item: #1 of 145 id: cord-000346-9b6yz3f4 author: Holder, Benjamin P. title: Assessing the In Vitro Fitness of an Oseltamivir-Resistant Seasonal A/H1N1 Influenza Strain Using a Mathematical Model date: 2011-03-24 words: 7509 flesch: 42 summary: The growth of viral plaques during the enlargment phase Replication of viruses in a growing plaque: A reactiondiffusion model Time-delayed spread of viruses in growing plaques Parameter identifiability and estimation of HIV/AIDS dynamic models New low-viscosity overlay medium for viral plaque assays A simple and fast method for determining colony forming units Assessing the viral fitness of oseltamivir-resistant influenza viruses in ferrets, using a competitive-mixtures model Fluorometric assay of neuraminidase with a sodium (4-methylumbelliferyl-a-D-N-acetylneruaminate) substrate Advanced biochemistry: Protein properties and kinetics (BTC 560) -Course website Exploring the effect of biological delays in kinetic models of influenza within a host or cell culture Induction of programmed cell death (apoptosis) by influenza virus infection in tissue culture cells Apoptosis: A mechanism of cell killing by influenza A and B viruses NS1 protein of influenza A virus down-regulates apoptosis Impairment of multicycle influenza virus growth in Vero (WHO) cells by loss of trypsin activity Mode of action of the anti-influenza virus activity of plant flavonoid, 5,7,49-trihydroxy-8-methoxyflavone, from the roots of Scutellaria baicalensis The primary function of RNA binding by the influenza A virus NS1 protein in infected cells: Inhibiting the 29-59 oligo(A) synthetase/ We have shown, however, in earlier work where influenza virus plaques were observed by immunostaining [41] , that the same plaque velocity can be measured from both the progress of dead cells, as we consider here, and the progress of newly infected cells. keywords: cell; growth; h275y; infection; influenza; mutant; plaque; rate; strain; time; titer; virus; yield cache: cord-000346-9b6yz3f4.txt plain text: cord-000346-9b6yz3f4.txt item: #2 of 145 id: cord-001340-kqcx7lrq author: Ladner, Jason T. title: Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing date: 2014-06-17 words: 2513 flesch: 34 summary: Despite the small sizes of viral genomes, complications related to limited RNA quantities, host contamination, and secondary structure mean that it is often not time-or cost-effective to finish every genome, and given the intended use, finishing may be unnecessary (5) . One of the most common and important applications for viral genomes is in the study of viral epidemiology, which encompasses our understanding of the patterns, causes, and effects of disease. keywords: characterization; coverage; genome; sequences; sequencing; viruses cache: cord-001340-kqcx7lrq.txt plain text: cord-001340-kqcx7lrq.txt item: #3 of 145 id: cord-001985-iwfidoer author: Urayama, Syun-ichi title: FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance date: 2016-02-13 words: 5024 flesch: 40 summary: This novel dsRNA targeting metagenomic method is characterized by an extremely high recovery rate of viral RNA sequences, the retrieval of terminal sequences, and uniform read coverage, which has not previously been reported in other metagenomic methods targeting RNA viruses. Microbes Environ DOI: 10.1264/jsme2.me15171 sha: doc_id: 1985 cord_uid: iwfidoer Knowledge of the distribution and diversity of RNA viruses is still limited in spite of their possible environmental and epidemiological impacts because RNA virus-specific metagenomic methods have not yet been developed. keywords: cdna; contigs; diatom; dsrna; flds; genome; method; reads; rna; sequences; terminal; total; viral; viruses cache: cord-001985-iwfidoer.txt plain text: cord-001985-iwfidoer.txt item: #4 of 145 id: cord-002608-zn7tm1ww author: Sokoloski, Kevin J. title: Identification of Interactions between Sindbis Virus Capsid Protein and Cytoplasmic vRNA as Novel Virulence Determinants date: 2017-06-29 words: 11247 flesch: 37 summary: These data support the identification of the C:R interaction sites as bona fide capsid: RNA interaction sites and indicate that the mutational approach is capable of reducing capsid interaction at these specific sites. However it should be noted that the direct interaction between the viral capsid protein and viral RNA has not been exhaustively characterized in the cytoplasm of infected cells, or in mature viral particles leaving our understanding of the molecular interactions between these essential components of the virus incomplete. keywords: analysis; binding; capsid; capsid protein; cells; data; fig; genomic rna; infection; interaction sites; mutants; mutation; particles; protein; r