novel avian paramyxovirus (putative serotype 15) isolated from wild birds Novel avulaviruses in penguins OIE, the World Organisation for Animal Health Newcastle Disease, Pneumovirus Infection and Other Paramyxoviruses The Biology of paramyxoviruses Experimental infection of hamsters with avian paramyxovirus serotypes 1 to 9 Newcastle disease in Nigeria: Epizootiology and current knowledge of circulating genotypes Isolation and properties of viruses from poultry in Hong Kong which represent a new (sixth) distinct group of avian paramyxoviruses Characterization of avian paramyxovirus type 6 isolated from a Eurasian teal in the intersection of migratory flyways in Russia Characterization of avian paramyxovirus serotype 14, a novel serotype, isolated from a duck fecal sample in Japan Novel avian paramyxovirus (APMV-15) isolated from a migratory bird in South America Complete nucleotide sequence of avian paramyxovirus type 6 strain JL isolated from mallard ducks in China Sensitive and broadly reactive reverse transcription-PCR assays to detect novel paramyxoviruses Surveillance of avian paramyxovirus in migratory waterfowls in the San-in region of western Japan from Prevalence of antibodies to different avian paramyxoviruses in commercial poultry in the United States Comparative study on the pathogenicity and immunogenicity of wild bird isolates of avian paramyxovirus 2, 4, and 6 in chickens Complete genome sequences of avian paramyxovirus serotype 6 prototype strain Hong Kong and a recent novel strain from Italy: Evidence for the existence of subgroups within the serotype Genetic diversity of the genotype VII Newcastle disease virus: Identification of a novel VIIj sub-genotype Identification and pathotypical analysis of a novel VIk sub-genotype Newcastle disease virus obtained from pigeon in China Completion of full length genome sequence of novel avian paramyxovirus strain APMV/Shimane67 isolated from migratory wild geese in Japan Characterization of novel avian paramyxovirus strain APMV/Shimane67 isolated from migratory wild geese in Japan Dispersal and transmission of avian paramyxovirus serotype 4 among wild birds and domestic poultry Enhanced replication of virulent newcastle disease virus in chicken macrophages is due to polarized activation of cells by inhibition of TLR7 High genetic diversity of newcastle disease virus in wild and domestic birds in Northeastern China from 2013 to 2015 reveals potential epidemic trends Biological and phylogenetic characterization of a novel hemagglutination-negative avian avulavirus 6 isolated from wild waterfowl in China Avian paramyxoviruses that have been isolated from birds; however, due to changes in taxonomy is now referred to as avian avulavirus (AAvV) (Amarasinghe et al., 2017 ). keywords: aavv-6; birds; china; disease; novel; paramyxovirus cache: cord-326596-8ux1q9xw.txt plain text: cord-326596-8ux1q9xw.txt item: #781 of 973 id: cord-327024-1k5jucae author: Zhang, Qingshui title: Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings date: 2018-04-19 words: 4173 flesch: 41 summary: Bidin et al. 18 reported the detection of avian nephritis virus infection in Croatian goose flocks and provided evidence that this AstV was associated with stunting and prehatching mortality of goose embryos. Infected goslings exhibited signs of depression from 3 dpi and this symptom persisted for 3-4 days. keywords: astrovirus; astv; birds; dpi; fig; goose; goslings; infection; isolate; rna; virus cache: cord-327024-1k5jucae.txt plain text: cord-327024-1k5jucae.txt item: #782 of 973 id: cord-327069-vjlisnui author: Driscoll, Amanda J. title: Standardization of Laboratory Methods for the PERCH Study date: 2017-06-15 words: 4734 flesch: 38 summary: Site laboratories received uniform training, equipment, and reagents for core testing methods. The standardization of laboratory methods in the PERCH study was equally important to ensure comparability across study sites and for accurate and meaningful interpretation of pneumonia etiology results. keywords: acid; blood; data; laboratory; methods; nucleic; pcr; perch; pneumonia; samples; sites; specimens; study; testing cache: cord-327069-vjlisnui.txt plain text: cord-327069-vjlisnui.txt item: #783 of 973 id: cord-327105-7dsgs2sd author: Zóka, András title: Distinct changes in the real-time PCR detectability of certain SARS-CoV-2 target sequences date: 2020-05-05 words: 341 flesch: 47 summary: However, certain patients initially presented with an undetectable RdRp, and subsequently became positive. Dynamic change process of target genes by RT-PCR testing of SARS-Cov-2 during the course of a Coronavirus Disease 2019 patient Profile of RT-PCR for SARS-CoV-2: a preliminary study from 56 COVID-19 patients Coronaviruses: An Overview of Their Replication and Pathogenesis keywords: pcr cache: cord-327105-7dsgs2sd.txt plain text: cord-327105-7dsgs2sd.txt item: #784 of 973 id: cord-327259-7o7fs4yb author: Correa, I. A. title: Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date: 2020-08-19 words: 4586 flesch: 50 summary: key: cord-327259-7o7fs4yb authors: Correa, I. A.; Rodrigues, T. d. S.; Queiroz, A.; Nascimento, L. d. F.; Wolff, T.; Akamine, R. N.; Kuriyama, S. N.; Costa, L.; Fidalgo-Neto, A. A. title: Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date: 2020-08-19 journal: nan DOI: 10.1101/2020.08.16.20167536 sha: doc_id: 327259 cord_uid: 7o7fs4yb qRT-PCR is the gold standard technique available for SARS-CoV-2 detection. Coronavirus Disease (COVID-19) Dashboard Considerations in adjusting public health and social measures in the context of COVID-19 COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation per million population Clinical management of COVID-19: interim guidance Coronavirus disease (COVID-19) technical guidance: Laboratory testing for 2019-nCoV in humans Pooling of sera for human immunodeficiency virus (HIV) testing: an economical method for use in developing countries Pooling Nasopharyngeal/Throat Swab Specimens To Increase Testing Capacity for Influenza Viruses by PCR Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources The Detection of Defective Members of Large Populations Pooling Samples: the Key to Sensitive, Specific and Cost-effective Genetic Diagnosis of Chlamydia trachomatis in Low-Resource Countries Utility of Pooled Urine Specimens for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Men Attending Public Sexually Transmitted Infection Clinics in Mumbai, India, by PCR Optimal pooled testing Evaluation of Group Testing for SARS-CoV-2 RNA. keywords: cost; pooling; pools; preprint; prevalence; rna; samples; sars; testing cache: cord-327259-7o7fs4yb.txt plain text: cord-327259-7o7fs4yb.txt item: #785 of 973 id: cord-327344-8gi1wb76 author: Gambarino, Stefano title: Development of a RT Real-Time PCR for the Detection and Quantification of Human Rhinoviruses date: 2009-03-17 words: 3510 flesch: 33 summary: Evidence demonstrating that HRV disease is not exclusively limited to the upper airways and may cause lower respiratory complications, together with the frequency of HRV infections and the increasing number of immunocompromised patients underline the need for including HRV in virological diagnostics of acute lower respiratory tract illness. Rapidity and quantitative results represent important advantages in the diagnostic workup of HRV infection and could be of relevance considering the future potential availability of antiviral agents. keywords: assay; detection; hrv; patients; pcr; reaction; specimens; time cache: cord-327344-8gi1wb76.txt plain text: cord-327344-8gi1wb76.txt item: #786 of 973 id: cord-327620-fwhhsnmq author: Agut, H title: Détection, quantification et analyse des génomes viraux dans les infections à herpèsvirus humains 6 et 7 (HHV-6, HHV-7) date: 2003-09-30 words: 4451 flesch: 43 summary: Les performances de cette approche dépendent étroitement de la spécificité antigénique des anticorps, de leur affinité pour leurs cibles protéiques, du maintien de la structure des épitopes après fixation cellulaire. La détection effectuée en continu au cours de l'amplification, d'où la dénomination de « temps réel », autorise de plus une quantification précise et reproductible de la quantité initiale d'ADN introduit dans la réaction. keywords: dans; des; est; hhv-6; human; infections; les; par; plus; pour; que; qui; sont; une; virus; été cache: cord-327620-fwhhsnmq.txt plain text: cord-327620-fwhhsnmq.txt item: #787 of 973 id: cord-327675-uo839gvc author: Salamatian, Iman title: In vitro Acquisition and Retention of Low-Pathogenic Avian Influenza H9N2 by Musca domestica (Diptera: Muscidae) date: 2019-10-11 words: 3659 flesch: 49 summary: The potential of house fly, Musca Domestica (L.) in the mechanical transmission of influenza A subtype H1N1 virus under laboratory conditions Persistence of low-pathogenic avian influenza H5N7 and H7N1 subtypes in house flies (Diptera: Muscidae) Natural cases and an experimental study of H9N2 avian influenza in commercial broiler chickens of Iran Pathogenesis of H9N2 virus in Chukar partridges Risk factors for highly pathogenic avian influenza (HPAI) H5N1 infection in backyard chicken farms Detection and isolation of highly pathogenic H5N1 avian influenza A viruses from blow flies collected in the vicinity of an infected poultry farm in Kyoto Survival of avian H5N1 influenza A viruses in Calliphora nigribarbis (Diptera: Calliphoridae) Epidemiology of avian influenza in agricultural and other man-made systems Mechanical transport of rotavirus by the legs and wings of Musca domestica (Diptera: Muscidae) Avian influenza virus H5N1 remained exist in gastrointestinal tracts of house flies 24 hours post-infection The role of rodents in avian influenza outbreaks in poultry farms: a review The potential of house flies to act as a vector of avian influenza subtype H5N1 under experimental conditions Experimental assessment of houseflies as vectors in avian influenza subtype H5N1 transmission in chickens Experimental evaluation of Musca domestica (Diptera: Muscidae) as a vector of Newcastle disease virus World Health Organisation for Animal Health (OIE) Moreover, viral RNAs concentration declined during the time after exposure to AIV H9N2 either outside or within house flies. keywords: avian; et al; flies; fly; h9n2; house; influenza; pcr; virus cache: cord-327675-uo839gvc.txt plain text: cord-327675-uo839gvc.txt item: #788 of 973 id: cord-327682-i3uim0zi author: Santti, Juhana title: Molecular detection and typing of human picornaviruses date: 1999-08-25 words: 2440 flesch: 36 summary: It has been shown in a number of studies that virtually all the enterovirus serotypes and most of the HRV isolates can be detected using these primer sequences (Hyypiä et , 1989; Horsnell et al., 1995; Pulli et al., 1995; Arola et al., 1996; Huttunen et al., 1996; Pitkäranta et al., 1997; The outcome of enterovirus infections in man varies from minor respiratory illnesses to paralysis, myocarditis, meningoencephalitis and generalized infections with multiorgan failure in newborns (Grist et al., 1978) . keywords: enterovirus; infections; molecular; pcr; serotypes cache: cord-327682-i3uim0zi.txt plain text: cord-327682-i3uim0zi.txt item: #789 of 973 id: cord-327894-b0bsseui author: Pecellín, Lidia Gestoso title: Recomendaciones y uso de los diferentes tipos de test para detección de infección por SARS-COV-2 date: 2020-10-14 words: 4899 flesch: 42 summary: La enfermera que proceda a la obtención de muestra deberá llevar un equipo de protección individual para prevenir la transmisión de la infección de acuerdo con el riesgo de exposición 31 . La táctica para la contención de la epidemia fue la realización de tests masivos para conocer el número de personas contagiadas 1 . keywords: anticuerpos; casos; centros; como; con; coronavirus; cov-2; covid-19; de la; del; detección; diagnóstico; infección; las; los; muestras; más; pacientes; para; para la; pcr; por; pruebas; que; recogida; sars; según; ser; son; tests; toma; una; virus cache: cord-327894-b0bsseui.txt plain text: cord-327894-b0bsseui.txt item: #790 of 973 id: cord-328206-iylw1bvw author: Yu, Daojun title: Simultaneous Detection and Differentiation of Human Papillomavirus Genotypes 6, 11, 16 and 18 by AllGlo Quadruplex Quantitative PCR date: 2012-11-09 words: 4073 flesch: 42 summary: In addition, AllGlo probe quadruplex fluorescence quantitative PCR also has the advantages of relatively high throughput, time savings, simple operation, and lower cost, which are key factors that are needed in order to be qualified for clinical applications. AllGlo quadruplex quantitative PCR in a single tube has the advantages of relatively high throughput, good reproducibility, high sensitivity, high specificity, and a wide linear range of detection. keywords: allglo; detection; dna; fluorescence; hpv; pcr; probe; qpcr; quadruplex; test cache: cord-328206-iylw1bvw.txt plain text: cord-328206-iylw1bvw.txt item: #791 of 973 id: cord-328373-cubp1cc1 author: Jiang, Yanfang title: Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications date: 2020-11-04 words: 3569 flesch: 42 summary: Clinical patient samples and samples obtained from potentially contaminated environments were analyzed. Pathogenic evidence: Nucleic acid test (real-time RT PCR) was used to detect SARS-CoV-2 in the respiratory tract. keywords: cov-2; detection; digital; nucleic; patients; pcr; samples; sars cache: cord-328373-cubp1cc1.txt plain text: cord-328373-cubp1cc1.txt item: #792 of 973 id: cord-328409-px92ff89 author: Hornuss, Daniel title: COVID-19-assoziierte Pneumonie trotz persistierend negativen PCR-Tests aus oropharyngealen Abstrichen date: 2020-05-13 words: 1588 flesch: 34 summary: Aufgrund der geringen Invasivität und der einfachen Durchführung ist die PCR-Analyse aus tiefen Rachen-oder Nasenabstrichen weiterhin die diagnostische Testmethode der ersten Wahl, insbesondere im Rahmen von Screening-Untersuchungen. Folgerung Die Kasuistik beschreibt einen Fall von COVID-19, bei dem trotz typischer klinischer Symptomatik sowie typischen radiologischen und laborchemischen Befunden ein Virusnachweis in mehrfach korrekt durchgeführten tiefen Rachenabstrichen nicht möglich war. keywords: analysis; bei; cov-2; covid-19; der; die; findings; patient; pcr; sars; und cache: cord-328409-px92ff89.txt plain text: cord-328409-px92ff89.txt item: #793 of 973 id: cord-328460-thx9zh11 author: Zanoli, Laura Maria title: Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices date: 2012-12-27 words: 8976 flesch: 31 summary: Although PCR is the most widespread technology for DNA amplification, the need for an electrically powered thermal cycler with a precise temperature control and for an optimized experimental setup makes the use of PCR at point-of-care settings more complex and increases the cost of PCR-based devices. Symmetrical mode of DNA replication TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing Optimization of the polymerase chain reaction with regard to fidelity: Modified T7, Taq, and vent DNA polymerases Fidelity of DNA polymerases in DNA amplification Unbiased whole genome amplification directly from clinical samples Genomic DNA amplification from a single bacterium Nanoliter reactors improve multiple displacement amplification of genomes from single cells Single-Molecule DNA Amplification and analysis using microfluidics DNA detection using recombination proteins A phaseguided passive batch microfluidic mixing chamber for isothermal amplification Phaseguides: A paradigm shift in microfluidic priming and emptying Hot start PCR Digital isothermal quantification of nucleic acids via simultaneous chemical initiation of recombinase polymerase amplification reactions on SlipChip Nucleic acid sequence-based amplification Characteristics and applications of nucleic acid sequence-based amplification (NASBA) Quantitative detection of hepatitis B virus DNA by real-time nucleic acid sequence-based amplification with molecular beacon detection A one-tube quantitative HIV-1 RNA NASBA nucleic acid amplification assay using electrochemiluminiscent (ECL) labelled probes Comparison of nucleic acid-based detection of avian influenza H5N1 with virus isolation Human pathogenic Cryptosporidium species bioanalytical detection method with single oocyst detection capability PMMA biosensor for nucleic acids with integrated mixer and electrochemical detection Strategy for molecular beacon binding readout: Separating molecular recognition element and signal reporter Molecular engineering of DNA: Molecular beacons Real-time molecular beacon NASBA reveals hblc expression from Bacillus spp. keywords: acid; amplification; detection; device; dna; dna amplification; helicase; isothermal; nasba; nucleic; pcr; polymerase; reaction; rna; sample; sequence; target; temperature; time cache: cord-328460-thx9zh11.txt plain text: cord-328460-thx9zh11.txt item: #794 of 973 id: cord-328526-es8t6t0j author: Hoppes, Sharman title: The Isolation, Pathogenesis, Diagnosis, Transmission, and Control of Avian Bornavirus and Proventricular Dilatation Disease date: 2010-08-02 words: 5509 flesch: 52 summary: A group of 15 'healthy' cockatiels from a single aviary, with no history of PDD or exposure to other birds, was screened for ABV by fecal PCR. Recent findings on the transmission, epidemiology, pathogenesis, diagnosis, and control of ABV infection and PDD are also reviewed. keywords: abv; authors; birds; bornavirus; colleagues; dilatation; disease; pcr; pdd; protein; proventricular; virus cache: cord-328526-es8t6t0j.txt plain text: cord-328526-es8t6t0j.txt item: #795 of 973 id: cord-328534-66c2tg5r author: Nidzworski, Dawid title: Detection of avian influenza virus and newcastle disease virus by duplex one step RT PCR date: 2013-03-16 words: 2537 flesch: 45 summary: The ability to detect both these major, avian pathogens, even in co-infections, through a very easy procedure, makes this method very attractive for application in veterinary laboratories. Avian influenza and human health A review of avian influenza in different bird species Immunology of avian influenza virus: a review Family paramyxoviridae Disease of Poultry Pathogenicity and phylogenetic evaluation of the variant Newcastle disease viruses termed pigeon PMV-1 viruses based on the nucleotide sequence of the fusion protein gene Proteolytic cleavage of the viral glycoproteins and its significance for the virulence of Newcastle disease virus Role of fusion protein cleavage site in the virulence of Newcastle disease virus Characterization of Newcastle disease virus isolates by reverse transcription PCR coupled to direct nucleotide sequencing and development of sequence database for pathotype prediction and molecular epidemiological analysis Detection and differentiation of pathogenicity of avian paramyxovirus serotype 1 from field cases using one-step reverse transcriptasepolymerase chain reaction Rapid discrimination of H5 and H9 subtypes of avian influenza viruses and Newcastle disease virus by multiplex RT-PCR Detection of a broad range of class I and II Newcastle disease viruses using a multiplex real time reverse transcription polymerase chain reaction assay A multiplex RT-PCR assay for detection and differentiation of avian H3, H5, and H9 subtype influenza viruses and Newcastle disease viruses Development and Application of a Multiplex Polymerase Chain Reaction for Avian Respiratory Agents Standardization of a duplex RT-PCR for the detection of Influenza A and Newcastle disease viruses in migratory birds Rapid and Simultaneous Detection of Avian Influenza and Newcastle Disease Viruses by Duplex Polymerase Chain Reaction Assay Identification of sensitive and specific avian influenza polymerase chain reaction methods through blind ring trials organized in the European Union Multiplex polymerase chain reaction for the detection and differentiation of avian influenza viruses and other poultry respiratory pathogens Development of a Real-Time Reverse Transcriptase PCR Assay for Type A Influenza Virus and the Avian H5 and H7 Hemagglutinin Subtypes Immuno-PCR for one step detection of H5N1 avian influenza virus and Newcastle disease virus using magnetic gold particles as carriers Detection of three avian respiratory viruses by single-tube multiplex reverse transcription-polymerase chain reaction assay approving a Diagnostic Manual for avian influenza as provided for in Council Directive 2005/94/EC (notified under document number C(2006) 3477) Avian influenza viruses (AIV) are also divided into: low pathogenic (LPAI) and highly pathogenic (HPAI) strains. keywords: avian; detection; influenza; ndv; pcr; virus; viruses cache: cord-328534-66c2tg5r.txt plain text: cord-328534-66c2tg5r.txt item: #796 of 973 id: cord-328633-c31xsyeo author: Moser, Michael J. title: Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme date: 2012-06-04 words: 7878 flesch: 48 summary: The AMV and MMLV had higher RT activity at 37uC while the 3173 Pol RT was much more active at 65uC using the fluorogenic incorporation assay ( Figure 3A ). Soluble proteins were collected from the supernatant after centrifugation at 11,000 rcf for 10 minutes and assayed for DNA Pol activity based on their ability to extend a 59 fluorescently labeled oligonucleotide primer. keywords: activity; amplification; dna; enzyme; exonuclease; fidelity; figure; mmlv; ms2; pcr; pol; polymerase; primer; reverse; rna; step; taq; target cache: cord-328633-c31xsyeo.txt plain text: cord-328633-c31xsyeo.txt item: #797 of 973 id: cord-328795-rs1sd42z author: Falsey, Ann R. title: Rhinoviruses date: 2016-10-24 words: 4514 flesch: 40 summary: Infection of the upper airways is the most common site of infection, although lower airways disease is also well documented, as is the link between HRV infection and exacerbations of asthma. Infection of the upper airways is the most common site of infection, although lower airways disease is also now well documented, as is the link between HRV infection and exacerbations of asthma. keywords: asthma; disease; hrv; illness; infection; rhinovirus; symptoms; turner cache: cord-328795-rs1sd42z.txt plain text: cord-328795-rs1sd42z.txt item: #798 of 973 id: cord-328961-waxtb759 author: Pratelli, Annamaria title: PCR assay for the detection and the identification of atypical canine coronavirus in dogs date: 2002-10-01 words: 1890 flesch: 47 summary: A total of 177 faecal samples from dogs CCoV positive previously with the PCR assay were analysed. This note describes a PCR assay to identify atypical CCoV strains with nucleotide substitutions in the M gene. keywords: ccov; pcr; pratelli; sequence cache: cord-328961-waxtb759.txt plain text: cord-328961-waxtb759.txt item: #799 of 973 id: cord-329052-jan20ljs author: Gombar, Saurabh title: Persistent detection of SARS-CoV-2 RNA in patients and healthcare workers with COVID-19 date: 2020-05-30 words: 865 flesch: 49 summary: To better understand the appropriate length of symptom based return to work and contact precaution strategies. Objectives: To better understand the appropriate length of symptom based return to work and contact precaution strategies. keywords: pcr cache: cord-329052-jan20ljs.txt plain text: cord-329052-jan20ljs.txt item: #800 of 973 id: cord-329069-ejdunj41 author: Yang, He S title: Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning date: 2020-08-21 words: 2370 flesch: 40 summary: This model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-CoV-2 infected patients before their RT-PCR results are available. Laboratory test results obtained within two days before the release of SARS-CoV-2-RT-PCR result were used to train a gradient boosted decision tree (GBDT) model from 3,356 SARS-CoV-2 RT-PCR tested patients (1,402 positive and 1,954 negative) evaluated at a metropolitan hospital. keywords: laboratory; patients; pcr; sars; testing; tests cache: cord-329069-ejdunj41.txt plain text: cord-329069-ejdunj41.txt item: #801 of 973 id: cord-329148-zs18ez5q author: Geng, Yunyun title: Development of real-time recombinase polymerase amplification assay for rapid and sensitive detection of canine parvovirus 2 date: 2017-11-06 words: 3898 flesch: 51 summary: The recombinant plasmid, pCPV-VP2, was 10-fold serially diluted to achieve DNA concentrations ranging from 10 5 to 10 0 copies/μL, which were used as the standard DNA for the CPV-2 RPA sensitivity assay. No discrepancy was found in samples (14/76) containing low levels of CPV-2 DNA (Ct > 35, real-time PCR), indicating that the established real-time RPA reliably detected low amounts of CPV-2 in clinical samples. keywords: amplification; assay; canine; detection; dna; pcr; rpa; samples; time; time rpa cache: cord-329148-zs18ez5q.txt plain text: cord-329148-zs18ez5q.txt item: #802 of 973 id: cord-329162-6w8qcv1c author: Ayginin, Andrey A. title: The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels date: 2018-08-12 words: 4840 flesch: 44 summary: The software BLAST was then employed to first compare the representative sequences (RS) against virus-only nucleotide and protein databases that were collected by selection of virus sequences from GenBank NT and GenBank NR databases, respectively, to identify viral nucleotide candidate RS (nRS) and protein candidate RS (pRS) with E-value cutoffs of 10 -5 and 10 -3 , respectively. We also observed a considerable number of viral reads corresponding to various genera in some samples (B27, B46, B49, B58, B66, and B69), despite the absence of specific primers in the panel for their enrichment. keywords: detection; enrichment; genus; number; panel; pcr; primer; reads; samples; sequences; sequencing; viruses cache: cord-329162-6w8qcv1c.txt plain text: cord-329162-6w8qcv1c.txt item: #803 of 973 id: cord-329395-4k8js9v2 author: Ratcliff, Jeremy title: Evaluation of Different PCR Assay Formats for Sensitive and Specific Detection of SARS-CoV-2 RNA date: 2020-07-01 words: 1667 flesch: 35 summary: As determined by 50% endpoint detection, the sensitivities of three RT-qPCRs and nested PCR methods varied substantially depending on the transcript target with no method approaching single copy detection. 