# bib

id: cord-027649-6xn9swsq
author: Addetia, Amin
date: 2020-06-23
extension: .txt
mime: text/plain
words: 453
sentence: 13
flesch: 27
cache: cache/cord-027649-6xn9swsq.txt
txt: txt/cord-027649-6xn9swsq.txt
title:
  Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates

summary:
  We predict global sequencing projects may yield additional clinical SARS-CoV-2 isolates with deletions in ORF6 or ORF7a, but not both. Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization Rapid Metagenomic Next-Generation Sequencing during an Investigation of Hospital-Acquired Human Parainfluenza Virus 3 Infections Trimmomatic: a flexible trimmer for Illumina sequence data Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data An 81 nucleotide deletion in SARS-CoV ORF7a identified from sentinel surveillance in Arizona Structure and intracellular targeting of the SARS-coronavirus Orf7a accessory protein A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology A SARS-CoV-2 protein interaction map reveals targets for drug repurposing Severe Acute Respiratory Syndrome Coronavirus Inhibits Cellular Protein Synthesis and Activates p38 Mitogen-Activated Protein Kinase WA-UW-4570 and resulted in the fusion of ORF7a and ORF8. key: cord-027649-6xn9swsq authors: Addetia, Amin; Xie, Hong; Roychoudhury, Pavitra; Shrestha, Lasata; Loprieno, Michelle; Huang, Meei-Li; Jerome, Keith R.; Greninger, Alexander L. title: Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates date: 2020-06-23 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104523 sha: doc_id: 27649 cord_uid: 6xn9swsq nan SARS-CoV-2 xGen enrichment panel (NC_045512; IDT).


id: cord-010155-g5fk567p
author: Schildgen, Verena
title: Absence of Melaka-virus in European children with respiratory disease
date: 2008-03-24
extension: .txt
mime: text/plain
words: 674
sentence: 21
flesch: 43
cache: cache/cord-010155-g5fk567p.txt
txt: txt/cord-010155-g5fk567p.txt
summary:
  All rights reserved Human metapneumovirus infections cause similar symptoms and clinical severity as respiratory syncytial virus infections In similar epidemiological studies that we have performed for other viruses, the phenomenon that a newly described virus was not found in patient populations with corresponding symptoms was not observed.


id: cord-026099-97luq10a
author: Kok, J
date: 2020-06-05
extension: .txt
mime: text/plain
words: 763
sentence: 25
flesch: 42
cache: cache/cord-026099-97luq10a.txt
txt: txt/cord-026099-97luq10a.txt
title:
  Response to correspondence received on our paper:Interpret with caution: an evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus

summary:
  False positive results of other AusDiagnostics assays using the same methodology have been previously attributed to incorrectly calibrated equipment and poor quality power supply [Meunier] . As Stanley correctly points out, it is important that diagnostic assays have high sensitivity in order to detect all persons with suspected COVID-19 and limit further transmission of infection.


id: cord-010160-wk8k2igu
author: Chandrasekaran, Alamelu
date: 2012-01-04
extension: .txt
mime: text/plain
words: 920
sentence: 29
flesch: 41
cache: cache/cord-010160-wk8k2igu.txt
txt: txt/cord-010160-wk8k2igu.txt
title:
  Broad reactivity of the Luminex xTAG Respiratory Virus Panel (RVP) assay for the detection of human rhinoviruses

summary:
  In conclusion, the xTAG RVP can detect a broad range of HRV serotypes, including HRV A, B and C strains. NL63, OC43, HKU-1 and 229E. A multicenter study demonstrated that RVP can detect culture isolates of HRV serotypes 39 and 54 and HRV strains of phylogenetic groups A, B, C, E and F from clinical samples.


id: cord-265760-ch4pcy21
author: Zhifeng, Jiang
title: Consistency analysis of COVID-19 nucleic acid tests and the changes of lung CT
date: 2020-04-10
extension: .txt
mime: text/plain
words: 1412
sentence: 63
flesch: 52
cache: cache/cord-265760-ch4pcy21.txt
txt: txt/cord-265760-ch4pcy21.txt
summary:
  The Kappa coefficient of initial nucleic acid positive changes and lung CT changes was −1.52. This study aimed to explore the relationships between positive initial nucleic acid test and the consistency of lung CT changes, as an attempt to facilitate the effective screening of suspected patients.


id: cord-282576-mcx0xq0w
author: Boutin, Catherine-Audrey
date: 2020-09-04
extension: .txt
mime: text/plain
words: 1366
sentence: 45
flesch: 47
cache: cache/cord-282576-mcx0xq0w.txt
txt: txt/cord-282576-mcx0xq0w.txt
title:
  Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument

summary:
  The correlation between Ct values obtained in the LD RT-PCR test and cobas SARS CoV-2 ORF-1 target for positive samples in both assays was good (r 2 = 0.82, data not shown). An excellent correlation (r(2) = 0.98) was obtained between Ct values of the ORF-1 and E targets in the cobas assays and a good correlation was obtained between LD RT-PCR test and cobas SARS CoV-2 ORF-1 target (r(2) = 0.82).


id: cord-259558-remrzrq1
author: LeBlanc, Jason J.
date: 2020-05-16
extension: .txt
mime: text/plain
words: 1462
sentence: 50
flesch: 38
cache: cache/cord-259558-remrzrq1.txt
txt: txt/cord-259558-remrzrq1.txt
title:
  A combined oropharyngeal/nares swab is a suitable alternative to nasopharyngeal swabs for the detection of SARS-CoV-2

summary:
  The limited and unpredictable supply of NP swabs during the COVID-19 pandemic prompted the evaluation of swabs that were readily available and commonly used for sexually transmitted infections. Infectious Diseases (except HIV/AIDS) Effect of throat washings on detection of 2019 novel coronavirus Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs Avaniss-Aghajani A. 2020.


id: cord-285018-l26px1bc
author: Ong, David S.Y.
date: 2020-09-07
extension: .txt
mime: text/plain
words: 1496
sentence: 59
flesch: 46
cache: cache/cord-285018-l26px1bc.txt
txt: txt/cord-285018-l26px1bc.txt
title:
  Comparison of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the sample-to-result Platform ELITe InGenius to the national reference method: an added value of N gene target detection?

summary:
  In these samples, the InGenius® platform detected all three genes in 47 (84%) samples, E gene and N gene only in 1 (2%), RdRp and N gene only in 2 (3%), and N gene only in 8 (14%). key: cord-285018-l26px1bc authors: Ong, David S.Y.; Claas, Eric C.J.; Breijer, Simone; Vaessen, Norbert title: Comparison of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the sample-to-result Platform ELITe InGenius to the national reference method: an added value of N gene target detection? date: 2020-09-07 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104632 sha: doc_id: 285018 cord_uid: l26px1bc BACKGROUND: Due to the emergence of the coronavirus disease 2019 (COVID-19) pandemic there is an urgent need for rapid and accurate testing on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).


id: cord-256699-d2tf2g7f
author: Brochot, Etienne
title: Comparison of different serological assays for SARS-CoV-2 in real life
date: 2020-08-02
extension: .txt
mime: text/plain
words: 1864
sentence: 68
flesch: 43
cache: cache/cord-256699-d2tf2g7f.txt
txt: txt/cord-256699-d2tf2g7f.txt
summary:
  In addition, more than 50 days after a positive PCR for CoV-2-SARS the proportion of positive patients seem to decrease. We For these 168 samples divided into 4 groups for which the five serological techniques were performed, we compared the number of positive samples two by two and calculated the overall percent agreement (negative and positive samples) and Kappa index ( Table 2) .


id: cord-279563-4lu1n0s7
author: Gorzalski, Andrew J.
date: 2020-06-10
extension: .txt
mime: text/plain
words: 1722
sentence: 74
flesch: 39
cache: cache/cord-279563-4lu1n0s7.txt
txt: txt/cord-279563-4lu1n0s7.txt
title:
  High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2

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.


id: cord-263389-m6x9gxwe
author: AlGhounaim, M.
date: 2017-07-29
extension: .txt
mime: text/plain
words: 1931
sentence: 93
flesch: 38
cache: cache/cord-263389-m6x9gxwe.txt
txt: txt/cord-263389-m6x9gxwe.txt
title:
  Diagnostic yield and clinical impact of routine cell culture for respiratory viruses among children with a negative multiplex RT-PCR result

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.


id: cord-291553-j9nn5g70
author: Fridholm, Helena
title: Human pegivirus detected in a patient with severe encephalitis using a metagenomic pan-virus array
date: 2016-01-29
extension: .txt
mime: text/plain
words: 2018
sentence: 85
flesch: 43
cache: cache/cord-291553-j9nn5g70.txt
txt: txt/cord-291553-j9nn5g70.txt
summary:
  A reassessment of the literature on the hepatitis G virus GB virus-C-a virus without a disease: we cannot give it chronic fatigue syndrome Lack of GB virus C/hepatitis G virus sequences in cerebrospinal fluid in patients with central nervous system infections A case-control study of transmission routes for GB virus C/hepatitis G virus in Swedish blood donors lacking markers for hepatitis C virus infection GB virus C/hepatitis G virus infection in patients investigated for chronic liver disease and in the general population in southern Sweden Prevalence of GB virus C (also called hepatitis G virus) markers in Norwegian blood donors Seroprevalence of GB virus C and persistence of RNA and antibody A novel T cell evasion mechanism in persistent RNA virus infection Humoral immune response to the E2 protein of hepatitis G virus is associated with long-term recovery from infection and reveals a high frequency of hepatitis G virus exposure among healthy blood donors GB Virus C epidemiology in denmark: different routes of transmission in children and low-and high-risk adults Detection of antibodies to a putative hepatitis G virus envelope protein Antibody to GBV-C second envelope glycoprotein (anti-GBV-C E2): is it a marker for immunity? Prevalence of GBV-C/hepatitis G virus RNA and E2 antibody among subjects infected with human immunodeficiency virus type 1 after parenteral or sexual exposure Evidence that the GBV-C/Hepatitis G virus is primarily a lymphotropic virus Causes of encephalitis and differences in their clinical presentations in England: a multicentre, population-based prospective study Etiology of encephalitis in Australia Actionable diagnosis of neuroleptospirosis by next-generation sequencing Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing The authors declare no conflicts of interests. Diagnostic value of anti-GBV-C antibodies in HIV-infected patients GB virus C coinfections in West African Ebola patients Acquisition of GB virus type C and lower mortality in patients with advanced HIV disease The microbial detection array for detection of emerging viruses in clinical samples-a useful panmicrobial diagnostic tool A microbial detection array (MDA) for viral and bacterial detection Multiplex real-time PCR for the detection and quantification of latent and persistent viral genomes in cellular or plasma blood fractions Hepatitis C virus and GB virus C/hepatitis G virus viremia in Swedish blood donors with different alanine aminotransferase levels Evidence for extensive genotypic diversity and recombination of GB virus C (GBV-C) in Germany The GB viruses: a review and proposed classification of GBV-A, GBV-C (HGV), and GBV-D in genus Pegivirus within the family Flaviviridae G-pers creepers, where'd you get those papers?


id: cord-262045-r2iqpmmc
author: Smits, Saskia L.
title: Reliable typing of MERS-CoV variants with a small genome fragment
date: 2014-12-15
extension: .txt
mime: text/plain
words: 2154
sentence: 86
flesch: 44
cache: cache/cord-262045-r2iqpmmc.txt
txt: txt/cord-262045-r2iqpmmc.txt
summary:
  The continued occurrence of transmission between humans in health care and family settings is an ongoing concern as stated by the World Health Organization (http://www.who.int/csr/disease/coronavirus infections/MERS CoV Update 27 March 2014.pdf?ua=1), although the outbreaks appear to be self-limiting or extinguishable with rigorous implementation of appropriate infection control guidelines at present. State of knowledge and data gaps of Middle East Respiratory Syndrome coronavirus (MERS-CoV) in humans Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia MERS coronaviruses in dromedary camels Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation Middle East Respiratory Syndrome (MERS) coronavirus seroprevalence in domestic livestock in Saudi Arabia Human infection with MERS coronavirus after exposure to infected camels Antibodies against MERS coronavirus in dromedary camels Seroepidemiology for MERS coronavirus using microneutralisation and pseudoparticle virus neutralisation assays reveal a high prevalence of antibody in dromedary camels in Egypt Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study Middle East respiratory syndrome coronavirus quasispecies that include homologues of human isolates revealed through whole-genome analysis and virus cultured from dromedary camels in Saudi Arabia Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels Isolation of MERS coronavirus from a dromedary camel Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans 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 Middle East respiratory syndrome coronavirus (MERS-CoV) infections in two returning travellers in the Netherlands This work was funded by ZonMW TOP project 91213058Z.


id: cord-289740-nsiycudn
author: Smithgall, Marie C.
date: 2020-05-13
extension: .txt
mime: text/plain
words: 2231
sentence: 82
flesch: 45
cache: cache/cord-289740-nsiycudn.txt
txt: txt/cord-289740-nsiycudn.txt
title:
  Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2

summary:
  Influenza Other Respir Viruses Evaluation of the molecular Xpert Xpress Flu/RSV assay vs. Alere i Influenza A & B assay for rapid detection of influenza viruses Multicenter Clinical Evaluation of the Alere i Respiratory Syncytial Virus Isothermal Nucleic Acid Amplification Assay Direct Comparison of Alere i and cobas Liat Influenza A and B Tests for Rapid Detection of Influenza Virus Infection Table 2: Positive and negative agreement of Abbott ID Now SARS-CoV-2 and Cepheid Xpert Xpress SARS-CoV-2 with Roche cobas SARS Total Total Positive 65 (73.9 Declarations of interest: none J o u r n a l P r e -p r o o f However, robust data are lacking on the relative performance of available rapid molecular tests across a full range of viral concentrations.


id: cord-260267-nau9kayk
author: Ren, Lili
date: 2011-06-01
extension: .txt
mime: text/plain
words: 2015
sentence: 101
flesch: 50
cache: cache/cord-260267-nau9kayk.txt
txt: txt/cord-260267-nau9kayk.txt
title:
  Human parainfluenza virus type 4 infection in Chinese children with lower respiratory tract infections: A comparison study

summary:
  Although HPIV-4 has been associated with mild ARTIs for years, recent investigations have also associated HPIV-4 infection with severe respiratory syndromes and with outbreaks of ARTIs in children. The median patient age was 20 months for HPIV-4 infections and 7–11 months for HPIV-1, -2, and -3 infections, but the clinical manifestations did not differ significantly between HPIV-1, -2, -3, and -4 infections.


id: cord-264360-eroqjkoh
author: Risku, Minna
title: Detection of human coronaviruses in children with acute gastroenteritis
date: 2010-03-15
extension: .txt
mime: text/plain
words: 2372
sentence: 106
flesch: 53
cache: cache/cord-264360-eroqjkoh.txt
txt: txt/cord-264360-eroqjkoh.txt
summary:
  A new virus isolated from the human respiratory tract The morphology of three previously uncharacterized human respiratory viruses that grow in organ culture Recovery in tracheal organ cultures of novel viruses from patients with respiratory disease Growth in suckling-mouse brain of IBVlike viruses from patients with upper respiratory tract disease Occurrence and frequency of coronavirus infections in humans as determined by enzyme-linked immunosorbent assay Viruses and bacteria in the etiology of the common cold An outbreak of coronavirus OC43 respiratory infection in Normandy, France Rhinovirus and coronavirus infectionassociated hospitalizations among older adults Spectrum of clinical illness in hospitalized patients with common cold virus infections The human enteric coronaviruses Adaptation of human enteric coronavirus to growth in cell lines Coronavirus as a possible cause of severe acute respiratory syndrome A novel coronavirus associated with severe acute respiratory syndrome Identification of a novel coronavirus in patients with severe acute respiratory syndrome A cluster of cases of severe acute respiratory syndrome in Hong Kong A major outbreak of severe acute respiratory syndrome in Hong Kong Identification of severe acute respiratory syndrome in Canada Enteric involvement of severe acute respiratory syndrome-associated coronavirus infection Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Viral replication in the nasopharynx is associated with diarrhea in patients with severe acute respiratory syndrome Identification of a new human coronavirus A previously undescribed coronavirus associated with respiratory disease in humans Human coronavirus NL63 infection in Canada New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia Human Coronavirus-NL63 infections in Korean children Human coronavirus NL63, France Croup is associated with the novel coronavirus NL63 Seroepidemiology of group I human coronaviruses in children Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia Human respiratory coronavirus HKU1 versus other coronavirus infections in Italian hospitalised patients A prospective hospital-based study of the clinical impact of non-severe acute respiratory syndrome (Non-SARS)-related human coronavirus infection Evidence of human coronavirus HKU1 and human bocavirus in Australian children Coronavirus HKU1 infection in the United States Detection of the new human coronavirus HKU1: a report of 6 cases Multiplex real time RT-PCR for the detection and quantitation of norovirus genogroups I and II in patients with acute gastroenteritis We thank Professor Tobias Allander and Professor Lia van der Hoek for providing control samples for setting up the PCR method. Since the discovery, NL63 has been detected in patients with respiratory tract infection in several countries around the world, including Canada, Australia, Korea and France.