interaction; rna; rnas; sequence; sinv; type; virus cache: cord-002608-zn7tm1ww.txt plain text: cord-002608-zn7tm1ww.txt item: #5 of 145 id: cord-003045-r707jl16 author: Bhuvaneshwar, Krithika title: viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors date: 2018-06-05 words: 6547 flesch: 48 summary: We compared various viral detection pipeline using the several criteria (Table 1) . In this paper, we present our pipeline viGEN to not only detect and quantify read counts at the individual viral-gene level, but also detect viral variants from human RNA-seq data. keywords: cancer; data; gene; hepatitis; human; patients; pipeline; rna; vigen; viruses cache: cord-003045-r707jl16.txt plain text: cord-003045-r707jl16.txt item: #6 of 145 id: cord-004501-guiy89x8 author: Cojocaru, Florina-Daniela title: Nanomaterials Designed for Antiviral Drug Delivery Transport across Biological Barriers date: 2020-02-18 words: 14004 flesch: 30 summary: A reality for diagnosis of HCV infectious disease HIV biosensors for early diagnosis of infection: The intertwine of nanotechnology with sensing strategies Chitosan as a bioactive polymer: Processing, properties and applications Anti-Herpes Simplex Virus (HSV-1 and HSV-2) activity of biogenic gold and silver nanoparticles using seaweed Sargassum wightii A novel extracellular synthesis of monodisperse gold nanoparticles using marine alga, Sargassum wightii Greville Broad-spectrum non-toxic antiviral nanoparticles with a virucidal inhibition mechanism Inhibition of Human Metapneumovirus Binding to Heparan Sulfate Blocks Infection in Human Lung Cells and Airway Tissues Pathogen Inhibition by Multivalent Ligand Architectures Surface-structureregulated cell-membrane penetration by monolayer-protected nanoparticles Antiherpes evaluation of soybean isoflavonoids Topical Delivery of Coumestrol from Lipid Nanoemulsions Thickened with Hydroxyethylcellulose for Antiherpes Treatment Lecithin based nanoemulsions: A comparative study of the influence of non-ionic surfactants and the cationic phytosphingosine on physicochemical behaviour and skin permeation Reverse Transcriptase Inhibitors Nanosystems Designed for Drug Stability and Controlled Delivery Novel dendritic structure of alginate hybrid nanoparticles for effective anti-viral drug delivery Design of antiretroviral drug-polymeric nanoparticles laden buccal films for chronic HIV therapy in paediatrics Influence of Solvent Evaporation Technique Parameters on Diameter of Submicron Lamivudine-Poly-ε-Caprolactone Conjugate Particles Nanoencapsulation of water-soluble drug, lamivudine, using a double emulsion spray-drying technique for improving HIV treatment Formulation and characterisation of chitosan based lamivudine nanoparticles The Antiretroviral Agent Nelfinavir Mesylate: A Potential Therapy for Systemic Sclerosis Inhibition of HIV Fusion with Multivalent Gold Nanoparticles Gold Nanoparticles as an HIV Entry Inhibitor Gold nanoparticles to improve HIV drug delivery The role of nanotechnology in the treatment of viral infections Epaxal ® : A virosomal vaccine to prevent hepatitis A infection Pharmacokinetics and Pharmacodynamics Modeling and Simulation Systems to Support the Development and Regulation of Liposomal Drugs Eleven years of Inflexal ® V-A virosomal adjuvanted influenza vaccine Package Insert PEG-IntronTM (Peginterferon alfa-2b) Powder for Injection, Schering Corporation Progress in Nanomedicine: Approved and Investigational Nanodrugs Tolerability and Immune Response to LC002, an Experimental Therapeutic Vaccine Bioavailability of MK-1439 Experimental Nano Formulations in Healthy Adults (MK-1439-046)-ClinicalTrials.gov There are several factors that hinder the development of antiviral drugs: • Dependence of viruses replication on host cell biosynthetic machinery keywords: activity; acv; antiviral; barrier; bbb; blood; brain; cell; costs; delivery; dna; drug; drug delivery; hiv; impact; infection; inhibitors; mechanism; membrane; nanoparticles; nanotechnology; nps; review; skin; studies; therapy; treatment; virus; viruses; vitro cache: cord-004501-guiy89x8.txt plain text: cord-004501-guiy89x8.txt item: #7 of 145 id: cord-006129-5rog0s98 author: Hemida, Maged Gomaa title: Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases: Expectations and Limitations date: 2012-08-16 words: 7449 flesch: 39 summary: [12] We will discuss the roles and therapeutic potential of cellular as well as viral miRNAs (if any) in the pathogenesis and treatment of different viral diseases. HPyVs are able to encode viral miRNAs for their own benefit. keywords: cellular; diseases; expression; gene; host; human; immune; infection; micrornas; mirnas; replication; target; targeting; virus; viruses