19 An alternative, more cost-effective diagnostic method for SARS-CoV-2 RNA is nested PCR. 20 Nested PCR is based on the use of two sequential PCR amplifications wherein the secondary set 21 of primers target sequences nested within the amplicon produced by the first round amplification. keywords: cov-2; detection; pcr; rna; sars cache: cord-329395-4k8js9v2.txt plain text: cord-329395-4k8js9v2.txt item: #804 of 973 id: cord-329517-3yn80r9h author: Yang, Jin-Long title: Development of a fluorescent quantitative real-time polymerase chain reaction assay for the detection of Goose parvovirus in vivo date: 2009-09-15 words: 3582 flesch: 49 summary: Previous studies have examined the distribution of GPV in infected Muscovy ducks by qualitative PCR [9] , including a study that used quantitative PCR [20] . Real-time PCR and qualitative PCR assays keywords: assay; detection; dna; gpv; pcr; plasmid; pvp3; time cache: cord-329517-3yn80r9h.txt plain text: cord-329517-3yn80r9h.txt item: #805 of 973 id: cord-329564-tmi1u224 author: Arashiro, Takeshi title: COVID-19 in 2 Persons with Mild Upper Respiratory Tract Symptoms on a Cruise Ship, Japan date: 2020-06-17 words: 1998 flesch: 52 summary: Coronavirus disease (COVID-19) outbreak Regarding COVID-19 cases on a cruise ship Cabinet order to designate novel coronavirus infection 2019 as designated infectious disease Clinical features of patients infected with 2019 novel coronavirus in Wuhan Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study Epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside Wuhan, China A novel coronavirus emerging in China-key questions for impact assessment Emergency ministerial meeting on COVID-19 organized by the African Union and the Africa Centres for Disease Control and Prevention Discharge criteria for COVID-19 patients SARS-CoV-2 viral load in upper respiratory specimens of infected patients The work was supported by Major Project of Wenzhou Municipal Science and Technology Bureau (ZY202004). Other case-patients who had been on other floors denied any direct contact with confirmed patients from floor 7, but they shared common building facilities (e.g., restrooms, elevators). keywords: case; day; patients; ship; symptoms cache: cord-329564-tmi1u224.txt plain text: cord-329564-tmi1u224.txt item: #806 of 973 id: cord-329643-hhk900c1 author: Skalina, K. A. title: Extended Storage of SARS-CoV2 Nasopharyngeal Swabs Does Not Negatively Impact Results of Molecular-Based Testing date: 2020-05-20 words: 1871 flesch: 37 summary: This study utilized three different automated real-time reverse-transcriptase polymerase chain reaction (RT-PCR) in vitro diagnostic platforms (Luminex ARIES, Panther Fusion, and Abbott m2000) currently in use for clinical testing of SARS-CoV-2 at the Department of Pathology, Division of Virology, Montefiore Medical Center, Bronx, NY. These varied assay constructs may be differentially affected by storage conditions and degradation. keywords: cov-2; sars; storage; testing; time cache: cord-329643-hhk900c1.txt plain text: cord-329643-hhk900c1.txt item: #807 of 973 id: cord-330079-pdaowkop author: Xu, Lin title: Surveillance and Genome Analysis of Human Bocavirus in Patients with Respiratory Infection in Guangzhou, China date: 2012-09-11 words: 4479 flesch: 44 summary: Many reports of adult HBoV infection enrolled no more than 100 samples [2, 8, 12, 29, 30] . In contrast, HBoV positive adults were mainly diagnosed as acute upper respiratory tract infection (AURI) ( Table 3) . keywords: bocavirus; children; hbov; human; infection; patients; pcr; strains; virus cache: cord-330079-pdaowkop.txt plain text: cord-330079-pdaowkop.txt item: #808 of 973 id: cord-330594-uq2h8rmv author: Nishizono, Akira title: A simple and rapid immunochromatographic test kit for rabies diagnosis date: 2008-04-21 words: 3490 flesch: 46 summary: Biological and serological characterization T cell responses to cleaved rabies virus glycoprotein and to synthetic peptides Antigenic properties of rabies virus components Re-evaluating the burden of rabies in Africa and Asia Estimating the public health impact of rabies Comparative field evaluation of the fluorescent-antibody test, virus isolation from tissue culture, and enzyme immunodiagnosis for rapid laboratory diagnosis of rabies Laboratory techniques in rabies Intravitam diagnosis of human rabies by PCR using saliva and cerebrospinal fluid Nucleic-acid sequence based amplification in the rapid diagnosis of rabies Suppression of cell-mediated immunity by street rabies virus infection Essential role of T cell in the postexposure prophylaxis of rabies in mice Isolation and assay of rabies serogroup viruses in CER cells Characterization of Oita virus296/1972 of Rhabdoviridae isolated from a horseshoe bat bearing characteristics of both lyssavirus and vesiculovirus Genetic analysis of rabies virus isolates in the Philippines Resistance of mice vaccinated with rabies virus internal structural proteins to lethal infection Linear and conformation-dependent antigenic sites on the nucleoprotein of rabies virus Cross-reactive antigenicity of nucleoproteins of lyssaviruses recognized by a monospecific antirabies virus nucleoprotein antiserum on paraffin sections of formalin-fixed tissues Development, evaluation, and application of lateral-flow immunoassay (Immunochromatography) for detection of rotavirus in bovine fecal samples Evaluation of the ESPLINE INFLUENZA A&B-N kit for the diagnosis of avian and swine influenza Comparison of an immunochromatography test with multiplex reverse transcription-PCR for rapid diagnosis of respiratory syncytial virus infections Detection of rabies virus antigen in dog saliva using a latex agglutination test Evaluation of a direct, rapid immunohistochemical test for rabies diagnosis This work was partially supported by grants-in-aid no. 19406016 from the Japan Society for the Promotion of Science and by the Program of Founding Research Centers for Emerging and Reemerging Infectious Diseases, MEXT, founded by the Ministry of Education, Culture, Sports, Science and Technology, Japan. These were developed using monoclonal antibodies which recognize epitope II and III of the nucleoprotein of rabies virus. keywords: brain; diagnosis; ict; protein; rabies; rabv; samples; test; type; virus cache: cord-330594-uq2h8rmv.txt plain text: cord-330594-uq2h8rmv.txt item: #809 of 973 id: cord-330602-g0xaonxv author: Sugiura, Hiroaki title: Prescription Surveillance and Polymerase Chain Reaction Testing to Identify Pathogens during Outbreaks of Infection date: 2013-02-07 words: 3232 flesch: 30 summary: Therefore, syndromic surveillance systems have been implemented in many countries since 1995 The scheme proposed by the present study uses PCR testing triggered by detection alerts from syndromic surveillance systems. keywords: infections; patients; pcr; pneumoniae; respiratory; surveillance cache: cord-330602-g0xaonxv.txt plain text: cord-330602-g0xaonxv.txt item: #810 of 973 id: cord-330800-s91zfzfi author: Reta, Daniel Hussien title: Molecular and Immunological Diagnostic Techniques of Medical Viruses date: 2020-09-04 words: 10553 flesch: 40 summary: A H1N1 Virus 2009 by reverse-transcription loop-mediated isothermal amplification with hydroxynaphthol blue dye An updated loop-mediated isothermal amplification method for rapid diagnosis of H5N1 avian influenza viruses Loop-mediated isothermal amplification assay for rapid detection of hepatitis C virus Detection of acute HIV-1 infection by RT-LAMP Detection of Zika virus using reverse-transcription LAMP coupled with reverse dot blot analysis in saliva Infectious diseases detection by microarray: an overview of clinical relevant infections Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children Detection of herpesvirus and adenovirus co-infections with diagnostic DNA-microarrays DNA microarrays for virus detection in cases of central nervous system infection DNA microarray for detection of gastrointestinal viruses DNA microarray platform for detection and surveillance of viruses transmitted by small mammals and arthropods DNA probe array for the simultaneous identification of herpesviruses, enteroviruses, and flaviviruses Characterization of real-time microarrays for simultaneous detection of HIV-1, HIV-2, and hepatitis viruses A DNA microarray-based assay to detect dual infection with two dengue virus serotypes An efficient microarray-based genotyping platform for the identification of drug-resistance mutations in majority and minority subpopulations of HIV-1 Quasispecies Development of a simple microarray for genotyping HIV-1 drug resistance mutations in the reverse transcriptase gene in rural Tanzania Microarray-based genotyping and detection of drug-resistant HBV mutations from 620 Chinese patients with chronic HBV infection Development of a single nucleotide polymorphism DNA microarray for the detection and genotyping of the SARS coronavirus Diagnostic microarray for influenza B viruses Viral discovery and sequence recovery using DNA microarrays Metagenomics and the molecular identification of novel viruses DNA microarrays: types, applications and their future Next-generation sequencing for infectious disease diagnosis and management Current approaches for diagnosis of influenza virus infections in humans Application of next generation sequencing in clinical microbiology and infection prevention Assessing the performance of the Oxford nanopore technologies MinION Nanopore sequencing and assembly of a human genome with ultra-long reads Rapid and accurate sequencing of enterovirus genomes using MinION nanopore sequencer Whole genome sequencing of influenza A and B viruses with the MinION sequencer in the clinical setting: a pilot study Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples A method to identify respiratory virus infections in clinical samples using nextgeneration sequencing Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis First evaluation of the Next-Generation Sequencing platform for the detection of HIV-1 drug resistance mutations in Belgium Newly discovered Ebola virus associated with hemorrhagic fever outbreak in Uganda Next-generation sequencing and bioinformatic approaches to detect and analyze influenza virus in ferrets Metagenomic nextgeneration sequencing aids the diagnosis of viral infections in febrile returning travellers Nucleoprotein-based indirect enzyme-linked immunosorbent assay (indirect ELISA) for detecting antibodies specific to Ebola virus and Marbug virus Evaluation of antibody testing for SARS-CoV-2 using ELISA and lateral flow immunoassays Evaluation of ELISA tests for the qualitative determination of IgG, IgM and IgA to SARS-CoV-2 Development of an enzyme-linked immunosorbent assay for rapid detection of dengue virus (DENV) NS1 and differentiation of DENV serotypes during early infection Transmission of Herpes simplex virus type 2 among factory workers in Ethiopia Detection of severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in SARS patients by enzyme-linked immunosorbent assay Detection of hepatitis A, B, and C virus-specific antibodies using oral fluid for epidemiological studies Newly established monoclonal antibodies for immunological detection of H5N1 influenza virus High specificity of a novel Zika virus ELISA in European patients after exposure to different flaviviruses Laboratory diagnostics for HIV infection Development of a Western blot assay for detection of antibodies against coronavirus causing severe acute respiratory syndrome Western blot detection of human anti-Chikungunya virus antibody with recombinant envelope 2 protein Western blot-based logistic regression model for the identification of recent HIV-1 infection: a promising HIV-1 surveillance approach for resource-limited regions Early detection of anti-HCc antibody in acute hepatitis C virus (HCV) by western blot (immunoblot) using a recombinant HCV core protein fragment Detection of human immunodeficiency virus type 1 (HIV-1) antibody by western blotting and HIV-1 DNA by PCR in patients with AIDS Western blot profile in HIV infection Accuracy of rapid influenza diagnostic test and immunofluorescence assay compared to real time RT-PCR in children with influenza A(H1N1)pdm09 infection Immunofluorescence assay for serologic diagnosis of SARS Detection of herpes simplex virus in direct specimens by immunofluorescence assay using a monoclonal antibody Comparative evaluation of a simple indirect immunofluorescence test and mouse neutralization test for assaying rabies antibodies Molecular diagnostic techniques provide rapid viral detection in patient sample. keywords: amplification; assay; detection; diagnosis; dna; elisa; human; infection; influenza; pcr; reaction; rna; samples; sars; sensitivity; specificity; time; virus; viruses cache: cord-330800-s91zfzfi.txt plain text: cord-330800-s91zfzfi.txt item: #811 of 973 id: cord-331413-fejho1of author: Nakayama, Eiichi title: Rapid optimization of antimicrobial chemotherapy given to pediatric patients with community-acquired pneumonia using PCR techniques with serology and standard culture date: 2007-12-31 words: 3958 flesch: 36 summary: The median values (50%) of the white blood cell count (WBC) and C-reactive protein (CRP) using the box-and-whisker and plot method, respectively, were 11.7 × 103 mm−3 and 1.4mg/dl in viral infections, 15.6 × 103 mm−3 and 4.8mg/dl in mixed infections with virus and bacteria, 17.8 × 103 mm−3 and 6.3mg/dl in bacterial infections, 6.7 × 103 mm−3 and 1.4mg/dl in M. pneumoniae infections, and 21.5 × 103 mm−3 and 6.4mg/dl in mixed infections with M. pneumoniae and other bacterial infections. Sulbactam/ampicillin (n =61), carbapenems (n =12), and ceftriaxone (n =7) were selected for the patients suspected of having bacterial infections alone or mixed infections with bacterial and viruses in accordance with our criteria defined tentatively. keywords: bacterial; cases; children; infections; pathogens; patients; pcr; pneumoniae cache: cord-331413-fejho1of.txt plain text: cord-331413-fejho1of.txt item: #812 of 973 id: cord-331455-dfnn9mrf author: Shah, Aditya S. title: The utility of chest computed tomography (CT) and RT-PCR screening of asymptomatic patients for SARS-CoV-2 prior to semiurgent or urgent hospital procedures date: 2020-07-16 words: 2381 flesch: 41 summary: The CT chest study was interpreted as typical, indeterminate, atypical, or normal using the criteria set forth in the publication Radiological Society of North America Expert Consensus statement on reporting chest CT findings related to COVID-19, endorsed by the Society of Thoracic Radiology, the American College of Radiology, and RSNA and the corresponding suggested reporting language accompanied each category in the impression of the CT report. Infectious Diseases Society of America website Chest CT for detecting COVID-19: a systematic review and meta-analysis of diagnostic accuracy Radiological Society of North America Expert Consensus statement on reporting chest CT findings related to COVID-19. keywords: chest; covid-19; patients; pcr cache: cord-331455-dfnn9mrf.txt plain text: cord-331455-dfnn9mrf.txt item: #813 of 973 id: cord-331475-mmcu18c8 author: Sahu, Amit Ranjan title: Selection and validation of suitable reference genes for qPCR gene expression analysis in goats and sheep under Peste des petits ruminants virus (PPRV), lineage IV infection date: 2018-10-29 words: 4740 flesch: 40 summary: Design and validation issues in RNA-seq experiments RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays Understanding mechanisms underlying human gene expression variation with RNA sequencing Mapping and quantifying mammalian transcriptomes by RNA-Seq RNA-Seq: a revolutionary tool for transcriptomics Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq Validation' in genome-scale research Infection of bovine dendritic cells by rinderpest or measles viruses induces different changes in host transcription Identification of suitable reference gene in goat peripheral blood mononuclear cells (PBMCs) infected with peste des petits ruminants virus (PPRV) Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays The need for transparency and good practices in the qPCR literature Quantification of mRNA using real-time RT-PCR Validation of reference genes for gene expression studies in virus-infected Nicotiana benthamiana using quantitative real-time PCR Evaluation and validation of candidate endogenous control genes for real-time quantitative PCR studies of breast cancer Real-time RT-PCR normalisation; strategies and considerations Selection of reliable reference genes for gene expression studies using real-time PCR in tung tree during seed development Apparent versus true gene expression changes of three hypoxia-related genes in autopsy derived tissue and the importance of normalisation Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of references Evaluation of suitable reference genes for gene expression studies in porcine PBMCs in response to LPS and LTA 18S rRNA is a reliable normalisation gene for real time PCR based on influenza virus infected cells Careful selection of reference genes is required for reliable performance of RT-qPCR in human normal and cancer cell lines Use of Maximum Likelihood-Mixed Models to select stable reference genes: a case of heat stress response in sheep Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Evaluation of internal reference genes for quantitative expression analysis by real-time reverse transcription-PCR in somatic cells from goat milk Global distribution of peste des petits ruminants virus and prospects for improved diagnosis and control Peste des petits ruminants Expression kinetics of ISG15, IRF3, IFNgamma, IL10, IL2 and IL4 genes vis-a-vis virus shedding, tissue tropism and antibody dynamics in PPRV vaccinated, challenged, infected sheep and goats Peste des Petits Ruminants Virus Supporting Livelihoods and Supporting Livelihoods and Peste Des Petits Ruminants (PPR) and Small Ruminant Diseases Control Reference gene selection for quantitative real-time PCR analysis in virus infected cells: SARS corona virus, Yellow fever virus, Human Herpesvirus-6, Camelpox virus and Cytomegalovirus infections Using host 28S ribosomal RNA as a housekeeping gene for quantitative real-time reverse transcription-PCR (qRT-PCR) in virus-infected animal cells Selection of reference genes for quantitative real-time PCR normalisation in adipose tissue, muscle, liver and mammary gland from ruminants Early changes in cytokine expression in peste des petits ruminants disease Toll-like receptor responses to Peste des petits ruminants virus in goats and water buffalo The validation of housekeeping genes as a reference in quantitative Real Time PCR analysis: application in the milk somatic cells and frozen whole blood of goats infected with caprine arthritis encephalitis virus Real-time PCR in virology Cytokines expression profile and kinetics of Peste des petits ruminants virus antigen and antibody in infected and vaccinated goats Selection of reference genes for quantitative real-time PCR analysis in chicken embryo fibroblasts infected with avian leukosis virus subgroup Systematic selection of housekeeping genes for gene expression normalization in chicken embryo fibroblasts infected with Newcastle disease virus Reference gene selection for normalization of PCR analysis in chicken embryo fibroblast infected with H5N1 AIV Reference gene screening for analyzing gene expression across goat tissue RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization Selection of reference genes for gene expression studies related to intramuscular fat deposition in Capra hircus skeletal muscle The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments Quantitative PCR pitfalls: the case of the human placenta Guideline to reference gene selection for quantitative real-time PCR Reference gene validation for RT-qPCR, a note on different available software packages Selection of reliable reference genes for RT-qPCR analysis Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets Validation of Suitable Reference Genes for Assessing Gene Expression of MicroRNAs in Lonicera japonica Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pair-wise correlations Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR Reference genes selection for quantitative real-time PCR using RankAggreg method in different tissues of Capra hircus Antiviral activity of innate immune protein A total of ten candidate reference genes were selected based on, their use as reference genes in diverse studies on gene expression in goats and sheep, availability of their sequences in databases and their function in the cell ( Table 3) . keywords: control; expression; genes; goats; hmbs; pcr; pprv; reference; sheep; tissues cache: cord-331475-mmcu18c8.txt plain text: cord-331475-mmcu18c8.txt item: #814 of 973 id: cord-331496-5xak7z6b author: Garnett, Emily title: Clinical Validation and Performance Evaluation of the Automated Vitros Total Anti–SARS-CoV-2 Antibodies Assay for Screening of Serostatus in COVID-19 date: 2020-08-31 words: 3450 flesch: 34 summary: Accuracy studies were performed using 57 healthy volunteers who were negative for SARS CoV-2 by RT-PCR and who had no known exposure, travel history, or symptoms of COVID-19 and 79 patient samples that were positive for SARS CoV-2 by RT-PCR. The CoV2T assay exhibited 100% negative predictive agreement (56/56) and 71% positive predictive agreement (56/79) with RT-PCR across all patient samples and was concordant with other serologic assays. keywords: assay; cov-2; cov2; sars; serologic; testing cache: cord-331496-5xak7z6b.txt plain text: cord-331496-5xak7z6b.txt item: #815 of 973 id: cord-331557-8axi74nn author: Raoult, Didier title: What does the future hold for clinical microbiology? date: 2004 words: 6513 flesch: 28 summary: key: cord-331557-8axi74nn authors: Raoult, Didier; Fournier, Pierre Edouard; Drancourt, Michel title: What does the future hold for clinical microbiology? date: 2004 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro820 sha: doc_id: 331557 cord_uid: 8axi74nn In the past decade, clinical microbiology laboratories have undergone important changes with the introduction of molecular biology techniques and laboratory automation. Worldwide -mainly because of the cost of containment measures for infectious diseases -there has been a general tendency over the past 10 years to centralize clinical microbiology laboratories such that they serve several hospitals, therefore maximizing the efficiency of testing at the lowest cost 4 . keywords: bacteria; detection; diagnosis; diseases; dna; fcm; future; identification; laboratories; microarrays; microbiology; microorganisms; molecular; pcr; tests cache: cord-331557-8axi74nn.txt plain text: cord-331557-8axi74nn.txt item: #816 of 973 id: cord-331558-6rqd3fmj author: Sun, Chuan-bin title: Role of the Eye in Transmitting Human Coronavirus: What We Know and What We Do Not Know date: 2020-04-24 words: 5514 flesch: 40 summary: However, the number of 2019-nCoV infected patients in the first two months was nearly 10 times that of SARS patients in total, which indicated that 2019-nCoV is more transmissible than SARS-CoV and MERS-CoV (16) . Patients infected by 2019-nCoV, similar to SARS cases, mostly present with non-specific symptoms such as fever, dry cough, and dyspnoea, or, in some cases, no evident symptoms, at the early phase of the disease (9, 16, (23) (24) (25) (26) (27) 48) . keywords: conjunctival; coronavirus; cov; covid-19; covs; human; infection; mers; ncov; patients; sars cache: cord-331558-6rqd3fmj.txt plain text: cord-331558-6rqd3fmj.txt item: #817 of 973 id: cord-331616-arnuoufn author: Blank, Walter A. title: Virus PCR Assay Panels: An Alternative to the Mouse Antibody Production Test date: 2004 words: 3519 flesch: 29 summary: PCR testing requires personnel trained in molecular biology techniques and specialized equipment, which includes still-air work hoods for sample processing, thermal cyclers, and gel electrophoresis equipment and/or fluorometric detection systems. By contrast, PCR testing can detect infectious and noninfectious virus particles alike, provided that the sample has not been mishandled to such an extent that the nucleic acid has degraded. keywords: assays; detection; map; pcr; reaction; testing; use; virus; viruses cache: cord-331616-arnuoufn.txt plain text: cord-331616-arnuoufn.txt item: #818 of 973 id: cord-331740-yjt3q9ph author: Jones, R. M. title: Development and Validation of RT‐PCR Tests for the Detection and S1 Genotyping of Infectious Bronchitis Virus and Other Closely Related Gammacoronaviruses Within Clinical Samples date: 2011-04-07 words: 5873 flesch: 41 summary: Transport and initial processing of field samples Tissue samples (kidney, brain, liver, oviduct, bursa and respiratory and intestinal tracts) were collected from a variety of bird species (chicken, turkey, pheasant and pigeon) at post-mortem from cases with respiratory disease or suspected coronavirus infection based on clinical observations. The IBV S1 sequence files were taken from the public access Genbank database and included representatives of the major groups of IBV strains that are currently circulating in Europe alongside other IBV strains (see Fig. 1 ). keywords: bronchitis; diagnostic; field; ibv; pcr; samples; sequence; strains; time; time rt; virus cache: cord-331740-yjt3q9ph.txt plain text: cord-331740-yjt3q9ph.txt item: #819 of 973 id: cord-331932-oujdl459 author: Lung, O. title: Multiplex PCR and Microarray for Detection of Swine Respiratory Pathogens date: 2015-12-12 words: 6365 flesch: 33 summary: Duplex and triplex real-time PCR for porcine respiratory viruses have also been recently described (Chang et al., 2014; Wu et al., 2014) . The DNeasy Blood and Tissue Kit and the Viral RNA Mini extraction kit were the most efficient for the tested bacteria and virus targets, respectively (data not shown). keywords: assay; bacteria; control; detection; electronic; et al; microarray; multiplex; pcr; porcine; probes; target; viruses cache: cord-331932-oujdl459.txt plain text: cord-331932-oujdl459.txt item: #820 of 973 id: cord-332024-jk983q4p author: Briese, Thomas title: Diagnostic System for Rapid and Sensitive Differential Detection of Pathogens date: 2005-02-17 words: 1745 flesch: 26 summary: Multiplex primer sets were designed to identify up to 22 respiratory pathogens in a single Mass Tag PCR reaction; sensitivity was established by using synthetic DNA and RNA standards as well as titered viral stocks; the utility of Mass Tag PCR was determined in blinded analysis of previously diagnosed clinical specimens. After quantita-tion by UV spectrometry, RNA was serially diluted in 2.5µg/mL yeast tRNA (Sigma), reverse transcribed with random hexamers by using Superscript II (Invitrogen, Carlsbad, CA, USA), and used as template for Mass Tag PCR. keywords: detection; mass; multiplex; pathogens; pcr; rna; tag cache: cord-332024-jk983q4p.txt plain text: cord-332024-jk983q4p.txt item: #821 of 973 id: cord-332042-bqtflk7r author: LeBlanc, J. J. title: Validation of the Seegene RV15 multiplex PCR for the detection of influenza A subtypes and influenza B lineages during national influenza surveillance in hospitalized adults date: 2019-07-02 words: 4565 flesch: 39 summary: Within 7 days of onset of illness, consenting patients were enrolled and tested for influenza viruses A and B from NP swabs collected in universal transport media (UTM) (Copan Diagnostics). This study focuses on molecular detection of influenza viruses for the purpose of surveillance. keywords: detection; influenza; methods; pcr; respiratory; rv15; study; surveillance; time; viruses cache: cord-332042-bqtflk7r.txt plain text: cord-332042-bqtflk7r.txt item: #822 of 973 id: cord-332053-df44guu7 author: Malka, Jonathan title: The Effect of Viral Infection on Exhaled Nitric Oxide in Children with Acute Asthma Exacerbations date: 2015-07-26 words: 4759 flesch: 47 summary: In this study of children with asthma, we sought to determine whether FENO levels were elevated during acute asthma exacerbations. We found FENO levels to be the highest in children with acute asthma exacerbations that were not associated with viral infections [PCR(À)]. keywords: asthma; baseline; children; exacerbation; feno; levels; nitric; oxide; pcr; virus cache: cord-332053-df44guu7.txt plain text: cord-332053-df44guu7.txt item: #823 of 973 id: cord-332333-vw5ogccq author: Montenegro-López, Diego title: Uso de tecnologías en el lugar de atención para el manejo de la pandemia por COVID-19 en Colombia date: 2020-08-14 words: 3007 flesch: 40 summary: en Colombia Detección Temprana SARS CoV-2/ COVID-19 MInisterio de Salud y de la Proteccion Social Colombia: 25 de marzo 2020 Guidelines for point-of-care testing: Según el reporte de la Procuraduría de Colombia (40), el costo de cada PCR es de 380 mil pesos colombianos (aprox. keywords: atención; casos; colombia; con; coronavirus; covid-19; del; diagnóstico; las; los; para; pcr; por; pruebas; que; rápido; salud; una cache: cord-332333-vw5ogccq.txt plain text: cord-332333-vw5ogccq.txt item: #824 of 973 id: cord-332510-x3znuwc0 author: Freire-Álvarez, Eric title: COVID-19-associated encephalitis successfully treated with combination therapy date: 2020-11-01 words: 1908 flesch: 30 summary: Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Middle East respiratory syndrome coronavirus causes multiple organ damage and lethal disease in mice transgenic for human dipeptidyl peptidase 4 Detection of severe acute respiratory syndrome coronavirus in the brain: potential role of the chemokine mig in pathogenesis COVID-19: consider cytokine storm syndromes and immunosuppression The cytokine release syndrome (CRS) of severe COVID-19 and interleukin-6 receptor (IL-6R) antagonist tocilizumab may be the key to reduce the mortality A first case of meningitis/encephalitis associated with SARS-Coronavirus-2 COVID-19-associated acute hemorrhagic necrotizing encephalopathy: CT and MRI features Neurological manifestations of influenza infection in children and adults: results of a National British Surveillance Study Encephalitis after influenza and vaccination: a nationwide population-based registry study from Norway Neurological and neuropsychiatric complications of COVID-19 in 153 patients: a UK-wide surveillance study Neurologic manifestations in 1760 COVID-19 patients admitted to Papa Giovanni XXIII Hospital Acute disseminated encephalomyelitis: current knowledge and open questions Severe neurologic syndrome associated with Middle East respiratory syndrome corona virus (MERS-CoV) Multiple organ infection and the pathogenesis of SARS Based on clinical characteristics, CSF data and neuroimaging, the diagnosis of encephalitis was established in five patients, among whom one was herpes simplex virus 1-related, one necrotizing encephalitis, and two patients had SARS CoV-2 detected in CSF by RT-PCR. keywords: acute; brain; covid-19; encephalitis; sars cache: cord-332510-x3znuwc0.txt plain text: cord-332510-x3znuwc0.txt item: #825 of 973 id: cord-332522-adul9nzf author: Wu, Qingfa title: Development of Taqman RT-nested PCR system for clinical SARS-CoV detection date: 2004-04-02 words: 2815 flesch: 57 summary: To compare the reverse transcribed efficiency of random primer versus specific primer, seven sets of nested primers covering each known gene were chosen for testing. In this study, 12 sets of nested primers covering the SARS-CoV genome have been screened and showed sufficient sensitivity to detect SARS-CoV in RNA isolated from virus cultured in Vero 6 cells. keywords: cov; pcr; primer; rna; sars cache: cord-332522-adul9nzf.txt plain text: cord-332522-adul9nzf.txt item: #826 of 973 id: cord-332539-v1bfm57x author: Gohl, Daryl M. title: A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2 date: 2020-05-11 words: 5055 flesch: 46 summary: The tailed amplicon approach, developed here, enriches first strand cDNA using ARTIC v3 primers containing adapter tails. We thank Sean Wang and Matt Plumb from the Minnesota Department of Heath for helpful discussions and for sharing ARTIC v3 primers. keywords: amplicon; artic; cov-2; coverage; figure; read; samples; sars; sequencing cache: cord-332539-v1bfm57x.txt plain text: cord-332539-v1bfm57x.txt item: #827 of 973 id: cord-333216-fdwmsnz9 author: Gonzalez, J. E. title: ESTIMATING PREVALENCE AND TIME COURSE OF SARS-CoV-2 BASED ON NEW HOSPITAL ADMISSIONS AND PCR TESTS date: 2020-08-17 words: 3678 flesch: 51 summary: FIGURES AND TABLES Figure 1 shows the relationship of the 7-day moving average of positive % PCR versus the daily number of tests with the 7-day moving average of the total number of daily PCR tests. Figure 2A exhibits the relationship between the 7-day moving average of positive %PCR and NHA. keywords: cases; new; nha; pcr; population; preprint cache: cord-333216-fdwmsnz9.txt plain text: cord-333216-fdwmsnz9.txt item: #828 of 973 id: cord-333261-knj2rrut author: Albright, Catherine J. title: An exercise in molecular epidemiology: Human rhinovirus prevalence and genetics date: 2011-11-11 words: 3417 flesch: 56 summary: HRV PCR