id: cord-263118-6sf41rsj
author: Landry, Marie L.
date: 2008-07-18
extension: .txt
mime: text/plain
words: 2587
sentence: 106
flesch: 50
cache: cache/cord-263118-6sf41rsj.txt
txt: txt/cord-263118-6sf41rsj.txt
title:
  Real-time PCR compared to Binax NOW and cytospin-immunofluorescence for detection of influenza in hospitalized patients

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.


id: cord-289139-5ljqnc39
author: Mengelle, C.
date: 2014-09-03
extension: .txt
mime: text/plain
words: 2574
sentence: 122
flesch: 47
cache: cache/cord-289139-5ljqnc39.txt
txt: txt/cord-289139-5ljqnc39.txt
title:
  The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit

summary:
  respiratory viral panel with in-house nucleic acid amplification tests for diagnosis of respiratory virus infections Epidemiology of viral respiratory tract infections in a prospective cohort of infants and toddlers attending daycare Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children Severe lower respiratory tract infection in infants and toddlers from a nonaffluent population: viral etiology and co-detection as risk factors Dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis Single versus dual respiratory virus infections in hospitalized infants: impact on clinical course of disease and interferon-gamma response The 2009 pandemic influenza A(H1N1) coincides with changes in the epidemiology of other viral pathogens causing acute respiratory tract infections in children Rates of hospitalisation for influenza, respiratory syncytial virus and human metapneumovirus among infants and young children Spectrum and frequency of illness presenting to a pediatric emergency department Relative quantification of 40 nucleic acid sequences by multiplex ligationdependent probe amplification Performance of a rapid molecular multiplex assay for the detection of influenza and picornaviruses Pathogen chip for respiratory tract infections A Prospective Study of Agents associated with acute respiratory infection among young American Indian 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 Viral etiology of common cold in children Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens-duration of symptoms significantly affects detection rate Do rhinoviruses cause pneumonia in children? Lower respiratory tract infections associated with rhinovirus during infancy and increased risk of wheezing during childhood.


id: cord-276316-7ot9ds34
author: Lei, Chunliang
date: 2020-10-14
extension: .txt
mime: text/plain
words: 2381
sentence: 107
flesch: 50
cache: cache/cord-276316-7ot9ds34.txt
txt: txt/cord-276316-7ot9ds34.txt
title:
  Factors associated with clinical outcomes in patients with Coronavirus Disease 2019 in Guangzhou, China

summary:
  CONCLUSIONS: Most of COVID-19 patients in Guangzhou are mild/moderate, and presence of extrapulmonary virus and higher CD4/CD8 ratio are associated with higher risk of worse outcomes. 7 One of the main challenges for the clinicians is how to quickly identify COVID-19 patients at high risk for worse outcomes.


id: cord-253148-3t4o27xp
author: Chow, Brian D.W.
title: Evidence of human bocavirus circulating in children and adults, Cleveland, Ohio
date: 2008-09-19
extension: .txt
mime: text/plain
words: 2702
sentence: 158
flesch: 46
cache: cache/cord-253148-3t4o27xp.txt
txt: txt/cord-253148-3t4o27xp.txt
summary:
  To define the clinical and epidemiologic characteristics in adult and pediatric patients with evidence of HBoV. STUDY DESIGN: From October 2005 through October 2006, we screened respiratory samples from children and adults negative for common respiratory pathogens for HBoV by PCR. The 12-18 month age group had the highest prevalence, with HBoV detected in 6.0% of respiratory samples screened (Fig. 2) .


id: cord-259798-fnm1im98
author: Lee, Brian R.
date: 2018-11-23
extension: .txt
mime: text/plain
words: 2956
sentence: 116
flesch: 36
cache: cache/cord-259798-fnm1im98.txt
txt: txt/cord-259798-fnm1im98.txt
title:
  Impact of multiplex molecular assay turn-around-time on antibiotic utilization and clinical management of hospitalized children with acute respiratory tract infections

summary:
  While research has demonstrated that MRPs may have a positive impact on patient outcomes such as decreasing empiric antibiotic exposures, length of hospital stay (LOS), and improving timely oseltamivir treatment for influenza patients [9] [10] [11] [12] However, since some of these studies have been restricted to adult patients [11] , examined clinical impact for influenza patients only [12] or only included data from peak respiratory seasons


id: cord-266359-uf1ao1x1
author: Hakki, Morgan
date: 2015-04-15
extension: .txt
mime: text/plain
words: 3263
sentence: 127
flesch: 33
cache: cache/cord-266359-uf1ao1x1.txt
txt: txt/cord-266359-uf1ao1x1.txt
title:
  The clinical impact of coronavirus infection in patients with hematologic malignancies and hematopoietic stem cell transplant recipients

summary:
  Mortality was attributed to respiratory virus infection if death was due to respiratory failure without identification of a cause other than a respiratory virus We conducted a retrospective review of all cases of CoV infection documented by polymerase chain reaction, (PCR)-based testing on nasopharyngeal and bronchoalveolar lavage fluid samples between June 2010 and 2013.


id: cord-263279-afdmegq0
author: Uhteg, Katharine
title: Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays
date: 2020-04-26
extension: .txt
mime: text/plain
words: 3181
sentence: 123
flesch: 42
cache: cache/cord-263279-afdmegq0.txt
txt: txt/cord-263279-afdmegq0.txt
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.


id: cord-268567-2xoubkxb
author: Samannodi, Mohammed
title: Compliance with international guidelines in adults with encephalitis
date: 2020-04-14
extension: .txt
mime: text/plain
words: 3278
sentence: 171
flesch: 40
cache: cache/cord-268567-2xoubkxb.txt
txt: txt/cord-268567-2xoubkxb.txt
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.


id: cord-295189-bz3gi15h
author: Jennings, Lance C.
date: 2015-03-14
extension: .txt
mime: text/plain
words: 3265
sentence: 130
flesch: 42
cache: cache/cord-295189-bz3gi15h.txt
txt: txt/cord-295189-bz3gi15h.txt
title:
  Respiratory viruses in airline travellers with influenza symptoms: Results of an airport screening study

summary:
  Even though fever and cough were most frequently identified in association with influenza infections, surveillance data were often obtained over long periods with varying levels of influenza virus activity, resulting in a low PPV for these symptoms for influenza virus infection [26] . While, these and previous reports documenting seasonal influenza among air travelers [2, [9] [10] [11] have focused primarily on the in-flight transmission of influenza, clearly air travellers are responsible for the introduction of influenza viruses into countries on an ongoing basis


id: cord-268093-ta6k0uyz
author: Etemadi, Mohammad Reza
date: 2013-08-07
extension: .txt
mime: text/plain
words: 3355
sentence: 135
flesch: 44
cache: cache/cord-268093-ta6k0uyz.txt
txt: txt/cord-268093-ta6k0uyz.txt
title:
  Biodiversity and clinico-demographic characteristics of human rhinoviruses from hospitalized children with acute lower respiratory tract infections in Malaysia()

summary:
  However, fever occurred less often in HRV infections than in RSV and IFV-A. Temperature equal or above 38 • C was presented in 17% of HRV as compared with 33% of RSV and 30% of IFV-A infections. A significant burden of HRV infection, was found in 54 out of 165 patients (33%), and this concurs with previous studies with a rate varying from 26% to 33% in a hospitalized pediatric patient [8, [16]


id: cord-268830-8li6xhbu
author: Kozak, Robert
date: 2020-03-29
extension: .txt
mime: text/plain
words: 3136
sentence: 127
flesch: 39
cache: cache/cord-268830-8li6xhbu.txt
txt: txt/cord-268830-8li6xhbu.txt
title:
  Severity of coronavirus respiratory tract infections in adults admitted to acute care in Toronto, Ontario

summary:
  Effects of a new human respiratory virus in volunteers Human coronavirus circulation in the United States Clinical significance of human coronavirus in Bronchoalveolar Lavage samples from hematopoietic cell transplant recipients and patients with hematologic malignancies Prolonged shedding of human coronavirus in hematopoietic cell transplant recipients: risk factors and viral genome evolution Viral infection in adults hospitalized with community-acquired pneumonia: prevalence, pathogens, and presentation Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015: a systematic review and modelling study Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance Receptor-binding loops in alphacoronavirus adaptation and evolution Identification and evolutionary dynamics of two novel human coronavirus OC43 genotypes associated with acute respiratory infections: phylogenetic, spatiotemporal and transmission network analyses 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, Eur Human Coronavirus-HKU1 Infection Among Adults in MERS transmission and risk factors: a systematic review The predictors of 3-and 30-day mortality in 660 MERS-CoV patients Influenza surveillance-United States, 1992-93 and 1993-94 Severe morbidity and mortality associated with respiratory syncytial virus versus influenza infection in hospitalized older adults Clinical determinants of the severity of Middle East respiratory syndrome (MERS): a systematic review and meta-analysis Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia Sex matters -a preliminary analysis of Middle East respiratory syndrome in the Republic of Korea Presence of Middle East respiratory syndrome coronavirus antibodies in Saudi Arabia: a nationwide, cross-sectional, serological study SARS in Singapore-predictors of disease severity Isolation of rhinoviruses and coronaviruses from 38 colds in adults Species-specific clinical characteristics of human coronavirus infection among otherwise healthy adolescents and adults, Influenza Other Respir Molecular epidemiology of human coronavirus OC43 reveals evolution of different genotypes over time and recent emergence of a novel genotype due to natural recombination Dual respiratory virus infections Human coronavirus alone or in co-infection with rhinovirus C is a risk factor for severe respiratory disease and admission to the pediatric intensive care unit: a one-year study in Southeast Brazil Epidemiology and microbiological investigations of communityacquired pneumonia in children admitted at the emergency department of a university hospital Coronavirus HKU1 and other coronavirus infections in Hong Kong Detection of respiratory viruses and Legionella spp. A bivariate analysis identified both This cross-sectional study spanning 6-years suggests that CoV accounts for an important burden of respiratory infection, representing 1 out of 9 viral respiratory infections, with a propensity to cause lowerrespiratory tract infection and severe outcomes.


id: cord-253333-cwunxhyw
author: Echavarría, M.
date: 2018-09-14
extension: .txt
mime: text/plain
words: 4010
sentence: 164
flesch: 40
cache: cache/cord-253333-cwunxhyw.txt
txt: txt/cord-253333-cwunxhyw.txt
title:
  Clinical impact of rapid molecular detection of respiratory pathogens in patients with acute respiratory infection

summary:
  Alejandro Seoane: Investigation, Writing Review & Editing; Martin Ypas: Investigation, Writing Review & Editing; Cristina Videla: Resources, Writing Review & Editing Guadalupe Carballal: Conceptualization, Writing original Draft Principles and Practice of Infectious Diseases Community-acquired pneumonia requiring hospitalization among Antibiotic prescribing practice for acute, uncomplicated respiratory tract infections in primary care settings Antibiotic prescribing in ambulatory pediatrics in the United States Accuracy of rapid influenza diagnostic tests: a meta-analysis Epidemiology of viral respiratory tract infections in a prospective cohort of infants and toddlers attending daycare Viral etiology of acute respiratory infections in hospitalized and outpatient children in 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 Respiratory viral diagnosis by using an automated system of multiplex PCR (FilmArray) compared to conventional methods Influenza Other Respir Viral infections in outpatients with medically attended acute respiratory illness during the 2012-2013 influenza season Rapid viral diagnosis for acute febrile respiratory illness in children in the emergency department Antibiotics for acute respiratory infections: shrinking benefit, increasing risk, and the irrelevance of antimicrobial resistance Clinical impact of RT-PCR for pediatric acute respiratory infections: a controlled clinical trial Clinical utility of on-demand multiplex respiratory pathogen testing among adult outpatients Impact of Rapid diagnosis on management of adults hospitalized with influenza 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 Impact of Rapid influenza PCR testing on hospitalization and antiviral use: a retrospective cohort study Computed tomography -an increasing source of radiation exposure Impact of the rapid diagnosis of influenza on physician decision-making and patient management in the pediatric emergency department: results of a randomized, prospective, controlled trial Incidence of viral respiratory infections in a prospective cohort of outpatient and hospitalized children aged ≤5 years and its associated cost in Clinical and financial benefits of Rapid detection of respiratory viruses: an outcomes study Multiplex PCR point of care testing versus routine, laboratory-based testing in the treatment of adults with respiratory tract infections: a quasi-randomised study assessing impact on length of stay and antimicrobial use We would like to thank all physicians from the Pediatric and Adult Emergency Departments for patient enrollment, in particular, Drs. The greatest change was observed in adult patients with bronchitis (31% in the FilmArray-RP group versus 0% in the IFA group; p = 0.005)


id: cord-269407-6i66zf0e
author: Rutvisuttinunt, Wiriya
date: 2017-07-14
extension: .txt
mime: text/plain
words: 3869
sentence: 160
flesch: 42
cache: cache/cord-269407-6i66zf0e.txt
txt: txt/cord-269407-6i66zf0e.txt
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

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.


id: cord-268335-mfcjldu3
author: Dimeglio, Chloé
title: Children are protected against SARS-CoV-2 infection
date: 2020-05-20
extension: .txt
mime: text/plain
words: 557
sentence: 23
flesch: 46
cache: cache/cord-268335-mfcjldu3.txt
txt: txt/cord-268335-mfcjldu3.txt
summary:
  As infants and young children infected with respiratory tract viruses are particularly at risk of hospitalization (3) the paucity of pediatric patients with COVID-19 has raised many questions for clinicians, epidemiologists and scientists. key: cord-268335-mfcjldu3 authors: Dimeglio, Chloé; Mansuy, Jean-Michel; Charpentier, Sandrine; Claudet, Isabelle; Izopet, Jacques title: Children are protected against SARS-CoV-2 infection date: 2020-05-20 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104451 sha: doc_id: 268335 cord_uid: mfcjldu3 nan 1 Chloé Dimeglio 1,2* , Jean-Michel Mansuy 2 , Sandrine Charpentier 3,4 , Isabelle Claudet 4,5 , and Jacques Izopet 1 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China in December 2019.


id: cord-273229-c1jws3ol
author: Blairon, Laurent
date: 2020-05-30
extension: .txt
mime: text/plain
words: 1339
sentence: 59
flesch: 47
cache: cache/cord-273229-c1jws3ol.txt
txt: txt/cord-273229-c1jws3ol.txt
title:
  Implementation of rapid SARS-CoV-2 antigenic testing in a laboratory without access to molecular methods: experiences of a general hospital

summary:
  Under routine conditions, the sensitivity of the antigen detection of SARS-CoV-2 with the immunochromatographic COVID-19 Ag Respi-Strip kit was significantly lower than that announced by the manufacturer or reported by Vandenberg [2] , although we limited ourselves to using qRT-PCR as the comparison method. Using this immunochromatographic assay as a triage test did not significantly reduce the number of samples outsourced for COVID-19 confirmation by qRT-PCR.