cache: cord-006129-5rog0s98.txt plain text: cord-006129-5rog0s98.txt item: #8 of 145 id: cord-006450-si5168pb author: Jouneau, S. title: Which patients should be tested for viruses on bronchoalveolar lavage fluid? date: 2012-12-14 words: 3121 flesch: 32 summary: To better inform the use of viral tests in patients with respiratory diseases, we performed an observational, retrospective study in our institution, with three aims: (i) to assess the diagnostic value of viral tests on BALF in routine practice; (ii) to analyze the characteristics of patients with virus-positive BALF; and (iii) to identify the factors predictive of positive viral tests in BALF. The variables associated with positive viral tests on univariate analysis were immunosuppression [human immunodeficiency virus (HIV), corticosteroids >10 mg/day for ≥3 weeks, or other immunosuppressive therapy], ground-glass attenuations on computed tomography (CT) scanning, late-onset ventilator-associated pneumonia (VAP), and durations of (i) hospital stay, (ii) intensive care unit (ICU) stay, and (iii) mechanical ventilation before BAL (p < 0.01 for each comparison). keywords: balf; cmv; patients; pcr; study; tests; virus; viruses cache: cord-006450-si5168pb.txt plain text: cord-006450-si5168pb.txt item: #9 of 145 id: cord-007255-jmjolo9p author: Pulliam, Juliet R. C. title: Ability to replicate in the cytoplasm predicts zoonotic transmission of livestock viruses date: 2009-02-15 words: 2460 flesch: 36 summary: Humans have regular contact with all potentially infectious bodily fluids of domestic food animals; we thus ensure that the target species has contact with all viral groups infecting the source hosts by analyzing the pool of viral species known to infect sheep, goats, cattle, and pigs. Methods. Because influenza virus A infects domestic artiodactyls but was excluded from our database because it is maintained through continuous transmission in humans, we confirmed the robustness of our results to this exclusion; we also confirmed that our findings were robust to the inclusion of viral species for which human infection data were based solely on serology (see table B1 in appendix B, which appears only in the electronic edition of the Journal). keywords: ability; infect; replication; species; viruses cache: cord-007255-jmjolo9p.txt plain text: cord-007255-jmjolo9p.txt item: #10 of 145 id: cord-009101-376snefs author: Strodtbeck, Frances title: Viral Infections of the Newborn date: 2015-12-16 words: 3386 flesch: 37 summary: The fetus and newborn are particularly wlnerable to viral infection. The incidence of viral infections in the newborn is estimated at 6-8% of all live births (Smith, 1993) . keywords: care; disease; infection; newborn; strodtbeck; virus; viruses cache: cord-009101-376snefs.txt plain text: cord-009101-376snefs.txt item: #11 of 145 id: cord-009577-29u7pdpk author: Gonzalez‐Scarano, F. title: Molecular pathogenesis of neurotropic viral infections date: 2004-10-08 words: 6378 flesch: 35 summary: In the case of influenza virus, a trypsin-like protease present in host cells cleaves the hemagglutinin protein into two smaller peptides, HA1 and HA2, held together by a tlisulfide bond. If influenza virus is grown in cells that lack this peptidase activity, H A cleavage does not occur, and, though the virus still binds to cellular receptors, it is not infectious [20, 41, 67, 681. keywords: cells; cns; host; infection; influenza; proteins; rabies; receptor; reovirus; spread; system; type; virus; viruses cache: cord-009577-29u7pdpk.txt plain text: cord-009577-29u7pdpk.txt item: #12 of 145 id: cord-010233-772e35kx author: Monto, Arnold S. title: Respiratory illness caused by picornavirus infection: a review of clinical outcomes date: 2002-01-03 words: 4599 flesch: 30 summary: The search terms used were picornavirus, rhinovirus, enterovirus, viral respiratory infection, upper respiratory infection, disease burden, economic, cost, complications, asthma, COPD, immunocompromised, elderly, otitis media, and sinusitis. Younger children appear to be more susceptible to viral respiratory infections, as demonstrated by the fact that preschool children can have 5 to 9 respiratory infections per year. keywords: asthma; children; infections; patients; picornavirus; rhinovirus; study; tract cache: cord-010233-772e35kx.txt plain text: cord-010233-772e35kx.txt item: #13 of 145 id: cord-011095-79ce5900 author: Meskill, Sarah D. title: Respiratory Virus Co-infection in Acute Respiratory Infections in Children date: 2020-01-24 words: 4979 flesch: 27 summary: mSphere Respiratory pathogens in children with and without respiratory symptoms Clinical utility of PCR for common viruses