products were sequenced to determine the genetic makeup of each field isolate. The average symptom, sleep, and stress scores were compared between HRV positive and HRV negative subjects and between reported sick and healthy subjects (Figs. 4a-4c) . keywords: hrv; pcr; rna; samples; stress; students; subjects; viruses cache: cord-333261-knj2rrut.txt plain text: cord-333261-knj2rrut.txt item: #829 of 973 id: cord-333413-8buawes0 author: Liebing, J. title: Health status of free-ranging ring-necked pheasant chicks (Phasianus colchicus) in North-Western Germany date: 2020-06-16 words: 5556 flesch: 47 summary: Based on these findings, our study focused on pheasant chicks up to eleven weeks of age. Previous studies on pheasants indicated that the most sensitive age class for infectious diseases was pheasant chicks, possibly due to a higher susceptibility keywords: ac1; ac2; ac3; age; animals; birds; chicks; germany; inflammation; mycoplasma; pcr; pheasant; population; samples; virus cache: cord-333413-8buawes0.txt plain text: cord-333413-8buawes0.txt item: #830 of 973 id: cord-333453-v3gap8kj author: Dima, Mirabela title: First neonates with severe acute respiratory syndrome coronavirus 2 infection in Romania: Three case reports date: 2020-08-14 words: 3022 flesch: 44 summary: A novel coronavirus from patients with pneumonia in China Prevalence of comorbidities and its effects in patients infected with SARS-CoV-2: a systematic review and metaanalysis SARS-CoV-2 infection in children Epidemiology of COVID-19 among children in China Kawasaki-like disease: emerging complication during the COVID-19 pandemic A case report of neonatal acute respiratory failure due to SARS-CoV-2 Systematic review of COVID-19 in children shows milder cases and a better prognosis than adults First case of neonate infected with novel coronavirus pneumonia in China National Institute of Public Health Neonatal early-onset infection with SARS-CoV-2 in 33 neonates born to mothers with COVID-19 in Vertical transmission of coronavirus disease 19 (COVID-19) from infected pregnant mothers to neonates: a review Severe COVID-19 during pregnancy and possible vertical transmission Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia Detection of SARS-CoV-2 in human breastmilk Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target Towards definition, clinical and laboratory criteria, and a scoring system for disseminated intravascular coagulation Flowchart showing the reverse transcription polymerase chain reaction test results of the newborns and their mothers Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases Clinical characteristics of fatal and recovered cases of coronavirus disease 2019 (COVID-19) in Wuhan, China: a retrospective study Venous and arterial thromboembolic complications in COVID-19 patients admitted to an academic hospital in COVID-19 and thrombotic or thromboembolic disease: implications for prevention, antithrombotic therapy, and follow-up Epidemiology and prevention of neonatal candidiasis: fluconazole for all neonates? [9] In Romania, at the moment the official national registry for COVID-19 cases states that the group age 0 to 9 years accounts for approximately 2.5% of the cases. keywords: candidiasis; cases; cov-2; covid-19; patients; sars cache: cord-333453-v3gap8kj.txt plain text: cord-333453-v3gap8kj.txt item: #831 of 973 id: cord-333524-a6p6ma8r author: Khan, Pavana title: Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date: 2020-09-23 words: 8847 flesch: 42 summary: Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV Virus An Ultrasensitive, Rapid, and Portable Coronavirus SARS-CoV SARS-CoV-2 Detection with CRISPR Diagnostics CDetection: CRISPR-Cas12b-Based DNA Detection with Sub-Attomolar Sensitivity and Single-Base Specificity Development and Evaluation of Recombinase-Aided Amplification Assays Incorporating Competitive Internal Controls for Detection of Human Adenovirus Serotypes 3 and 7 Direct Observation of DNA Target Searching and Cleavage by CRISPR-Cas12a SHERLOCK: Nucleic Acid Detection with CRISPR Nucleases Pointof-Care Testing for COVID-19 Using SHERLOCK. CRISPR-based detection uses both primer-specific amplification and guide RNA directed detection, thus increasing sequence specificity in two different ways. keywords: amplification; cov-2; crispr; detection; dna; isothermal; lamp; nucleic; pcr; polymerase; primers; reaction; rna; rpa; sars; sequence; use cache: cord-333524-a6p6ma8r.txt plain text: cord-333524-a6p6ma8r.txt item: #832 of 973 id: cord-333805-xmqs2ax7 author: Romoli, Michele title: A systematic review of neurological manifestations of SARS‐CoV‐2 infection: the devil is hidden in the details date: 2020-06-05 words: 4032 flesch: 41 summary: They found that COVID-19 patients were significantly younger (81%) and a high rate of smell (45%) and taste disorders (90.%). A multicentre retrospective study evaluated the occurrence of seizures in COVID-19 patients [19] . keywords: case; covid-19; csf; disease; infection; patients; pcr; sars; study cache: cord-333805-xmqs2ax7.txt plain text: cord-333805-xmqs2ax7.txt item: #833 of 973 id: cord-334090-66d8c75g author: Seger, Waleed title: Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015 date: 2016-02-18 words: 3624 flesch: 49 summary: Molecular detection of infectious bronchitis virus and it is relation with avian influenza virus (H9) and Mycoplasma gallisepticum from different geographical regions in Iraq Molecular detection of infectious bronchitis and avian metapneumoviruses in Oman backyard poultry Molecular detection of infectious bronchitis and avian metapneumoviruses in Oman backyard poultry Circulation of QX-like infectious bronchitis virus in the Middle East Completion of the sequence of the genome of the coronavirus avian infectious bronchitis virus Detection of the Chinese genotype of infectious bronchitis virus (QX-type) in Iran Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens Coronaviruses in poultry and other birds Variation in the spike protein of the 793/B type of infectious bronchitis virus, in the field and during alternate passage in chickens and embryonated eggs Factors influencing the outcome of infectious bronchitis vaccination and challenge experiments Analysis of S1 gene of avian infectious bronchitis virus isolated in southern China during Genotypes of infectious bronchitis viruses circulating in the Middle East between Turkey coronavirus is more closely related to avian infectious bronchitis virus than to mammalian coronaviruses: a review Phylogenetic study of Iranian infectious bronchitis virus isolates during 2010-2011 using glycoprotein S1 gene Review of infectious bronchitis virus around the world Efficacy of live infectious bronchitis vaccines against a novel European genotype, Italy 02 Development and validation of RT-PCR tests for the detection and S1 genotyping of infectious bronchitis virus and other closely related gammacoronaviruses within clinical samples Presence of IS/1494/06 genotype-related infectious bronchitis virus in breeder and broiler flocks in Turkey Evolutionary and bioinformatics analysis of the spike glycoprotein gene of H120 vaccine strain protectotype of infectious bronchitis virus from India Fenner's veterinary virology Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East Infectious Bronchitis Virus: a major cause of respiratory disease outbreaks in chickens in Ghana Identification of a novel nephropathogenic infectious bronchitis virus in Israel Complete genome sequences of two Chinese virulent avian coronavirus infectious bronchitis virus variants Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand Investigation and molecular characterization of avian infectious bronchitis virus in suspected broiler farms in Slemani Governorate. key: cord-334090-66d8c75g authors: Seger, Waleed; GhalyanchiLangeroudi, Arash; Karimi, Vahid; Madadgar, Omid; Marandi, Mehdi Vasfi; Hashemzadeh, Masoud title: Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015 date: 2016-02-18 journal: Arch Virol DOI: 10.1007/s00705-016-2790-2 sha: doc_id: 334090 cord_uid: 66d8c75g Infectious bronchitis virus (IBV) is one of the most critical pathogens in the poultry industry, causing serious economic losses in all countries including Iraq. keywords: bronchitis; ibv; iraq; like; pcr; strains; study; virus cache: cord-334090-66d8c75g.txt plain text: cord-334090-66d8c75g.txt item: #834 of 973 id: cord-334688-0i1pu8wc author: Martos Pérez, F. title: Comorbidity and prognostic factors on admission in a COVID-19 cohort of a general hospital date: 2020-08-19 words: 3447 flesch: 50 summary: Caused by SARS-CoV-2: A Prospective Cohort Study Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan ACP risk grade: a simple mortality index for patients with confirmed or suspected severe acute respiratory syndrome coronavirus 2 disease (COVID-19) during the early stage of outbreak in Wuhan Development and external validation of a prognostic multivariable model on admission for hospitalized patients with Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. Informe sobre el reporte de casos de COVID-19 Enfermedad por el coronavirus (COVID-19) Gobierno de España; 2020 abr Prediction models for diagnosis and prognosis of covid-19 infection: systematic review and critical appraisal Prediction of criticality in patients with severe Covid-19 infection using three clinical features: a machine learning-based prognostic model with clinical data in Wuhan Association of radiologic findings with mortality of patients infected with 2019 novel coronavirus in Wuhan Predicting COVID-19 malignant progression with AI techniques Predictors of Mortality for Patients with COVID-19 Pneumonia keywords: cov-2; covid-19; hospital; mean; mortality; patients; sars; study cache: cord-334688-0i1pu8wc.txt plain text: cord-334688-0i1pu8wc.txt item: #835 of 973 id: cord-335085-7pxkhgbq author: Dessau, R. B. title: Coronaviruses in spinal fluid of patients with acute monosymptomatic optic neuritis date: 2009-01-29 words: 2147 flesch: 57 summary: The CSF from patients with MS and controls with other neurological disease were analyzed for the presence of human coronaviral RNA sequences. key: cord-335085-7pxkhgbq authors: Dessau, R. B.; Lisby, G.; Frederiksen, J. L. title: Coronaviruses in spinal fluid of patients with acute monosymptomatic optic neuritis date: 2009-01-29 journal: Acta Neurol Scand DOI: 10.1111/j.1600-0404.1999.tb01043.x sha: doc_id: 335085 cord_uid: 7pxkhgbq Acute monosymptomatic optic neuritis (AMON) may be an initial symptom of multiple sclerosis (MS). keywords: amon; controls; hcv; patients; pcr; primers cache: cord-335085-7pxkhgbq.txt plain text: cord-335085-7pxkhgbq.txt item: #836 of 973 id: cord-335323-p7cv79ig author: DeSerres, Joshua J. title: Best Practice Guidelines for the Management of Acute Craniomaxillofacial Trauma During the COVID-19 Pandemic date: 2020-05-11 words: 4208 flesch: 37 summary: For this reason, we recommend secondary correction of malunited fractures in COVID-19 positive patients for those deformities that are more easily corrected (eg, most zygoma fractures, Lefort I fractures). This has been created to ensure continued care for CMF trauma patients while attempting to minimize risk of exposure and transmission to surgeons and other healthcare providers. keywords: cmf; covid-19; disease; pandemic; patients; pcr; procedures; risk; trauma cache: cord-335323-p7cv79ig.txt plain text: cord-335323-p7cv79ig.txt item: #837 of 973 id: cord-335359-4rcj75tc author: Jia, Bei title: Evaluation of a PCR-electrospray ionization mass spectrometry platform for detection and identification of fungal pathogens directly from prospectively collected bronchoalveolar lavage specimens date: 2020-01-15 words: 5130 flesch: 33 summary: Aspergillus was detected in 35 BAL samples by culture and/or PCR/ ESI-MS, 20 of which were considered to be related to lung infection by clinical context including underlying conditions, clinical features, and lung CT findings (Fig. 3) . Eighteen of them were detected by PCR/ ESI-MS; of which fifteen were verified by culture, and of which ten matched culture-based identification at the species level. keywords: assay; culture; detection; esi; fungal; fungi; patients; pcr; specimens cache: cord-335359-4rcj75tc.txt plain text: cord-335359-4rcj75tc.txt item: #838 of 973 id: cord-335393-4buooi2d author: Xiang, Yangxi title: Comparative transcriptome analysis reveals the role of p53 signalling pathway during red‐spotted grouper nervous necrosis virus infection in Lateolabrax japonicus brain cells date: 2019-01-18 words: 3895 flesch: 37 summary: In addition, significantly higher level of caspase 3 activities was observed in Ljp53 overexpressing cells post-RGNNV infection. Many aquatic species have been sequenced to study pathogenic processes during virus infection, including mandarin , orange-spotted grouper (Huang et al., 2011) , Pacific white shrimp (Zeng et al., 2013) and rainbow trout (Aquilino, Castro, Fischer, & Tafalla, 2014) . keywords: cells; expression; infection; ljb; ljp53; perch; rgnnv; sea; virus cache: cord-335393-4buooi2d.txt plain text: cord-335393-4buooi2d.txt item: #839 of 973 id: cord-335459-tq4fwigw author: Chen, Hui Juan title: Early chest CT features of patients with 2019 novel coronavirus (COVID-19) pneumonia: relationship to diagnosis and prognosis date: 2020-06-09 words: 2804 flesch: 58 summary: Whether a given treatment is beneficial could also be assessed with chest CT. 33 (97%) normal, 0 decreased, 1 (3%) increased Red blood cell count female (normal range, 115-150 g/L) 29 (85%) normal, 5 (15%) decreased, 0 increased Hematocrit female (normal range, 0.35-0.45) 27 (79%) normal, 6 (18%) decreased, 1 (3%) increased 82-100 fL) 32 (94%) normal, 2 (6%) decreased, 0 increased Mean corpuscular hemoglobin (normal range, 27-34 pg) 32 (94%) normal, 2 (6%) decreased, 0 increased Mean corpuscular hemoglobin concentration (MCHC) (normal range, 316-354 g/L) 32 (94%) normal, 2 (6%) decreased, 0 increased Red blood cell volume distribution width RDW-CV (normal range 25-70 mg/L) 12 (43%) normal, 16 (57%) decreased, 0 increased C-reactive protein (normal range, 0.068-8.2 mg/L) 8 (24%) normal, 0 decreased Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases Sensitivity of chest CT for COVID-19: comparison to RT-PCR Diagnostic performance of CT and reverse transcriptase-polymerase chain reaction for coronavirus disease 2019: keywords: covid-19; lesions; patients; pcr cache: cord-335459-tq4fwigw.txt plain text: cord-335459-tq4fwigw.txt item: #840 of 973 id: cord-335784-v7nbck0n author: Barak, N. title: Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests date: 2020-10-20 words: 3151 flesch: 43 summary: One promising solution is the application of sample pooling or group testing, a well-developed field in mathematics that allows the identification of carriers in a population of N using a number of tests that is smaller than N. Group testing can alleviate the supply-chain blocks and cut costs while increasing testing throughput. We and others, have recently described the validation and early implementation of sample pooling for SARS-CoV-2 detection (2, [6] [7] [8] [9] keywords: cov-2; medrxiv; pooling; preprint; samples; sars cache: cord-335784-v7nbck0n.txt plain text: cord-335784-v7nbck0n.txt item: #841 of 973 id: cord-336453-cbq0ui4p author: Machitori, Akihiro title: Computed tomography surveillance helps tracking COVID-19 outbreak date: 2020-08-07 words: 3807 flesch: 48 summary: We call the program 'Computed Tomography Imaging Surveillance of Viral Pneumonia,' (hereinafter referred to as CT surveillance) as it is designed to identify suspected or confirmed COVID-19 carriers with CT findings that are similar to those of COVID-19 pneumonia. We also analyzed CT findings, age distribution, gender differences, and clinical diagnoses obtained by CT surveillance. keywords: covid-19; findings; number; patients; pcr; surveillance cache: cord-336453-cbq0ui4p.txt plain text: cord-336453-cbq0ui4p.txt item: #842 of 973 id: cord-336636-xgfw21hk author: Spezia, Pietro Giorgio title: Redondovirus DNA in human respiratory samples date: 2020-08-15 words: 1893 flesch: 39 summary: Further defining the human virome using NGS: identification of Redondoviridae Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample Consensus statement: virus taxonomy in the age of metagenomics Genomoviridae: a new family of widespread single-stranded DNA viruses Smacoviridae: a new family of animal-associated single-stranded DNA viruses Molecular properties, biology, and clinical implications of TT virus, a recently identified widespread infectious agent of humans Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria A new superfamily of putative NTP-binding domains encoded by genomes of a small DNA and RNA viruses Torquetenovirus: the human virome from bench to bedside A novel rolling circle amplification assay to detect members of the family Anelloviridae in pigs and humans The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin Human bocavirus and paediatric infections Respiratory viruses other than influenza virus: impact and therapeutic advances The aminoacidic (A) and nt (B) trees based on a 582-bp segment from the capsid gene of the viral genome was obtained by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using Jones-Thornton-Taylor (JTT) and Maximum Composite Likelihood (MCL) models, respectively. The finding might indicate that, similar to other respiratory viruses [18, 19] , ReDoV may not remain restricted to the respiratory tract. keywords: dna; patients; redov; samples; virus; viruses cache: cord-336636-xgfw21hk.txt plain text: cord-336636-xgfw21hk.txt item: #843 of 973 id: cord-336639-jaue41mv author: Simons, Fermin A. title: A mRNA PCR for the diagnosis of feline infectious peritonitis date: 2004-12-21 words: 3046 flesch: 48 summary: Proteins of plasma and ascitic fluid Detection of feline coronaviruses by culture and reverse transcriptase-polymerase chain reaction of blood samples from healthy cats and cats with clinical feline infectious peritonitis Detection of feline coronavirus RNA in feces, tissues, and body fluids of naturally infected cats by reverse transcriptase PCR Elimination of feline coronavirus infection from a large experimental specific pathogen-free catbreeding colony by serologic testing and isolation The prevalence of type I and II feline coronavirus infections in cats Some important disorders of cats The virology and pathogenesis of felineinfectious peritonitis Sequence analysis of the porcine transmissible gastroenteritis coronavirus nucleocapsid protein gene Histopathological alterations of lymphatic tissues in cats without feline infectious peritonitis after long-term exposure to FIP virus The molecular biology of coronaviruses Isolation of Feline Coronaviruses from two cats with divers disease manifestations High viral loads despite absence of clinical and pathological findings in cats experimentally infected with feline coronavirus (FCoV) type I and in naturally FCoV-infected cats Feline infectious peritonitis: Isolation of a coronavirus Feline Infectious Peritonitis (FIP) virus; propagation in suckling rat and hamster brain Virologic and immunologic aspects of feline infectious peritonitis virus infection Infection studies in kittens, using feline infectious peritonitis virus propagated in cell culture An enteric coronavirus infection of cats and its relationship to feline infectious peritonitis Experimental studies with three new strains of feline infectious peritonitis virus: FIPV-UCD2, FIPV-UCD3, and FIPV-UCD4. Although the percentage of PCR-positive healthy animals is much lower when compared to FIP cats, a positive PCR result alone does not allow a definite diagnosis Gunn-Moore et al., 1998 ). keywords: blood; cats; fcov; feline; fip; pcr cache: cord-336639-jaue41mv.txt plain text: cord-336639-jaue41mv.txt item: #844 of 973 id: cord-336671-vfq5ft08 author: Ai, Jing-Wen title: Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned date: 2020-03-16 words: 1884 flesch: 46 summary: Recent advances in the detection of respiratory virus infection in humans A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster A pneumonia outbreak associated with a new coronavirus of probable bat origin A new coronavirus associated with human respiratory disease in China RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis Comparison of the filmarray respiratory panel and prodesse realtime PCR assays for detection of respiratory pathogens However, these methods were not able to detect novel pathogens as in the case of Hubei Province. keywords: crispr; novel; pcr; pneumonia; sars cache: cord-336671-vfq5ft08.txt plain text: cord-336671-vfq5ft08.txt item: #845 of 973 id: cord-336975-28mtmw2z author: Sadeghi, Christine D title: Twelve years' detection of respiratory viruses by immunofluorescence in hospitalised children: impact of the introduction of a new respiratory picornavirus assay date: 2011-02-07 words: 3033 flesch: 35 summary: multiplex PCR for the detection of respiratory picornavirus infections in children Epidemiological and clinical study of viral respiratory tract infections in children from Italy Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Use of monoclonal antibodies for rapid diagnosis of respiratory viruses in a community hospital Viral pathogens of acute lower respiratory tract infection in China Rapid detection of respiratory picornaviruses in nasopharyngeal aspirates by immunofluorescence assay Respiratory picornaviruses and respiratory syncytial virus as causative agents of acute expiratory wheezing in children Ten years' experience with year-round active surveillance of up to 19 respiratory pathogens in children Epidemiology of viral infections and evaluation of the potential benefit of OM-85 BV on the virologic status of children attending day-care centers Human rhinoviruses: the cold wars resume Rhinovirus associated with severe lower respiratory tract infections in children Human picornavirus and coronavirus RNA in nasopharynx of children without concurrent respiratory symptoms Frequency of detection of picornaviruses and seven other respiratory pathogens in infants Single versus dual respiratory virus infections in hospitalized infants: impact on clinical course of disease and interferon-gamma response Respiratory syncytial virus, human bocavirus and rhinovirus bronchiolitis in infants Two-year periodicity of respiratory syncytial virus epidemics in Switzerland Monto AS: Epidemiology of influenza Biennial spring activity of human metapneumovirus in Austria Human metapneumovirus infections-biannual epidemics and clinical findings in children in the region of Basel, Switzerland Epidemiologic characteristics and seasonal distribution of human metapneumovirus infections in five epidemic seasons in Prospective study of human metapneumovirus detection in clinical samples by use of light diagnostics direct immunofluorescence reagent and real-time PCR We gratefully acknowledge the technical support of the staff of our Virology Laboratory. key: cord-336975-28mtmw2z authors: Sadeghi, Christine D; Aebi, Christoph; Gorgievski-Hrisoho, Meri; Mühlemann, Kathrin; Barbani, Maria Teresa title: Twelve years' detection of respiratory viruses by immunofluorescence in hospitalised children: impact of the introduction of a new respiratory picornavirus assay date: 2011-02-07 journal: BMC Infect Dis DOI: 10.1186/1471-2334-11-41 sha: doc_id: 336975 cord_uid: 28mtmw2z BACKGROUND: Direct immunofluorescence assays (DFA) are a rapid and inexpensive method for the detection of respiratory viruses and may therefore be used for surveillance. keywords: children; detection; dfa; hmpv; pcr; picornaviruses cache: cord-336975-28mtmw2z.txt plain text: cord-336975-28mtmw2z.txt item: #846 of 973 id: cord-337003-7ygcfzii author: Mehrbod, Parvaneh title: Association of IFITM3 rs12252 polymorphisms, BMI, diabetes, and hypercholesterolemia with mild flu in an Iranian population date: 2017-11-09 words: 4429 flesch: 44 summary: Population stratification is related to situations when cases and controls are of different ethnic backgrounds with different genetic compositions, and has been noted as the most important type of the bias in genetic association studies. The mean BMI value was slightly higher among mild flu patients rather than in controls (P value: 0.034). keywords: allele; association; diabetes; flu; ifitm3; influenza; rs12252; study; susceptibility; virus cache: cord-337003-7ygcfzii.txt plain text: cord-337003-7ygcfzii.txt item: #847 of 973 id: cord-337096-ulc7mnwb author: Okazawa, Mitsushi title: Japanese tactics for suppressing COVID-19 spread date: 2020-07-14 words: 952 flesch: 48 summary: During the spread of infection, the effective reproduction number Rt, which is the average number of subjects who become infected by infectious subjects, was calculated using daily data. Rt was larger than 1 from mid-March to the end of March, indicating that infectious subjects increased toward a peak, as shown in Figure 2 . keywords: patients; pcr; spread cache: cord-337096-ulc7mnwb.txt plain text: cord-337096-ulc7mnwb.txt item: #848 of 973 id: cord-337198-4sors3bg author: Clementi, Nicola title: Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-SARS-CoV-2 Effects in vitro date: 2020-07-10 words: 4273 flesch: 46 summary: For secondary (P2) virus stock, Vero E6 cells seeded into 25 cm 2 tissue culture flasks were infected with 0.5 mL of P1 stored aliquot, and infected cells and supernatant were collected 48 hpi and stored at −80 • C. For tertiary (P3) virus stock, Vero E6 cells seeded into 75 cm 2 tissue culture flasks were infected with 1.5 mL of P2 stored aliquot and prepared as above described. A clinical isolate hCoV-19/Italy/UniSR1/2020 (GISAID accession ID: EPI_ISL_413489) was isolated and propagated in Vero E6 cells, and viral titer was determined by 50% tissue culture infective dose (TCID 50 ) and plaque assay for confirming the obtained titer. keywords: adsorption; cells; cpe; hcq; infection; pcr; sars; virus cache: cord-337198-4sors3bg.txt plain text: cord-337198-4sors3bg.txt item: #849 of 973 id: cord-337206-jo29nx9b author: Lee, Jong-Han title: Identification of Adenovirus, Influenza Virus, Parainfluenza Virus, and Respiratory Syncytial Virus by Two Kinds of Multiplex Polymerase Chain Reaction (PCR) and a Shell Vial Culture in Pediatric Patients with Viral Pneumonia date: 2010-09-01 words: 2955 flesch: 45 summary: Viral etiology of acute respiratory infections with cough in infancy: a community-based birth cohort study Detection of respiratory syncytial virus A and B and parainfluenzavirus 3 sequences in respiratory tracts of infants by a single PCR with primers targeted to the L-polymerase gene and differential hybridization Diagnosis of viral respiratory tract infections in children by using a reverse transcription-PCR panel Respiratory virus infections after stem cell transplantation: a prospective study from the Infectious Diseases Working Party of the European Group for Blood and Marrow Transplantation Community respiratory virus infections in immunocompromised patients with cancer Effectiveness of neuraminidase inhibitors in treatment and prevention of influenza A and B: systematic review and metaanalyses of randomised controlled trials Clinical potential of the acyclic nucleoside phosphonates cidofovir, adefovir, and tenofovir in treatment of DNA virus and retrovirus infections Enterovirus infections A sensitive, specific, and cost-effective multiplex reverse transcriptase-PCR assay for the detection of seven common respiratory viruses in respiratory samples Rapid identification of nine microorganisms causing acute respiratory tract infections by single-tube multiplex reverse transcription-PCR: feasibility study Evaluation of the Hexaplex assay for detection of respiratory viruses in children Comparison of a multiplex reverse transcription-PCRenzyme hybridization assay with conventional viral culture and immunofluorescence techniques for the detection of seven viral respiratory pathogens Rapid simultaneous diagnosis of infections with respiratory syncytial viruses A and B, influenza viruses A and B, and human parainfluenza virus types 1, 2, and 3 by multiplex quantitative reverse transcription-polymerase chain reaction-enzyme hybridization assay (Hexaplex) [10] [11] [12] The virus culture is still considered the gold standard for respiratory virus detection, but it has limitations in turnaround time, specimen transport, and storage conditions in maintaining the infectivity of the virus. keywords: culture; kit; pcr; samples; virus cache: cord-337206-jo29nx9b.txt plain text: cord-337206-jo29nx9b.txt item: #850 of 973 id: cord-337396-g69bb60d author: Ogawa, Yoshihiko title: Assessing the effects of exposure to a SARS-CoV-2 re-positive patient in healthcare personnel date: 2020-11-07 words: 1789 flesch: 48 summary: In conclusion, no HCP were infected by contact with and aerosol exposures to SARS-CoV-2 re-positive patients in our hospital. Thus, the hypothesis that a patient with re-positive PCR is not infectious is plausible. keywords: covid-19; hcp; pcr; results; sars cache: cord-337396-g69bb60d.txt plain text: cord-337396-g69bb60d.txt item: #851 of 973 id: cord-337406-25285u24 author: Wu, Xiaodong title: Incidence of Respiratory Viral Infections Detected by PCR and Real-Time PCR in Adult Patients with Community-Acquired Pneumonia: A Meta-Analysis date: 2015-03-12 words: 3534 flesch: 35 summary: A Meta-Analysis date: 2015-03-12 journal: Respiration DOI: 10.1159/000369561 sha: doc_id: 337406 cord_uid: 25285u24 BACKGROUND: With