id: cord-289947-z2dw2eaz
author: Wong, River Chun-Wai
date: 2020-08-16
extension: .txt
mime: text/plain
words: 802
sentence: 36
flesch: 52
cache: cache/cord-289947-z2dw2eaz.txt
txt: txt/cord-289947-z2dw2eaz.txt
title:
  Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay

summary:
  Emerg Microbes Infect Deep throat saliva as an alternative diagnostic specimen type for the detection of SARS-CoV-2 Saliva as an Alternate Specimen Source for Detection of SARS-CoV-2 in Symptomatic Patients Using Cepheid Xpert Xpress SARS-CoV-2 Saliva as a Noninvasive Specimen for Detection of SARS-CoV-2 Posterior oropharyngeal saliva for the detection of SARS-CoV-2 Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2 Test Clinical Evaluation of Three Sample-to-Answer Platforms for Detection of SARS-CoV-2 Brief validation of the novel GeneXpert Xpress SARS We would like to thank all the technical staff who provide technical assistance and contribute to SARS-CoV-2 testing in our department. Xpert® Xpress SARS-CoV-2 assay is only validated on nasopharyngeal specimens for detection of SARS-CoV-2.


id: cord-260338-or4faju7
author: Völz, Sebastian
date: 2007-09-11
extension: .txt
mime: text/plain
words: 4326
sentence: 172
flesch: 42
cache: cache/cord-260338-or4faju7.txt
txt: txt/cord-260338-or4faju7.txt
title:
  Prospective study of Human Bocavirus (HBoV) infection in a pediatric university hospital in Germany 2005/2006

summary:
  Unlike patients with RSV-infection (Ogra, 2004; Simon et al., 2006) , and similar to those with HMPV-associated respiratory tract infection , children older than 6 months seem to be most at risk (Kesebir et al., 2006; Manning et al., 2006; Weissbrich et al., 2006) . Two recently published studies included control groups of asymptomatic children (Kesebir et al., 2006; Manning et al., 2006) .


id: cord-264713-38dlh3wg
author: Vernet, Guy
title: Molecular diagnostics in virology
date: 2004-08-20
extension: .txt
mime: text/plain
words: 4802
sentence: 176
flesch: 36
cache: cache/cord-264713-38dlh3wg.txt
txt: txt/cord-264713-38dlh3wg.txt
summary:
  in 2001 illustrate the interest of multiplex detection of respiratory viruses by NAT. Table 6 Multiplex Nat for the detection of respiratory viruses (Hexaplex, Prodesse Inc.) DNA-microarrays or DNA-Chips are very powerful detection tools that can be combined with amplification techniques to detect viruses or virus variants (reviewed in Clewley, 2004) .


id: cord-268993-2sjh17mw
author: Rödel, Jürgen
date: 2020-08-31
extension: .txt
mime: text/plain
words: 2456
sentence: 108
flesch: 51
cache: cache/cord-268993-2sjh17mw.txt
txt: txt/cord-268993-2sjh17mw.txt
title:
  Use of the variplex(TM) SARS-CoV-2 RT-LAMP as a rapid molecular assay to complement RT-PCR for COVID-19 diagnosis

summary:
  For a single test 15 l of RT master mix and 8 l of eluted RNA were pipetted into two wells of a Genie test strip (Amplex Diagnostics). The combination of RT with Bst polymerase possessing a DNA strand displacement activity allows amplification of target genes at a constant temperature in less than one hour.


id: cord-271445-eft2vwgb
author: Xepapadaki, Paraskevi
title: Human metapneumovirus as a causative agent of acute bronchiolitis in infants
date: 2004-05-06
extension: .txt
mime: text/plain
words: 2001
sentence: 70
flesch: 37
cache: cache/cord-271445-eft2vwgb.txt
txt: txt/cord-271445-eft2vwgb.txt
summary:
  However, several epidemiological as well as clinical aspects of hMPV infection are still to be firmly established and in this context the analysis of well defined respiratory disease cohorts is of particular importance (Jartti et al., 2002; Rawlinson et al., 2003) . Finally, it should be noted that this is the first report of hMPV infection in Greece and the East Mediterranean area, further confirming the worldwide distribution of this virus (van den Hoogen et al., 2001; Stockton et al., 2002; Peret et al., 2002; Howe, 2002; Jartti et al., 2002; Freymouth et al., 2003; Viazov et al., 2003; Peiris et al., 2003; Vicente et al., 2003; Maggi et al., 2003) .


id: cord-301254-093yih5n
author: Brittain-Long, Robin
date: 2010-01-18
extension: .txt
mime: text/plain
words: 2860
sentence: 110
flesch: 40
cache: cache/cord-301254-093yih5n.txt
txt: txt/cord-301254-093yih5n.txt
title:
  Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens—Duration of symptoms significantly affects detection rate

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).


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
extension: .txt
mime: text/plain
words: 1361
sentence: 58
flesch: 45
cache: cache/cord-294155-94skyx5f.txt
txt: txt/cord-294155-94skyx5f.txt
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.


id: cord-272734-kawim93f
author: Freire-Paspuel, Byron
date: 2020-05-22
extension: .txt
mime: text/plain
words: 1249
sentence: 55
flesch: 51
cache: cache/cord-272734-kawim93f.txt
txt: txt/cord-272734-kawim93f.txt
title:
  Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies

summary:
  key: cord-272734-kawim93f authors: Freire-Paspuel, Byron; Vega-Mariño, Patricio; Velez, Alberto; Castillo, Paulina; Cruz, Marilyn; Garcia-Bereguiain, Miguel Angel title: Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies date: 2020-05-22 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104454 sha: doc_id: 272734 cord_uid: kawim93f BACKGROUND: Several qPCR kits are available for SARS-CoV-2 diagnosis, mostly lacking of evaluation due to covid19 emergency. Both CoV-QS and 2019-nCoV CDC EUA kits were used at SARS-CoV-2 diagnosis laboratory LabGal at Agencia de Regulación y Control de la Bioseguridad y Cuarentena para Galápagos at Puerto Ayora in Galapagos Islands (Ecuador), where we considered this validation necessary to guarantee the sensibility of SARS-CoV-2 during the surveillance.


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
extension: .txt
mime: text/plain
words: 6856
sentence: 289
flesch: 51
cache: cache/cord-277909-rn1dow26.txt
txt: txt/cord-277909-rn1dow26.txt
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


id: cord-297365-11es4w0u
author: Peng, Hui
title: Coronavirus Disease 2019 in Children: Characteristics, Antimicrobial Treatment, and Outcomes
date: 2020-05-07
extension: .txt
mime: text/plain
words: 1697
sentence: 87
flesch: 52
cache: cache/cord-297365-11es4w0u.txt
txt: txt/cord-297365-11es4w0u.txt
summary:
  Young children are more dependent on their family members and infants are not suitable for wearing masks, which may explain why children younger than 2 years are the most vulnerable group to COVID-19. On February 19, arbidol was included in A Case Series of children with 2019 novel coronavirus infection: clinical and epidemiological features Pediatric Branch of Hubei Medical Association; Pediatric Branch of Wuhan Medical Association Recommendation for the diagnosis and treatment of novel coronavirus infection in children in Hubei Diagnosis and treatment recommendations for pediatric respiratory infection caused by the 2019 novel coronavirus Cardiovascular Complications in Patients with COVID-19: Consequences of Viral Toxicities and Host Immune Response Clinical Characteristics of Children with Coronavirus Disease COVID-19 epidemic: Disease characteristics in children Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study Epidemiology of COVID-19 Among Children in China COVID-19 in Children: Initial Characterization of the Pediatric Disease Treatment of SARS with human interferons Treatment efficacy analysis of traditional Chinese medicine for novel coronavirus pneumonia (COVID-19): an empirical study from Wuhan Ribavirin and interferon alfa-2a for severe Middle East respiratory syndrome coronavirus infection: a retrospective cohort study Clinical Features of 69 Cases with Coronavirus Disease Arbidol combined with LPV/r versus LPV/r alone against Corona Virus Disease 2019:a retrospective cohort study Arbidol monotherapy is superior to lopinavir/ritonavir in treating COVID-19


id: cord-300018-3uzau7if
author: Mak, Gannon C.K.
date: 2020-07-24
extension: .txt
mime: text/plain
words: 650
sentence: 18
flesch: 37
cache: cache/cord-300018-3uzau7if.txt
txt: txt/cord-300018-3uzau7if.txt
title:
  The D614G substitution in the S gene and clinical information for patients with COVID-19 detected in Hong Kong

summary:
  Of 11 severe cases, 4 (36.4%) showed D614G substitution while 39 (38.2%) non-severe cases showed D614G substitution. key: cord-300018-3uzau7if authors: Mak, Gannon C.K.; Lau, Angela W.L.; Chan, Andy M.Y.; Chan, Desmond Y.W.; Tsang, Dominic N.C. title: The D614G substitution in the S gene and clinical information for patients with COVID-19 detected in Hong Kong date: 2020-07-24 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104550 sha: doc_id: 300018 cord_uid: 3uzau7if nan In an attempt to understand the relevance of D614G substitution among COVID-19 patients in Hong Kong, full length S gene sequences from severe and non-severe cases were examined.


id: cord-281495-beb164oy
author: Charpentier, Charlotte
date: 2020-09-03
extension: .txt
mime: text/plain
words: 2379
sentence: 87
flesch: 51
cache: cache/cord-281495-beb164oy.txt
txt: txt/cord-281495-beb164oy.txt
title:
  Performance evaluation of two SARS-CoV-2 IgG/IgM rapid tests (Covid-Presto and NG-Test) and one IgG automated immunoassay (Abbott)

summary:
  Sensitivity of Abbott IgG test was 67% (n=4/6), 100% (n=22/22) and 100% (n=29/29) for samples collected between days 7 and 9, between days 10 and 14, and after 14 days after onset of symptoms, respectively. On the other hand, although a very large number of rapid tests have been developed, few of them have been reliably evaluated with a suitable serum panel.


id: cord-264406-s5c0grz0
author: Miró-Cañís, Sílvia
title: Multiplex PCR reveals that viruses are more frequent than bacteria in children with cystic fibrosis
date: 2016-11-13
extension: .txt
mime: text/plain
words: 2087
sentence: 94
flesch: 41
cache: cache/cord-264406-s5c0grz0.txt
txt: txt/cord-264406-s5c0grz0.txt
summary:
  Multiplex PCR screening for respiratory viruses is feasible in children with cystic fibrosis; the clinical implications of screening warrant further study. Conclusions: Multiplex PCR screening for respiratory viruses is feasible in children with cystic fibrosis; the clinical implications of screening warrant further study.


id: cord-295957-s17z2ccf
author: Bordi, Licia
title: Rapid and sensitive detection of SARS-CoV-2 RNA using the Simplexa™ COVID-19 direct assay
date: 2020-05-04
extension: .txt
mime: text/plain
words: 1928
sentence: 60
flesch: 38
cache: cache/cord-295957-s17z2ccf.txt
txt: txt/cord-295957-s17z2ccf.txt
summary:
  This study was performed at two regional reference laboratories, with the following aims: I) to assess the analytical performances of the newly designed Simplexa™ COVID-19 Direct assay; II) to evaluate its clinical performance as compared to WHO protocols (7, 8) using different types of clinical specimens from patients with laboratory-confirmed COVID-19. All the SARS-CoV-2 samples resulted positive with the reference test (Cormans method), also resulted positive with Simplexa™ COVID-19 Direct assay, with a diagnostic sensitivity of 100% and almost perfect concordance.


id: cord-302528-wmxw9e0c
author: Mitchell, Stephanie L.
title: Evaluation of the COVID19 ID NOW EUA Assay
date: 2020-05-15
extension: .txt
mime: text/plain
words: 910
sentence: 34
flesch: 44
cache: cache/cord-302528-wmxw9e0c.txt
txt: txt/cord-302528-wmxw9e0c.txt
summary:
  • All the false-negative results occurred with weakly positive samples, with reference method C(T) values ≥35.  All the false-negative results occurred with weakly positive samples, with reference method CT values ≥35.


id: cord-295600-xe3ruu9a
author: Calarota, Sandra A.
date: 2015-06-17
extension: .txt
mime: text/plain
words: 3595
sentence: 123
flesch: 41
cache: cache/cord-295600-xe3ruu9a.txt
txt: txt/cord-295600-xe3ruu9a.txt
title:
  T-lymphocyte subsets in lung transplant recipients: association between nadir CD4 T-cell count and viral infections after transplantation

summary:
  Common infections in the lung transplant recipient Cytomegalovirus replication within the lung allograft is associated with bronchiolitis obliterans syndrome Detection of Epstein-Barr virus DNA in peripheral blood is associated with the development of bronchiolitis obliterans syndrome after lung transplantation Rate, causes, and clinical implications of presenting with low CD4+ cell counts in the era of highly active antiretroviral therapy Interruptions of cART limits CD4 T-cell recovery and increases the risk for opportunistic complications and death Immunodeficiency as a risk factor for non-AIDS-defining malignancies in HIV-1-infected patients receiving combination antiretroviral therapy Association of virus load, CD4 cell count, and treatment with clinical progression in human immunodeficiency virus-infected patients with very low CD4 cell counts HIV disease progression in a patient cohort treated via a clinical research network in a resource limited setting Lower CD4+ T lymphocyte nadirs may indicate limited immune reconstitution in HIV-1 infected individuals on potent antiretroviral therapy: analysis of immunophenotypic marker results of AACTG 5067 CD4 + T-lymphocyte nadir and the effect of highly active antiretroviral therapy on phenotypic and functional immune restoration in HIV-1 infection Nadir CD4 T cell count as predictor and high CD4 T cell intrinsic apoptosis as final mechanism of poor CD4 T cell recovery in virologically suppressed HIV-infected patients: clinical implications Kinetics of T-lymphocyte subsets and posttransplant opportunistic infections in heart and kidney transplant recipients Kinetics of peripheral blood lymphocyte subpopulations predicts the occurrence of opportunistic infection after kidney transplantation Blood and alveolar lymphocyte subsets in pulmonary cytomegalovirus infection after lung transplantation peripheral blood obtained from patients after thoracic organ transplantation Evaluation of cytomegalovirus DNAaemia versus pp65-antigenaemia cutoff for guiding preemptive therapy in transplant recipients: a randomized study Preemptive therapy for systemic and pulmonary human cytomegalovirus infection in lung transplant recipients In another study, a decrease in the percentage of CD4 T cells was observed at one year post-transplant in 17 LTR compared with normal ranges; a decrease in the percentage of CD8 T cells in patients with HCMV infection was also observed [15] .


id: cord-292578-co5essuw
author: Johnson, Marina
date: 2020-08-02
extension: .txt
mime: text/plain
words: 2114
sentence: 74
flesch: 41
cache: cache/cord-292578-co5essuw.txt
txt: txt/cord-292578-co5essuw.txt
title:
  Evaluation of a novel multiplexed assay for determining IgG levels and functional activity to SARS-CoV-2

summary:
  Samples were screened for IgG to SARS-CoV-2 N protein using a commercially available kit (Epitope Diagnostics Inc, San Diego, USA) as previously described (8) . An advantage of this assay is its ability to measure antibody induced inhibition of ACE-2 receptor-spike interaction thought to be the major mechanism by which SARS viruses, including SARS-CoV-2 attach to host cell surfaces (11, 12) .