in acute respiratory illness Rates of asymptomatic respiratory virus infection across age groups Respiratory syncytial virus: infection, detection, and new options for prevention and treatment The burden of respiratory syncytial virus infection in young children Community-acquired pneumonia requiring hospitalization among U.S. children Human rhinoviruses Prospective multicenter study of viral etiology and hospital length of stay in children with severe bronchiolitis Insights into the interaction between influenza virus and pneumococcus Preventing and treating influenza Quantitative review of antibody response to inactivated seasonal influenza vaccines. Of those participants who tested negative for respiratory viral infections, 81.9-99.6% reported to be asymptomatic depending on the definition applied. keywords: children; disease; infections; influenza; patients; rsv; study; virus; viruses cache: cord-011095-79ce5900.txt plain text: cord-011095-79ce5900.txt item: #14 of 145 id: cord-014397-7b88ycv8 author: Gavora, JS title: Resistance of livestock to viruses: mechanisms and strategies for genetic engineering date: 1996-12-15 words: 11586 flesch: 35 summary: The transgenic birds that expressed only the viral envelope coding region of the recombinant genome were shown to be resistant to the corresponding subgroup of the avian leukosis virus (Salter and Crittenden, 1989; Gavora et al, 1995a) , due to a blockage of virus receptors by the viral envelope proteins. and 1 Erythrocyte P antigen: cellular receptor for B 19 parvovirus Resistance to parvovirus B19 infection due to lack of virus receptor (erythrocyte P antigen) keywords: avian; cells; disease; et al; gene; genome; host; infection; livestock; mechanisms; plants; protein; receptor; replication; resistance; resistance mechanisms; rna; strategies; virus; viruses cache: cord-014397-7b88ycv8.txt plain text: cord-014397-7b88ycv8.txt item: #15 of 145 id: cord-015893-e0fofgxq author: Ryhal, Bruce title: Viral Disease, Air Pollutants, Nanoparticles, and Asthma date: 2011-05-03 words: 6332 flesch: 43 summary: The causal direction in the association between respiratory syncytial virus hospitalization and asthma Evidence of a causal role of winter virus infection during infancy in early childhood asthma The effect of respiratory syncytial virus on subsequent recurrent wheezing in atopic and nonatopic children Siblings, day-care attendance, and the risk of asthma and wheezing during childhood Day-care attendance, position in sibship, and early childhood wheezing: A population-based birth cohort study Day care, siblings, and asthma-Please, sneeze on my child A novel group of rhinoviruses is associated with asthma hospitalizations Association between human rhinovirus and severity of acute asthma in children Effects of allergic inflammation of the nasal mucosa on the severity of rhinovirus 16 cold Oral prednisolone for preschool children with acute virus-induced wheezing The Asthma Predictive Index: A very useful tool for predicting asthma in young children Preemptive use of high-dose fluticasone for virus induced wheezing in young children Montelukast reduces asthma exacerbations in 2-to 5-year-old children with intermittent asthma Computed tomographic study of the common cold Effect of amoxicillin-clavulanate in clinically diagnosed acute rhinosinusitis Antibiotics for acute maxillary sinusitis Cluster analysis and clinical asthma phenotypes Infectious asthma: a reemerging clinical entity? Epidemiology of asthma exacerbations A cluster analysis divided asthma patients into five different groups. keywords: air; asthma; children; disease; hrv; illness; infection; patients; pollution; respiratory; study; wheezing cache: cord-015893-e0fofgxq.txt plain text: cord-015893-e0fofgxq.txt item: #16 of 145 id: cord-016475-7ldxvbpz author: Pleschka, Stephan title: Anti-viral approaches against influenza viruses date: 2006 words: 17141 flesch: 32 summary: Apoptosis is mainly regarded to be a host cell defense against virus viruses (reviewed in: Julkunen et al., 2000; Ludwig et al., 2003; infections since many viruses express anti-apoptotic proteins to prevent this cellular response. The etiological agent of the disease, influenza virus is responsible E. Bogner and A. Holzenburg (eds.) , New Concepts of Antiviral Therapy, 115-167. keywords: activation; activity; anti; apoptosis; cell; disease; et al; human; immunity; induction; infection; influenza; influenza virus; inhibitors; kinase; mek; neuraminidase; oseltamivir; pathway; production; protein; replication; response; strain; treatment; type; vaccine; viral; virus; viruses; zanamivir cache: cord-016475-7ldxvbpz.txt plain text: cord-016475-7ldxvbpz.txt item: #17 of 