the development of more rapid and sensitive detection methods based on PCR techniques, the contributions of respiratory viral infections to community-acquired pneumonia (CAP) in adult patients are being more and more recognized. Yet, up to now, there has been a lack of synthetic data that clearly demonstrates the incidence of respiratory viral infections in adult patients with CAP. keywords: cap; community; incidence; infections; patients; pneumonia cache: cord-337406-25285u24.txt plain text: cord-337406-25285u24.txt item: #852 of 973 id: cord-337636-3yc0ribg author: Morehouse, Zachary P. title: A novel two-step, direct-to-PCR method for virus detection off swabs using human coronavirus 229E date: 2020-08-25 words: 2981 flesch: 43 summary: Herein, we are proposing a novel method for viral pathogen detection off swabs as an improvement or alternative to the current PCR based assays commonly used for viral detection This novel two-step, directto-PCR method for viral detection off swabs has shown a lower limit of reliable detection at 1.2 × 10 3 viral copies/mL with 96.30% sensitivity in vitro when screening for HcoV-229E. Herein, we have demonstrated the success of this methodology in vitro and propose it as a novel approach to viral detection that allows for decrease run time in comparison to traditional PCR based viral detection assay protocols, as well as a reduction in the materials needed for successful viral detection. keywords: copies; detection; methodology; pcr; swabs; virus cache: cord-337636-3yc0ribg.txt plain text: cord-337636-3yc0ribg.txt item: #853 of 973 id: cord-337701-56tmg38b author: Xiao, Yan title: Comparison of three TaqMan Real-Time Reverse Transcription-PCR assays in detecting SARS-CoV-2 date: 2020-07-06 words: 2124 flesch: 41 summary: For the ORF 1b gene assay, the CVs of mean Ct 145 values were 0.26%-4.45%, 0.29%-1.76%, 0.71%-6.52% in intra-assay, and 146 2.17%-5.12%, 0.30-1.57%, 2.63%-4.34% in inter-assay of IPBCAMS assays, WHO 147 assays, and CCDC assays, respectively. A LOD of 10 genomic copies per 127 reaction was observed for both the N gene assay and the ORF 1b gene assay of all the 128 three qRT-PCR assays, although the Ct values for N gene assay of WHO assays and 129 ORF 1b gene assay of CCDC assays were higher than 35 cycles (Table 2) . keywords: assays; gene; pcr cache: cord-337701-56tmg38b.txt plain text: cord-337701-56tmg38b.txt item: #854 of 973 id: cord-338205-sy91rnse author: Li, Chenxi title: Laboratory Diagnosis of Coronavirus Disease-2019 (COVID-19) date: 2020-07-02 words: 7542 flesch: 45 summary: A data-driven analysis in the early phase of the outbreak High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2 World Health Organization, Consensus document on theepidemiology of severe acuterespiratory syndrome (SARS) Virology, Epidemiology, Pathogenesis, and Control of COVID-19 Aerosol and Surface Distribution of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospital Wards Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1 Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity First Case of 2019 Novel Coronavirus in the United States World Health Organization, Laboratory testing for 2019 novel coronavirus (2019-nCoV) in suspected human cases A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster Identification of Coronavirus Isolated from a Patient in Korea with COVID-19 Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients Transmission of 2019-nCoV Infection from an Asymptomatic Contact in Germany A new coronavirus associated with human respiratory disease in China Clinical Characteristics of Coronavirus Disease 2019 in China SARS-CoV-2 can be detected in urine, blood, anal swabs, and oropharyngeal swabs specimens Consistent detection of 2019 novel coronavirus in saliva, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study Evaluating the use of posterior oropharyngeal saliva in a point-of-care assay for the detection of SARS-CoV-2 Duration of viral detection in throat and rectum of a patient with COVID-19 Ophthalmologic evidence against the interpersonal transmission of 2019 novel coronavirus through conjunctiva Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS-CoV-2 infection Guidelines for Laboratory Diagnosis of Coronavirus Disease 2019 (COVID-19) in Korea Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples World Health Organization, Coronavirus disease (COVID-19) technical guidance: There are currently 7 CoVs (including SARS-CoV-2) that can cause human respiratory diseases, but to date, only SARS-CoV, MERS-CoV, and SARS-CoV-2 have caused a large outbreak with high mortality. keywords: assay; coronavirus; cov-2; covid-19; detection; igg; patients; pcr; protein; samples; sars; sensitivity; tests cache: cord-338205-sy91rnse.txt plain text: cord-338205-sy91rnse.txt item: #855 of 973 id: cord-338582-o976nab9 author: Dahlhausen, Bob title: Future Veterinary Diagnostics date: 2010-09-19 words: 9203 flesch: 30 summary: Antibodies in an immunoassay format have been widely used and are well established as highly sensitive tools for disease detection. 26, 27 Researchers led by Joseph DeRisi of the University of California at San Francisco have combined genome databases of sequenced viruses with DNA microarray technology. keywords: amplification; analysis; cancer; detection; diagnostic; disease; dna; expression; gene; microarrays; nucleic; pcr; protein; rna; sequence; target; technology; testing; viral; viruses cache: cord-338582-o976nab9.txt plain text: cord-338582-o976nab9.txt item: #856 of 973 id: cord-338607-22f04uqe author: Verbeek, A. title: Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes date: 1991 words: 4132 flesch: 41 summary: In conclusion, BCV or TCV probes may be valuable in molecular hybridization for routine clinical diagnosis of either virus but may be problematic when these two viruses have to be distinguished. Double-stranded probes, synthesized in PCR with 1/3 of the dCTP being radiolabelled were efficient in BCV detection but resulted in strong background after only 8 h of autoradiography keywords: bcv; detection; fig; hybridization; pcr; probes; samples; signals; specific; tcv; virus cache: cord-338607-22f04uqe.txt plain text: cord-338607-22f04uqe.txt item: #857 of 973 id: cord-338641-s006a7m0 author: Black, W. D. title: Reverse transcriptase-polymerase chain reaction for the detection equine rhinitis B viruses and cell culture isolation of the virus date: 2006-08-24 words: 4049 flesch: 48 summary: Other cells used for virus culture, including virus isolation attempts, were Vero cells (passage 130-200), RK13 cells (passage 195-250) and equine foetal kidney (EFK) cells (passage 4). We especially thank Marianne Weiss, University of Berne, P. J. Timoney and W. H. McCollum, University of Kentucky, and Dorothy Holmes and Ed Dubovi, Cornell University, for providing virus isolates and culture history. keywords: cell; culture; equine; erbv; horses; pcr; samples; swab; virus cache: cord-338641-s006a7m0.txt plain text: cord-338641-s006a7m0.txt item: #858 of 973 id: cord-338899-qt17jhg0 author: Lakshmi, Vemu title: Clinical Features and Molecular Diagnosis of Chikungunya Fever from South India date: 2008-05-01 words: 3630 flesch: 45 summary: In the present study, the detection of CHIK virus RNA in 48.6% of samples by RT-PCR and in 55.4% of samples by RT-LAMP, as well as the detection of IgM antibodies in 21.5% of samples, confi med that the causative agent of this epidemic was CHIK virus. As is the case for most alphaviruses, detection of CHIK virus depends on isolation of the virus in blood specimens obtained from viremic patients or in infected tissue specimens obtained from blood-feeding arthropods, which are time-consuming. keywords: chik; chikungunya; fever; infection; lamp; patients; pcr; samples; time; virus cache: cord-338899-qt17jhg0.txt plain text: cord-338899-qt17jhg0.txt item: #859 of 973 id: cord-338942-q4neat3x author: Zhang, Haoqing title: LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification date: 2019-01-31 words: 5759 flesch: 38 summary: A modified visual loop-mediated isothermal amplification method for diagnosis and differentiation of main pathogens from Mycobacterium tuberculosis complex Colorimetric LAMP microfluidic chip for detecting three allergens: peanut, sesame and soybean Development of mitochondrial loop-mediated isothermal amplification for detection of the small liver fluke Opisthorchis viverrini (Opisthorchiidae; Trematoda Rapid detection of food-borne Listeria monocytogenes by real-time quantitative loop-mediated isothermal amplification Real time loop-mediated isothermal amplification using a portable fluorescence scanner for rapid and simple detection of Vibrio parahaemolyticus A CCD-based fluorescence imaging system for real-time loopmediated isothermal amplification-based rapid and sensitive detection of waterborne pathogens on microchips Microfluidic electrochemical assay for rapid detection and quantification of Escherichia coli Detection of roundup ready soybean by loop-mediated isothermal amplification combined with a lateral-flow dipstick Evaluation of reverse transcription loopmediated isothermal amplification in conjunction with ELISA-hybridization assay for molecular detection of Mycobacterium tuberculosis Loop-mediated isothermal amplification combined with colorimetric nanogold for detection of the microsporidian Enterocytozoon hepatopenaei in penaeid shrimp Ion sensing (EIS) real-time quantitative monitorization of isothermal DNA amplification A polycarbonate based surface plasmon resonance sensing cartridge for high sensitivity HBV loop-mediated isothermal amplification GMO detection using a bioluminescent real time reporter (BART) of loop mediated isothermal amplification (LAMP) suitable for field use On-chip LAMP-BART reaction for viral DNA real-time bioluminescence detection A novel HBV genotypes detecting system combined with microfluidic chip, loop-mediated isothermal amplification and GMR sensors Loop-mediated isothermal amplification (LAMP): recent progress in research and development A device for point-ofcare genetic testing using a smartphone Rapid isolation and detection of aquaculture pathogens in an integrated microfluidic system using loop-mediated isothermal amplification A microfluidic lab-on-a-disc integrated loop mediated isothermal amplification for foodborne pathogen detection Development of a high-throughput centrifugal loop-mediated isothermal amplification microdevice for multiplex foodborne pathogenic bacteria detection Identifying multiple bacterial pathogens by loop-mediated isothermal amplification on a rotate & react slipchip Development and evaluation of a loop-mediated isothermal amplification assay for the rapid detection of Staphylococcus aureus in food Development and application of a rapid and simple loopmediated isothermal amplification method for food-borne Salmonella detection Handheld device for real-time, quantitative, LAMP-based detection of Salmonella enterica using assimilating probes Loop-mediated isothermal amplification for Salmonella detection in food and feed: current applications and future directions A facile cascade signal amplification strategy using DNAzyme loop-mediated isothermal amplification for the ultrasensitive colorimetric detection of Salmonella Development and application of a loop-mediated isothermal amplification method on rapid detection Escherichia coli O157 strains from food samples Centrifugal loop-mediated isothermal amplification microdevice for rapid, multiplex and colorimetric foodborne pathogen detection Integrated glass microdevice for nucleic acid purification, loop-mediated isothermal amplification, and online detection Monte Carlo modelingbased digital loop-mediated isothermal amplification on a spiral chip for absolute quantification of nucleic acids This work was supported by the Foreign Experts Program of P.R. China (W099109). Isothermal amplification techniques require simple hardware and they are rather insensitive to polymerase inhibitors, making the amplification process robust. keywords: amplification; chip; detection; dna; fig; isothermal; lamp; loop; methods; pcr; sample; system; temperature; time cache: cord-338942-q4neat3x.txt plain text: cord-338942-q4neat3x.txt item: #860 of 973 id: cord-339278-9luefzyo author: Zayet, Souheil title: Contribution of anosmia and dysgeusia for diagnostic of COVID-19 in outpatients date: 2020-05-14 words: 2072 flesch: 55 summary: Amongst patients complaining of dysgeusia and anosmia, eleven patients were in G2 (PCR-negative) and 52 patients were in G1 (PCR-positive). More than 80% of patients with COVID-19 present with influenza-like illness (ILI) or mild pneumonia keywords: covid-19; patients; pcr; sars cache: cord-339278-9luefzyo.txt plain text: cord-339278-9luefzyo.txt item: #861 of 973 id: cord-339419-b6tr2zyx author: Lee, Thomas Ming-Hung title: DNA-based bioanalytical microsystems for handheld device applications date: 2006-01-18 words: 5432 flesch: 48 summary: After many years of tremendous research efforts in the area of lab-on-a-chip for DNA analysis, almost all individual analytical processes of sample preparation, target amplification, and target detection have reached a mature stage. For instance, Northrup et al. developed DNA amplification chips keywords: amplification; cell; detection; dna; gold; hybridization; pcr; probe; sample; sequence; silicon; surface; target cache: cord-339419-b6tr2zyx.txt plain text: cord-339419-b6tr2zyx.txt item: #862 of 973 id: cord-339456-82iks0xf author: Mikel, P. title: Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens date: 2015-02-25 words: 10037 flesch: 42 summary: Process control viruses can also be constructed artificially using technology for production of MS2 phage-like particles, which have many advantages in comparison with other used controls and are especially suited for controlling the detection and quantification of certain types of RNA viruses. The use of process control virus in RT-PCR and qRT-PCR detection of RNA viruses from clinical specimens is necessary, but so far there is no ISO/TS, which would describe the use of specific process control viruses. keywords: bacteriophage; coat; control; control viruses; detection; et al; ms2; ms2 phage; packaging; particles; pcr; phage; process; process control; protein; rna; system; virus; viruses cache: cord-339456-82iks0xf.txt plain text: cord-339456-82iks0xf.txt item: #863 of 973 id: cord-339656-u0cpklsv author: de Groot-Mijnes, Jolanda D.F. title: Identification of New Pathogens in the Intraocular Fluid of Patients With Uveitis date: 2010-11-30 words: 4020 flesch: 40 summary: Of the human parechovirus–positive patients, 1 was immunocompromised and had panuveitis. To determine infectious causes in patients with uveitis of unknown origin by intraocular fluids analysis. keywords: hsv; human; intraocular; patients; pcr; rubella; samples; uveitis; virus cache: cord-339656-u0cpklsv.txt plain text: cord-339656-u0cpklsv.txt item: #864 of 973 id: cord-339804-hktedla3 author: Papillard‐Marechal, Solesne title: Monitoring epidemic viral respiratory infections using one‐step real‐Time Triplex RT‐PCR targeting influenza A and B viruses and respiratory syncytial virus date: 2011-02-15 words: 3590 flesch: 40 summary: I. Periods of prevalence of H1N1 and H3N2 influenza A strains, their relative rates of isolation in different age groups, and detection of antigenic variants Comparison of real-time PCR assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children Quantification of hepatitis delta virus RNA in serum by consensus real-time PCR indicates different patterns of virological response to interferon therapy in chronically infected patients Rapid influenza antigen test for diagnosis of pandemic (H1N1) Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: A systematic review and meta-analysis The effect of influenza on hospitalizations, outpatient visits, and courses of antibiotics in children The underrecognized burden of influenza in young children Respiratory syncytial virus infection The impact of influenza epidemics on hospitalizations Effectiveness of reverse transcription-PCR, virus isolation, and enzyme-linked immunosorbent assay for diagnosis of influenza A virus infection in different age groups Increased detection of respiratory syncytial virus, influenza viruses, parainfluenza viruses, and adenoviruses with real-time PCR in samples from patients with respiratory symptoms Influenza surveillance in France Contribution of influenza and respiratory syncytial virus to community cases of influenza-like illness: An observational study Influenza viruses were detected by hemagglutination assay with guinea-pig erythrocytes. keywords: assay; infections; influenza; pcr; respiratory; rsv cache: cord-339804-hktedla3.txt plain text: cord-339804-hktedla3.txt item: #865 of 973 id: cord-339973-kj56zi59 author: Coleman, Kristen K. title: Bioaerosol Sampling for Respiratory Viruses in Singapore’s Mass Rapid Transit Network date: 2018-11-30 words: 4779 flesch: 40 summary: key: cord-339973-kj56zi59 authors: Coleman, Kristen K.; Nguyen, Tham T.; Yadana, Su; Hansen-Estruch, Christophe; Lindsley, William G.; Gray, Gregory C. title: Bioaerosol Sampling for Respiratory Viruses in Singapore’s Mass Rapid Transit Network date: 2018-11-30 journal: Sci Rep DOI: 10.1038/s41598-018-35896-1 sha: doc_id: 339973 cord_uid: kj56zi59 As a leading global city with a high population density, Singapore is at risk for the introduction of novel biological threats. In an effort to enhance respiratory virus surveillance in Singapore, our team conducted a pilot study employing a noninvasive bioaerosol sampling method to detect respiratory viruses in Singapore’s Mass Rapid Transit (MRT) network. keywords: aerosol; bioaerosol; influenza; mrt; pcr; samples; sampling; singapore; study; time; virus; viruses cache: cord-339973-kj56zi59.txt plain text: cord-339973-kj56zi59.txt item: #866 of 973 id: cord-339976-tg2jkss7 author: Wang, Haibin title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date: 2004-07-01 words: 2582 flesch: 36 summary: RT-PCR was successfully used to detect SARS CoV in nasopharyngeal aspirates, nasopharyngeal swabs, throat swabs, and broncheoalveolar lavage of SARS patients (6, 7 ) . This finding provides evidence that lymphocytes are a target or reservoir for SARS CoV and that they are a better sample source than plasma for detecting SARS CoV. keywords: acute; cov; patients; pcr; plasma; sample; sars cache: cord-339976-tg2jkss7.txt plain text: cord-339976-tg2jkss7.txt item: #867 of 973 id: cord-339995-0pbknb32 author: Feng, Hao title: A case report of COVID-19 with false negative RT-PCR test: necessity of chest CT date: 2020-04-07 words: 974 flesch: 54 summary: On the basis of epidemiologic characteristics, clinical manifestations, chest CT images, and laboratory findings, the diagnosis of COVID-19 pneumonia was made. It is difficult to distinguish COVID-19 pneumonia from other viral pneumonia on CT findings alone; however, we emphasize the utility of chest CT to detect early change of COVID-19 in cases which RT-PCR tests show negative results. keywords: covid-19; pcr cache: cord-339995-0pbknb32.txt plain text: cord-339995-0pbknb32.txt item: #868 of 973 id: cord-340021-pj6fywwc author: Norooznezhad, Amir Hossein title: Primary Symptoms, Comorbidities, and Outcomes of 431 Hospitalized Patients with Confirmative RT-PCR Results for COVID-19 date: 2020-06-24 words: 1961 flesch: 43 summary: Thus, it seems that this study has added some new findings regarding a large number of confirmed COVID-19 patients in three age-groups by their symptoms. This analytical cross-sectional study was performed in Farabi and Imam-Reza hospitals as two designated centers for COVID-19 patients hospitalization by the Ministry of Health in Kermanshah (a western province), Iran. keywords: covid-19; patients; pcr cache: cord-340021-pj6fywwc.txt plain text: cord-340021-pj6fywwc.txt item: #869 of 973 id: cord-340046-kgbvld0y author: Houspie, Lieselot title: Exhaled breath condensate sampling is not a new method for detection of respiratory viruses date: 2011-03-04 words: 4082 flesch: 48 summary: key: cord-340046-kgbvld0y authors: Houspie, Lieselot; De Coster, Sarah; Keyaerts, Els; Narongsack, Phouthalack; De Roy, Rikka; Talboom, Ive; Sisk, Maura; Maes, Piet; Verbeeck, Jannick; Van Ranst, Marc title: Exhaled breath condensate sampling is not a new method for detection of respiratory viruses date: 2011-03-04 journal: Virol J DOI: 10.1186/1743-422x-8-98 sha: doc_id: 340046 cord_uid: kgbvld0y BACKGROUND: Exhaled breath condensate (EBC) sampling has been considered an inventive and novel method for the isolation of respiratory viruses. This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. keywords: collection; detection; ebc; pcr; samples; study; viruses; volunteers cache: cord-340046-kgbvld0y.txt plain text: cord-340046-kgbvld0y.txt item: #870 of 973 id: cord-340317-gwqy6u9x author: Dora, Amy V title: Using Serologic Testing to Assess the Effectiveness of Outbreak Control Efforts, Serial PCR Testing, and Cohorting of Positive SARS-CoV-2 Patients in a Skilled Nursing Facility date: 2020-08-28 words: 1600 flesch: 43 summary: To assess unrecognized SARS-CoV-2 exposure, we reviewed serologic testing in a cohort of SNF residents who had been serially tested for SARS-CoV-2 infection by nasopharyngeal swab RT-PCR following a COVID-19 outbreak at this SNF Despite numerous outbreaks, the performance of serologic testing for SARS-CoV-2 in residents of skilled nursing facilities (SNF) is not well described; its utility in epidemiologic sero-surveillance studies and outbreak reporting is under evaluation. keywords: pcr; testing cache: cord-340317-gwqy6u9x.txt plain text: cord-340317-gwqy6u9x.txt item: #871 of 973 id: cord-340336-u59l0taa author: Perchetti, Garrett A. title: Multiplexing primer/probe sets for detection of SARS-CoV-2 by qRT-PCR date: 2020-06-08 words: 1397 flesch: 41 summary: Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) - a CDC-based quantitative reverse transcriptase PCR reaction - and analyzed for agreement between the multiplexed assay. CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. keywords: assay; cov-2; pcr; sars cache: cord-340336-u59l0taa.txt plain text: cord-340336-u59l0taa.txt item: #872 of 973 id: cord-340481-i3qrxnpr author: Pozo, Francisco title: Aplicación de los métodos moleculares al diagnóstico y el estudio epidemiológico de las infecciones respiratorias causadas por virus date: 2008-07-31 words: 9089 flesch: 29 summary: Los iniciadores de reacción, por consiguiente, no son 2, sino un conjunto de especies moleculares diferentes, cuyo número dependerá de la cantidad de posiciones variables y de la variabilidad de éstas. La detección de infecciones en humanos causadas por virus gripales pertenecientes a subtipos distintos de los habituales (H5N1, H7N7, H7N3 y H9N2) ha favorecido en los últimos años el diseño y la comercialización de técnicas de subtipado de los virus gripales A, y especialmente de detección del subtipo H5N1, ya sea mediante PCR 6,7 , sistemas de detección basados en microarrays o biochips 8 , e incluso arrays de ADN en fase líquida 9 . keywords: arn; clinical; como; con; cov; de la; de los; del; detección; detection; diagnóstico; diferentes; en el; entre; estos; estudios; genes; genoma; han; human; infecciones; infección; ira; las; los; los virus; mediante; molecular; muy; más; métodos; para; parainfluenza; pcr; por; proteínas; que; real; secuenciación; son; también; tiempo; técnicas; una; viral; virus; viruses; vrsh; y la cache: cord-340481-i3qrxnpr.txt plain text: cord-340481-i3qrxnpr.txt item: #873 of 973 id: cord-340627-xyvzgkxl author: Ornaghi, Sara title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy date: 2020-09-15 words: 3810 flesch: 46 summary: Admission questionnaires may have limitations since they rely on honest answering. However, our detailed investigation of minor SARS-CoV-2 triage questionnaire in obstetric patients symptoms, such as loss of smell or taste, may also have played an important role [3, 29] . keywords: admission; cov-2; infection; patients; questionnaire; sars; women cache: cord-340627-xyvzgkxl.txt plain text: cord-340627-xyvzgkxl.txt item: #874 of 973 id: cord-340710-dmow5p7k author: Lagana, Stephen M. title: Hepatic pathology in patients dying of COVID-19: a series of 40 cases including clinical, histologic, and virologic data date: 2020-08-13 words: 4542 flesch: 45 summary: As the focus of this study is liver pathology, the lungs were considered only in the context of how the pulmonary findings may relate to liver injury. The role of immunosuppression and allograft recipient status on liver injury associated with COVID-19 will need further study. keywords: acute; cases; covid-19; hepatitis; injury; liver; patients; pcr; steatosis cache: cord-340710-dmow5p7k.txt plain text: cord-340710-dmow5p7k.txt item: #875 of 973 id: cord-340788-p02v46xu author: Zitek, Tony title: The Appropriate Use of Testing for COVID-19 date: 2020-04-13 words: 1602 flesch: 53 summary: Interestingly, some patients had positive tests, and then negative tests, and then positive tests again, all within the same hospitalization. West J Emerg Med DOI: 10.5811/westjem.2020.4.47370 sha: doc_id: 340788 cord_uid: p02v46xu Many public officials are calling for increased testing for the 2019 novel coronavirus disease (COVID-19), and some governments have taken extraordinary measures to increase the availability of testing. keywords: covid-19; pcr; testing cache: cord-340788-p02v46xu.txt plain text: cord-340788-p02v46xu.txt item: #876 of 973 id: cord-340883-zf8jbhdl author: He, Zhongping title: Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) date: 2007-03-27 words: 2894 flesch: 53 summary: There were 92 (33.9%) healthcare workers who acquired SARS, including 51 nurses, 30 physicians, 5 logistics staff, 3 pharmacists and 2 laboratory technicians (one of whom was believed to be infected after handling sputum and stool samples from SARS patients in a diagnostic laboratory). A total of 112 people were infected following exposure to SARS patients in the hospital setting, either as healthcare workers, patients or visitors, and another 62 cases were household contacts of known SARS cases. keywords: cov; days; pcr; samples; sars cache: cord-340883-zf8jbhdl.txt plain text: cord-340883-zf8jbhdl.txt item: #877 of 973 id: cord-341141-bgrgzfoo author: Hou, Peili title: Rapid detection of infectious bovine Rhinotracheitis virus using recombinase polymerase amplification assays date: 2017-12-13 words: 4699 flesch: 44 summary: Lane 1 to 9 were represented IBRV RPA reactions extracted from ten-fold serially diluted IBRV templates range from 5 × 10 6 to 5 × 10 −1 DNA copies per reaction. The amplified products in the IBRV LFD RPA reaction were also detected by subsequent agarose gel electrophoresis (Fig. 2b) . keywords: amplification; assay; bovine; detection; dna; ibrv; lfd; pcr; primers; reaction; rpa cache: cord-341141-bgrgzfoo.txt plain text: cord-341141-bgrgzfoo.txt item: #878 of 973 id: cord-341434-2xrdv92m author: Nowland, Megan H. title: Biology and Diseases of Rabbits date: 2015-07-10 words: 31614 flesch: 40 summary: Rabbits provided with objects (toys) spent significantly more time chewing than rabbits without toys (Poggiagliolmi et al., 2011) . that originated on cattle, mountain sheep, or rabbits Colonization of rabbits by Pasteurella multocida: serum IgG responses following intranasal challenge with serologically distinct isolates Identification and characterization of three Encephalitozoon cuniculi strains Treponema paraluis-cuniculi infection in a commercial rabbitry: epidemiology and serodiagnosis Atrophic rhinitis in New Zealand White rabbits infected with Pasteurella multocida Naturally acquired Pasteurella multocida infection in rabbits: immunological aspects Naturally acquired Pasteurella multocida infection in rabbits: clinicopathological aspects Hypervitaminosis A and reproductive disorders in rabbits Ferrets, Rabbits, and Rodents Production of recombinant human protein C in the milk of transgenic rabbits from the F3 generation Development of PCR protocols for specific identification of Clostridium spiroforme and detection of sas and sbs genes Vaccination against Eimeria magna coccidiosis using spray dispersion of precocious line oocysts in the nest box A quantitative polymerase chain reaction assay for detection and quantification of Lawsonia intracellularis Subclinical proliferative enteropathy in sentinel rabbits associated with Lawsonia intracellularis Assignment of the agent of Tyzzer's disease to Clostridium piliforme comb. keywords: age; allen et; animals; blood; cas et; cases; cells; chermette et; clostridium; coli; colony; complications; control; cuniculus; days; diagnosis; diarrhea; difficile; disease; eimeria; escherichia; et al; etiology; fox; human; infection; intestinal; intracellularis; isolates; laboratory; laboratory rabbits; lawsonia; lesions; liver; model; multocida; new; pasteurella; pathology; pcr; piliforme; prevention; rabbits; research; schoeb et; signs; skin; species; spiroforme; strains; studies; study; time; toxin; treatment; virus; white; zealand cache: cord-341434-2xrdv92m.txt plain text: cord-341434-2xrdv92m.txt item: #879 of 973 id: cord-342277-v6310fjh author: Carducci, A. title: Environmental survey to assess viral contamination of air and surfaces in hospital settings date: 2011-01-31 words: 3032 flesch: 39 summary: For virus detection, 1000 L of air were sampled on Rodac plates containing Tryptone Soy Agar (TSA). Although biomolecular