id: cord-296847-r752bcsu
author: Campanini, Giulia
date: 2007-04-23
extension: .txt
mime: text/plain
words: 3048
sentence: 85
flesch: 37
cache: cache/cord-296847-r752bcsu.txt
txt: txt/cord-296847-r752bcsu.txt
title:
  Human respiratory syncytial virus (hRSV) RNA quantification in nasopharyngeal secretions identifies the hRSV etiologic role in acute respiratory tract infections of hospitalized infants

summary:
  Observation of 8 consecutive epidemics between 1982 and 1990 Nasal quantity of respiratory syncytial virus correlates with disease severity in hospitalized infants A randomised, double-blind, placebo-controlled trial of dexamethasone in severe respiratory syncytial virus (RSV) infections: effects on RSV quantity and clinical outcome Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription-nested PCR assay Natural infection of infants with respiratory syncytial virus subgroups A and B: a study of frequency, disease severity and viral load Diagnosis of respiratory syncytial virus infection: comparison of reverse transcription-PCR to viral culture and serology in adults with respiratory illness Comparison of quantitative reverse transcription-PCR to viral culture for assessment of respiratory syncytial virus shedding Evaluation of R-Mix fresh cells in shell vials for detection of respiratory viruses Detection of respiratory syncytial virus by reverse-transcription-PCR and hybridization with a DNA enzyme immunoassay Occurrence of groups A and B respiratory syncytial virus over 15 years: associated epidemiologic and clinical characteristics in hospitalized and ambulatory children Evaluation of five methods for respiratory syncytial virus detection Evaluation of direct immunofluorescence, enzyme immunoassay, centrifugation culture, and conventional culture for the detection of respiratory syncytial virus SimulFluor respiratory screen for rapid detection of multiple respiratory viruses in clinical specimens by immunofluorescence staining Respiratory syncytial virus-coded pediatric hospitalisation, 1997-1999 Reduction of respiratory syncytial virus (RSV) in tracheal aspirates in intubated infants using humanized monoclonal antibody to RSV F protein A singleseason epidemic with respiratory syncytial virus subgroup B2 during 10 epidemic years, 1978 to 1988 Rapid detection of respiratory syncytial virus in nasopharyngeal aspirates by reverse transcription and polymerase chain reaction amplification Comparison of a real-time reverse transcription PCR assay and a culture technique for quantitative assessment of viral load in children naturally infected with respiratory syncytial virus Monoclonal antibodies versus reverse transcription-PCR for detection of respiratory viruses in a patient population with respiratory tract infections admitted to hospital Detection and molecular characterization of Ebola viruses causing disease in human and nonhuman primates Anderson LJ. Bronchiolitis-associated hospitalizations among US children Severity of respiratory virus infection is related to virus strain We thank all the technical staff of the Servizio di Virologia for performing all the assays.


id: cord-310171-1fmsxx2s
author: Goffard, Anne
title: Virus and cystic fibrosis: Rhinoviruses are associated with exacerbations in adult patients()
date: 2014-02-25
extension: .txt
mime: text/plain
words: 3326
sentence: 123
flesch: 33
cache: cache/cord-310171-1fmsxx2s.txt
txt: txt/cord-310171-1fmsxx2s.txt
summary:
  Here, we performed a mechanical pre-treatment of each sputum sample before nucleic acid extraction; this pretreatment is newly recommended for respiratory virus detection in sputa from patients with asthma or CF [26, 27] . key: cord-310171-1fmsxx2s authors: Goffard, Anne; Lambert, Valérie; Salleron, Julia; Herwegh, Stéphanie; Engelmann, Ilka; Pinel, Claudine; Pin, Isabelle; Perrez, Thierry; Prévotat, Anne; Dewilde, Anny; Delhaes, Laurence title: Virus and cystic fibrosis: Rhinoviruses are associated with exacerbations in adult patients() date: 2014-02-25 journal: J Clin Virol DOI: 10.1016/j.jcv.2014.02.005 sha: doc_id: 310171 cord_uid: 1fmsxx2s BACKGROUND: Few studies have suggested the potential role of respiratory viruses in cystic fibrosis (CF) exacerbation, but their real impact is probably underestimated.


id: cord-279570-lgbqpfh5
author: Fragkou, Paraskevi C.
date: 2020-08-26
extension: .txt
mime: text/plain
words: 2748
sentence: 118
flesch: 42
cache: cache/cord-279570-lgbqpfh5.txt
txt: txt/cord-279570-lgbqpfh5.txt
title:
  Clinical characteristics and outcomes of measles outbreak in adults: a multicenter retrospective observational study of 93 hospitalized adults in Greece

summary:
  2019 global summary National Update on Measles Cases and Outbreaks -United States Ongoing measles outbreak in Greece related to the recent European-wide epidemic The ORION statement: guidelines for transparent reporting of outbreak reports and intervention studies of nosocomial infection -on the communicable diseases and related special health issues to be covered by epidemiological surveillance as well as relevant case definitions Investigators, Adult patients hospitalized for measles in France, in the 21st century Clinical and laboratory features of measles in hospitalized adults Measles-related hospitalizations and associated complications in Jerusalem Cocirculation of genotypes D4 and D6 in Greece during the 2005 to 2006 measles epidemic Epidemiological, clinical and laboratory characteristics of the measles resurgence in the Republic of Serbia Clinical and immunological analysis of measles patients admitted to a Beijing hospital in 2014 during an outbreak in China Impact and longevity of measles-associated immune suppression: a matched cohort study using data from the THIN general practice database in the UK Measles virus infection diminishes preexisting antibodies that offer protection from other pathogens Incomplete genetic reconstitution of B cell pools contributes to prolonged immunosuppression after measles C-reactive protein as a biomarker of severe H1N1 influenza C-Reactive Protein and Respiratory Viral Infection The course of Creactive protein response in untreated upper respiratory tract infection Changes in serum C-reactive protein during complicated and uncomplicated measles virus infections Bacterial pneumonia as a suprainfection in young adults with measles Severe measles pneumonia in adults with respiratory failure: role of ribavirin and high-dose vitamin A Severe measles pneumonitis in adults: evaluation of clinical characteristics and therapy with intravenous ribavirin Acute Myocardial Infarction after Laboratory-Confirmed Influenza Infection H1N1-Induced Venous Thromboembolic Events? In this study we aim to describe the clinical characteristics and complications of measles infection in hospitalized adults during the recent epidemic in Greece


id: cord-273783-z71bquck
author: Dijkman, Ronald
title: The dominance of human coronavirus OC43 and NL63 infections in infants
date: 2011-12-19
extension: .txt
mime: text/plain
words: 3076
sentence: 124
flesch: 47
cache: cache/cord-273783-z71bquck.txt
txt: txt/cord-273783-z71bquck.txt
summary:
  The severe acute respiratory syndrome (SARS) outbreak in 2002/2003 by a novel coronavirus, followed by the recent identification of HCoV-NL63 (2004) and HCoV-HKU1 (2005) renewed research interest into HCoV infections and their ability to seriously affect human health. Some studies addressed the frequency of HCoV infection during childhood and suggested that HCoV-NL63 infections were associated with more hospitalization compared to HCoV-OC43. 3, 19, 20 In the majority of the abovementioned studies only 1 year was sampled and for HCoVs a large year-to-year periodicity is known.


id: cord-299388-okiqmy6e
author: Wollmeister, Elinara
title: Respiratory syncytial virus in Brazilian infants – Ten years, two cohorts
date: 2017-12-06
extension: .txt
mime: text/plain
words: 2289
sentence: 97
flesch: 41
cache: cache/cord-299388-okiqmy6e.txt
txt: txt/cord-299388-okiqmy6e.txt
summary:
  Risk factors for bronchiolitis hospitalization during the first year of life in a multicenter Italian birth cohort Epidemiological and genetic characteristics associated with the severity of acute viral bronchiolitis by respiratory syncytial virus Concurrent detection of other respiratory viruses in children shedding viable human respiratory syncytial virus Single-and multiple viral respiratory infections in children: disease and management cannot be related to a specific pathogen Genotypes and clinical data of respiratory syncytial virus and metapneumovirus in Brazilian infants: a new perspective Etiology and seasonality of viral respiratory infections in rural Honduran children Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China Prospective validation of a prognostic model for respiratory syncytial virus bronchiolitis in late preterm infants: a multicenter birth cohort study Maternal milk protects infants against bronchiolitis during the first year of life. key: cord-299388-okiqmy6e authors: Wollmeister, Elinara; Alvarez, Alfonso Eduardo; Bastos, Juliana Cristina Santiago; Marson, Fernando Augusto Lima; Ribeiro, José Dirceu; Baracat, Emílio Carlos Elias; Arns, Clarice Weis; Riccetto, Adriana Gut Lopes title: Respiratory syncytial virus in Brazilian infants – Ten years, two cohorts date: 2017-12-06 journal: J Clin Virol DOI: 10.1016/j.jcv.2017.12.002 sha: doc_id: 299388 cord_uid: okiqmy6e BACKGROUND: Each year, a considerable amount of children will experience at least one episode of acute viral bronchiolitis (AVB) during their first year of life.


id: cord-310631-ru5f69qg
author: Joachim, Denner
title: SARS-CoV-2 and enhancing antibodies
date: 2020-05-07
extension: .txt
mime: text/plain
words: 567
sentence: 23
flesch: 39
cache: cache/cord-310631-ru5f69qg.txt
txt: txt/cord-310631-ru5f69qg.txt
summary:
  CoV infections were shown to induce an effective antibody response, however in addition to neutralising antibodies also enhancing antibodies were described, e. g., in the case of SARS-CoV To induce enhancing antibodies after immunisation of a healthy person is certainly not the goal of this preventive measure.


id: cord-267928-dflkggjt
author: Kantola, Kalle
date: 2009-05-22
extension: .txt
mime: text/plain
words: 2735
sentence: 95
flesch: 46
cache: cache/cord-267928-dflkggjt.txt
txt: txt/cord-267928-dflkggjt.txt
title:
  Merkel cell polyomavirus DNA in tumor-free tonsillar tissues and upper respiratory tract samples: Implications for respiratory transmission and latency

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.


id: cord-264676-k531q3ir
author: Liu, Yi
date: 2009-07-09
extension: .txt
mime: text/plain
words: 3930
sentence: 146
flesch: 42
cache: cache/cord-264676-k531q3ir.txt
txt: txt/cord-264676-k531q3ir.txt
title:
  In situ reverse-transcription loop-mediated isothermal amplification (in situ RT-LAMP) for detection of Japanese encephalitis viral RNA in host cells

summary:
  Fields virology Japanese encephalitis: current worldwide status New initiatives for the control of Japanese encephalitis by vaccination Viral infections of humans An intranasal challenge model for testing Japanese encephalitis vaccines in rhesus monkeys Rapid diagnosis of Japanese encephalitis by using an immunoglobulin M dot enzyme immunoassay Identification of dengue sequences by genomic amplification: rapid diagnosis of dengue virus serotypes in peripheral blood Rapid identification of flavivirus using the polymerase chain reaction Detection of Japanese encephalitis virus in mouse peripheral blood mononuclear cells using an in situ reverse transcriptase polymerase chain reaction Accelerated reaction by loop mediated isothermal amplification using loop primers Loop-mediated isothermal amplification of DNA Rapid detection and quantification of Japanese encephalitis virus by real-time reverse transcription loop-mediated isothermal amplification Potential role of Armigeres subalbatus (Diptera: Culcidae) in the transmission of Japanese encephalitis virus in the absence of rice culture on Liu-Chiu islet A model to study neurotropism and persistency of Japanese encephalitis virus infection in human neuroblastoma cells and leukocytes Analysis of Japanese encephalitis epidemic in western Nepal in 1997 A survey of the clinical sequelae of Japanese encephalitis A hospital-based surveillance for Japanese encephalitis in Bali Sensitive and specific detection of strains of Japanese encephalitis using a one-step TaqMan RT-PCR technique Development and evaluation of SYBR Green I-based one-step real-time RT-PCR assay for detection and quantization of Japanese encephalitis virus Detection of West Nile and Japanese encephalitis viral genome sequences in cerebrospinal fluid from acute encephalitis cases in Karachi NASBA and other transcription-based amplification methods for research and diagnostic microbiology TaqMan reverse transcription polymerase chain reaction for the detection of Japanese encephalitis virus Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation Development and evaluation of a novel loop-mediated isothermal amplification method for rapid detection of severe acute respiratory syndrome coronavirus Development of H5-RT-LAMP (loop-mediated isothermal amplification) system for rapid diagnosis of H5 avian influenza virus infection Rapid detection and differentiation of Dengue virus serotypes by real-time reverse transcription loop-mediated isothermal amplification assay Rapid and real-time detection of hepatitis A virus by reverse transcription loop-mediated isothermal amplification assay Evaluation of loop-mediated isothermal amplification (LAMP) to rapidly detect arbuscular mycorrhizal fungi Specific and rapid detection of food-borne Salmonella by loop-mediated isothermal amplification method Development of a multiplex loop-mediated isothermal amplification (mLAMP) method for the simultaneous detection of bovine Babesia parasites Species-specific loop-mediated isothermal amplification (LAMP) for diagnosis of trypanosomosis Evaluation of loop-mediated isothermal amplification (LAMP), PCR and parasitological tests for detection of Trypanosoma evansi in experimentally infected pigs Rapid sexing of water buffalo (Bubalus bubalis) embryos using loop-mediated isothermal amplification Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of West Nile virus Development and evaluation of reverse transcription-loop-mediated isothermal amplification assay for rapid and real-time detection of Japanese encephalitis virus Rapid and real-time detection of Chikungunya virus by reverse transcription loop-mediated isothermal amplification assay Persistence, latency and reactivation of Japanese encephalitis virus infection in mice Persistence of Japanese encephalitis virus in the human nervous system Japanese encephalitis virus latency in peripheral blood lymphocytes and recurrence of infection in children Detection and isolation of Japanese encephalitis virus from blood clots collected during the acute phase of infection The blood-brain barrier in the cerebrum is the initial site for the Japanese encephalitis virus entering the central nervous system Funding: This work was financially supported by grants from Chang Gung Memorial Hospital (CMRPD160162 and EMREPD180191). 27 Application of RT-LAMP to JE virus detection has been shown to be relatively rapid and allows for virus quantification.


id: cord-293890-thfros7x
author: Carbo, Ellen C.
title: Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness
date: 2020-08-21
extension: .txt
mime: text/plain
words: 2318
sentence: 88
flesch: 40
cache: cache/cord-293890-thfros7x.txt
txt: txt/cord-293890-thfros7x.txt
summary:
  Identification of a Novel Coronavirus in Patients with Severe Acute Respiratory Syndrome A Novel Coronavirus Associated with Severe Acute Respiratory Syndrome Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid VIP: an integrated pipeline for metagenomics of virus identification and discovery Metagenomics for pathogen detection in public health Genome Detective: an automated system for virus identification from highthroughput sequencing data Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis', mBio Enhanced virome sequencing using targeted sequence capture Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR Mechanisms and enzymes involved in SARS coronavirus genome expression Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease Fast gapped-read alignment with Bowtie 2 Centrifuge: rapid and sensitive classification of metagenomic sequences Interactive metagenomic visualization in a Web browser SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Basic local alignment search tool Trimmomatic: a flexible trimmer for Illumina sequence data Fast and sensitive protein alignment using DIAMOND metaSPAdes: a new versatile metagenomic assembler The efficacy of a metagenomic sequencing protocol using capture probes targeting vertebrate virus sequences designed before the emergence of SARS-CoV-2, was studied in the context of virus discovery.


id: cord-316723-srenbxa7
author: Zhao, Jincun
date: 2004-11-23
extension: .txt
mime: text/plain
words: 3111
sentence: 125
flesch: 57
cache: cache/cord-316723-srenbxa7.txt
txt: txt/cord-316723-srenbxa7.txt
title:
  Development and evaluation of an enzyme-linked immunosorbent assay for detection of antibodies against the spike protein of SARS-coronavirus

summary:
  Amino acids 270 to 510 of the severe acute respiratory syndrome coronavirus spike protein are required for interaction with receptor Antibody detection of SARS-CoV spike and nucleocapsid protein The secret life of ACE2 as a receptor for the SARS virus Development of a Western blot assay for detection of antibodies against coronavirus causing severe acute respiratory syndrome Antigenicity and receptor-binding ability of recombinant SARS coronavirus spike protein Mass spectrometric characterization of proteins from the SARS virus: a preliminary report Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus Immunological characterization of the spike protein of SARS-coronavirus The genome sequence of the SARS-associated coronavirus Coronavirus as a possible cause of severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome Molecular modeling of S1 and S2 subunits of SARS coronavirus spike glycoprotein Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association Profiles of antibody responses against severe acute respiratory syndrome coronavirus recombinant proteins and their potential use as diagnostic markers Structural characterization of the SARS-coronavirus spike S fusion protein core Expression cloning of functional receptor used by SARS coronavirus A 193-amino acid fragment of the SARS coronavirus S protein efficiently binds angiotensinconverting enzyme 2 Relative rates of non-pneumonic SARS coronavirus infection and SARS coronavirus pneumonia Early detection of antibodies against various structural proteins of the SARS-associated coronavirus in SARS patients The SARS-CoV S glycoprotein: expression and functional characterization SARS-associated coronavirus quasispecies in individual patients Proteomic analysis on structural proteins of severe acute respiratory syndrome coronavirus An exposed domain in the severe acute respiratory syndrome coronavirus spike protein induces neutralizing antibodies The first two authors contributed equally to this work. DNA coding for S450-650 of SARS CoV S protein was PCR amplified using high fidelity Taq DNA polymerase (TaKaRa Biotech Co. Ltd., Japan).


id: cord-307602-2cmgu7rf
author: McErlean, P.
date: 2007-05-07
extension: .txt
mime: text/plain
words: 3272
sentence: 121
flesch: 42
cache: cache/cord-307602-2cmgu7rf.txt
txt: txt/cord-307602-2cmgu7rf.txt
title:
  Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis

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.


id: cord-269519-8hr8wyrr
author: Hirotsu, Yosuke
date: 2020-07-07
extension: .txt
mime: text/plain
words: 1599
sentence: 80
flesch: 48
cache: cache/cord-269519-8hr8wyrr.txt
txt: txt/cord-269519-8hr8wyrr.txt
title:
  Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan

summary:
  key: cord-269519-8hr8wyrr authors: Hirotsu, Yosuke; Maejima, Makoto; Shibusawa, Masahiro; Amemiya, Kenji; Nagakubo, Yuki; Hosaka, Kazuhiro; Sueki, Hitomi; Mochizuki, Hitoshi; Tsutsui, Toshiharu; Kakizaki, Yumiko; Miyashita, Yoshihiro; Omata, Masao title: Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan date: 2020-07-07 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104543 sha: doc_id: 269519 cord_uid: 8hr8wyrr BACKGROUND: Severe acute respiratory coronavirus 2 (SARS-CoV-2) has spread and caused death worldwide. However, the extent to which SARS-CoV-2, influenza viruses and other causative viruses have prevailed since implementing preventive measures is unclear.


id: cord-299664-nexq5ntj
author: Butt, S.A.
title: Comparison of three commercial RT-PCR systems for the detection of respiratory viruses
date: 2014-08-18
extension: .txt
mime: text/plain
words: 2875
sentence: 110
flesch: 43
cache: cache/cord-299664-nexq5ntj.txt
txt: txt/cord-299664-nexq5ntj.txt
summary:
  RVP fast multiplex assays for detection of respiratory viruses Comparison of xTAG respiratory virus panel and Verigene respiratory virus plus for detecting influenza Virus and respiratory syncytial virus Evaluation of three influenza A and B real-time reverse transcription-PCR assays and a new 2009 H1N1 assay for detection of influenza viruses Influenza and respiratory syncytial virus detection in clinical specimens without nucleic acid extraction using FOCUS direct disc assay is substantially equivalent to the traditional methods and the FOCUS nucleic acid extraction-dependent RT-PCR assay A one-step RT-PCR assay using an enzyme-linked detection system for the diagnosis of enterovirus meningitis The clinical utility of a near patient care rapid microarray-based diagnostic test for influenza and respiratory syncytial virus infections in the pediatric setting Comparison of the Luminex xTAG RVP Fast assay and the Idaho Technology FilmArray RP assay for detection of respiratory viruses in pediatric patients at a cancer hospital Comparison of the FilmArray RP, Verigene RV+, and Prodesse ProFLU+/FAST+ multiplex platforms for detection of influenza viruses in clinical samples from the 2011-2012 influenza season in Belgium Evaluation and implementation of FilmArray version 1.7 for improved detection of adenovirus respiratory tract infection We thank the Molecular Diagnostics staff for their help with collecting respiratory specimens and performing Pro.


id: cord-287206-ois4gnqx
author: Eberhardt, J.N.
title: Multi-Stage Group Testing Improves Efficiency of Large-Scale COVID-19 Screening
date: 2020-04-23
extension: .txt
mime: text/plain
words: 3350
sentence: 159
flesch: 60
cache: cache/cord-287206-ois4gnqx.txt
txt: txt/cord-287206-ois4gnqx.txt
summary:
  Two-stage group testing applies this construction with setting = 2. To compare the performance of group testing schemes, we defined a quantity called improvement factor. We designed group testing schemes with the goal of testing large numbers of samples more efficiently.


id: cord-291029-oldket3n
author: Sefers, Susan E.
date: 2005-07-21
extension: .txt
mime: text/plain
words: 3537
sentence: 130
flesch: 46
cache: cache/cord-291029-oldket3n.txt
txt: txt/cord-291029-oldket3n.txt
title:
  QIAamp MinElute Virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs()

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.


id: cord-283028-g2rjjq48
author: Christensen, Andreas
date: 2010-09-15
extension: .txt
mime: text/plain
words: 3123
sentence: 140
flesch: 56
cache: cache/cord-283028-g2rjjq48.txt
txt: txt/cord-283028-g2rjjq48.txt
title:
  Human bocavirus in children: Mono-detection, high viral load and viraemia are associated with respiratory tract infection

summary:
  Cloning of a human parvovirus by molecular screening of respiratory tract samples Frequent detection of highly diverse variants of cardiovirus, cosavirus, bocavirus and circovirus in sewage samples collected in the United States Human bocavirus: a novel parvovirus epidemiologically associated with pneumonia requiring hospitalization in Thailand Disseminated bocavirus infection after stem cell transplant Human bocavirus in an immunocompromised child presenting with severe diarrhea Impact of human bocavirus on children and their families Human bocavirus commonly involved in multiple viral airway infections Human bocavirus infection in young children in the United States: molecular epidemiological profile and clinical characteristics of a newly emerging respiratory virus Human bocavirus and acute wheezing in children Human bocavirus infection in children with respiratory tract disease Clinical assessment and improved diagnosis of bocavirus-induced wheezing in children Prevalence and clinical aspects of human bocavirus infections in children Seroepidemiology of human bocavirus in Hokkaido prefecture High prevalence of human parvovirus B19 DNA in myocardial autopsy samples from subjects without myocarditis or dilative cardiomyopathy Persistence of novel human parvovirus PARV4 in liver tissue of adults 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 detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction Duration of enterovirus shedding in stool Prolonged detection of human bocavirus DNA in nasopharyngeal aspirates of children with respiratory tract disease Latent species C adenoviruses in human tonsil tissues None. [3] [4] [5] However, HBoV1 is frequently found together with other respiratory viruses and consequently its causative role in childhood RTI may be questioned.


id: cord-314829-tmgmqtjq
author: Scohy, Anaïs
title: Low performance of rapid antigen detection test as frontline testing for COVID-19 diagnosis
date: 2020-05-21
extension: .txt
mime: text/plain
words: 1193
sentence: 48
flesch: 48
cache: cache/cord-314829-tmgmqtjq.txt
txt: txt/cord-314829-tmgmqtjq.txt
summary:
  key: cord-314829-tmgmqtjq authors: Scohy, Anaïs; Anantharajah, Ahalieyah; Bodéus, Monique; Kabamba-Mukadi, Benoît; Verroken, Alexia; Rodriguez-Villalobos, Hector title: Low performance of rapid antigen detection test as frontline testing for COVID-19 diagnosis date: 2020-05-21 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104455 sha: doc_id: 314829 cord_uid: tmgmqtjq BACKGROUND: Recently, several easy to perform rapid antigen detection tests were developed and recommended in some countries as the first line of diagnostic.


id: cord-312971-r9sggqh8
author: Mancino, Enrica
date: 2020-04-29
extension: .txt
mime: text/plain
words: 1309
sentence: 57
flesch: 39
cache: cache/cord-312971-r9sggqh8.txt
txt: txt/cord-312971-r9sggqh8.txt
title:
  A single centre study of viral community-acquired pneumonia in children: no evidence of SARS-CoV-2 from October 2019 to March 2020

summary:
  We described viral aetiologies, with particular interest in detecting SARS-CoV-2, in hospitalized pneumonia children. Our aim was to describe viral aetiologies, with particular interest in detecting SARS-CoV-2, in hospitalized pneumonia children under 14 years of age.


id: cord-310140-h7uwl0pb
author: Templeton, K.E.
date: 2005-07-12
extension: .txt
mime: text/plain
words: 4187
sentence: 150
flesch: 43
cache: cache/cord-310140-h7uwl0pb.txt
txt: txt/cord-310140-h7uwl0pb.txt
title:
  A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses

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.


id: cord-300316-r54ksiy3
author: Moesker, F.M.
date: 2016-03-25
extension: .txt
mime: text/plain
words: 3353
sentence: 173
flesch: 53
cache: cache/cord-300316-r54ksiy3.txt
txt: txt/cord-300316-r54ksiy3.txt
title:
  Diagnostic performance of influenza viruses and RSV rapid antigen detection tests in children in tertiary care

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:


id: cord-302125-96w0nh9q
author: Péré, Hélène
date: 2020-09-03
extension: .txt
mime: text/plain
words: 373
sentence: 9
flesch: 31
cache: cache/cord-302125-96w0nh9q.txt
txt: txt/cord-302125-96w0nh9q.txt
title:
  Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris

summary:
  key: cord-302125-96w0nh9q authors: Péré, Hélène; Wack, Maxime; Védie, Benoit; Guinet, Nathalie Demory; Najiby, Kassis Chikani; Janot, Laurence; Bélec, Laurent; Veyer, David title: Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris date: 2020-09-03 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104617 sha: doc_id: 302125 cord_uid: 96w0nh9q nan Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris Running title: Sequential SARS-CoV-2 serology testing in health-workers Hélène Péré 1,2,3 , Maxime Wack 4 , Benoit Védie 5 , Nathalie Demory Guinet 6 , Kassis Chikani Najiby 7 , Laurence Janot 6 , Laurent Bélec 1,2,3 , David Veyer 1, 8 surface protein, with the high-throughput UniCel DxI 800 Access Immunoassay System (Beckman Coulter), to increase hospital productivity in SARS-CoV-2 IgG serology testing. The virology laboratory of Hôpital Européen Georges Pompidou was then called upon to test all hospital staff exposed to the virus during the epidemic peak.


id: cord-324125-wau2xq0x
author: Qiu, Chao
date: 2013-12-16
extension: .txt
mime: text/plain
words: 1821
sentence: 88
flesch: 48
cache: cache/cord-324125-wau2xq0x.txt
txt: txt/cord-324125-wau2xq0x.txt
title:
  Epidemiologic report and serologic findings for household contacts of three cases of influenza A (H7N9) virus infection

summary:
  Consistent with the observations in studies of H7N9 virus transmission in animal models, our results indicate that compared with globally disseminated seasonal and pandemic influenza viruses, the H7N9 virus is not readily transmitted in certain household settings Antibodies against H7N9 virus in serum samples were tested using hemagglutination inhibition and pseudovirus based neutralization assays.


id: cord-314028-sf8zt9r9
author: Esposito, Susanna
title: Telemedicine for management of paediatric infectious diseases during COVID-19 outbreak
date: 2020-06-23
extension: .txt
mime: text/plain
words: 586
sentence: 21
flesch: 39
cache: cache/cord-314028-sf8zt9r9.txt
txt: txt/cord-314028-sf8zt9r9.txt
summary:
  key: cord-314028-sf8zt9r9 authors: Esposito, Susanna; Voccia, Emanuele; Cantarelli, Angelo; Canali, Andrea; Principi, Nicola; Prati, Andrea title: Telemedicine for management of paediatric infectious diseases during COVID-19 outbreak date: 2020-06-23 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104522 sha: doc_id: 314028 cord_uid: sf8zt9r9 nan problems. This experience shows that during the COVID-19 outbreak, the use of telemedicine for the management of paediatric infectious diseases permitted us to avoid hospital access J o u r n a l P r e


id: cord-284841-flhfagp3
author: Nicol, Thomas
date: 2020-06-15
extension: .txt
mime: text/plain
words: 2811
sentence: 130
flesch: 50
cache: cache/cord-284841-flhfagp3.txt
txt: txt/cord-284841-flhfagp3.txt
title:
  Assessment of SARS-CoV-2 serological tests for the diagnosis of COVID-19 through the evaluation of three immunoassays: two automated immunoassays (Euroimmun and Abbott) and one rapid lateral flow immunoassay (NG Biotech)

summary:
  [ELISA] or chemiluminescence enzyme immunoassays [CLIA]) or rapid detection test (lateral flow immunoassays, LFIA). Serological tests can be used for symptomatic individuals for which RT-PCR testing was either not performed at the time of acute illness or for which nasopharyngeal swab result was found to be negative, and also for epidemiological studies (close contacts screening, screening of health care workers …)


id: cord-311633-i9ret7bw
author: Péré, Hélène
title: Unexpected diagnosis of COVID-19-associated disorders by SARS-CoV-2-specific serology
date: 2020-08-04
extension: .txt
mime: text/plain
words: 1683
sentence: 64
flesch: 42
cache: cache/cord-311633-i9ret7bw.txt
txt: txt/cord-311633-i9ret7bw.txt
summary:
  Abbott SARS-CoV-2 IgG assay sensitivity. Thus, the frequency of SARS-CoV-2-specific IgG was around 10-fold higher in COVID-19 areas than COVID-19 free areas (75% versus 8%; P < 0.001).


id: cord-315782-tx2vqr64
author: Han, Tae Hee
title: Human Coronavirus-NL63 infections in Korean children, 2004–2006
date: 2006-11-29
extension: .txt
mime: text/plain
words: 2254
sentence: 94
flesch: 51
cache: cache/cord-315782-tx2vqr64.txt
txt: txt/cord-315782-tx2vqr64.txt
summary:
  New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia Human coronavirus NL63 infection in Canada Infections by human coronavirus-NL in hospitalized children Human coronavirus NL63 infection and other coronavirus infections in children hospitalized with acute respiratory disease in Hong Kong Detection of human coronavirus NL63 in young children with bronchiolitis Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children A previously undescribed coronavirus associated with respiratory disease in humans Human coronavirus NL63 associated with lower respiratory tract symptoms in early life A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium The Tecumseh study of respiratory illness. CONCLUSIONS: HCoV-NL63 may be one of the causative agents of acute respiratory tract infection, especially croup.