methods for virus detection do not enable infectivity assessment, positive results indicate previous viral contamination. keywords: air; contamination; detection; samples; surfaces; ttv; virus; viruses cache: cord-342277-v6310fjh.txt plain text: cord-342277-v6310fjh.txt item: #880 of 973 id: cord-342344-jjnf4yje author: Mello, C. J. title: Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date: 2020-06-26 words: 3130 flesch: 45 summary: The coronavirus pandemic and aerosols: Does COVID-19 transmit via expiratory particles? Temporal dynamics in viral shedding and transmissibility of COVID-19 SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Detection of a novel human coronavirus by real-time reversetranscription polymerase chain reaction Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections Identification of a novel coronavirus in patients with severe acute respiratory syndrome A one step quantitative RT-PCR for detection of SARS coronavirus with an internal control for PCR inhibitors Talking the talk, but not walking the walk: RT-qPCR as a paradigm for the lack of reproducibility in molecular research How good is a PCR efficiency estimate: 56% linked molecules) between these sequences (Fig. 4b, Table 1) , similar to the level of linkage (58%) was detected in a control RNA sample that was not exposed to saliva (Fig. 4c, Table 1 ). . keywords: cov-2; droplets; license; positive; preprint; rna; sars; sequences cache: cord-342344-jjnf4yje.txt plain text: cord-342344-jjnf4yje.txt item: #881 of 973 id: cord-342380-lihz7h1k author: Meguid Kassem, Abdel title: SARS-CoV-2 infection among healthcare workers of a gastroenterological service in a tertiary care facility date: 2020-07-21 words: 3048 flesch: 46 summary: Among HCWs with symptoms at time of swab, the frequency of positive tests was 50%, while among asymptomatic HCWs the frequency was significantly lower (16.1%). Date: 17 Occupational health response to SARS Deaths in healthcare workers due to COVID-19: the need for robust data and analysis SARS-CoV-2 in the Employees of a Large University Hospital Prevalence and clinical presentation of health care workers with symptoms of coronavirus disease 2019 in 2 Dutch hospitals during an early phase of the pandemic Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano Roll-out of SARS-CoV-2 testing for healthcare workers at a large NHS Foundation Trust in the United Kingdom SARS-CoV-2 infection in Health Care Workers Coronavirus: 511 healthworkers positive, 26 hospitalised and 2 have died -Zweli Mkhize Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China COVID-19 Exposure risk of healthcare personnel in digestive endoscopy: a prospective study On behalf of the ITALIAN GI-COVID19 Working Group, et al. Low Risk of covid-19 Transmission in GI Endoscopy The Laboratory Diagnosis of COVID-19 Infection: Current Issues and Challenges Sensitivity of Chest CT for COVID-19: Comparison to RT-PCR Personal protective equipment for preventing highly infectious diseases due to exposure to contaminated body fluids in healthcare staff COVID-19: the case for health-care worker screening to prevent hospital transmission We would like to acknowledge the valuable logistic support provided by Dr. Tarek El-Mahdy keywords: cov-2; covid-19; hcws; infection; pcr; positive; sars; study cache: cord-342380-lihz7h1k.txt plain text: cord-342380-lihz7h1k.txt item: #882 of 973 id: cord-342383-ckswlo9o author: Pawlowski, C. title: Exploratory analysis of immunization records highlights decreased SARS-CoV-2 rates in individuals with recent non-COVID-19 vaccinations date: 2020-07-28 words: 5487 flesch: 44 summary: There are several ongoing/recruiting clinical trials testing the protective effects of existing vaccines against SARS-CoV-2 infection, including: Polio 8 , Measles-Mumps-Rubella vaccine 9 , Influenza vaccine 10 , and BCG vaccine 11, 12, 13, 14 . From the limited data available, there were 51 individuals in the study population who had taken BCG vaccine in the past 5 years, and among these 0 individuals tested positive for SARS-CoV-2 infection (95% CI: (0.0%, 7.0%)). keywords: cov-2; individuals; infection; rates; sars; time; vaccines; year cache: cord-342383-ckswlo9o.txt plain text: cord-342383-ckswlo9o.txt item: #883 of 973 id: cord-342476-0rupk21u author: van Rijn, Anneloes L. title: The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease date: 2019-10-24 words: 4038 flesch: 39 summary: Correlation between qPCR Cq value and logarithm of normalized numbers of mNGS viral reads was tested with population Pearson correlation coefficient. No correlation was found between viral reads and clinical markers. keywords: copd; exacerbations; mngs; pathogens; patients; pcr; reads; samples; study; virome; viruses cache: cord-342476-0rupk21u.txt plain text: cord-342476-0rupk21u.txt item: #884 of 973 id: cord-342568-3sj235rm author: Bald-Blume, Niklas title: Development of a molecular assay for the general detection of tospoviruses and the distinction between tospoviral species date: 2017-02-11 words: 5369 flesch: 49 summary: The standard method for virus detection (ELISA) lacks this potential and is quite labor-and time-intensive as it only allows to test for one virus at a time. In this study a new method for plant virus diagnosis is described using the Luminex xTAG keywords: detection; luminex; pcr; plant; primers; species; tospoviruses; tswv; virus; wsmov cache: cord-342568-3sj235rm.txt plain text: cord-342568-3sj235rm.txt item: #885 of 973 id: cord-342783-85b4lwh3 author: Prazuck, T. title: Evaluation of performance of two SARS-CoV-2 Rapid whole-blood finger-stick IgM-IgGCombined Antibody Tests date: 2020-05-27 words: 2643 flesch: 53 summary: According 110 to severity of disease, patients RT-PCR positive were either hospitalized in the infectious 111 diseases ward, only devoted to treat COVID-19 infected patients, or invited to have regular 112 medical visits in the outpatient consultation. These tests use anti-human IgM antibody (test line IgM), anti-human IgG 144 antibody (test line IgG) and rabbit IgG (control line C) immobilized on a nitrocellulose strip. keywords: cov-2; license; medrxiv; patients; preprint; sars cache: cord-342783-85b4lwh3.txt plain text: cord-342783-85b4lwh3.txt item: #886 of 973 id: cord-342785-55r01n0x author: Lemmon, Gordon H title: Predicting the sensitivity and specificity of published real-time PCR assays date: 2008-09-25 words: 4319 flesch: 46 summary: GL found real time PCR signatures in the literature, wrote Perl scripts, and performed the analysis of published signatures. It has been estimated that a minimum of 3-4 genomes are needed in order to computationally design TaqMan PCR signatures likely to detect most strains, with those isolates chosen for sequencing that have been selected to span gradients of geographic, phenotypic, and temporal variation [19] . keywords: assay; detection; pcr; primer; probe; sensitivity; sequences; signatures; time; virus cache: cord-342785-55r01n0x.txt plain text: cord-342785-55r01n0x.txt item: #887 of 973 id: cord-343377-6muareue author: Kidszun, André title: Viral Infections in Neonates with Suspected Late-Onset Bacterial Sepsis—A Prospective Cohort Study date: 2016-05-16 words: 2357 flesch: 41 summary: 27 Funding None. Prevention of nosocomial infections in the neonatal intensive care unit Development of a surveillance system for nosocomial infections: the component for neonatal intensive care units in Germany Molecular detection of lateonset neonatal sepsis in premature infants using small blood volumes: proof-of-concept Nosocomial infections in very low birthweight infants in Germany: current data from the National Surveillance System NEO-KISS Hospital-acquired viral pathogens in the neonatal intensive care unit Clinical and epidemiologic characteristics of viral infections in a neonatal intensive care unit during a 12-year period Nosocomial rhinovirus infection in preterm infants Pandemic A/H1N1(2009) influenza infections in very-low-birth-weight infants-a case series from the German Neonatal Network Human rhinovirus causes severe infection in preterm infants Respiratory viral infections are not uncommon in neonatal intensive care units Viral outbreaks in neonatal intensive care units: what we do not know Medical and economic impact of a respiratory syncytial virus outbreak in a neonatal intensive care unit The role of multiplex PCR in respiratory tract infections in children Detection of multiple respiratory pathogens during primary respiratory infection: nasal swab versus nasopharyngeal aspirate using real-time polymerase chain reaction Detection of respiratory viral infections in neonates treated for suspicion of nosocomial bacterial sepsis: a feasibility study Viral respiratory tract infections in the neonatal intensive care unit: the VIRIoN-I study Unrecognized viral respiratory tract infections in premature infants during their birth hospitalization: a prospective surveillance study in two neonatal intensive care units Validation of a multiplex reverse transcriptase PCR ELISA for the detection of 19 respiratory tract pathogens Viral respiratory tract infections in the Neonatal Intensive Care Unit Viral infections of the lower respiratory tract: old viruses, new viruses, and the role of diagnosis Predominance of rhinovirus in the nose of symptomatic and asymptomatic infants Clinical utility of PCR for common viruses in acute respiratory illness Association of respiratory picornaviruses with acute bronchiolitis in French infants Prebiotic and probiotic supplementation prevents rhinovirus infections in preterm infants: a randomized, placebo-controlled trial A host-based RT-PCR gene expression signature to identify acute respiratory viral infection Human parechovirus infection in neonatal intensive care 5ICCN_006: Viral infections in neonates with suspected nosocomial bacterial sepsis Viral Infections in Neonates Kidszun et None. Respiratory viral infections did not occur in clusters in the NICU and none of the virus-positive infants had been discharged home previously. keywords: infants; infections; sepsis; study; virus cache: cord-343377-6muareue.txt plain text: cord-343377-6muareue.txt item: #888 of 973 id: cord-343441-z849jvq5 author: Li, Yan title: Simultaneous detection of hemagglutinin and neuraminidase genes of novel influenza A (H7N9) by duplex real-time reverse transcription polymerase chain reaction date: 2013-09-01 words: 2239 flesch: 48 summary: In this study, a duplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assay was developed for the simultaneous detection of hemagglutinin (HA) and neuraminidase (NA) genes of H7N9 influenza viruses. In this study, a duplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assay was developed for the simultaneous detection of hemagglutinin (HA) and neuraminidase (NA) genes of H7N9 influenza viruses. keywords: assay; genes; h7n9; pcr; rrt; virus cache: cord-343441-z849jvq5.txt plain text: cord-343441-z849jvq5.txt item: #889 of 973 id: cord-343784-zgvxl4h3 author: Cho, Chi Hyun title: Evaluation of the AdvanSure™ real-time RT-PCR compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses date: 2014-05-31 words: 3713 flesch: 42 summary: New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses Comparative evaluation of the Seegene Seeplex RV15 and real-time PCR for respiratory virus detection Comparison of two commercial molecular assays for simultaneous detection of respiratory viruses in clinical samples using two automatic electrophoresis detection systems Multiplex PCR, and emerging technologies for the detection of respiratory pathogens Development of a multiplex one step RT-PCR that detects eighteen respiratory viruses in clinical specimens and comparison with real time RT-PCR Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-PCR assay Evaluation of the FilmArray(R) Respiratory Panel for clinical use in a large children's hospital Use of the Seeplex RV Detection kit for surveillance of respiratory viral outbreaks in Ten years of human metapneumovirus research Evaluation of multiple commercial molecular and conventional diagnostic assays for the detection of respiratory viruses in children Rapid molecular detection of influenza outbreaks in nursing homes Update on rhinovirus and coronavirus infections Cyclic-CMTA: an innovative concept in multiplex quantification Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent in enteric infections Utilization of nucleic acid amplification assays for the detection of respiratory viruses Comparison of Anyplex II RV16 with the xTAG respiratory viral panel and Seeplex RV15 for detection of respiratory viruses Rapid multiplex nested PCR for detection of respiratory viruses High-throughput, sensitive, and accurate multiplex PCR-microsphere flow cytometry system for large-scale comprehensive detection of respiratory viruses Epidemiology of multiple respiratory viruses in childcare attendees PCR for detection of respiratory viruses: seasonal variations of virus infections Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens Clinical evaluation of multiplex real-time PCR panels for rapid detection of respiratory viral infections Mortality associated with influenza and respiratory syncytial virus in the United States Clinical and economical impact of multiplex respiratory virus assays Simultaneous detection of respiratory viruses in children with acute respiratory infection using two different multiplex reverse transcription-PCR assays High incidence of multiple viral infections identified in upper respiratory tract infected children under three years of age in Shanghai. All of our samples (nasopharyngeal aspirates or flocked nasopharyngeal swabs) had been transported in 3 mL of UTM (COPAN, Murrieta, CA, USA) and were freshly used for virus culture, Seeplex® RV 15 assay, and AdvanSure™ real-time RT-PCR (LG Life Science). keywords: advansure; culture; pcr; positive; rv15; viruses cache: cord-343784-zgvxl4h3.txt plain text: cord-343784-zgvxl4h3.txt item: #890 of 973 id: cord-343860-2j7nbryv author: Thiberville, S.D. title: The viral etiology of an influenza‐like illness during the 2009 pandemic date: 2012-05-14 words: 3730 flesch: 43 summary: None are satisfactorily sensitive and specific for defining influenza virus infection All patient samples were tested for influenza virus, and 286 negative nasal swabs were tested further for 18 other respiratory viruses using real‐time RT‐PCR. keywords: et al; h1n1p; illness; influenza; patients; pcr; positive; viruses cache: cord-343860-2j7nbryv.txt plain text: cord-343860-2j7nbryv.txt item: #891 of 973 id: cord-344745-sgkq1l93 author: Selim, Karim title: Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 date: 2013-11-18 words: 2765 flesch: 50 summary: One of a series of the Veterinary Medicine-Large Animal Clinical Sciences Department, Florida Cooperative Extension Service Avian infectious bronchitis virus Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand Severe acute respiratory syndrome vaccine development experiences of vaccination against avian infectious bronchitis coronavirus Identification of five bronchitis virus (IBV) strains isolated in China and phylogenetic analysis of the S1gene Complete genomic sequence analysis of infectious bronchitis virus Ark DPI, strain and its evolution by recombination Isolation and molecular characterization of infectious bronchitis virus isolate Shiraz IBV, by RT PCR and restriction enzyme analysis S1 gene sequence analysis of a nephro-pathogenic strain of avian infectious bronchitis virus in Egypt Studies on infectious bronchitis in broiler chickens in El-Menia Governorate Present status of infectious bronchitis in Egypt Emergence of a novel genotype of avian infectious bronchitis virus in Egypt Molecular characterization of infectious bronchitis virus isolates foreign to the United States and comparison with United States isolates Molecular analysis of the 793/B serotype of IBV in great Britain CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods Detection of infectious bronchitis Laboratory manual for the isolation and identification of avian pathogens Molecular epizootiology of avian infectious bronchitis in Russia Isolation and molecular characterization of Sul/01/09avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East Antigenic and S-1 genomic characterization of the Delaware variant serotype of infectious bronchitis virus Spike gene analysis of the DE072 strain of infectious bronchitis virus: origin and evolution Isolation and characterization of infectious bronchitis virus strain 4/91 from commercial layer chickens in the Sudan Identification of a novel nephropathogenic infectious bronchitis virus in Israel Presence of IS/1494/06 genotype-related infectious bronchitis virus in breeder and broiler flocks in Turkey It is very critical to complete genetic characterization of circulating IBV viruses to study the genetic relatedness among viruses and vaccine strains. keywords: acc; bronchitis; gene; group; ibv; isolates; pcr; virus cache: cord-344745-sgkq1l93.txt plain text: cord-344745-sgkq1l93.txt item: #892 of 973 id: cord-344749-omzhhr0k author: Kaya, Sariye Irem title: Electrochemical virus detections with nanobiosensors date: 2020-02-14 words: 8406 flesch: 32 summary: key: cord-344749-omzhhr0k authors: Kaya, Sariye Irem; Karadurmus, Leyla; Ozcelikay, Goksu; Bakirhan, Nurgul K.; Ozkan, Sibel A. title: Electrochemical virus detections with nanobiosensors date: 2020-02-14 journal: Nanosensors for Smart Cities DOI: 10.1016/b978-0-12-819870-4.00017-7 sha: doc_id: 344749 cord_uid: omzhhr0k Infectious diseases are caused from pathogens, which need a reliable and fast diagnosis. Recent progress in electrochemical studies shows that biosensors are very simple, accurate, precise, and cheap at virus detection, for which researchers find great interest in this field. keywords: antigen; biosensor; carbon; cells; detection; disease; dna; electrochemical; electrode; gold; hepatitis; humans; immunosensor; influenza; methods; nanoparticles; pcr; rna; surface; virus; viruses cache: cord-344749-omzhhr0k.txt plain text: cord-344749-omzhhr0k.txt item: #893 of 973 id: cord-344751-i4qnrtjq author: Van Praet, Jens T. title: Comparison of four commercial SARS-CoV-2 IgG immuno-assays in RT-PCR negative patients with suspect CT findings date: 2020-09-10 words: 2402 flesch: 45 summary: Furthermore, we could not test serum samples from included patients on all time points. Indeed, the misdiagnosis of admitted patients as Covid-19 may have serious consequences since these patients are isolated in a specific ward. keywords: cov-2; patients; pcr; sars cache: cord-344751-i4qnrtjq.txt plain text: cord-344751-i4qnrtjq.txt item: #894 of 973 id: cord-344770-aoi42xq4 author: Bialasiewicz, Seweryn title: Detection of a divergent Parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing date: 2014-05-19 words: 2704 flesch: 43 summary: PCR primers used to amplify and sequence PIV4 strain QLD-01. These findings further support a possible role for Parainfluenza 4 in the aetiology of adult respiratory disease within the community setting, and highlight the caution needed to be used in designing PCR assays from limited sequence information or in using proprietary commercial PCR assays. keywords: genome; parainfluenza; pcr; piv4; qld-01; study; virus; viruses cache: cord-344770-aoi42xq4.txt plain text: cord-344770-aoi42xq4.txt item: #895 of 973 id: cord-344782-ond1ziu5 author: Zhang, Jing title: Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date: 2018-10-24 words: 6005 flesch: 45 summary: Similarity to other viruses for each of the ORFs and their predicted amino acid sequences were determined by searches using BLASTn and BLASTp [13] algorithms through the NCBI server (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Ball Python Nidovirus: a Candidate Etiologic Agent for Severe Respiratory Disease in Python regius Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius) Novel divergent nidovirus in a python with pneumonia Nidovirus-Associated Proliferative Pneumonia in the Green Tree Python (Morelia viridis) Discovery and partial genomic characterisation of a novel nidovirus associated with respiratory disease in wild shingleback lizards (Tiliqua rugosa) Redefining the invertebrate RNA virosphere The evolutionary history of vertebrate RNA viruses Programmed translational frameshifting Ribosomal frameshifting on viral RNAs The primary structure and expression of the second open reading frame of the polymerase gene of the coronavirus MHV-A59 a highly conserved polymerase is expressed by an efficient ribosomal frameshifting mechanism An RNA Pseudoknot in the 3' end of the Arterivirus genome has a critical role in regulating viral RNA synthesis Changes to taxonomy and the international code of virus classification and Nomenclature ratified by the international committee on taxonomy of viruses Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates Molecular comparison of isolates of an emerging fish pathogen, Koi herpesvirus, and the effect of water temperature on mortality of experimentally infected Koi Is horizontal transmission of the ostreid herpesvirus OsHV-1 in Crassostrea gigas affected by unselected or selected survival status in adults to juveniles? keywords: acid; animals; disease; georgesi; min; nidovirus; pcr; python; river; rna; samples; sequence; species; tissues; turtle; virus cache: cord-344782-ond1ziu5.txt plain text: cord-344782-ond1ziu5.txt item: #896 of 973 id: cord-344889-1y4ieamp author: Cameron, Robert J. title: Virus infection in exacerbations of chronic obstructive pulmonary disease requiring ventilation date: 2006-05-24 words: 4314 flesch: 42 summary: An attempt to evaluate the relationship Infectious exacerbations of chronic obstructive pulmonary disease associated with respiratory viruses and non-typeable Haemophilus influenzae Respiratory viruses in exacerbations of chronic obstructive pulmonary disease requiring hospitalisation: a case-control study Bronchial microbial patterns in severe exacerbations of chronic obstructive pulmonary disease (COPD) requiring mechanical ventilation Characterization of distal bronchial microflora during acute exacerbation of chronic bronchitis. Role of inflammatory cells and mediators A model of viral wheeze in nonasthmatic adults: symptoms and physiology Virus-induced asthma attacks Human metapneumovirus and lower respiratory tract disease in otherwise healthy infants and children Respiratory picornaviruses and respiratory syncytial virus as causative agents of acute expiratory wheezing in children Field's virology, 4th edn Standards for the diagnosis and treatment of patients with COPD: a summary of the ATS/ERS position paper Noninvasive ventilation in acute respiratory failure Evaluation of antimicrobial treatment in mechanically ventilated patients with severe chronic obstructive pulmonary disease exacerbations Noninvasive positivepressure ventilation via face mask during bronchoscopy with BAL in high-risk hypoxemic patients Evaluation of a quantitative real-time PCR for the detection of respiratory syncytial virus in pulmonary diseases Detection of rhinovirus in induced sputum at exacerbation of chronic obstructive pulmonary disease Recent advances in diagnosis and management of chronic bronchitis and emphysema Evidencebased approach to acute exacerbations of COPD Exacerbations of chronic obstructive pulmonary disease: when are bacteria important? Impact of sputum bacteria on airway inflammation and health status in clinical stable COPD Relationship between bacterial colonisation and the frequency, character, and severity of COPD exacerbations Natural and experimental rhinovirus infections of the lower respiratory tract Virus-induced airway hyperresponsiveness in man Low grade rhinovirus infection induces a prolonged release of IL-8 in pulmonary epithelium Detection of rhinovirus RNA in lower airway cells during experimentally induced infection Respiratory viruses, symptoms, and inflammatory markers in acute exacerbations and stable chronic obstructive pulmonary disease Lower respiratory viral illnesses: improved diagnosis by molecular methods and clinical impact Impact of respiratory virus infections on persons with chronic underlying conditions Epidemiology and treatment of chronic bronchitis and its exacerbations Respiratory viral infections in adults Respiratory viral infections in adults with and without chronic obstructive pulmonary disease Rapid and sensitive routine detection of all members of the genus enterovirus in different clinical specimens by real-time PCR keywords: cases; chronic; copd; exacerbations; infection; patients; pcr; study; virus cache: cord-344889-1y4ieamp.txt plain text: cord-344889-1y4ieamp.txt item: #897 of 973 id: cord-345211-4ivqlsgt author: Murdoch, David R. title: How recent advances in molecular tests could impact the diagnosis of pneumonia date: 2016-03-07 words: 5996 flesch: 30 summary: A wide variety of microorganisms are listed as pneumonia pathogens key: cord-345211-4ivqlsgt authors: Murdoch, David R. title: How recent advances in molecular tests could impact the diagnosis of pneumonia date: 2016-03-07 journal: Expert Rev Mol Diagn DOI: 10.1586/14737159.2016.1156536 sha: doc_id: 345211 cord_uid: 4ivqlsgt Molecular diagnostic tests have been the single major development in pneumonia diagnostics over recent years. keywords: children; detection; diagnostic; disease; etiology; nats; pathogens; pcr; pneumococcal; pneumonia; tests cache: cord-345211-4ivqlsgt.txt plain text: cord-345211-4ivqlsgt.txt item: #898 of 973 id: cord-345312-i7soyabu author: Wabe, Nasir title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients date: 2019-03-05 words: 2884 flesch: 40 summary: In this study, we analysed routinely collected data to determine whether rapid PCR testing for influenza and RSV infections in EDs is associated with improved patient and laboratory outcomes. During July-December 2016, patients were tested with the standard PCR system, a central laboratory-based multiplex PCR test for sixteen respiratory viruses (including RSV and influenza viruses A and B), available as a referral test at the central laboratory in Hospital B. During July-December 2017, patients were tested with the rapid PCR system, a hospital laboratory-based test specific for RSV and influenza viruses A and B. Hospitals A, B and D have onsite laboratories that perform rapid PCR testing; Hospital C sends samples to the nearby Hospital A. keywords: influenza; patients; pcr; testing; tests cache: cord-345312-i7soyabu.txt plain text: cord-345312-i7soyabu.txt item: #899 of 973 id: cord-345338-pf4tsh3v author: Shaw, Brian title: The lingering manifestations of COVID-19 during and after convalescence: update on long-term pulmonary consequences of coronavirus disease 2019 (COVID-19) date: 2020-10-01 words: 3658 flesch: 43 summary: Serial CT features in discharged COVID-19 patients with positive RT-PCR re-test Patient follow-up after discharge after COVID-19 pneumonia: considerations for infectious control Abnormal pulmonary function in COVID-19 patients at time of hospital discharge Post-discharge surveillance and positive virus detection in two medical staff recovered from coronavirus disease 2019 (COVID-19), China Three cases of re-detectable positive SARS-CoV-2 RNA in recovered COVID-19 patients with antibodies Pathological evidence for residual SARS-CoV-2 in pulmonary tissues of a ready-fordischarge patient Initial CT findings and temporal changes in patients with the novel coronavirus pneumonia (2019-nCoV): a study of 63 patients in Wuhan, China Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan, China: a descriptive study Evolution of CT findings in patients with mild COVID-19 pneumonia Chest CT findings of COVID-19 pneumonia by duration of symptoms Time course of lung changes on chest CT during recovery from 2019 novel coronavirus (COVID-19) pneumonia CT scans of patients with 2019 novel coronavirus (COVID-19) pneumonia Radiologic findings of coronavirus disease (COVID-19): clinical correlation is recommended Lung fibrosis: an undervalued finding in COVID-19 pathological series Radiology-pathology correlation in recovered COVID-19, demonstrating organizing pneumonia Pneumonia Low-dose CT in COVID-19 outbreak: radiation safety, image wisely, and image gently pledge Radiology-pathology correlation in recovered COVID-19, demonstrating organizing Organizing pneumonia: chest HRCT findings The role of chest imaging in patient management during the COVID-19 pandemic: a multinational consensus statement from the fleischner society Role of chest CT in resource-driven healthcare systems COVID-19) infection: findings and correlation with clinical outcome Coronavirus disease 2019 (COVID-19) diagnostic technologies: a country-based retrospective analysis of screening and containment procedures during the first wave of the pandemic Considerations for postacute rehabilitation for survivors of COVID-19 Coronavirus (COVID-19) The discharge criteria in many of these studies are unclear, and few have reported short-term (1-2 months) follow-ups on COVID-19 patients after hospital discharge. keywords: covid-19; days; discharge; findings; patients; pneumonia; studies cache: cord-345338-pf4tsh3v.txt plain text: cord-345338-pf4tsh3v.txt item: #900 of 973 id: cord-345475-ttrcmtu4 author: de Oliveira, Luisa Abruzzi title: Reference Genes for the Normalization of Gene Expression in Eucalyptus Species date: 2011-12-24 words: 9769 flesch: 41 summary: Method Reference gene selection for quantitative real-time PCR normalization in tomato subjected to nitrogen, cold, and light