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
extension: .txt
mime: text/plain
words: 3883
sentence: 140
flesch: 43
cache: cache/cord-309763-8eywr57j.txt
txt: txt/cord-309763-8eywr57j.txt
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) .


id: cord-295873-kykyubdq
author: Morikawa, Saeko
title: Seasonal variations of respiratory viruses and etiology of human rhinovirus infection in children
date: 2015-10-22
extension: .txt
mime: text/plain
words: 2890
sentence: 130
flesch: 44
cache: cache/cord-295873-kykyubdq.txt
txt: txt/cord-295873-kykyubdq.txt
summary:
  Review on long-term outcome until adulthood after early childhood wheezing Seasonal variations of 15 respiratory agents illustrated by the application of a multiplex polymerase chain reaction assay, Scand Clinical impact of RT-PCR for pediatric acute respiratory infections: a controlled clinical trial Viral etiology of respiratory infections in children in southwestern Saudi Arabia using multiplex reverse-transcriptase polymerase chain reaction Ten years' experience with year-round active surveillance of up to 19 respiratory pathogens in children High incidence but low burden of coronaviruses and preferential associations between respiratory viruses Human coronavirus in young children hospitalized for acute respiratory illness and asymptomatic controls Detection of respiratory viruses in gargle specimens of healthy children Molecular diagnosis of human enteroviruses by phylogeny-based classification by use of the VP4 sequence The neighbor-joining method: a new method for reconstructing phylogenetic trees Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types Prospective genotyping of human rhinoviruses in children and adults during the winter of Molecular epidemiology of human rhinovirus C in patients with acute respiratory tract infections in Osaka City Proposals for the classification of human rhinovirus species C into genotypically assigned types Picornaviridae study group Comparison of real-time PCR assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children Epidemiological study of respiratory viruses detected in patients under two years old who required admission because of lower respiratory disease Phylogenetic analysis reveals the global migration of seasonal influenza A viruses Do rhinoviruses reduce the probability of viral co-detection during acute respiratory tract infections? key: cord-295873-kykyubdq authors: Morikawa, Saeko; Kohdera, Urara; Hosaka, Taisuke; Ishii, Kousuke; Akagawa, Shohei; Hiroi, Satoshi; Kase, Tetsuo title: Seasonal variations of respiratory viruses and etiology of human rhinovirus infection in children date: 2015-10-22 journal: J Clin Virol DOI: 10.1016/j.jcv.2015.10.001 sha: doc_id: 295873 cord_uid: kykyubdq BACKGROUND: Using the polymerase chain reaction (PCR) method it is possible to detect uncultivable viruses and discover multiple viral infections.


id: cord-323567-1397kds0
author: Bialasiewicz, S.
date: 2007-08-21
extension: .txt
mime: text/plain
words: 2878
sentence: 110
flesch: 44
cache: cache/cord-323567-1397kds0.txt
txt: txt/cord-323567-1397kds0.txt
title:
  Development and evaluation of real-time PCR assays for the detection of the newly identified KI and WU polyomaviruses

summary:
  Clinical sensitivity and specificity were determined by retrospectively testing 200 nasopharyngeal aspirate (NPA) specimens by the five rtPCR methods and comparing the results to those obtained using previously described WUV and KIV conventional PCR assays. One specimen provided positive results for both KIV and WUV in all real-time and conventional PCR assays and was considered a co-infection (Sample 22; Table 4 ).


id: cord-313375-rs3jjiuj
author: Panning, Marcus
date: 2010-11-13
extension: .txt
mime: text/plain
words: 2310
sentence: 105
flesch: 50
cache: cache/cord-313375-rs3jjiuj.txt
txt: txt/cord-313375-rs3jjiuj.txt
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

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.


id: cord-310680-klywz85w
author: Li, Qihan
date: 2005-04-06
extension: .txt
mime: text/plain
words: 4412
sentence: 163
flesch: 47
cache: cache/cord-310680-klywz85w.txt
txt: txt/cord-310680-klywz85w.txt
title:
  The interaction of the SARS coronavirus non-structural protein 10 with the cellular oxido-reductase system causes an extensive cytopathic effect

summary:
  The observation of nsp10-GFP fusion protein expressed in KMB-17 cells shows that nsp10 protein is accumulated as a distributed cluster in the cytoplasm (Fig. 2c) . Approximately 4 ug expressed and purified GST-nsp10 fusion protein and GST protein were respectively mixed with the 500 ul labeled extract of KMB-17 cells (5 × 10 6 cells), which were lysed in lysis buffer at 4 • C overnight.


id: cord-322220-mlphue1r
author: Bosis, Samantha
title: Coronavirus HKU1 in an Italian pre-term infant with bronchiolitis
date: 2007-02-21
extension: .txt
mime: text/plain
words: 1593
sentence: 37
flesch: 24
cache: cache/cord-322220-mlphue1r.txt
txt: txt/cord-322220-mlphue1r.txt
summary:
  Human coronavirus NL-63 infections in children: a 1-year study Impact of human metapneumovirus in childhood: comparison with respiratory syncytial virus and influenza viruses Human coronavirus NL63 infection and other coronavirus infections in children hospitalized with acute respiratory disease in Hong Kong Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-PCR assay Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children Coronavirus HKU1 infection in the United States Clinical and socioeconomic impact of influenza and respiratory syncytial virus (RSV) infection on healthy children and their households A previously undescribed coronavirus associated with respiratory disease in humans Newer respiratory virus infections: human metapneumovirus, avian influenza virus, and human coronaviruses Pring-Akerblom P. Rapid and quantitative detection of human adenovirus DNA by real-time PCR History and recent advances in coronavirus discovery Realtime PCR for rapid diagnosis of entero-and rhinovirus infections using LightCycler Prevalence of respiratory syncytial virus infection in Italian infants hospitalized for acute lower respiratory tract infections, and association between respiratory syncytial virus infection risk factors and disease severity Coronavirus HKU1 and other coronavirus infections in Hong Kong Frequency of detection of picoronaviruses and seven other respiratory pathogens in infants Real-time reverse transcriptase PCR assay for detection of human metapneumovirus from all known genetic lineages Clinical virology in real time Human metapneumovirus infection in pediatric age Human metapneumovirus in otherwise healthy infants and children Children's Hospital Respiratory Syncytial Virus Database Risk factors, treatment and hospital course in 3308 infants and young children Evidence of human coronavirus HKU1 and human bocavirus in Australian children A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses Detection of the new human coronavirus HKU1: a report of 6 cases Identification of a new human coronavirus Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia Phylogenetic and recombination analysis of coronavirus HKU1, a novel coronavirus from patients with pneumonia Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia Comparative analysis of 22 coronavirus HKU1 genomes reveals a novel genotype and evidence of natural recombination in coronavirus HKU1 However, further epidemiological and clinical investigations are needed to precisely define the role of HCoV-HKU1 in respiratory infections.


id: cord-314888-i7nn2e3m
author: DeGroote, Nicholas P.
title: Human parainfluenza virus circulation, United States, 2011–2019
date: 2020-01-09
extension: .txt
mime: text/plain
words: 2419
sentence: 102
flesch: 39
cache: cache/cord-314888-i7nn2e3m.txt
txt: txt/cord-314888-i7nn2e3m.txt
summary:
  Among HPIV detections where age was known, the majority were aged ≤ 2 years. We analyzed tests determined by molecular diagnostic assays as they were the most prevalent test type reported (encompassing approximately 75 % of HPIV detections) and limited to laboratories that reported at least one HPIV test and one detection during the analysis period.


id: cord-321287-mh2j2koa
author: Trémeaux, Pauline
date: 2020-07-06
extension: .txt
mime: text/plain
words: 1146
sentence: 63
flesch: 58
cache: cache/cord-321287-mh2j2koa.txt
txt: txt/cord-321287-mh2j2koa.txt
title:
  Evaluation of the Aptima™ Transcription-Mediated Amplification assay (Hologic®) for detecting SARS-CoV-2 in clinical specimens

summary:
  The final Cohen’s kappa coefficients were: κ = 0.978 between the Aptima™ and Panther Fusion™ assays, κ = 0.945 between the Aptima™ and MagNA/LC480 assays and κ = 0.956 between the MagNA/LC480 and Panther Fusion™ assays. The prospective study provided 2 positive and 98 negative samples, and there was perfect concordance between results of the Aptima™ assay and those of the Panther Fusion™ assay and very good concordance between the Aptima™ assay and the MagNA/LC480 assay.


id: cord-302896-3zvjyl3g
author: Minosse, C.
title: Phylogenetic analysis of human coronavirus NL63 circulating in Italy
date: 2008-07-03
extension: .txt
mime: text/plain
words: 2491
sentence: 96
flesch: 44
cache: cache/cord-302896-3zvjyl3g.txt
txt: txt/cord-302896-3zvjyl3g.txt
summary:
  HCoV-NL63 can be considered as a new important cause of respiratory illness, although the available data mainly refer to pediatric populations (Arden et al., 2005; Bastien et al., 2005b; Boivin et al., 2005; Chiu et al., 2005; Ebihara et al., 2005; Kuypers et al., 2007; Moës et al., 2005) . Based on phylogenetic analysis of different genome regions, several subtypes, currently co-circulating in the human population, have been identified in France, Canada, Australia, Belgium, Netherlands, Sweden, China and Korean (Arden et al., 2005; Bastien et al., 2005a; Chiu et al., 2005; Han et al., 2007; Koetz et al., 2006; Moës et al., 2005; Vabret et al., 2005; van der Hoek et al., 2004) .


id: cord-302864-2xnq1oq7
author: Quartuccio, Luca
date: 2020-05-15
extension: .txt
mime: text/plain
words: 3186
sentence: 136
flesch: 43
cache: cache/cord-302864-2xnq1oq7.txt
txt: txt/cord-302864-2xnq1oq7.txt
title:
  Profiling COVID-19 pneumonia progressing into the cytokine storm syndrome: results from a single Italian Centre study on tocilizumab versus standard of care

summary:
  To conclude, our study showed that TOCI treated patients COVID-19 pneumonia were at the highest risk of cytokine storm [32] . Aging (Albany NY) Prognostic role of neutrophil-to-lymphocyte ratio in solid tumors: a systematic review and meta-analysis Prediction for Progression Risk in Patients with COVID-19 Pneumonia: the CALL Score Clinical Course and Outcomes of Critically Ill Patients With SARS-CoV-2 Pneumonia in Wuhan, China: A Single-Centered, Retrospective, Observational Study Clinical Characteristics of Coronavirus Disease 2019 in China Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients Airway Memory CD4(+) T Cells Mediate Protective Immunity against Emerging Respiratory Coronaviruses Microvascular COVID-19 lung vessels obstructive thromboinflammatory syndrome (MicroCLOTS): an atypical acute respiratory distress syndrome working hypothesis Anticoagulant treatment is associated with decreased mortality in severe coronavirus disease 2019 patients with coagulopathy Risk of thrombosis in Sjögren syndrome: the open question of endothelial function immune-mediated dysregulation Risk factors for severity and mortality in adult COVID-19 inpatients in Wuhan On the alert for cytokine storm: Immunopathology in COVID-19.


id: cord-290352-0pc5eji4
author: de Jong, Menno D.
title: Avian influenza A (H5N1)
date: 2005-10-06
extension: .txt
mime: text/plain
words: 9178
sentence: 282
flesch: 31
cache: cache/cord-290352-0pc5eji4.txt
txt: txt/cord-290352-0pc5eji4.txt
summary:
  The structure and receptor binding properties of the 1918 influenza hemagglutinin Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: the role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza Comparison of efficacies of RWJ-270201, zanamivir, and oseltamivir against H5N1, H9N2, and other avian influenza viruses Emergence of multiple genotypes of H5N1 avian influenza viruses in Hong Kong SAR H5N1 influenza: a protean pandemic threat Molecular characterization of H9N2 influenza viruses: were they the donors of the internal genes of H5N1 viruses in Hong Kong? Characterization of influenza A/HongKong/156/97 (H5N1) virus in a mouse model and protective effect of zanamivir on H5N1 infection in mice Avian influenza-a challenge to global health care structures Replication of avian influenza A viruses in mammals Role of domestic ducks in the propagation and biological evolution of highly pathogenic H5N1 influenza viruses in Asia Molecular basis for the generation in pigs of influenza A viruses with pandemic potential Antibody response in individuals infected with avian influenza A (H5N1) viruses and detection of anti-H5 antibody among household and social contacts Avian-to-human transmission of the PB1 gene of influenza A viruses in the 1957 and 1968 pandemics Avian influenza H5N1 in tigers and leopards Potential for transmission of avian influenza viruses to pigs Enhanced virulence of influenza A viruses with the haemagglutinin of the 1918 pandemic virus DNA vaccine encoding hemagglutinin provides protective immunity against H5N1 influenza virus infection in mice Transmission of H7N7 avian influenza While there has been no evidence of efficient transmission of influenza H5N1 virus between humans to date, caution and detailed investigations remain warranted in case of any cluster of infections, especially in view of the relatively rapid evolution H5N1 viruses have exhibited in recent years.


id: cord-291930-n7wq09rq
author: Arden, K.E.
date: 2010-01-27
extension: .txt
mime: text/plain
words: 3297
sentence: 108
flesch: 38
cache: cache/cord-291930-n7wq09rq.txt
txt: txt/cord-291930-n7wq09rq.txt
title:
  Molecular characterization and distinguishing features of a novel human rhinovirus (HRV) C, HRVC-QCE, detected in children with fever, cough and wheeze during 2003

summary:
  Disappointingly, the possibility that discrete HRV strains exist as distinct viral entities is not accounted for in asymptomatic control populations because strain identification is not routinely conducted. Many HRV strains have distinct genetic, antigenic, immunogenic and epidemiologic profiles which are similar in nature to those of other respiratory virus species including human respiratory syncytial virus (HRSV).


id: cord-307261-0a3iztns
author: Hayden, Randall T.
date: 2012-01-30
extension: .txt
mime: text/plain
words: 4054
sentence: 164
flesch: 43
cache: cache/cord-307261-0a3iztns.txt
txt: txt/cord-307261-0a3iztns.txt
title:
  Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children

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


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
extension: .txt
mime: text/plain
words: 865
sentence: 35
flesch: 49
cache: cache/cord-329052-jan20ljs.txt
txt: txt/cord-329052-jan20ljs.txt
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.


id: cord-308921-lpcjhxvg
author: Stellrecht, Kathleen A.
date: 2019-11-09
extension: .txt
mime: text/plain
words: 3335
sentence: 143
flesch: 46
cache: cache/cord-308921-lpcjhxvg.txt
txt: txt/cord-308921-lpcjhxvg.txt
title:
  Panther Fusion® Respiratory Virus Assays for the detection of influenza and other respiratory viruses()

summary:
  Nucleic acid amplification tests (NAATs), such as PCR, are preferred for respiratory virus testing, due to superior diagnostic accuracy and faster turnaround time. There are many options for respiratory virus testing, each with their own niche.


id: cord-326816-a7yovhvk
author: Piralla, Antonio
date: 2018-01-12
extension: .txt
mime: text/plain
words: 3844
sentence: 155
flesch: 47
cache: cache/cord-326816-a7yovhvk.txt
txt: txt/cord-326816-a7yovhvk.txt
title:
  Enterovirus-D68 (EV-D68) in pediatric patients with respiratory infection: The circulation of a new B3 clade in Italy

summary:
  Numbering of amino acidic changes is according Acute respiratory infections due to enterovirus 68 in Yamagata outbreak of enterovirus D68 in North America Enterovirus D68: a focused review and clinical highlights from the 2014 United States outbreak Global reemergence of enterovirus D68 as an important pathogen for acute respiratory infections Severe respiratory illness associated with enterovirus D68-Missouri and Illinois Continued seasonal circulation of enterovirus D68 in the Netherlands Molecular epidemiology of enterovirus D68 from 2013 to 2014 in Philippines Genome sequence of enterovirus D68 and clinical disease Genome sequence of enterovirus D68 from St Louis Enterovirus D68-associated severe pneumonia Low-level circulation of enterovirus D68-associated acute respiratory infections A fatal central nervous system enterovirus 68 infection Enterovirus-D68 in the cerebrospinal fluid of two children with aseptic meningitis Acute flaccid myelitis associated with enterovirus-D68 infection in an otherwise healthy child Molecular evolution and intraclade recombination of enterovirus D68 during the 2014 outbreak in the United States European surveillance for enterovirus D68 during the emerging North-American outbreak in 2014 Phylogenetic patterns of human respiratory picornavirus species, including the newly identified group C rhinoviruses, during a 1-year surveillance of a hospitalized patient population in Italy FilmArray ® respiratory panel performance in respiratory samples from neonatal care units A new real-time reverse transcription-PCR assay for detection of human enterovirus 68 in respiratory samples MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets JPred4: a protein secondary structure prediction server Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology Not so different after all: a comparison of methods for detecting amino acid sites under selection Sialic acid-dependent cell entry of human enterovirus D68 European surveillance for enterovirus D68 during the emerging North-American outbreak in 2014 Outbreak of enterovirus D68 of the new B3 lineage in Identification and whole-genome sequencing of four enterovirus D68 strains in Southern China inlate Complete genome sequences of nine enterovirus D68 strains from patients of the lower Hudson Valley Enterovirus D68 in hospitalized children: sequence variation, viral loads and clinical outcomes Clinical course of enterovirus D68 in hospitalized children Enterovirus D68 infection among children with medically attended acute respiratory illness Enterovirus D68-associated community-acquired pneumonia in the pediatric age group A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study Molecular evolution and the global reemergence of enterovirus D68 by genome-wide analysis Genetic divergence of enterovirus D68 in China and the United States Enterovirus D68 infections associated with severe respiratory illness in elderly patients and emergence of a novel clade in Hong Kong Global distribution and evolutionary history of enterovirus D68, with emphasis on the Enterovirus D68 subclade B3 strain circulating and causing an outbreak in the United States in 2016


id: cord-320156-xs936r6u
author: Nunes, Marta C.
title: Polyomaviruses-associated respiratory infections in HIV-infected and HIV-uninfected children
date: 2014-10-28
extension: .txt
mime: text/plain
words: 3694
sentence: 143
flesch: 38
cache: cache/cord-320156-xs936r6u.txt
txt: txt/cord-320156-xs936r6u.txt
summary:
  Although our study was not designed to establish whether polyomavirus infections caused more severe disease in HIV-infected children, among hospitalized children in whom polyomaviruses were detected HIV-infected were more likely to present with pneumonia rather than bronchiolitis, had a longer duration of hospitalization and higher CFR compared to HIV-uninfected children. key: cord-320156-xs936r6u authors: Nunes, Marta C.; Kuschner, Zachary; Rabede, Zelda; Cutland, Clare L.; Madimabe, Richard; Kuwanda, Locadiah; Klugman, Keith P.; Adrian, Peter V.; Madhi, Shabir A. title: Polyomaviruses-associated respiratory infections in HIV-infected and HIV-uninfected children date: 2014-10-28 journal: J Clin Virol DOI: 10.1016/j.jcv.2014.10.013 sha: doc_id: 320156 cord_uid: xs936r6u BACKGROUND: Two recently discovered polyomaviruses (PyV), WU and KI, have been identified in respiratory-tract specimens from children with acute respiratory infections, although there are limited data in HIV-infected children.


id: cord-319864-t6ql9hz2
author: Lima, Amorce
date: 2020-11-11
extension: .txt
mime: text/plain
words: 3053
sentence: 105
flesch: 52
cache: cache/cord-319864-t6ql9hz2.txt
txt: txt/cord-319864-t6ql9hz2.txt
title:
  Validation of a Modified CDC Assay and Performance Comparison with the NeuMoDx™ and DiaSorin® automated assays for Rapid Detection of SARS-CoV-2 in Respiratory Specimens

summary:
  f the First Rapid Multiplex PCR Commercial Assay for SARS-CoV-2 Detection Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting Rapid and sensitive detection of SARS-CoV-2 RNA using the Simplexa™ COVID-19 direct assay Clinical Evaluation of the cobas SARS-CoV-2 Test and a Diagnostic Platform Switch during 48 Hours in the Midst of the COVID-19 Pandemic US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 Comparison of Abbott ID Now, Diasorin Simplexa, and CDC FDA EUA methods for the detection of SARS-CoV-2 from nasopharyngeal and nasal swabs from individuals diagnosed with COVID-19 Comparison of Commercially Available and Laboratory Developed Assays for in vitro Detection of SARS-CoV-2 in Clinical Laboratories Clinical Evaluation of Three Sample-To-Answer Platforms for the Detection of SARS-CoV-2 We are grateful to University of Texas Medical Branch for providing SARS CoV-2 RNA Template for the validation of the modified CDC SARS-CoV-2 assay. Our laboratory at Tampa General Hospital validated a modified version of the CDC assay following the FDA EUA guidelines and brought in commercial assays to help respond to the testing demand.


id: cord-311275-ysr9nqun
author: Chuaychoo, Benjamas
date: 2019-07-03
extension: .txt
mime: text/plain
words: 3167
sentence: 166
flesch: 38
cache: cache/cord-311275-ysr9nqun.txt
txt: txt/cord-311275-ysr9nqun.txt
title:
  Clinical manifestations and outcomes of respiratory syncytial virus infection in adult hospitalized patients

summary:
  key: cord-311275-ysr9nqun authors: Chuaychoo, Benjamas; Ngamwongwan, Sopita; Kaewnaphan, Bualan; Athipanyasilp, Niracha; Horthongkham, Navin; Kantakamalakul, Wannee; Muangman, Nisa title: Clinical manifestations and outcomes of respiratory syncytial virus infection in adult hospitalized patients date: 2019-07-03 journal: J Clin Virol DOI: 10.1016/j.jcv.2019.07.001 sha: doc_id: 311275 cord_uid: ysr9nqun BACKGROUND: Respiratory syncytial virus (RSV) is an important virus found in adult hospitalized patients. There were a few data of adult hospitalized patients with RSV infection, with high complications, in Thailand; [3, 12, 13] however, additional clinical data are required for planning patient management and also disease prevention in this region.


id: cord-318012-bg9y2nsp
author: Cantais, Aymeric
date: 2014-05-22
extension: .txt
mime: text/plain
words: 3548
sentence: 124
flesch: 36
cache: cache/cord-318012-bg9y2nsp.txt
txt: txt/cord-318012-bg9y2nsp.txt
title:
  Epidemiology and microbiological investigations of community-acquired pneumonia in children admitted at the emergency department of a university hospital

summary:
  Breathing new life into pneumonia diagnostics Blood culture is poor method of confirming pneumococcus as cause of childhood pneumonia Association of human metapneumovirus with radiologically diagnosed community-acquired alveolar pneumonia in young children Comprehensive detection of causative pathogens using real-time PCR to diagnose pediatric community-acquired pneumonia Viruses in community-acquired pneumonia in children aged less than 3 years old: high rate of viral coinfection Etiology of community-acquired pneumonia in hospitalized school-age children: evidence for high prevalence of viral infections Etiology of community-acquired pneumonia in hospitalized children based on WHO clinical guidelines Community acquired pneumonia -a prospective UK study Epidemiology and clinical characteristics of community-acquired pneumonia in hospitalized children Human metapneumovirus and community-acquired pneumonia in children Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses Role of Mycoplasma pneumoniae and Chlamydia pneumoniae in children with community-acquired lower respiratory tract infections Diagnostic value of tachypnoea in pneumonia defined radiologically Comparing nose-throat swabs and nasopharyngeal aspirates collected from children with symptoms for respiratory virus identification using real-time polymerase chain reaction Induced sputum in the diagnosis of childhood community-acquired pneumonia Development and evaluation of Chlamylege, a new commercial test allowing simultaneous detection and identification of Legionella, Chlamydophila pneumoniae, and Mycoplasma pneumoniae in clinical respiratory specimens by multiplex PCR Comparative evaluation of six commercialized multiplex PCR kits for the diagnosis of respiratory infections European manual of clinical microbiology Pneumonia Methods Working Group, et al. These findings highlight the huge proportion of CAP of viral origin, the high number of co-infection by multiple viruses and the low number of bacterial CAP, notably in children under 5 years, and address the need to re-evaluate the indications of empiric antimicrobial treatment in this age group.


id: cord-313749-f2ct57em
author: Brittain-Long, Robin
title: Multiplex real-time PCR for detection of respiratory tract infections
date: 2007-12-26
extension: .txt
mime: text/plain
words: 1568
sentence: 57
flesch: 40
cache: cache/cord-313749-f2ct57em.txt
txt: txt/cord-313749-f2ct57em.txt
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.


id: cord-332723-rz1iilsv
author: Creager, Hannah M.
title: Clinical evaluation of the BioFire® Respiratory Panel 2.1 and detection of SARS-CoV-2
date: 2020-07-06
extension: .txt
mime: text/plain
words: 1479
sentence: 45
flesch: 40
cache: cache/cord-332723-rz1iilsv.txt
txt: txt/cord-332723-rz1iilsv.txt
summary:
  key: cord-332723-rz1iilsv authors: Creager, Hannah M.; Cabrera, Barbara; Schnaubelt, Andy; Cox, Jesse L.; Cushman-Vokoun, Allison M.; Shakir, Salika M.; Tardif, Keith D.; Huang, Meei-Li; Jerome, Keith R.; Greninger, Alexander L.; Drobysheva, Daria; Spaulding, Usha; Rogatcheva, Margarita; Bourzac, Kevin M.; Hinrichs, S.H.; Broadhurst, M.J.; Fey, P.D. title: Clinical evaluation of the BioFire® Respiratory Panel 2.1 and detection of SARS-CoV-2 date: 2020-07-06 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104538 sha: doc_id: 332723 cord_uid: rz1iilsv We evaluated the performance of the BioFire® Respiratory Panel 2.1 (RP2.1) in the detection of SARS CoV-2 in comparison against three other SARS CoV-2 EUA assays. Since 30% of nasopharyngeal swab specimens have a SARS CoV-2 Ct >30 and thus detection of virus in low titers is clinically relevant, a sample with a high titer was diluted and each 10 fold dilution was tested in triplicate and compared against 6 other EUA approved SARS CoV-2 assays.


id: cord-328290-kbysppgb
author: Beckmann, Christiane
title: Diagnostic performance of near-patient testing for influenza
date: 2015-03-31
extension: .txt
mime: text/plain
words: 1991
sentence: 91
flesch: 47
cache: cache/cord-328290-kbysppgb.txt
txt: txt/cord-328290-kbysppgb.txt
summary:
  Conclusion: Simple sample processing and a TAT of 15 min render isothermal NAT Alere TM Influenza A&B suitable for sequential near-patient testing, but the TAT advantage is lost when testing of larger series. Isothermal NAT was 10-100-fold more sensitive compared to DAD for influenza virus culture supernatants with a lower limit of detection of 5000-50,000 copies/mL. The average turn-around time (TAT) of isothermal NAT and DADs was 15 min, but increased to 110 min for Alere TM Influenza A&B, 30 min for BinaxNOW ® Influenza A&B, and 45 min for Sofia ® Influenza A + B, when analyzing batches of 6 samples.


id: cord-299537-lbx1plqx
author: Wang, Wei
date: 2010-09-19
extension: .txt
mime: text/plain
words: 4012
sentence: 155
flesch: 45
cache: cache/cord-299537-lbx1plqx.txt
txt: txt/cord-299537-lbx1plqx.txt
title:
  Molecular monitoring of causative viruses in child acute respiratory infection in endemo-epidemic situations in Shanghai

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.


id: cord-336237-hmczy0am
author: Kitagawa, Yutaro
date: 2020-05-21
extension: .txt
mime: text/plain
words: 1206
sentence: 41
flesch: 41
cache: cache/cord-336237-hmczy0am.txt
txt: txt/cord-336237-hmczy0am.txt
title:
  Evaluation of rapid diagnosis of novel coronavirus disease (COVID-19) using loop-mediated isothermal amplification

summary:
  Shinichi Takeuchi: Provided scientific guidance, Reviewed and Edited Shigefumi Maesaki: Provided scientific guidance Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia Exploring the reasons for healthcare workers infected with novel coronavirus disease 2019 (COVID-19) in China Operational feasibility of using loop mediated isothermal amplification (LAMP) for the diagnosis of pulmonary TB in microscopy centers of developing countries Evaluation of a simple loop mediated isothermal amplification test kit for the diagnosis of tuberculosis Manual for the Detection of Pathogen 2019-nCoV Ver.2.6 Development of Reverse Transcription Loopmediated Isothermal Amplification (RT-LAMP) In this protocol, cDNA is synthesized from SARS-CoV-2 RNA using reverse transcriptase, followed by DNA amplification under isothermal conditions in one step.


id: cord-349541-7g50vg14
author: Poulikakos, Dimitrios
title: SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England
date: 2020-07-07
extension: .txt
mime: text/plain
words: 428
sentence: 16
flesch: 50
cache: cache/cord-349541-7g50vg14.txt
txt: txt/cord-349541-7g50vg14.txt
summary:
  key: cord-349541-7g50vg14 authors: Poulikakos, Dimitrios; Sinha, Smeeta; Kalra, Philip A. title: SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England date: 2020-07-07 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104545 sha: doc_id: 349541 cord_uid: 7g50vg14 nan Please cite this article as: Poulikakos D, Sinha S, Kalra PA, SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England, Journal of Clinical Virology (2020), doi: https://doi.org/10.1016/j.jcv.2020.104545 This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. England most likely reflect general community transmission rather than hospital exposure SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients Hospital-Wide SARS-CoV-2 Antibody Screening Analytical performances of a chemiluminescence immunoassay for SARS-CoV-2 IgM/IgG and antibody kinetics First experience of COVID-19 screening of health-care workers in England Evaluating the National PPE Guidance for NHS Healthcare Workers During the COVID-19 Pandemic


id: cord-349921-v1tewoi0
author: Giorgi Rossi, Paolo
date: 2020-05-05
extension: .txt
mime: text/plain
words: 657
sentence: 24
flesch: 47
cache: cache/cord-349921-v1tewoi0.txt
txt: txt/cord-349921-v1tewoi0.txt
title:
  Case fatality rate in patients with COVID-19 infection and its relationship with length of follow up()

summary:
  Prevalence and severity of corona virus disease 2019 (COVID-19): A systematic review and meta-analysis Clinical features of patients infected with 2019 novel coronavirus in Wuhan An interactive web-based dashboard to track COVID-19 in real time Clinical characteristics of coronavirus disease 2019 (COVID-19) in China: a systematic review and meta-analysis Case-Fatality Rate and Characteristics of Patients Dying in Relation to COVID-19 in Italy Epidemiological characteristics of COVID-19 cases in Italy and estimates of the reproductive numbers one month into the epidemic The following are members of the Emilia-Romagna COVID-19 working group: Andrea Mattivi, Giulio Matteo, key: cord-349921-v1tewoi0 authors: Giorgi Rossi, Paolo; Broccoli, Serena; Angelini, Paola title: Case fatality rate in patients with COVID-19 infection and its relationship with length of follow up() date: 2020-05-05 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104415 sha: doc_id: 349921 cord_uid: v1tewoi0 nan In their systematic review on the clinical characteristics of COVID-19, Wu and colleagues report a 3.2% case fatality rate (CFR), ranging from 2% to 4% 1 with strong heterogeneity between studies (I 2 =100%).


id: cord-313821-5f5b107l
author: Poelman, Randy
date: 2014-11-15
extension: .txt
mime: text/plain
words: 3040
sentence: 135
flesch: 52
cache: cache/cord-313821-5f5b107l.txt
txt: txt/cord-313821-5f5b107l.txt
title:
  The emergence of enterovirus D68 in a Dutch University Medical Center and the necessity for routinely screening for respiratory viruses

summary:
  key: cord-313821-5f5b107l authors: Poelman, Randy; Schölvinck, Elisabeth H.; Borger, Renze; Niesters, Hubert G.M.; van Leer-Buter, Coretta title: The emergence of enterovirus D68 in a Dutch University Medical Center and the necessity for routinely screening for respiratory viruses date: 2014-11-15 journal: J Clin Virol DOI: 10.1016/j.jcv.2014.11.011 sha: doc_id: 313821 cord_uid: 5f5b107l BACKGROUND: Since August 2014, an increase in infections caused by enterovirus D68 (EV-D68) was reported in the USA and Canada, for the most part in children presenting with severe respiratory symptoms. Since August 2014, an increase in infections caused by enterovirus D68 (EV-D68) has been reported in the USA and Canada.