stress Validation of reference genes for gene expression analysis in chicory (Cichorium intybus) using quantitative real-time PCR Evaluation of reference genes for quantitative RT-PCR in Lolium perenne Growthrelated gene expression in Nicotiana tabacum mesophyll protoplasts The two ribosomal protein L23A genes are differentially transcribed in Arabidopsis thaliana Global analysis of the core cell cycle regulators of Arabidopsis identifies novel genes, reveals multiple and highly specific profiles of expression and provides a coherent model for plant cell cycle control Characterization of the structure and expression of a highly conserved ribosomal protein gene, L9, from pea Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress Identification and validation of reference genes for quantitative RT-PCR normalization in wheat Reference gene selection for quantitative real-time PCR analysis in virus infected cells: SARS corona virus, Yellow fever virus, Human Herpesvirus-6, Camelpox virus and Cytomegalovirus infections Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development Normalisation of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations A new genomic resource dedicated to wood formation in Eucalyptus Involvement of Arabidopsis thaliana ribosomal protein S27 in mRNA degradation triggered by genotoxic stress Accumulation and nuclear targeting of BnC24, a Brassica napus ribosomal protein corresponding to a mRNA accumulating in response to cold treatment Stable internal reference genes for normalization of real-time RT-PCR in tobacco (Nicotiana tabacum) during development and abiotic stress Selection of reference genes for quantitative real-time PCR expression studies in the apomictic and sexual grass Brachiaria brizantha Properties of the reverse transcription reaction in mRNA quantification Real-time quantitative RT-PCR for low-abundance transcripts in the inner ear: analysis of neurotrophic factor expression Higher-level relationships among the eucalypts are resolved by ITS-sequence data Differential expression and sequence analysis of ribosomal protein genes induced in stolon tips of potato (Solanum tuberosum L.) during the early stages of tuberization A practical approach to RT-qPCR-publishing data that conform to the MIQE guidelines Housekeeping genes as internal standards: use and limits Selection of reliable reference genes for gene expression studies in peach using real-time PCR Significance analysis of microarrays applied to the ionizing radiation response Control of cell division and transcription by cyclin-dependent kinase-activating kinases in plants Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Heat-stressdependency and developmental modulation of gene expression: the potential of house-keeping genes as internal standards in mRNA expression profiling using real-time RT-PCR Selection of appropriate reference genes for gene expression studies by quantitative real-time polymerase chain reaction in cucumber Developmental regulation of ribosomal protein L16 genes in Arabidopsis thaliana Transcription elongation factor SII Extraribosomal functions of ribosomal proteins Cloning and characterization of the 1-deoxy-D-xylulose 5-phosphate reductoisomerase gene for diterpenoid tanshinone biosynthesis in Salvia miltiorrhiza (Chinese sage) hairy roots Molecular characterization and expression of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) gene from Salvia miltiorrhiza Characterization of reference genes for quantitative real-time PCR analysis in various tissues of Salvia miltiorrhiza An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression Normalization with genes encoding ribosomal proteins but not GAPDH provides an accurate quantification of gene expressions in neuronal differentiation of PC12 cells We acknowledge M.Sc. Given the increasing interest in the functional genomics of Eucalyptus, we sought to identify and experimentally verify suitable reference genes for the normalization of gene expression associated with the flower, leaf and xylem of six species of the genus. keywords: 2010; analysis; data; et al; eucalyptus; expression; genes; grandis; microarray; normalization; qpcr; reference; stability; studies; time; tissues; xylem cache: cord-345475-ttrcmtu4.txt plain text: cord-345475-ttrcmtu4.txt item: #901 of 973 id: cord-345518-athy5yg7 author: Meurs, Kathryn M title: Molecular Screening by Polymerase Chain Reaction Detects Panleukopenia Virus DNA in Formalin-Fixed Hearts from Cats with Idiopathic Cardiomyopathy and Myocarditis date: 2000-04-30 words: 4014 flesch: 34 summary: Domestic cats are noted for naturally occurring cardiomyopathy (3, 5, 7, 34) , and viral myocarditis has been suspected on the basis of histopathologic abnormalities (1, 2) . Because of the continuing interest in the potential relationship between viral myocarditis and cardiomyopathy, we evaluated hearts from cats with spontaneous, idiopathic cardiomyopathy for viral genomic material within myocytes by polymerase chain reaction, and for the presence of myocarditis by light microscopy. keywords: cardiomyopathy; cats; dna; feline; genome; myocarditis; panleukopenia; pcr; virus cache: cord-345518-athy5yg7.txt plain text: cord-345518-athy5yg7.txt item: #902 of 973 id: cord-345820-0n1pea70 author: Wiener, Renda Soylemez title: Angiotensin converting enzyme 2 is primarily epithelial and is developmentally regulated in the mouse lung date: 2007-03-05 words: 7002 flesch: 52 summary: Immunohistochemistry localizes ACE2 protein to Clara cells, type II cells, and endothelium and smooth muscle of small and medium vessels in the mouse lung. [2005] have suggested that ACE2 protein is localized to alveolar macrophages and type II cells based on immunohistochemistry. keywords: ace2; angiotensin; cell; et al; exon; expression; fig; kda; kidney; lung; mouse; mrna; pcr; protein cache: cord-345820-0n1pea70.txt plain text: cord-345820-0n1pea70.txt item: #903 of 973 id: cord-346054-k84rcpav author: Niespodziana, Katarzyna title: PreDicta chip-based high resolution diagnosis of rhinovirus-induced wheeze date: 2018-06-18 words: 7427 flesch: 39 summary: 3a (right column) results from the PCR testing performed using VP4-VP2specific primers in 108 of the 120 children 35 , which showed that the nucleic acid-based detection of virus strains was negative for approximately 25% of children with increases of RV peptide-specific IgG levels which may indicate a higher sensitivity of serology vs. PCR in these children. There were also 14 children without increases of RV peptide-specific antibody responses who had positive PCR results (Fig. 3a, bottom) . keywords: antibody; asthma; children; chip; fig; igg; increases; pcr; peptides; proteins; responses; rhinovirus; species; supplementary; vp1; wheeze cache: cord-346054-k84rcpav.txt plain text: cord-346054-k84rcpav.txt item: #904 of 973 id: cord-346096-aml84iv1 author: Bailey, Emily S. title: Molecular surveillance of respiratory viruses with bioaerosol sampling in an airport date: 2018-09-17 words: 2507 flesch: 42 summary: key: cord-346096-aml84iv1 authors: Bailey, Emily S.; Choi, Jessica Y.; Zemke, Juliana; Yondon, Myagmarsukh; Gray, Gregory C. title: Molecular surveillance of respiratory viruses with bioaerosol sampling in an airport date: 2018-09-17 journal: Trop Dis Travel Med Vaccines DOI: 10.1186/s40794-018-0071-7 sha: doc_id: 346096 cord_uid: aml84iv1 Recognizing that crowded, high-traffic airports and airplanes have been implicated in respiratory disease transmission, we partnered with administrators of Raleigh Durham International Airport (RDU) in conducting a pilot study of aerosol surveillance for respiratory viruses at RDU. This bioaerosol sampling technique has been adapted for respiratory virus screening in swine production facilities [5] , poultry markets keywords: adenovirus; aerosol; airport; human; influenza; samples; sampling; study; viruses cache: cord-346096-aml84iv1.txt plain text: cord-346096-aml84iv1.txt item: #905 of 973 id: cord-346104-18x8u2oe author: Black, Wendy title: Identification of gammaherpesvirus infection in free-ranging black bears (Ursus americanus) date: 2019-01-02 words: 5167 flesch: 49 summary: Interestingly, black bear herpesvirus infections were also found in bears without neurological signs. shown in Fig. 6 , the amplicons from bear tissues and UrHV-1 branch out together and have smaller distance to members of Rhadinvirus, such as HHV-8 and Rhadinovirus 1 (RHV-1). keywords: bear; black; dna; fig; herpesvirus; pcr; primers; tissue cache: cord-346104-18x8u2oe.txt plain text: cord-346104-18x8u2oe.txt item: #906 of 973 id: cord-346138-ip42zcld author: Zhurakivska, Khrystyna title: An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens date: 2020-08-20 words: 3956 flesch: 48 summary: All patients, except one in Kim's report (12) and four reported by Liu et al. (27) had negative viral detection in urine. Results on viral RNA detection in saliva are reported in two papers (17, 18) . Aimed at identifying viral RNA in the various compartments of the organism of sick subjects, diagnostic tests are carried out. keywords: disease; load; patients; rna; sars; studies; virus cache: cord-346138-ip42zcld.txt plain text: cord-346138-ip42zcld.txt item: #907 of 973 id: cord-346308-9h2fk9qt author: Kaur, Rajwinder title: Microbiology of hospital wastewater date: 2020-05-01 words: 14679 flesch: 30 summary: and Enterobacteriaceae in sewage Hospital wastewater releases of carbapenem-resistance pathogens and genes in urban India Assessment of antibiotic-and disinfectant-resistant bacteria in hospital wastewater, south Ethiopia: a cross-sectional study Antibiotic susceptibilities of Enterococcus species isolated from hospital and domestic wastewater effluents in Alice, Eastern Cape Province of South Africa Beta-lactamase-producing Enterobacteriaceae in hospital effluents Insights into the relationship between antimicrobial residues and bacterial populations in a hospital-urban wastewater treatment plant system Influence of hospital wastewater discharged from University of Benin Teaching Hospital (UBTH) Multiresistance, beta-lactamaseencoding genes and bacterial diversity in hospital wastewater in Rio de Janeiro, Brazil Enumeration and characterization of antimicrobial-resistant Escherichia coli bacteria in effluent from municipal, hospital, and secondary treatment facility sources Antibiotic resistance and antibiotic resistance genes in Escherichia coli isolates from hospital wastewater in Vietnam Antibiotic resistant bacteria in hospital wastewaters and sewage treatment plants Dissemination of antibiotic resistance in methicillin-resistant Staphylococcus aureus and vancomycin-resistant S aureus strains isolated from hospital effluents Detection of antimicrobial-resistant Gram-negative bacteria in hospital effluents and in the sewage treatment station of Goiânia Brazil Antimicrobial resistance of 3 types of gram-negative bacteria isolated from hospital surfaces and the hands of health care workers Abundance of antibiotics, antibiotic resistance genes and bacterial community composition in wastewater effluents from different Romanian hospitals Vancomycin resistant enterococci: from the hospital effluent to the urban wastewater treatment plant The role of aquatic ecosystems as reservoirs of antibiotic resistance Environmental dissemination of antibiotic resistance genes and correlation to anthropogenic contamination with antibiotics Occurrence of antibiotics and antibiotic resistance genes in hospital and urban wastewaters and their impact on the receiving river Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review Levels of antibiotic resistance genes in manure, biosolids, and fertilized soil Epidemiology of resistance to antibiotics: links between animals and humans Detection of antibiotic resistance genes in source and drinking water samples from a first nation community in Canada Prevalence of antibiotic resistance in drinking water treatment and distribution systems Antimicrobial Resistance: Global Report on Surveillance, World Health Organization Society's failure to protect a precious resource: antibiotics Hospital effluents are one of several sources of metal, antibiotic resistance genes, and bacterial markers disseminated in Sub-Saharan urban rivers Identifying antimicrobial resistance genes with DNA microarrays Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940 Antibiotic resistance genes in water environment Prevalence of antibiotic resistance genes and their relationship with antibiotics in the Huangpu River and the drinking water sources Multiple drug resistance and biocide resistance in Escherichia coli environmental isolates from hospital and household settings Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes Tackling antibiotic resistance: the environmental framework Screening methods for the detection of antimicrobial resistance genes present in bacterial isolates and the microbiota Culture-based methods for detection of antibiotic resistance in agroecosystems: advantages, challenges, and gaps in knowledge Insights into antibiotic resistance through metagenomic approaches Molecular evaluation of antibiotic susceptibility: keywords: analysis; antibiotics; args; bacteria; detection; dna; environment; fungal; genes; health; hospital; host; human; hww; infections; methods; norovirus; pathogens; pcr; present; prevalence; resistance; resistance genes; rotavirus; samples; species; transfer; treatment; virus; viruses; wastewater cache: cord-346308-9h2fk9qt.txt plain text: cord-346308-9h2fk9qt.txt item: #908 of 973 id: cord-346325-grt67p73 author: Reilev, M. title: Characteristics and predictors of hospitalization and death in the first 9,519 cases with a positive RT-PCR test for SARS-CoV-2 in Denmark: A nationwide cohort date: 2020-05-26 words: 4664 flesch: 41 summary: Among PCR positive cases with 4 or more comorbidities, the ORs for hospitalization was 3.6 and 5.2 for death compared to PCR positive cases without any comorbidities ( Table 2) . We included PCR positive cases with an index date prior to April 30 th , We first assessed the number of SARS-CoV-2 PCR positive cases in Denmark as well as the number of individuals tested PCR negative for SARS-CoV-2. keywords: age; cases; comorbidities; cov-2; disease; pcr; preprint; sars cache: cord-346325-grt67p73.txt plain text: cord-346325-grt67p73.txt item: #909 of 973 id: cord-346436-p61mpc6t author: Onodera, Kenji title: Selection for 3′-End Triplets for Polymerase Chain Reaction Primers date: 2007 words: 3710 flesch: 67 summary: Complementarity of the 5 -end of a primer to the PCR template is not so critical as for the 3 -end, and it is known that longer primers at the 5 -end (such as 30 nt or longer) do not improve specificity of PCR primers. GC clamp has been used for point mutation detection by adding GC-rich sequences to 5 -end of PCR primer (11). keywords: -end; design; pcr; primer; sequences; triplets cache: cord-346436-p61mpc6t.txt plain text: cord-346436-p61mpc6t.txt item: #910 of 973 id: cord-346467-a0r4xh1c author: Cornelissen, Jan B. W. J. title: Mycoplasma detection by triplex real-time PCR in bronchoalveolar lavage fluid from bovine respiratory disease complex cases date: 2017-04-08 words: 4086 flesch: 44 summary: In the M. bovis and M. dispar PCR, the difference in Ct value between PCR positive/ DGGE positive and PCR positive/ DGGE negative samples is at least 3.2, which indicates a factor of 10 difference in concentration of M. bovis and M. dispar DNA between these two groups (Fig. 4) . In the M. bovis and M. dispar PCR, we found a 10 fold difference in the Ct values between the DGGE positive/ PCR positive and DGGE negative/ PCR positive samples, which indicates a higher diagnostic sensitivity of M. bovis and M. dispar PCR than the DGGE analyses. keywords: bovirhinis; bovis; dispar; m. bovis; m. dispar; mycoplasma; pcr; respocheck; samples; triplex cache: cord-346467-a0r4xh1c.txt plain text: cord-346467-a0r4xh1c.txt item: #911 of 973 id: cord-346574-u28y1ttw author: Chen, Keyan title: Development and evaluation of an immunochromatographic strip for rapid detection of porcine hemagglutinating encephalomyelitis virus date: 2012-08-24 words: 5526 flesch: 45 summary: Additionally, there was a strong agreement between the sandwich enzyme-linked immunosorbent assay (ELISA) and immunochromatographic strips (Kappa = 0.976). The disease is caused by PHE coronavirus (PHE-CoV), which comprises a single strain and is the only known neurotropic CoV affecting pigs keywords: cov; detection; elisa; gold; mab; pcr; phe; samples; strip; test; virus cache: cord-346574-u28y1ttw.txt plain text: cord-346574-u28y1ttw.txt item: #912 of 973 id: cord-346859-r1v6ir8u author: Mallett, Sue title: At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR-based tests? A systematic review of individual participant data date: 2020-11-04 words: 5027 flesch: 46 summary: For each domain, the percentage of studies by concern for potential risk of bias is shown: low (green), unclear (yellow), and high (red) Details of bias and applicability issues Impact on interpretation of study data In these studies, the reference test usually incorporates RT-PCR (index test). Table 3 provides an overview of the major methodological limitations and their potential impact on study results. keywords: cov-2; participants; pcr; sampling; sars; sites; studies; test; virus cache: cord-346859-r1v6ir8u.txt plain text: cord-346859-r1v6ir8u.txt item: #913 of 973 id: cord-346958-9eeqlkoq author: Caruso, Damiano title: Chest CT Features of COVID-19 in Rome, Italy date: 2020-04-03 words: 1827 flesch: 42 summary: The aim of this study was to investigate chest CT features of patients with COVID-19 in Rome, Italy, and to compare the diagnostic performance of chest CT with RT-PCR. Exclusion criteria were: chest CT with contrast medium performed for vascular indications, patients who refused chest CT or hospitalization, and severe CT motion artifact. keywords: chest; covid-19; patients cache: cord-346958-9eeqlkoq.txt plain text: cord-346958-9eeqlkoq.txt item: #914 of 973 id: cord-346989-604gho1u author: Chen-Harris, Haiyin title: Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs date: 2013-02-12 words: 7131 flesch: 46 summary: [29] , in which overlapping regions of the read pairs serve to extend read lengths and reduce sequencing errors. ORPs help distinguish PCR error rates from sequencing error rates Figure 3 shows the Q-score distributions for all matching ORPs (blue), mismatched ORPs (red) and those matching ORPs that were erroneous (green) in the BCV control data (representative sample). keywords: base; control; error; matching; mismatch; orp; orps; pairs; pcr; rates; read; samples; sequencing; variant cache: cord-346989-604gho1u.txt plain text: cord-346989-604gho1u.txt item: #915 of 973 id: cord-347443-0evqo01m author: Litwin, Christine M. title: Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center date: 2013-07-24 words: 3999 flesch: 46 summary: respiratory viral panels for the diagnosis of respiratory viral infections in adults Performance of a novel microarray multiplex PCR for the detection of 23 respiratory pathogens (SYMP-ARI study) Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens-duration of symptoms significantly affects detection rate Seasonal variations of 15 respiratory agents illustrated by the application of a multiplex polymerase chain reaction assay Respiratory infections by HMPV and RSV are clinically indistinguishable but induce different host response in aged individuals Provisional Pertussis Surveillance Report Burden of human metapneumovirus infection in young children Human metapneumovirus infections-biannual epidemics and clinical findings in children in the region of Basel, Switzerland Broad respiratory virus detection in infants hospitalized for bronchiolitis by use of a multiplex RT-PCR DNA microarray system Prevalence of human metapneumovirus in adults with acute respiratory tract infection in Beijing Comparison of viral isolation and multiplex real-time reverse transcription-PCR for confirmation of respiratory syncytial virus and influenza virus detection by antigen immunoassays Prospective controlled study of four infection-control procedures to prevent nosocomial infection with respiratory syncytial virus Seasonality of respiratory tract infections 71 Seasonality, incidence, and repeat human metapneumovirus lower respiratory tract infections in an area with a high prevalence of human immunodeficiency virus type-1 infection Detection of respiratory viruses by molecular methods The Tecumseh study of respiratory illness. RSV and hMPV were the second-and third-most common causes of respiratory infections in our study. keywords: age; cases; entero; hmpv; infections; pcr; rsv; virus cache: cord-347443-0evqo01m.txt plain text: cord-347443-0evqo01m.txt item: #916 of 973 id: cord-347462-yz67t10x author: Chan, Tak Yeung title: A Comparative Study of Clinical Features and Outcomes in Young and Older Adults with Severe Acute Respiratory Syndrome date: 2004-07-19 words: 3598 flesch: 51 summary: The aim was to compare the clinical course of SARS patients aged 60 and younger with that of patients older than 60 admitted to a single institution with a clinical diagnosis of SARS. The former incidence was comparable with findings from several large local studies reporting diarrhea in 11% to 19.6% of SARS patients. keywords: acute; cov; patients; pcr; sars; tests cache: cord-347462-yz67t10x.txt plain text: cord-347462-yz67t10x.txt item: #917 of 973 id: cord-348209-rkkhv4mw author: Noerz, Dominik title: Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting date: 2020-04-11 words: 1650 flesch: 55 summary: The copyright holder for this preprint (which was not peer-reviewed) is Step Denature: 6 sec, at 95°C, No Detect Step Anneal: 19 sec, at 60°C, Detect 73 Table 1 : NeuMoDx-Software run-protocol summary displaying settings and PCR protocol. Prior to analysis, 1ml Roche cobas PCR medium (≤ 40% guanidine 77 hydrochloride in Tris-HCL buffer) was added to the sample in order to inactivate potential pathogens 78 within and facilitate further handling. keywords: cov-2; pcr; preprint; sars cache: cord-348209-rkkhv4mw.txt plain text: cord-348209-rkkhv4mw.txt item: #918 of 973 id: cord-348522-r7ev9br6 author: Englund, Stina title: The occurrence of Chlamydia spp. in pigs with and without clinical disease date: 2012-01-26 words: 3893 flesch: 50 summary: Ferkel-Darm Intestinal lesions caused by two swine chlamydial isolates in gnotobiotic pigs Experimental enteric infection of gnotobiotic piglets with Chlamydia suis strain S45 Intestinal lesions caused by a strain of Chlamydia suis in weanling pigs infected at 21 days of age Small intestinal Chlamydia infection in piglets Intensively kept pigs pre-disposed to chlamydial associated conjunctivitis Conjunctivitis caused by a swine Chlamydia trachomatis-like organism in gnotobiotic pigs Chlamydial zoonoses. in pig herds. keywords: chlamydia; conjunctivitis; control; herds; infection; pcr; performance; pigs; samples cache: cord-348522-r7ev9br6.txt plain text: cord-348522-r7ev9br6.txt item: #919 of 973 id: cord-348914-6wzqitun author: Ahouach, B. title: Cutaneous lesions in a patient with COVID‐19: are they related? date: 2020-04-30 words: 315 flesch: 54 summary: Thorax computed tomography scan was typical of COVID‐19; nasopharyngeal swab polymerase chain reaction (PCR) confirmed SARS‐CoV‐2. Thorax computed tomography scan was typical of COVID-19; nasopharyngeal swab polymerase chain reaction (PCR) confirmed SARS-CoV-2. keywords: fever cache: cord-348914-6wzqitun.txt plain text: cord-348914-6wzqitun.txt item: #920 of 973 id: cord-348975-plne3xlz author: Wagner, Tyler title: Augmented curation of clinical notes from a massive EHR system reveals symptoms of impending COVID-19 diagnosis date: 2020-07-07 words: 4950 flesch: 33 summary: Expanding beyond one institution's COVID-19 diagnostic testing and clinical care to the EHR databases of other academic medical centers and health systems will provide a more holistic view of clinical symptoms enriched in COVID pos over COVID neg patients in the days preceding confirmed diagnostic testing. Rhinitis is also a potential early signal of COVID pos patients that requires some consideration (2.2-fold amplification, p-value = 2.25E-29). keywords: covid; covid pos; covid-19; day; neg; patients; pcr; pcr testing; pos; symptoms; testing cache: cord-348975-plne3xlz.txt plain text: cord-348975-plne3xlz.txt item: #921 of 973 id: cord-349070-bqv03u2e author: Jiang, Shih Sheng title: Sensitive and Quantitative Detection of Severe Acute Respiratory Syndrome Coronavirus Infection by Real-Time Nested Polymerase Chain Reaction date: 2004-01-15 words: 2476 flesch: 44 summary: To reduce the risk of random or carry-over contamination of nested PCR [10] , sample preparation, reagent preparation, and PCR amplification were performed in different buildings or rooms with separated air-conditioning using different sets of the pipette system. This dual real-time PCR method can be easily completed within 2 h using LightCycler, which includes a 45-min, 1-step RT-PCR followed by 40-min real-time nested PCR, making it an ideal routine protocol for high-throughput screening of SARS-CoV. Second, the assay had a detection limit of !10 copies of SARS-CoV, to reduce the rate of false-negative results for trace virus samples. keywords: assay; detection; pcr; rna; round; sars; time cache: cord-349070-bqv03u2e.txt plain text: cord-349070-bqv03u2e.txt item: #922 of 973 id: cord-349562-ivu632j2 author: Hernes, S. S. title: Swabbing for respiratory viral infections in older patients: a comparison of rayon and nylon flocked swabs date: 2010-09-18 words: 3366 flesch: 49 summary: An outbreak of severe respiratory tract infection due to human metapneumovirus in a long-term care facility Respiratory syncytial virus infection in elderly and highrisk adults Respiratory syncytial virus pneumonia among the elderly: an assessment of disease burden A summer outbreak of human metapneumovirus infection in a long-term-care facility Mortality associated with influenza and respiratory syncytial virus in the United States Is clinical recognition of respiratory syncytial virus infection in hospitalized elderly and high-risk adults possible? Evaluation of four methods for the diagnosis of respiratory syncytial virus infection in older adults Lack of sensitivity of rapid antigen tests for the diagnosis of respiratory syncytial virus infection in adults Rapid molecular detection of influenza outbreaks in nursing homes Viral pneumonia in older adults A simple and reproducible method for collecting nasal secretions in frail elderly adults, for measurement of virus-specific IgA Respiratory viruses and influenza-like illness: a survey in the area of Rome Comparison of flocked and rayon swabs for collection of respiratory epithelial cells from uninfected volunteers and symptomatic patients Comparison of nasopharyngeal flocked swabs and aspirates for rapid diagnosis of respiratory viruses in children Comparison of respiratory virus detection rates for infants and toddlers by use of flocked swabs, saline aspirates, and saline aspirates mixed in universal transport medium for room temperature storage and shipping Identification of respiratory viruses in adults: nasopharyngeal versus oropharyngeal sampling Comparison of nasopharyngeal aspirate and nasopharyngeal swab specimens for respiratory syncytial virus diagnosis by cell culture, indirect immunofluorescence assay, and enzymelinked immunosorbent assay Comparison between pernasal flocked swabs and nasopharyngeal aspirates for detection of common respiratory viruses in samples from children Nasal swab versus nasopharyngeal aspirate for isolation of respiratory viruses Surveillance of respiratory virus infections in adult hospital admissions using rapid methods Development of a genomics-based PCR assay for detection of Mycoplasma pneumoniae in a large outbreak in New York State Evaluation of real-time quantitative PCR for identification and quantification of Chlamydia pneumoniae by comparison with immunohistochemistry The use of TaqMan PCR assay for detection of Bordetella pertussis infection from clinical specimens Real-time quantitative PCR assays for detection and monitoring of pathogenic human viruses in immunosuppressed pediatric patients Clinical diagnosis of influenza virus infection: evaluation of diagnostic tools in general practice Increased detection of respiratory syncytial virus, influenza viruses, parainfluenza viruses, and adenoviruses with real-time PCR in samples from patients with respiratory symptoms Comparison of real-time PCR assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 Real-time reverse transcriptase PCR assay for detection of human metapneumoviruses from all known genetic lineages Acknowledgements keywords: nasopharyngeal; nylon; patients; pcr; samples; swabs; virus; viruses cache: cord-349562-ivu632j2.txt plain text: cord-349562-ivu632j2.txt item: #923 of 973 id: cord-349745-zlhu1jit author: Konrad, Regina title: Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020 date: 2020-03-05 words: 2425 flesch: 50 summary: They all showed comparable results in reduction of unspecific E gene signals. Moreover, we additionally included a newly launched commercial test kit in our study: RealStar SARS-CoV-2 RT-PCR kit 1.0 (Altona, Hamburg, Germany), which did not show unspecific E gene signals. keywords: assays; coronavirus; cov-2; gene; health; pcr; sars cache: cord-349745-zlhu1jit.txt plain text: cord-349745-zlhu1jit.txt item: #924 of 973 id: cord-349775-zwslhjju author: Brittain-Long, Robin title: Access to a polymerase chain reaction assay method targeting 13 respiratory viruses can reduce antibiotics: a randomised, controlled trial date: 2011-04-26 words: 4616 flesch: 39 summary: A recent retrospective study of primary care patients in a comparable Swedish region recorded an antibiotic prescription rate of 45% for all patients with ARTIs, 60% for patients with acute bronchitis and 16% for patients with the 'common cold' [13] . We conducted an investigator-initiated, multicentre, prospective, randomised, controlled trial with adult patients in a primary care setting. keywords: antibiotic; group; patients; pcr; prescription; result; study; use; visit cache: cord-349775-zwslhjju.txt plain text: cord-349775-zwslhjju.txt item: #925 of 973 id: cord-349782-djzxkus2 author: van Kasteren, Puck B. title: Response to letter of concern by Oladimeji and Pickford of PrimerDesign date: 2020-06-29 words: 998 flesch: 44 summary: Similar to the FIND initiative (3), although less in number, we have used a selection of archived clinical samples to obtain retrospectively an indication of the diagnostic performance of the evaluated kits (we used the terms clinical sensitivity and specificity to express the diagnostic performance with clinical samples). However, in the discussion section we do speculate that the detection rate we observe would translate to a clinical sensitivity in the field of >96% for all kits, as only 3.6% of clinical samples in our database have a Ct value >34.5 with our in-J o u r n a l P r e -p r o o f house RT-PCR and all kits detected samples with Ct values <34.5 with our in-house RT-PCR. keywords: kits; pcr; samples cache: cord-349782-djzxkus2.txt plain text: cord-349782-djzxkus2.txt item: #926 of 973 id: cord-349838-p6vfzbla author: Algwaiz, Ghada title: Real-world issues and potential solutions in HCT during the COVID-19 pandemic: Perspectives from the WBMT and the CIBMTR's Health Services and International Studies Committee date: 2020-07-24 words: 4064 flesch: 34 summary: Exposure (especially to contacts with COVID-19 patients) and symptom history, physical examination, and chest imaging are helpful to evaluate HCT patients. Realizing the challenges as a result of this pandemic affecting the daily practice of the HCT centers, and the recognition of the variability in practice worldwide, the Worldwide Network for Blood & Marrow Transplantation (WBMT) and the Center for International Blood and Marrow Transplant Research (CIBMTR) Health Services and International Studies Committee have jointly produced an expert opinion statement as a general guide to deal with certain aspects of HCT including diagnostics for SARS-CoV-2 in HCT patients, pre-and-post-HCT management, donor issues, medical tourism and facilities management. keywords: blood; cell; covid-19; hct; infection; patients; pcr; risk; sars; therapy; transplantation; treatment cache: cord-349838-p6vfzbla.txt plain text: cord-349838-p6vfzbla.txt item: #927 of 973 id: cord-350016-yxf7ykva author: Qin, Le title: A predictive model and scoring system combining clinical and CT characteristics for the diagnosis of COVID-19 date: 2020-07-01 words: 3925 flesch: 44 summary: Inclusion criteria for patients suspected of COVID-19 were set according to the sixth edition of the Diagnosis and Treatment Program of COVID-19 proposed by The National Health Commission of the People's Republic of China: (1) epidemiological history: history of travel to Wuhan or history of residence in Wuhan or other areas with continuous transmission of local cases within 14 days before the onset of the disease, history of contact with COVID-19 patients within 14 days before the onset of the disease, and clustering or epidemiological association with COVID-19, and (2) clinical features: fever and/or disorder of the respiratory system, imaging manifestations of COVID-19 pneumonia, normal or reduced leukocyte count, or reduced lymphocyte count. From January 19 to February 6, 2020, 88 confirmed COVID-19 patients presenting with pneumonia and 80 non-COVID-19 patients suffering from pneumonia of other origins were retrospectively enrolled. keywords: 2019; clinical; covid-19; patients; pcr; pneumonia cache: cord-350016-yxf7ykva.txt plain text: cord-350016-yxf7ykva.txt item: #928 of 973 id: cord-350172-w3yoxhsg author: Mertens, Pascal title: Development and Potential Usefulness of the COVID-19 Ag Respi-Strip Diagnostic Assay in a Pandemic Context date: 2020-05-08 words: 7577 flesch: 41 summary: The post-implementation analysis of the proposed algorithm using samples collected in the LHUB-ULB between the 31st of March and the 7th of April 2020 from patients in four hospitals from Brussels showed 33.3% (325/975) total positive COVID-19 test results, of which 39.7% (129/325) were detected by the COVID-19 Ag Respi-Strip. In the absence of a vaccine and specific antiviral treatment, the containment of the pandemic relies mainly on the rapid identification and isolation of COVID-19 patients (2) . keywords: ag respi; assay; clinical; covid-19; covid-19 ag; diagnostic; patients; pcr; respi; results; samples; sars; strip; study; test cache: cord-350172-w3yoxhsg.txt plain text: cord-350172-w3yoxhsg.txt item: #929 of 973 id: cord-350211-vuxs5wtt author: Johanna, Barón‐Sánchez title: Afectación del sentido del olfato y el gusto en la enfermedad leve por coronavirus (COVID-19) en pacientes españoles date: 2020-07-28 words: 4030 flesch: 41 summary: La duración media de la anosmia fue de 8,33 días, posteriormente los pacientes manifestaron hiposmia, con resolución completa en 17,79 días de media. f Se consideraron los siguientes criterios de exclusión: pacientes menores de 18 años, presencia de disfunciones olfativas o gustativas antes de la epidemia; pacientes ingresados en el momento del estudio y pacientes en tratamiento con corticoides inhalados. keywords: alteraciones; anosmia; como; con; coronavirus; cov-2; covid-19; del; días; estudio; gusto; las; los; olfato; pacientes; para; pcr; por; que; sars; sin; síntomas; una cache: cord-350211-vuxs5wtt.txt plain text: cord-350211-vuxs5wtt.txt item: #930 of 973 id: cord-350296-6bq0tps2 author: Olsvik, Pål A title: Selection of reference genes for qRT-PCR examination of wild populations of Atlantic cod Gadus morhua date: 2008-07-16 words: 2694 flesch: 49 summary: Overall, this work suggests that the Ubi and ARP can be useful as reference genes in qRT-PCR examination of gene expression studying wild populations of Atlantic cod. Analysis of mRNA expression by real-time PCR Real-time RT-PCR normalisation; strategies and considerations Guideline to reference gene selection for quantitative realtime PCR Validation of housekeeping genes for normalizing RNA expression in real-time PCR Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Normalization of real-time quantitative reverse transcription-PCR data: A model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets Determination of stable housekeeping genes, differently regulated target genes and sample integrity: BestKeeper -Excel-based tool using pair-wise correlations Fisheries management: The case of the North Atlantic cod Miljøvurdering av utfylling av sprengstein i Store Lungegårdsvann Monitoring the environmental conditions in the Sørfjord Quantitative real-time RT-PCR -a perspective Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon Development and validation of endogenous reference genes for expression profiling of medaka (Oryzias latipes) exposed to endocrine disrupting chemicals by quantitative real-time RT-PCR Validation of zebrafish (Danio rerio) reference genes for quantitative realtime RT-PCR normalization Selection of housekeeping genes for gene expression studies in larvae from flatfish using real-time PCR Selection of reference genes for quantitative RT-PCR studies in striped dolphin (Stenella coeruleoalba) skin biopsies Reference gene selection for quantitative real-time PCR analysis in virus infected cells: SARS corona virus, Yellow fever virus, Human Herpesvirus-6, Camelpox virus and Cytomegalovirus infections We gratefully acknowledge Eva Mykkeltvedt and Hui-Shan Tung, NIFES, for analytical help. keywords: cod; expression; genes; pcr; reference; ubi cache: cord-350296-6bq0tps2.txt plain text: cord-350296-6bq0tps2.txt item: #931 of 973 id: cord-350398-w75flrwv author: Sampath, Rangarajan title: Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry date: 2012-06-29 words: 11154 flesch: 47 summary: Assembly of this comprehensive collection of biothreat cluster primers into a single assay on the PLEX-ID has the potential to serve a variety of biosecurity needs. Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry. Technology for detecting biothreat agents requires accurate identification of a broad array of bacterial and viral organisms that can cause severe disease and/or death, whether they occur as a result of a biological attack or from a natural source in the environment. keywords: agents; analysis; anthracis; assay; base; biothreat; clusters; data; detection; organisms; pairs; pcr; pestis; primer; primer pairs; samples; signatures; species; strains; table; tularensis cache: cord-350398-w75flrwv.txt plain text: cord-350398-w75flrwv.txt item: #932 of 973 id: cord-350593-bvmg7f15 author: McDonald, R.S. title: Proportional mouse model for aerosol infection by influenza date: 2012-08-21 words: 6567 flesch: 41 summary: A two-year study of contagion in a tuberculosis ward Possible increased pathogenicity of pandemic (H1N1) 2009 influenza virus upon reassortment The use of an animal model to study transmission of influenza virus infection Experimental transmission of influenza virus infection in mice. Their low cost, small size, relative susceptibility to the virus and ease of handling make mice a favourable platform for studying influenza virus infections. keywords: aerosol; dose; exposure; infection; influenza; mice; min; mouse; pcr; study; tcid; time; virus cache: cord-350593-bvmg7f15.txt plain text: cord-350593-bvmg7f15.txt item: #933 of 973 id: cord-350807-qdq96723 author: Reckziegel, Maria title: Viruses and atypical bacteria in the respiratory tract of immunocompromised and immunocompetent patients with airway infection date: 2020-05-27 words: 4659 flesch: 37 summary: Seminars in respiratory and critical care medicine Respiratory syncytial virus: infection, detection, and new options for prevention and treatment Human metapneumovirus infection after allogeneic hematopoietic stem cell transplantation Laboratory diagnosis of infections in cancer patients: challenges and opportunities Impact of viral multiplex real-time PCR on management of respiratory tract infection: a retrospective cohort study Burden of human metapneumovirus infections in patients with cancer: risk factors and outcomes Infection in organ transplantation Antiviral therapy for respiratory viral infections in immunocompromised patients Respiratory viral infections in solid organ and hematopoietic stem cell transplantation Treatment of alpha and beta herpesvirus infections in solid organ transplant recipients Herpesvirus respiratory infections in immunocompromised patients: epidemiology, management, and outcomes Multiple viral infections after haploidentical hematopoietic stem cell transplantation in a child with acute lymphoblastic leukemia Virus-bacteria interactions: an emerging topic in human infection Viral-bacterial co-infections in the respiratory tract Bacterial pneumonia as an influenza complication An official American Thoracic Society research statement: noninfectious lung injury after hematopoietic stem cell transplantation: idiopathic pneumonia syndrome Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients Effective use of oral ribavirin for respiratory syncytial viral infections in allogeneic haematopoietic stem cell transplant recipients Consecutive yearly outbreaks of respiratory syncytial virus in a haemato-oncology ward and efficacy of infection control measures Parainfluenza 3 infections early after kidney or simultaneous pancreas-kidney transplantation In vivo persistence of human rhinoviruses in immunosuppressed patients The Virome of the human respiratory tract Generation of multipotent cell lines from a distinct population of male germ line stem cells Lack of p73 mutations and late occurrence of p73 allelic deletions in melanoma tissues and cell lines Establishment of PCR for the early diagnosis of herpes simplex encephalitis HSV-2 DNA persistence in astrocytes of the trigeminal root entry zone: double labeling by in situ PCR and immunohistochemistry Detection of varicella-zoster virus DNA by polymerase chain reaction in the cerebrospinal fluid of patients suffering from neurological complications associated with chicken pox or herpes zoster Evaluation of the polymerase chain reaction for diagnosis of herpes simplex virus encephalitis Monitoring of patients for cytomegalovirus after organ transplantation by centrifugation culture and PCR Laboratory diagnosis of herpes zoster Detection of herpes simplex virus (types 1 and 2) and human herpesvirus 6 DNA in human brain tissue by polymerase chain reaction Detection by PCR of HHV-6 and EBV DNA in blood and oropharynx of healthy adults and HIV-seropositives Comparison of a LightCyclerbased real-time PCR for quantitation of Epstein-Barr viral load in different clinical specimens with semiquantitative PCR Human parechovirus infections in Dutch children and the association between serotype and disease severity Prevalence, types, and RNA concentrations of human parechoviruses, including a sixth parechovirus type, in stool samples from patients with acute enteritis Screening respiratory samples for detection of human rhinoviruses (HRVs) and enteroviruses: comprehensive VP4-VP2 typing reveals high incidence and genetic diversity of HRV species C MEGA6: molecular evolutionary genetics analysis version 6.0 Viruses as sole causative agents of severe acute respiratory tract infections in children Seroprevalence of herpes simplex virus type 1 and type 2 in Thuringia Seroprevalence of varicella-zoster virus in the German population Evolution of EBV seroprevalence and primary infection age in a French hospital and a city laboratory network Cytomegalovirus seroprevalence among children and adolescents in Germany: data from the German health interview and examination survey for children and adolescents (KiGGS) Human herpesvirus 6 Herpesvirus infections in organ transplant recipients Clinical impact of HSV-1 detection in the lower respiratory tract from hospitalized adult patients Quantitative detection of Epstein-Barr virus in bronchoalveolar lavage from transplant and nontransplant patients Detection of herpesvirus EBV DNA in the lower respiratory tract of ICU patients: a marker of infection of the lower respiratory tract? Epstein-Barr virus-associated pneumonia in patients with posttransplant lymphoproliferative disease after hematopoietic stem cell transplantation The role of infection in interstitial lung diseases: a review Epstein-Barr virus-associated pneumonia and bronchiolitis obliterans syndrome in a lung transplant recipient Detection of Epstein-Barr virus DNA in peripheral blood is associated with the development of bronchiolitis obliterans syndrome after lung transplantation Chromosomally integrated human herpesvirus 6: questions and answers Human herpesvirus-6 infections in kidney, liver, lung, and heart transplantation: review Varicella pneumonia in adults Detection of respiratory viruses using a multiplex real-time PCR assay in Germany Respiratory syncytial virus infection-associated hospitalization in adults: a retrospective cohort study Human bocaviruses: possible etiologic role in respiratory infection Human bocavirus infection as a cause of severe acute respiratory tract infection in children Frequent detection of bocavirus DNA in German children with respiratory tract infections Current understanding of human enterovirus D68 Enterovirus and parechovirus infection in children: a brief overview A method to identify respiratory virus infections in clinical samples using next-generation sequencing Capnetz Study G (2015) keywords: cmv; detection; dna; ebv; infections; patients; pcr; samples; study; tract; viruses cache: cord-350807-qdq96723.txt plain text: cord-350807-qdq96723.txt item: #934 of 973 id: cord-350890-ajxvjkmq author: Hsieh, Yi-Fan title: A real-time convective PCR machine in a capillary tube instrumented with a CCD-based fluorometer date: 2013-07-05 words: 4226 flesch: 41 summary: A novel real time PCR machine with a miniature spectrometer for fluorescence sensing in a micro liter volume glass capillary Development of a CCD-based fluorimeter for real-time PCR machine The authors deeply appreciate the financial support offered by the National Science Council (NSC) of Taiwan, Republic of China, under Contract Numbers NSC 99-2221-E-002-119-MY3 and NSC 99-2221-E-002-081-MY3 . His current research interests include the micro-fluidic system for biology and real time PCR system for DNA quantitative sequencing. keywords: capillary; copies; cpcr; dna; flow; fluorescence; machine; pcr; temperature; time cache: cord-350890-ajxvjkmq.txt plain text: cord-350890-ajxvjkmq.txt item: #935 of 973 id: cord-351038-k2m6woow author: Arun Krishnan, R. title: COVID-19: Current Trends in Invitro Diagnostics date: 2020-06-27 words: 2901 flesch: 44 summary: In vitro diagnostic assays for COVID-19: recent advances and emerging trends Laboratory testing for 2019 novel coronavirus (2019-Ncov) in suspected human cases Real-time RT-PCR in COVID-19 detection: issues affecting the results Viral load kinetics of SARS-CoV-2 infection in first two patients in Korea Loop-mediated isothermal amplification of DNA Comparison of realtime PCR, reverse transcriptase real-time PCR, loop-mediated isothermal amplification, and the FDA conventional microbiological method for the detection of Salmonella spp. In case of antibody detection assay, both IgG and IgM antibodies against the COVID-19 are the target analytes where IgM appears in blood within a week of time and IgG expression will take more than 10 days. keywords: coronavirus; cov-2; covid-19; detection; pcr; protein; sars; test cache: cord-351038-k2m6woow.txt plain text: cord-351038-k2m6woow.txt item: #936 of 973 id: cord-351100-llyl97ry author: Cariani, Lisa title: Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study date: 2020-07-23 words: 3255 flesch: 48 summary: Additionally, we were able to consider healed, just over 30% of positive HCWs with respect to the period of study. Asymptomatic HCWs were 17.6% (32/182), and 58 healed at 30 April 2020. keywords: cov-2; covid-19; hcws; negative; pcr; sars cache: cord-351100-llyl97ry.txt plain text: cord-351100-llyl97ry.txt item: #937 of 973 id: cord-351125-asrezu1f author: Lee, Sangmin title: Identification of Cystoisospora ohioensis in a Diarrheal Dog in Korea date: 2018-08-31 words: 1723 flesch: 47 summary: C. cayetanensis, C. ohioensis, C. canis, C. timonii, and T. gondii were used as outgroup species. For diagnostic purposes, detection by the 18S rRNA gene has limitations in differentiating C. cayetanensis from C. ohioensis. keywords: 18s; analysis; cayetanensis; ohioensis; pcr cache: cord-351125-asrezu1f.txt plain text: cord-351125-asrezu1f.txt item: #938 of 973 id: cord-351492-8jv7ip67 author: Urwin, S. G. title: FebriDx point-of-care test in patients with suspected COVID-19: a pooled diagnostic accuracy study date: 2020-10-20 words: 7244 flesch: 42 summary: We aimed to undertake a systematic review and pooled diagnostic test accuracy study of available individual patient data (IPD) to evaluate the diagnostic accuracy of a commercial POC test (FebriDx) in patients with suspected COVID-19. We undertook a systematic review and pooled diagnostic test accuracy study of available individual patient data (IPD) to evaluate the diagnostic accuracy of the FebriDx LFD compared to contemporaneous reverse transcriptase polymerase chain reaction (RT-PCR) testing to understand the performance of FebriDx in the identification of patients with COVID-19. keywords: accuracy; covid-19; febridx; medrxiv; patients; preprint; results; review; studies; study; test cache: cord-351492-8jv7ip67.txt plain text: cord-351492-8jv7ip67.txt item: #939 of 973 id: cord-351643-8ce807ub author: Poon, LLM title: Rapid detection of reassortment of pandemic H1N1/2009 influenza virus date: 2010-08-01 words: 2090 flesch: 47 summary: An investigation into human pandemic influenza virus (H1N1) 2009 on an Alberta swine farm Rapid diagnosis of a coronavirus associated with severe acute respiratory syndrome (SARS) Molecular detection of a novel human influenza (H1N1) of pandemic potential by conventional and real-time quantitative RT-PCR assays Universal primer set for the full-length amplification of all influenza A viruses Cocirculation of avian H9N2 and contemporary human H3N2 influenza A viruses in pigs in southeastern China: potential for genetic reassortment? Hog in the limelight: swine flu's got new genes on Reassortment of pandemic H1N1/2009 influenza A virus in swine The global circulation and occasional introductions of pandemic H1N1/2009 virus in humans and in pigs, respectively, might provide opportunities for this virus to reassort with other influenza viruses. keywords: assays; influenza; pandemic; swine; virus; viruses cache: cord-351643-8ce807ub.txt plain text: cord-351643-8ce807ub.txt item: #940 of 973 id: cord-351854-5s03f0pp author: Ben-Ami, Roni title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date: 2020-04-22 words: 3321 flesch: 49 summary: As shown in Figure 1 , positive samples were readily detected, even when their individual Ct ranged between 35 and 38. Alternatively, it is possible to dynamically adapt pooling sizes, when the measured rate of positive samples is different than expected. keywords: medrxiv; pooling; preprint; rna; samples; sars cache: cord-351854-5s03f0pp.txt plain text: cord-351854-5s03f0pp.txt item: #941 of 973 id: cord-351864-zozrj7w5 author: Chappleboim, A. title: ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection date: 2020-08-13 words: 5787 flesch: 51 summary: After pooling samples are washed once in buffer A, twice in buffer B, and can then be kept in RNA later until they are processed further. To test cross-contamination levels in the RT stage, we hybridized positive (Ct 26) and negative samples with two differently barcoded primers, pooled them, performed RT and tested the amount of cross-contamination by barcode-specific qPCR ( Figure 3A and 3B). keywords: beads; figure; license; medrxiv; pcr; preprint; primers; rna; samples; sequencing cache: cord-351864-zozrj7w5.txt plain text: cord-351864-zozrj7w5.txt item: #942 of 973 id: cord-352554-hsbyznex author: Lee, Yeon Joo title: Quality of Ribonucleic Acid Extraction for Real-Time Reverse Transcription-PCR (rRT-PCR) of SARS-CoV-2: Importance of Internal Control Monitoring date: 2020-11-01 words: 1124 flesch: 50 summary: We found more prominent deterioration in PCR efficiency of IC with sputum samples than with NP samples. The average Ct value of IC was 22.60 ± 0.99 at the first run, which increased to a maximum of 34.97 ± 2.99 among the runs performed on 26th February 2020 for NP samples; a similar increase from 23.94 ± 1.48 to 38.67 was detected for sputum samples (Fig. 1) . keywords: pcr; samples cache: cord-352554-hsbyznex.txt plain text: cord-352554-hsbyznex.txt item: #943 of 973 id: cord-352562-qfb478sf author: Yamamoto, Lidia title: SARS-CoV-2 infections with emphasis on pediatric patients: a narrative review date: 2020-09-04 words: 7323 flesch: 34 summary: Xiang et al. 52 tested 126 serum samples from COVID-19 patients, with 57.1% IgM sensitivity, 100% specificity and 69% accuracy. Criteria for releasing COVID-19 patients from isolation SARS and MERS: recent insights into emerging coronaviruses Understanding evolution of SARS-CoV-2: a perspective from analysis of genetic diversity of RdRp gene Emerging genetic diversity among clinical isolates of SARS-CoV-2: lessons for today The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak Real estimates of mortality following COVID-19 infection Epidemiological and clinical characteristics of 26 asymptomatic SARS-CoV-2 carriers SARS-CoV-2 receptor and regulator of the Renin-Angiotensin system: celebrating the 20th anniversary of the discovery of ACE2 Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) infection in children and adolescents: a systematic review The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak -an update on the status Gastrointestinal manifestations of SARS-CoV-2 infection and virus load in fecal samples from the Hong Kong cohort and systematic review and meta-analysis Kidney involvement in COVID-19 and rationale for extracorporeal therapies Neurologic manifestations of hospitalized patients with coronavirus disease Computed tomographic imaging of 3 patients with Coronavirus disease 2019 pneumonia with negative virus real-time reversetranscription Polymerase Chain Reaction test Nasal gene expression of Angiotensin-converting enzyme 2 in children and adults Ocular manifestations of a hospitalised patient with confirmed 2019 novel coronavirus disease Chilblain-like lesions in children following suspected COVID-19 infection Androgen regulates SARS-CoV-2 receptor levels and is associated with severe COVID-19 symptoms in men Physiological and pathological regulation of ACE2, the SARS-CoV-2 receptor COVID-19 infection and circulating ACE2 levels: protective role in women and children Coronavirus infections in children including COVID-19: an overview of the epidemiology, clinical features, diagnosis, treatment and prevention options in children Coronavirus disease 2019 in critically ill children: a narrative review of the literature SARS-COV-2 infection in children and newborns: a systematic review SARS-CoV-2 infection in children COVID-19 in children and adolescents in Europe: a multinational, multicentre cohort study Coinfection of SARS-CoV-2 and multiple respiratory pathogens in children Multisystem inflammatory syndrome in U.S. children and adolescents Multisystem inflammatory syndrome in children in New York State Flash survey on severe acute respiratory syndrome Coronavirus-2 infections in paediatric patients on anticancer treatment e65 SARS-CoV-2 infections with emphasis on pediatric patients: a narrative review How is immunosuppressive status affecting children and adults in SARS-CoV-2 infection? keywords: ace2; antibodies; children; cov-2; covid-19; days; disease; infection; patients; pcr; sars; symptoms; syndrome; women cache: cord-352562-qfb478sf.txt plain text: cord-352562-qfb478sf.txt item: #944 of 973 id: cord-352640-fycwhyfv author: Goel, Ashish title: Profile of Patients Suspected to be COVID-19: A Retrospective Analysis of Early Pandemic Data date: 2020-08-29 words: 2758 flesch: 55 summary: In a retrospective study by Xiao et al. of 301 confirmed COVID-19 patients hospitalized at Tongji Hospital in Wuhan, China, the median age was 58 years and 51.2% were male [12] . As clinical data is being reported from around the globe, it becomes important to focus on local subjects in a global milieu, lest one misses the trees for the forest. keywords: age; analysis; covid-19; data; patients; subjects cache: cord-352640-fycwhyfv.txt plain text: cord-352640-fycwhyfv.txt item: #945 of 973 id: cord-352720-z1cvjc2y author: Díaz-Corvillón, Pilar title: Routine screening for SARS CoV-2 in unselected pregnant women at delivery date: 2020-09-29 words: 4063 flesch: 43 summary: All neonates born from mothers with confirmed SARS CoV-2 were isolated and tested for SARS CoV-2 infection. To assess the prevalence of SARS CoV-2 infection in an unselected obstetrical population and to describe their presentation and clinical evolution. keywords: cases; cov-2; infection; patients; population; prevalence; sars; study cache: cord-352720-z1cvjc2y.txt plain text: cord-352720-z1cvjc2y.txt item: #946 of 973 id: cord-352814-fcl2g5wr author: Balboni, Andrea title: A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys date: 2011-11-22 words: 4005 flesch: 39 summary: The interassay variability was tested on bat samples by testing the three samples with different viral concentrations (B1, B2, and B3) in triplicate on three different days (Table 2) . Bat samples were considered positive if the mean of three replicates was greater than the LOD. keywords: bat; bats; coronavirus; like; pcr; plasmid; rna; sars; standard; time cache: cord-352814-fcl2g5wr.txt plain text: cord-352814-fcl2g5wr.txt item: #947 of 973 id: cord-352831-ydlix2o7 author: Hase, Ryota title: A case of imported COVID-19 diagnosed by PCR-positive lower respiratory specimen but with PCR-negative throat swabs date: 2020-04-02 words: 1223 flesch: 50 summary: The CDC guideline suggests that lower respiratory specimens are the preferred clinical specimens for diagnosis of MERS [6] . However, PCR on sputum obtained on day 5 was positive but a second throat swab obtained on the same day was still negative, suggesting that lower respiratory specimens have higher sensitivity. keywords: pcr; sputum; throat cache: cord-352831-ydlix2o7.txt plain text: cord-352831-ydlix2o7.txt item: #948 of 973 id: cord-352872-y1qh5nig author: Herpe, Guillaume title: Efficacy of Chest CT for COVID-19 Pneumonia in France date: 2020-09-01 words: 3836 flesch: 45 summary: The survey included the following parameters: clinical patient data (age, sex), results of initial chest CT and initial and/or repeat RT-PCR tests, time intervals between chest CT and RT-PCR, and final discharge summary according to the hospital