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
extension: .txt
mime: text/plain
words: 998
sentence: 32
flesch: 44
cache: cache/cord-349782-djzxkus2.txt
txt: txt/cord-349782-djzxkus2.txt
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.


id: cord-353640-giznbcpd
author: Barza, Ruby
date: 2020-08-11
extension: .txt
mime: text/plain
words: 1206
sentence: 32
flesch: 37
cache: cache/cord-353640-giznbcpd.txt
txt: txt/cord-353640-giznbcpd.txt
title:
  Use of a Simplified Sample Processing step without RNA Extraction for direct SARS-CoV-2 RT-PCR Detection

summary:
  The authors declare that there are no conflicts of interest This work received no specific grant from any funding agency J o u r n a l P r e -p r o o f Response and the President's Plan for Opening America Up Again Failing the Test -The Tragic Data Gap Undermining the U.S. Pandemic Response Access to Lifesaving Medical Resources for African Countries: COVID-19 Testing and Response, Ethics, and Politics Direct RT-qPCR detection of SARS-COV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step Development of a TaqMan® RT-PCR assay without RNA extraction step for the detection and quantification of African Chikungunya viruses Bei Resources Product Information Sheet for NR-52286 Use of reverse transcription and PCR to discriminate between infectious and non-infectious hepatitis A virus The authors would like to thank ChromaCode for providing the ChromaCode HDPCR™ SARS-CoV-2 Research Use Only (ChromaCode RUO) assay kit We found that the direct detection of SARS-CoV-2 using a 65°C heat inactivation and release step for 20minutes without RNA extraction and purification performed very well compared to the use of an automated RNA extraction instrument.


id: cord-349485-iomk99lv
author: Eis-Hübinger, Anna M.
date: 2020-04-22
extension: .txt
mime: text/plain
words: 1637
sentence: 69
flesch: 49
cache: cache/cord-349485-iomk99lv.txt
txt: txt/cord-349485-iomk99lv.txt
title:
  Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples

summary:
  In perspective, this approach can be set up rather easily e. g. by public health laboratories, can be done on a daily basis and at reduced costs compared to individual patient testing. This approach proved its principle and might assist public health laboratories in Europe and elsewhere to rapidly detect SARS-CoV-2 cases which might otherwise remain undetected.


id: cord-336636-xgfw21hk
author: Spezia, Pietro Giorgio
title: Redondovirus DNA in human respiratory samples
date: 2020-08-15
extension: .txt
mime: text/plain
words: 1893
sentence: 73
flesch: 39
cache: cache/cord-336636-xgfw21hk.txt
txt: txt/cord-336636-xgfw21hk.txt
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.


id: cord-343800-nbydaoac
author: Cerutti, Francesco
date: 2020-09-29
extension: .txt
mime: text/plain
words: 1211
sentence: 41
flesch: 45
cache: cache/cord-343800-nbydaoac.txt
txt: txt/cord-343800-nbydaoac.txt
title:
  Urgent need of rapid tests for SARS CoV-2 antigen detection: evaluation of the SD-Biosensor antigen test for SARS-CoV-2

summary:
  key: cord-343800-nbydaoac authors: Cerutti, Francesco; Burdino, Elisa; Milia, Maria Grazia; Allice, Tiziano; Gregori, Gabriella; Bruzzone, Bianca; Ghisetti, Valeria title: Urgent need of rapid tests for SARS CoV-2 antigen detection: evaluation of the SD-Biosensor antigen test for SARS-CoV-2 date: 2020-09-29 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104654 sha: doc_id: 343800 cord_uid: nbydaoac At the time of writing, FIND has listed four CE-marked SARSCoV-2 antigen tests. The adoption of POCT for SARS CoV-2 testing is certainly more suitable in point of care centers for mass screening where the prevalence of COVID-19 is much lower and the pre-test probability of not having the disease is higher than that in the patients admitted to the emergency room were the pre-test probability of having COVID-19 is significantly higher and false negative results are relevant for the correct management of patients.


id: cord-325120-jlrievxl
author: Abd El Wahed, Ahmed
date: 2015-05-19
extension: .txt
mime: text/plain
words: 3183
sentence: 143
flesch: 53
cache: cache/cord-325120-jlrievxl.txt
txt: txt/cord-325120-jlrievxl.txt
title:
  Diagnostics-in-a-Suitcase: Development of a portable and rapid assay for the detection of the emerging avian influenza A (H7N9) virus

summary:
  Avian influenza A (H7N9) virus Detection of a novel avian influenza A (H7N9) virus in humans by multiplex one-step real-time RT-PCR assay Development of a reverse transcription loop-mediated isothermal amplification method for the rapid detection of subtype H7N9 avian influenza virus Rapid and sensitive detection of novel avian-origin influenza A (H7N9) virus by reverse transcription loopmediated isothermal amplification combined with a lateral-flow device Development of reversetranscription loop-mediated isothermal amplification assay for rapid detection of novel avian influenza A (H7N9) virus Development of a reverse transcription loop-mediated isothermal amplification assay for the rapid diagnosis of avian influenza A (H7N9) virus infection Rapid and sensitive detection of H7N9 avian influenza virus by use of reverse transcription-loop-mediated isothermal amplification Development of a Panel of Recombinase Polymerase Amplification Assays for Detection of Respiratory Viruses A systematic review and meta-analysis of the diagnostic accuracy of rapid immunochromatographic assays for the detection of dengue virus IgM antibodies during acute infection Evaluation of diagnostic tests: dengue Real-time RT-PCR for H5N1 avian influenza A virus detection Development of real time RT-PCR assays for detection of type A influenza virus and for subtyping of avian H5 and H7 hemagglutinin subtypes Development of real-time RT-PCR for the detection of avian influenza virus Portable nucleic acid thermocyclers DNA detection using recombination proteins A portable reverse transcription recombinase polymerase amplification assay for rapid detection of foot-and-mouth disease virus Reverse transcription recombinase polymerase amplification assay for the detection of Middle East respiratory syndrome coronavirus A new approach for diagnosis of bovine coronavirus using a reverse transcription recombinase polymerase amplification assay Recombinase polymerase amplification assay for rapid detection of Rift Valley fever virus Nucleic acid-based detection of influenza A virus subtypes H7 and N9 with a special emphasis on the avian H7N9 virus Specific detection by real-time reverse-transcription PCR assays of a novel avian influenza A(H7N9) strain associated with human spillover infections in China.


id: cord-335067-tg66h99q
author: Woolhouse, Mark E.J.
title: Ecological and taxonomic variation among human RNA viruses
date: 2013-03-19
extension: .txt
mime: text/plain
words: 1396
sentence: 64
flesch: 53
cache: cache/cord-335067-tg66h99q.txt
txt: txt/cord-335067-tg66h99q.txt
summary:
  The remaindercomprising almost half the total of human RNA virus species -is not known to be transmissible between humans at all. We can distinguish three categories of human RNA viruses based on their basic reproduction number in human populations (R 0 ).


id: cord-335208-xv2evahh
author: O Loughlin, D.W.
title: The role of rhinovirus infections in young children with cystic fibrosis
date: 2020-06-01
extension: .txt
mime: text/plain
words: 2022
sentence: 82
flesch: 47
cache: cache/cord-335208-xv2evahh.txt
txt: txt/cord-335208-xv2evahh.txt
summary:
  There was no difference in the frequency of RV species between symptomatic and asymptomatic subjects. While the role of RV species is well studied in children with asthma [15, 16] , there is limited evidence on their clinical impact in children with CF [12, 17] .


id: cord-336535-r3a57m57
author: Kohmer, Niko
title: Brief clinical evaluation of six high-throughput SARS-CoV-2 IgG antibody assays
date: 2020-06-01
extension: .txt
mime: text/plain
words: 1483
sentence: 54
flesch: 41
cache: cache/cord-336535-r3a57m57.txt
txt: txt/cord-336535-r3a57m57.txt
summary:
  Focusing on IgG and total antibodies, we demonstrate the performance of four automated immunoassays (Abbott Architect™ i2000 (N protein-based)), Roche cobas™ e 411 analyzer (N protein-based, not differentiating between IgA, IgM or IgG antibodies), LIAISON®XL platform (S1 and S2 protein-based), VIRCLIA® automation system (S1 and N protein-based) in comparison two ELISA assays (Euroimmun SARS-CoV-2 IgG (S1 protein-based) and Virotech SARS-CoV-2 IgG ELISA (N protein-based)) and an in-house developed plaque reduction neutralization test (PRNT). The Euroimmun SARS-CoV-2 IgG ELISA (Euroimmun, Lübeck, Germany) and Virotech SARS-CoV-2 IgG ELISA (Virotech Diagnostics GmbH, Rüsselsheim, Germany; TABLE 1) were used, in an identical manner, according to the manufacturer's recommendation.


id: cord-337799-mc1oqhf4
author: Mak, Gannon CK
date: 2020-10-29
extension: .txt
mime: text/plain
words: 2330
sentence: 109
flesch: 54
cache: cache/cord-337799-mc1oqhf4.txt
txt: txt/cord-337799-mc1oqhf4.txt
title:
  Analytical sensitivity and clinical sensitivity of the three rapid antigen detection kits for detection of SARS-CoV-2 virus

summary:
  Although RAD kits were less sensitive than RT-PCR, understanding the clinical characteristics of different RAD kits can guide us to obtain suitable specimens for testing. Clinical sensitivity of RAD kits ranged from 22.9% to 71.4% for detecting specimens from COVID-19 patients.


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
extension: .txt
mime: text/plain
words: 1397
sentence: 60
flesch: 41
cache: cache/cord-340336-u59l0taa.txt
txt: txt/cord-340336-u59l0taa.txt
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.


id: cord-345603-mirsz6m8
author: Wehrhahn, Michael C.
title: Self-collection: an appropriate alternative during the SARS-CoV-2 pandemic
date: 2020-05-04
extension: .txt
mime: text/plain
words: 2348
sentence: 84
flesch: 48
cache: cache/cord-345603-mirsz6m8.txt
txt: txt/cord-345603-mirsz6m8.txt
summary:
  CONCLUSIONS: Self-collection of throat and nasal swabs offers a reliable alternative to health worker collection for the diagnosis of SARS-CoV-2 and other respiratory viruses and provides patients with easier access to testing, reduces exposure of the community and health workers to those being tested and reduces requirement for PPE. When Ct values for COVID-19 cases were compared by collection method (Figure 1) , mean E-gene Ct did not differ between HC and SCNT or SCN (p=0·236, 0·083, against α'=0·0083) but was significantly higher in SCT compared with HC (β=7·31, p<0·001).


id: cord-338923-hc7gagnq
author: Jääskeläinen, AJ
title: Performance of six SARS-CoV-2 immunoassays in comparison with microneutralisation
date: 2020-06-15
extension: .txt
mime: text/plain
words: 2113
sentence: 78
flesch: 43
cache: cache/cord-338923-hc7gagnq.txt
txt: txt/cord-338923-hc7gagnq.txt
summary:
  The specificity and sensitivity values of the commercial tests against MNT, respectively, were as follows: 95.1%/80.5% (Abbott Architect SARS-CoV-2 IgG), 94.9%/43.8% (Diasorin Liaison SARS-CoV-2 IgG; RUO), 68.3%/87.8% (Euroimmun SARS-CoV-2 IgA), 86.6%/70.7% (Euroimmun SARS-CoV-2 IgG), 74.4%/56.1% (Acro 2019-nCoV IgG), 69.5%/46.3% (Acro 2019-nCoV IgM), 97.5%/71.9% (Xiamen Biotime SARS-CoV-2 IgG), and 88.8%/81.3% (Xiamen Biotime SARS-CoV-2 IgM). The CE marked Diasorin Liaison SARS-CoV-2 IgG assay was not available for this evaluation.


id: cord-331707-kfja1i6s
author: Andrés, Cristina
date: 2018-11-30
extension: .txt
mime: text/plain
words: 3477
sentence: 143
flesch: 39
cache: cache/cord-331707-kfja1i6s.txt
txt: txt/cord-331707-kfja1i6s.txt
title:
  Surveillance of enteroviruses from paediatric patients attended at a tertiary hospital in Catalonia from 2014 to 2017

summary:
  Specimens were collected from paediatric (<17 years old) cases with suspicion of respiratory tract infection or EV infection. EV infections are usually asymptomatic or mild, but infections can sometimes evolve to severe diseases.


id: cord-335891-j78pnwgk
author: Piñana, Maria
date: 2020-08-11
extension: .txt
mime: text/plain
words: 3198
sentence: 144
flesch: 44
cache: cache/cord-335891-j78pnwgk.txt
txt: txt/cord-335891-j78pnwgk.txt
title:
  Insights into immune evasion of human metapneumovirus: novel 180- and 111-nucleotide duplications within viral G gene throughout 2014-2017 seasons in Barcelona, Spain

summary:
  The 180- and 111-nucleotide duplications occurred in A2c lineage G protein increased in prevalence throughout the study, in addition to short genetic changes observed in other HMPV lineages. The 180-and 111-nucleotide duplications occurred in A2c lineage G protein increased in prevalence throughout the study, in addition to short genetic changes observed in other HMPV lineages.


id: cord-344979-ngujhhp6
author: Lübke, Nadine
date: 2020-08-05
extension: .txt
mime: text/plain
words: 3246
sentence: 120
flesch: 46
cache: cache/cord-344979-ngujhhp6.txt
txt: txt/cord-344979-ngujhhp6.txt
title:
  Extraction-free SARS-CoV-2 detection by rapid RT-qPCR universal for all primary respiratory materials

summary:
  Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-qPCR Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab samples Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal 1 specimens without extraction of viral RNA Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP Rapid SARS-CoV-2 testing in primary material based on a novel multiplex LAMP assay LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards Predicting infectious SARS-CoV-2 from diagnostic samples Figure 1: Analysis of PCR conditions for the detection of SARS-CoV-2 by direct RT-qPCR Direct RT-qPCR with the Sarbeco and the new CoV-E primers Patient matched respiratory crude samples (n=20) including swabs, tracheal secretion, brochoalveolare lavage and sputum were analyzed for the detection of SARS-CoV-2 by direct RT-qPCR with the Sarbeco primers and the new CoV-E primers Direct RT-qPCR with fresh and pre-frozen PCR-mixes Patient matched respiratory crude samples (n=8) including swabs, tracheal secretion and BAL were analyzed for the detection of SARS-CoV-2 by direct RT-qPCR with either fresh prepared master-mixes (MMX) or pre-frozen master-mixes The authors gratefully acknowledge the TaKaRa™ employees, especially Sascha Deppermann and Matthieu Lewis for continuous scientific and technical support in establishment and optimization of J o u r n a l P r e -p r o o f HBV-SynQ (internal control): a synthetical plasmid coding for an inactivated s-Antigen of Hepatitis B Next, we analyzed if an increase in crude sample material input increases detection of SARS-CoV-2.


# url

id: cord-263279-afdmegq0
domain: www.fda.gov
url:
  https://www.fda.gov/medical-devices/emergencysituations-medical-devices/emergency-use-authorizations


id: cord-263279-afdmegq0
domain: altonadiagnostics.com
url:
  https://altonadiagnostics.com/en/products/reagents-140/reagents/realstar-realtime-pcr-reagents/realstar-sars-cov-2-rt-pcr-kit-ruo.html


id: cord-321287-mh2j2koa
domain: www.who.int
url:
  https://www.who.int/docs/defaultsource/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2&download=true


id: cord-321287-mh2j2koa
domain: www.fda.gov
url:
  https://www.fda.gov/emergencypreparedness-and-response/mcm-legal-regulatory-and-policy-framework/emergency-use-authorization


# ent

id: cord-321287-mh2j2koa
sid: 61
eid: 1
type: PERSON
entity:
  https://www.fda.gov/emergencypreparedness-and-response/mcm-legal-regulatory-and-policy-framework/emergency-use-authorization covidinvitrodev