discharge report. The role and performance of chest CT in the diagnosis of the coronavirus disease 2019 (COVID-19) pandemic remains under active investigation. keywords: chest; covid-19; diagnosis; patients; pcr; prevalence cache: cord-352872-y1qh5nig.txt plain text: cord-352872-y1qh5nig.txt item: #949 of 973 id: cord-352894-88c46evj author: Yoon, Soon‐Seek title: Comparison of the diagnostic methods on the canine adenovirus type 2 infection date: 2010-06-02 words: 2577 flesch: 42 summary: 5 Histopathology is a reliable indicator of CAV-2 infection because large IN/IBs are easily visualized in the infected lung. Histopathology was not a reliable indicator of CAV-2 infection since IN/IBs were not evident in all cases. keywords: canine; cav-2; cells; dogs; ihc; infection; pcr cache: cord-352894-88c46evj.txt plain text: cord-352894-88c46evj.txt item: #950 of 973 id: cord-353190-7qcoxl81 author: Nicklas, Werner title: Viral Infections of Laboratory Mice date: 2012-05-17 words: 27792 flesch: 37 summary: The term murine hepatitis virus (MHV; commonly referred to as 'mouse hepatitis virus') A model for the study of viral infection, pathogenesis, and clearance Histopathological characterization of the naturally occurring hepatotropic virus infections of nude mice Detection methods for the identification of rodent viral and mycoplasmal infections Reverse transcriptionpolymerase chain reaction detection and nucleic acid sequence confirmation of reovirus infection in laboratory mice with discordant serologic indirect immunofluorescence assay and enzyme-linked immunosorbent assay results Diagnosis of murine infections in relation to test methods employed Reovirus 3 not detected by reverse transcriptase-mediated polymerase chain reaction analysis of preserved tissue from infants with cholestatic liver disease Detection of reovirus type 3 by use of fluorogenic nuclease reverse transcriptase polymerase chain reaction Detection of reovirus by reverse transcription-polymerase chain reaction using primers corresponding to conserved regions of the viral L1 genome segment Isolation of a non-pathogenic tumour-destroying virus from mouse ascites An oncolytic virus recovered from Swiss mice during passage of an ascites tumour Mouse hepatitis virus Enterotropic mouse hepatitis virus Effects of air temperature and relative humidity on coronavirus survival on surfaces Asymptomatic infection of mouse hepatitis virus in the rat Effects of experimental infection of the deer mouse (Peromyscus maniculatus) with mouse hepatitis virus Isolation of a latent murine hepatitis virus from cultured mouse liver cells Induction of lytic plaques by murine leukemia virus in murine sarcoma virus-transformed nonproducer mouse cells persistently infected with mouse hepatitis virus MHV-S Mouse hepatitis virus biology and epizootiology The cellular and molecular pathogenesis of coronaviruses Enterotropic coronavirus (mouse hepatitis virus) in mice: influence of host age and strain on infection and disease Response of genetically susceptible and resistant mice to intranasal inoculation with mouse hepatitis virus JHM Duration of mouse hepatitis virus infection: studies in immunocompetent and chemically immunosuppressed mice Effective clearance of mouse hepatitis virus from the central nervous system requires both CD4þ and CD8þ T cells Role of CD4þ and CD8þ T cells in mouse hepatitis virus infection in mice Antibody prevents virus reactivation within the central nervous system Mouse hepatitis virus Enterotropic mouse hepatitis virus infection in nude mice Persistent transmission of mouse hepatitis virus by transgenic mice Duration of challenge immunity to coronavirus JHM in mice Virus strain specificity of challenge immunity to coronavirus Duration and strain-specificity of immunity to enterotropic mouse hepatitis virus Passively acquired challenge immunity to enterotropic coronavirus in mice Epizootic coronaviral typhlocolitis in suckling mice Isolation of mouse hepatitis virus from infant mice with fatal diarrhea Thymus involution induced by mouse hepatitis virus A59 in BALB/c mice Adverse effects of mouse hepatitis virus on ascites myeloma passage in the BALB/eJ mouse Murine hepatitis virus strain 1 produces a clinically relevant model of severe acute respiratory syndrome in A/J mice Tolllike receptor 4 deficiency increases disease and mortality after mouse hepatitis virus type 1 infection of susceptible C3H mice Granulomatous peritonitis and pleuritis in interferon-gamma gene knockout mice naturally infected with mouse hepatitis virus Pathogenesis of enterotropic mouse hepatitis virus in immunocompetent and immunodeficient mice Vertical transmission of mouse hepatitis virus infection in mice Tissue distribution and duration of mouse hepatitis virus in naturally infected immunocompetent ICR (CD-1) and immunodeficient athymic nudenu mouse strains used for ovarian transplantation and in vitro fertilization Rederivation of inbred strains of mice by means of embryo transfer Risk assessment of mouse hepatitis virus infection via in vitro fertilization and embryo transfer by the use of zona-intact and laser-microdissected oocytes Mouse hepatitis virus immunofluorescence in formalin-or Bouin's-fixed tissues using trypsin digestion Comparison of isolation in cell culture with conventional and modified mouse antibody production tests for detection of murine viruses Monoclonal antibody solution hybridization assay for detection of mouse hepatitis virus infection Detection of rodent coronaviruses in tissues and cell cultures by using polymerase chain reaction Sequence analysis and molecular detection of mouse hepatitis virus using the polymerase chain reaction Detection of mouse hepatitis virus by the polymerase chain reaction and its application to the rapid diagnosis of infection Detection of rodent coronaviruses by use of fluorogenic reverse transcriptase-polymerase chain reaction analysis An immunofluorescence test for detection of serum antibody to rodent coronaviruses Simultaneous detection of antibodies to mouse hepatitis virus recombinant structural proteins by a microsphere-based multiplex fluorescence immunoassay Differences in antibody production against mouse hepatitis virus (MHV) among mouse strains Maternally-derived passive immunity to enterotropic mouse hepatitis virus Mouse hepatitis virus: molecular biology and implications for pathogenesis Maintenance of pluripotency in mouse embryonic stem cells persistently infected with murine coronavirus Replication of murine coronaviruses in mouse embryonic stem cell lines. keywords: age; animals; antibodies; antibody; cells; choriomeningitis; clinical; colonies; days; detection; disease; experimental; hepatitis; hepatitis virus; host; immune; infection; inoculation; laboratory; laboratory mice; lesions; mhv; mice; mouse; mousepox; murine; parvovirus; pcr; research; results; strains; testing; transmission; virus; virus infection; viruses; weeks cache: cord-353190-7qcoxl81.txt plain text: cord-353190-7qcoxl81.txt item: #951 of 973 id: cord-353241-ityhcak7 author: Zhu, Hanliang title: IoT PCR for pandemic disease detection and its spread monitoring date: 2020-01-15 words: 4302 flesch: 46 summary: Data transfer between the BT unit and PCR system is conducted bi-directionally via a universal asynchronous receiver-transmitter interface. His research interests include microfluidics and miniaturization and application of PCR systems keywords: data; dengue; denv; device; disease; iot; location; pcr; system; time cache: cord-353241-ityhcak7.txt plain text: cord-353241-ityhcak7.txt item: #952 of 973 id: cord-353246-q9qpec7t author: Nijhuis, R. H. T. title: Comparison of ePlex Respiratory Pathogen Panel with Laboratory-Developed Real-Time PCR Assays for Detection of Respiratory Pathogens date: 2017-05-23 words: 3433 flesch: 39 summary: The ePlex respiratory pathogen panel (RP panel) is a novel molecular biology-based assay, developed by GenMark Diagnostics, Inc. (Carlsbad, CA), to be performed within a single cartridge for the diagnosis of 25 respiratory pathogens (viral and bacterial). The ePlex respiratory pathogen panel (RP panel) is based on electrowetting technology, a digital microfluidic technology by which droplets of sample and reagents can be moved efficiently within a network of contiguous electrodes in the ePlex cartridge, enabling rapid thermal cycling for a short time to result. keywords: panel; pathogens; pcr; respiratory; specimens; time cache: cord-353246-q9qpec7t.txt plain text: cord-353246-q9qpec7t.txt item: #953 of 973 id: cord-353253-kk2q71vg author: Itokawa, Kentaro title: Disentangling primer interactions improves SARS-CoV-2 genome sequencing by multiplex tiling PCR date: 2020-09-18 words: 3331 flesch: 47 summary: In general, amplicons suffering from primer interactions were expected to drop rapidly as Ta decreases. These amplicons seemed equally weak in all three primer sets rather than specific in N1 primer set. keywords: amplicons; artic; coverage; pcr; primer; set cache: cord-353253-kk2q71vg.txt plain text: cord-353253-kk2q71vg.txt item: #954 of 973 id: cord-353353-njvalb44 author: Lau, Susanna K. P. title: Identification of Novel Rosavirus Species That Infects Diverse Rodent Species and Causes Multisystemic Dissemination in Mouse Model date: 2016-10-13 words: 6997 flesch: 38 summary: Immunohistochemical staining with guinea pig anti-serum against rosavirus C VP1 protein antibody revealed viral antigen expression in bronchiolar and bronchial epithelial cells in lung sections, and hepatocytes in liver sections (Fig 7) . Neutralization assays showed that five of the six rats with anti-rosavirus C antibodies by western blot analyses were positive for neutralizing antibodies against rosavirus C RASM14A with titer 1:10 to 1:40. keywords: day; human; mice; novel; pcr; picornaviruses; rasm14a; rat; rats; rodent; rosavirus; samples; sequences; species; strains; vp1 cache: cord-353353-njvalb44.txt plain text: cord-353353-njvalb44.txt item: #955 of 973 id: cord-353499-os328w9o author: Yang, H. S. title: Routine laboratory blood tests predict SARS-CoV-2 infection using machine learning date: 2020-06-19 words: 2857 flesch: 48 summary: Overall, this model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-COV-2 infected patients before their RT-PCR results are available. Currently in hospital EDs, the nationally recommended practice when evaluating patients with moderate to high risk for COVID-19 is SARS-CoV-2 RT-PCR testing, a panel of routine laboratory tests, a chest X-ray and symptomatology, whereas chest computed tomography (CT) is not recommended due to cost and TAT considerations . keywords: license; medrxiv; pcr; perpetuity; preprint cache: cord-353499-os328w9o.txt plain text: cord-353499-os328w9o.txt item: #956 of 973 id: cord-353573-y9jro9gt author: You, Huey-Ling title: Simultaneous detection of respiratory syncytial virus and human metapneumovirus by one-step multiplex real-time RT-PCR in patients with respiratory symptoms date: 2017-03-27 words: 3458 flesch: 47 summary: Based on this improved triplex qRT-PCR assay, we found that RSV infection was associated with severe inflammation by chest X-ray and occurrence of pneumonia which were not observed previously. key: cord-353573-y9jro9gt authors: You, Huey-Ling; Chang, Shun-Jen; Yu, Hong-Ren; Li, Chia-Chin; Chen, Chang-Han; Liao, Wei-Ting title: Simultaneous detection of respiratory syncytial virus and human metapneumovirus by one-step multiplex real-time RT-PCR in patients with respiratory symptoms date: 2017-03-27 journal: BMC Pediatr DOI: 10.1186/s12887-017-0843-7 sha: doc_id: 353573 cord_uid: y9jro9gt BACKGROUND: Both respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are important viral pathogens causing respiratory tract infection (RTI) in the pediatric population. keywords: assay; detection; hmpv; pcr; probe; respiratory; rsv; step; virus cache: cord-353573-y9jro9gt.txt plain text: cord-353573-y9jro9gt.txt item: #957 of 973 id: cord-353810-mf753ae9 author: Tan, Cedric Chih Shen title: A novel method for the capture-based purification of whole viral native RNA genomes date: 2019-04-08 words: 5950 flesch: 49 summary: key: cord-353810-mf753ae9 authors: Tan, Cedric Chih Shen; Maurer-Stroh, Sebastian; Wan, Yue; Sessions, October Michael; de Sessions, Paola Florez title: A novel method for the capture-based purification of whole viral native RNA genomes date: 2019-04-08 journal: AMB Express DOI: 10.1186/s13568-019-0772-y sha: doc_id: 353810 cord_uid: mf753ae9 Current technologies for targeted characterization and manipulation of viral RNA primarily involve amplification or ultracentrifugation with isopycnic gradients of viral particles to decrease host RNA background. We report that this protocol was able to successfully purify viral RNA by 561- to 791-fold. keywords: capture; denv1; direct; host; method; pcr; post; purification; rna; sequencing; strategy; viral cache: cord-353810-mf753ae9.txt plain text: cord-353810-mf753ae9.txt item: #958 of 973 id: cord-353957-0pjg25kn author: Chen, Shilong title: Avian Interferon-Inducible Transmembrane Protein Family Effectively Restricts Avian Tembusu Virus Infection date: 2017-04-20 words: 6581 flesch: 46 summary: Our previous experiments demonstrated that ATMUV infection effectively triggered host innate immune response through MDA5 and TLR3-dependent signaling pathways. However, little information is available on the role of interferon-stimulated genes (ISGs) in defending against ATMUV infection. keywords: atmuv; cells; chicken; df-1; duck; et al; expression; hpi; ifitm1; ifns; infection; type; virus cache: cord-353957-0pjg25kn.txt plain text: cord-353957-0pjg25kn.txt item: #959 of 973 id: cord-354035-i3sl2r0k author: Wylie, Kristine M. title: The Virome of the Human Respiratory Tract date: 2016-12-10 words: 3902 flesch: 41 summary: Highlander SK Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China Communityacquired pneumonia among U.S. children Community-acquired pneumonia requiring hospitalization among U.S. adults Detection of viruses in young children with fever without an apparent source Sequence analysis of the human virome in febrile and afebrile children Increased prevalence of anellovirus in pediatric patients with fever Digging through the obstruction: insight into the epithelial cell response to respiratory virus infection in patients with cystic fibrosis The role of viral infections in exacerbations of chronic obstructive pulmonary disease and asthma Incidence and clinical impact of respiratory viruses in adults with cystic fibrosis Virus and cystic fibrosis: rhinoviruses are associated with exacerbations in adult patients The role of respiratory viruses in cystic fibrosis Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients Temporal response of the human virome to immunosuppression and antiviral therapy Viral discovery and sequence recovery using DNA microarrays Identification of new respiratory viruses in the new millennium. In a recent study of 26 households in Utah that were followed weekly over 1 year, modern molecular methods were used to detect respiratory viruses in the anterior nares. keywords: assays; pcr; respiratory; study; tract; virome; viruses cache: cord-354035-i3sl2r0k.txt plain text: cord-354035-i3sl2r0k.txt item: #960 of 973 id: cord-354103-4dldgqzf author: Grubic, Andrew D title: COVID-19 outbreak and surgical practice: The rationale for suspending non-urgent surgeries and role of testing modalities date: 2020-06-27 words: 4875 flesch: 44 summary: ACE2 receptors are also located in the enterocytes of the small intestine which is considered to be an explanation for digestive symptoms in COVID-19 patients [13, 14] . Several studies have highlighted the presence of virus in the feces of COVID-19 patients, and now fecal-oral transmission has also been proposed as a mechanism of spread [8, 9] , which may profoundly impact underdeveloped countries. keywords: care; cases; coronavirus; cov-2; covid-19; disease; pandemic; patients; pcr; sars; transmission cache: cord-354103-4dldgqzf.txt plain text: cord-354103-4dldgqzf.txt item: #961 of 973 id: cord-354308-ol8twpay author: Mardani, title: COVID-19 infection recurrence presented with meningoencephalitis date: 2020-07-23 words: 1461 flesch: 35 summary: key: cord-354308-ol8twpay authors: Mardani,; Nadji, Seyed Alireza; Aghazadeh Sarhangipor, Kouros; Sharifi-Razavi, Athena; Baziborun, Mana title: COVID-19 infection recurrence presented with meningoencephalitis date: 2020-07-23 journal: New Microbes New Infect DOI: 10.1016/j.nmni.2020.100732 sha: doc_id: 354308 cord_uid: ol8twpay Results for COVID-19 RT-PCR from her cerebrospinal fluid, nasopharyngeal and tracheal aspiration specimens became positive again whereas, negative COVID-19 serum antibodies. keywords: covid-19; csf; patients; pcr; sars cache: cord-354308-ol8twpay.txt plain text: cord-354308-ol8twpay.txt item: #962 of 973 id: cord-354683-l07w3lc7 author: Wang, Ruyi title: One-step multiplex TaqMan probe-based method for real-time PCR detection of four canine diarrhea viruses date: 2020-06-10 words: 944 flesch: 49 summary: In this study, we developed a one-step multiplex TaqMan probe-based real-time PCR for the differential diagnosis of four viruses causing canine diarrhea including, CPV (Canine Parvovirus 2), CCoV (Canine Coronavirus), In this study, we developed a one-step multiplex TaqMan probe-based real-time PCR for the differential diagnosis of four viruses causing canine diarrhea. keywords: canine; copies/µl; pcr cache: cord-354683-l07w3lc7.txt plain text: cord-354683-l07w3lc7.txt item: #963 of 973 id: cord-354725-lqio7l8k author: Arumugam, Arunkumar title: A Rapid COVID-19 RT-PCR Detection Assay for Low Resource Settings date: 2020-04-30 words: 3492 flesch: 60 summary: (Table 3) Rapid PCR Rapid PCR was conducted using two water baths maintained at 95°C and 55°C ( Table 4) . PCR tubes used in this study was Cepheid SmartCycler reaction tubes and thin-walled polypropylene PCR tubes (Cat. keywords: covid-19; minutes; pcr; samples; tubes; water cache: cord-354725-lqio7l8k.txt plain text: cord-354725-lqio7l8k.txt item: #964 of 973 id: cord-354733-qxivrhj8 author: Gniazdowski, V. title: Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date: 2020-08-06 words: 3930 flesch: 47 summary: 354733 cord_uid: qxivrhj8 Repeat molecular testing for SARS-CoV-2 may result in scenarios including multiple positive results, positive test results after negative tests, and repeated false negative results in symptomatic individuals. Repeat molecular testing for SARS-CoV-2 may result in scenarios including multiple positive 24 results, positive test results after negative tests, and repeated false negative results in 25 symptomatic individuals. keywords: license; negative; patients; preprint; results; rna; sars; virus cache: cord-354733-qxivrhj8.txt plain text: cord-354733-qxivrhj8.txt item: #965 of 973 id: cord-354773-u86bdmvf author: Suo, Tao title: ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens date: 2020-06-07 words: 4507 flesch: 50 summary: Diagnosis and treatment of pneumonitis with a new type of coronavirus infection (trial version 5) Covert coronavirus infections could be seeding new outbreaks Characteristics of and important lessons from the coronavirus disease 2019 (COVID-19) outbreak in China: summary of a report of 72 314 cases from the chinese center for disease control and prevention Quantification using real-time PCR technology: applications and limitations Comparison and analysis of the detection performance of six new coronavirus nucleic acid detection reagents Applications of digital PCR for clinical microbiology Principle and applications of digital PCR Evaluation of digital PCR for absolute RNA quantification Digital PCR provides sensitive and absolute calibration for high throughput sequencing Highthroughput droplet digital PCR system for absolute quantitation of DNA copy number Absolute quantification by droplet digital PCR versus analog real-time PCR Dropletbased digital PCR and next generation sequencing for monitoring circulating tumor DNA: a cancer diagnostic perspective Detection and quantification of HDR and NHEJ induced by genome editing at endogenous gene loci using droplet digital PCR National Institute For viral Disease Control and prevention of PRC. These vast and highly consistent oil droplets substantially improve the detection dynamic range and accuracy of digital PCR in a low-cost and practical format [15] . keywords: cov-2; ddpcr; detection; negative; official; pcr; samples; sars cache: cord-354773-u86bdmvf.txt plain text: cord-354773-u86bdmvf.txt item: #966 of 973 id: cord-354943-wxhbwcfr author: Guo, Li title: Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19) date: 2020-03-21 words: 3497 flesch: 52 summary: To evaluate the potential cross-reactivities of N proteins between SARS-CoV-2 and other human coronaviruses, we examined the reactivities of the SARS-CoV-2 rNP and human plasma with positive antibodies against NL63, 229E, OC43, HKU1, and SARS-CoV, respectively, by using Western blot and ELISA assays. Novel coronavirus (2019-nCoV) early-stage importation risk to Europe Summary of probable SARS cases with onset of illness from 1 Acknowledgments. keywords: coronavirus; cov-2; days; detection; igm; patients; samples; sars cache: cord-354943-wxhbwcfr.txt plain text: cord-354943-wxhbwcfr.txt item: #967 of 973 id: cord-355014-los6q1k4 author: Ai, J. title: Analysis of factors associated early diagnosis in coronavirus disease 2019 (COVID-19) date: 2020-04-14 words: 3932 flesch: 53 summary: Therefore, this study also confirms the relatively high false negative rate, which can be miss diagnosis rate, of first nucleic acid test. Many studies had shown that the positive rate of RT-PCR could be low, especially the first time of nucleic acid test (12, 14) . keywords: covid-19; funder; medrxiv; patients; preprint; test cache: cord-355014-los6q1k4.txt plain text: cord-355014-los6q1k4.txt item: #968 of 973 id: cord-355102-jcyq8qve author: Avila, Eduardo title: Hemogram data as a tool for decision-making in COVID-19 management: applications to resource scarcity scenarios date: 2020-06-29 words: 4771 flesch: 34 summary: Also, our simulations suggest that the NB model has at least some degree of tolerance to missing data values, which can be advantageous when compared to other ML techniques. The Naïve Bayes (NB) method combines the previous probability of an event (also called prior probability, or simply prior) with additional evidence (as, e.g., a set of clinical data from a patient) to calculate a combined, conditional probability that includes the prior probability given the extra information. keywords: covid-19; data; hemogram; model; patients; pcr; prior; probability; results cache: cord-355102-jcyq8qve.txt plain text: cord-355102-jcyq8qve.txt item: #969 of 973 id: cord-355489-tkvfneje author: Mendez, Jairo A title: Phylogenetic history demonstrates two different lineages of dengue type 1 virus in Colombia date: 2010-09-14 words: 4616 flesch: 43 summary: Clinical Investigations Genetic variation and microevolution of dengue 2 virus in Southeast Asia Molecular evolution and distribution of dengue viruses type 1 and 2 in nature Phylogenetic relationships of dengue-2 viruses Molecular epidemiology of dengue-1 and dengue-4 viruses Molecular evolution and phylogeny of dengue-4 viruses Molecular evolution of dengue type 2 virus in Thailand Molecular epidemiology of dengue viruses in Brazil Molecular epidemiology of dengue type 2 virus in Venezuela: evidence for in situ virus evolution and recombination Phylogenetic relationships and differential selection pressures among genotypes of dengue-2 virus Molecular evolution and phylogeny of dengue type 4 virus in the Caribbean The origin, emergence and evolutionary genetics of dengue virus Molecular epidemiological study of dengue virus type 1 in Taiwan Genotipificación y análisis filogenético de cepas colombianas del virus dengue tipo 2 Molecular epidemiology of dengue virus type 3 in Venezuela Phylogeography and molecular evolution of dengue 2 in the Caribbean basin Introduction of the American/Asian genotype of dengue 2 virus into the Yucatan State of Mexico Dengue virus 3 genotype 1 assosiated with dengue fever and dengue hemorrhagic fever Use of a Short Fragment of the C-Terminal E Gene for Detection and Characterization of Two New Lineages of Dengue Virus 1 in India Simultaneous circulation of genotypes I and III of dengue virus 3 in Colombia Phylogenetic studies reveal existence of multiple lineages of a single genotype of DENV-1 (genotype III) in India during 1956-2007 Dengue virus structural differences that correlate with pathogenesis Effect of age on outcome of secondary dengue 2 infections Burden of symptomatic dengue infection in children at primary school in Thailand: a prospective study Race: a risk factor for dengue hemorrhagic fever Dengue virus evolution and virulence models Microevolution and virulence of dengue viruses Lineage extinction and replacement in dengue type 1 virus populations are due to stochastic events rather than to natural selection Invasion and maintenance of dengue virus type 2 and type 4 in the Americas Molecular epidemiology of dengue 2 viruses in the Philippines: genotype shift and local evolution Molecular evolution of dengue 2 virus in Puerto Rico: Positive selection in the viral envelope accompanies clade reintroduction CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions specific gap penalties and weight matrix choice MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 BEAST: Bayesian evolutionary analysis by sampling trees Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies Bayesian inference of phylogeny: a non-technical primer Relaxed phylogenetics and dating with confidence RNA virus mutations and fitness for survival The causes and consequences of genetic variation in dengue virus Phylogenetic evidence for adaptive evolution of dengue viruses in nature Selection-driven evolution of emergent dengue virus Patterns of intra-and interhost nonsynonymous variation reveal strong purifying selection in dengue virus keywords: colombia; dengue; denv-1; evolution; genotype; isolates; lineages; molecular; pcr; strains; time; virus; viruses cache: cord-355489-tkvfneje.txt plain text: cord-355489-tkvfneje.txt item: #970 of 973 id: cord-355874-nz6eqcdb author: Wang, Le title: A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia date: 2016-09-14 words: 3069 flesch: 46 summary: The assay covered a broad range of virus targets and a large size of samples were tested. Nucleic acid amplification methods such as PCR and RT-PCR have increasingly been explored for identification of pathogens including virus detection in infectious respiratory diseases [9, 16, 18] . keywords: assay; cap; children; gexp; pcr; viruses cache: cord-355874-nz6eqcdb.txt plain text: cord-355874-nz6eqcdb.txt item: #971 of 973 id: cord-355988-4eldkteb author: SAMPATH, RANGARAJAN title: Rapid Identification of Emerging Infectious Agents Using PCR and Electrospray Ionization Mass Spectrometry date: 2007-04-23 words: 3430 flesch: 34 summary: Based upon the analysis of multiple influenza sequence alignments, paninfluenza virus PCR primer sets have been developed that are capable of amplifying all three influenza virus species (A, B, and C) and subtypes (HxNy) from different animal hosts (human, avian, swine, etc.) and to distinguish their essential molecular features using base composition signatures (Sampath et al., Personal Observation) . The technology has been validated for a variety of applications, including emerging virus identification, 23 determination of the pathogens involved in acute pneumonia epidemics, 24 and identification of biological weapons agents in a variety of sample types. keywords: base; detection; identification; isolates; organisms; pcr; range; regions; sample; viruses cache: cord-355988-4eldkteb.txt plain text: cord-355988-4eldkteb.txt item: #972 of 973 id: cord-356007-6b0w36l9 author: Alanazi, Khalid H. title: Scope and extent of healthcare-associated Middle East respiratory syndrome coronavirus transmission during two contemporaneous outbreaks in Riyadh, Saudi Arabia, 2017 date: 2018-12-31 words: 4034 flesch: 43 summary: Furthermore, 2 physicians at clinic C tested seropositive after an indeterminate rRT-PCR test, suggesting transmission at clinic C. Thus, increased testing for MERS-CoV in an outpatient setting for individuals with known risk factors and worsening respiratory symptoms might facilitate early recognition of MERS cases. The hospital B cluster appears to have been more Age, y, median (range) 58 ( Among 38 cases linked to hospital A, 17 were patient cases, 17 were HCP cases, and 4 were family members (Table 1) . keywords: cases; cov; hcp; hospital; index; mers; patient; transmission cache: cord-356007-6b0w36l9.txt plain text: cord-356007-6b0w36l9.txt item: #973 of 973 id: cord-356370-jjl1hbeb author: Sahajpal, Nikhil Shri title: Role of clinical laboratories in response to the COVID-19 pandemic date: 2020-06-19 words: 1603 flesch: 35 summary: key: cord-356370-jjl1hbeb authors: Sahajpal, Nikhil Shri; Njau, Allan; Mondal, Ashis K; Ananth, Sudha; Chaubey, Alka; Rojiani, Amyn; Kolhe, Ravindra title: Role of clinical laboratories in response to the COVID-19 pandemic date: 2020-06-19 journal: In the US, clinical laboratories are required to perform 'bridging studies' on FDA approved SARS-CoV-2 diagnostic assays to implement testing under the EUA regulation. keywords: cov-2; covid-19; laboratories; sars; testing cache: cord-356370-jjl1hbeb.txt plain text: cord-356370-jjl1hbeb.txt