145 id: cord-016499-5iqpl23p author: Mackay, Ian M. title: Rhinoviruses date: 2014-02-27 words: 23417 flesch: 34 summary: ARIs linked to HRV infections are associated with excessive and perhaps inappropriate antibiotic prescribing and with significant direct and indirect healthcare expenditure. ARIs linked to HRV infections are associated with excessive and perhaps inappropriate antibiotic prescribing [ 4 ] and with signifi cant direct and indirect healthcare expenditure [ 5 , 6 ] . keywords: acute; adults; airway; antiviral; ari; asthma; cells; children; cold; culture; defi; detection; disease; exacerbations; host; hrsv; hrv; hrv infection; hrvs; human; identifi; ifn; illness; infection; infl; nasal; pcr; receptor; response; rhinovirus; rna; role; species; studies; study; symptoms; time; tract; type; viruses cache: cord-016499-5iqpl23p.txt plain text: cord-016499-5iqpl23p.txt item: #18 of 145 id: cord-016798-tv2ntug6 author: Gautam, Ablesh title: Bioinformatics Applications in Advancing Animal Virus Research date: 2019-06-06 words: 6983 flesch: 35 summary: VIDA retrieves virus sequences from GenBank and the files are parsed into subfields. VIDA also provides functional classification of virus proteins into broad functional classes based on typical virus processes such as DNA and RNA replication, virus structural proteins, nucleotide and nucleic acid metabolism, transcription, glycoproteins and others. keywords: analysis; annotation; bioinformatics; database; et al; gene; genome; host; influenza; information; prediction; proteins; sequence; tools; virus; viruses; web cache: cord-016798-tv2ntug6.txt plain text: cord-016798-tv2ntug6.txt item: #19 of 145 id: cord-018058-n3majqes author: Modrow, Susanne title: Historical Overview date: 2013-08-12 words: 5378 flesch: 42 summary: Slow virus infections principally affect the central nervous system and are caused, for example, by measles virus and JC polyomavirus. This is demonstrated, for example, by SARS virus infections (▶ Sect. 14.8), the pandemic with the new influenza A virus variant (Mexican flu, swine flu) and the threatening potential with regard to humans of new highly pathogenic influenza viruses (▶ Sect. 16.3). keywords: cancer; cells; development; disease; human; infections; pathogen; research; sect; smallpox; time; virus; viruses cache: cord-018058-n3majqes.txt plain text: cord-018058-n3majqes.txt item: #20 of 145 id: cord-018325-k69h9cc5 author: Çatlı, Tolgahan title: Acute Viral Rhinitis date: 2019-05-14 words: 2419 flesch: 31 summary: Generally, acute rhinitis is associated with environmental allergies or respiratory viral infections. Antiviral agents primarily decrease viral shedding, but other steps of viral infection may be targeted [18] . keywords: avr; nasal; rhinitis; rssc; symptoms; viruses cache: cord-018325-k69h9cc5.txt plain text: cord-018325-k69h9cc5.txt item: #21 of 145 id: cord-018430-u3k8pds6 author: Mason, Jay W. title: Myocarditis date: 2007 words: 21762 flesch: 28 summary: Evidence for a CD18-dependent mechanism Neutrophil-activating peptide-1/interleukin 8, a novel cytokine that activates neutrophils Interleukin-2: inception, impact, and implications Cytokines: coordinators of immune and inflammatory responses Induction of fibroblast proliferation by human mononuclear leukocyte-derived proteins Mechanisms of immune-mediated myocyte injury Interleukin 1 and tumor necrosis factor inhibit cardiac myocyte beta-adrenergic responsiveness Abnormal contractile function due to induction of nitric oxide synthesis in rat cardiac myocytes follows exposure to activated macrophageconditioned medium The role of the NO pathway in the control of cardiac function Contractile depression and expression of proinflammatory cytokines and iNOS in viral myocarditis The role of inducible nitric oxide synthase in the host response to Coxsackievirus myocarditis Suppression of cytokines and nitric oxide production, and protection against lethal endotoxemia and viral myocarditis by a new NF-kappaB inhibitor Nitric oxide production within cardiac myocytes reduces their contractility in endotoxemia Cellular basis for the negative inotropic effects of tumor necrosis factor-alpha in the adult mammalian heart Cardiac failure in transgenic mice with myocardial expression of tumor necrosis factor-alpha Increased serum levels of circulating intercellular adhesion molecule-1 in patients with myocarditis Increased circulating cytokines in patients with myocarditis and cardiomyopathy Augmentation of pathogenesis of coxsackievirus B3 infections in mice by exogenous administration of interleukin-1 and interleukin-2 Detection of transforming growth factor-b1 in Coxsackie B3 virus-induced murine myocarditis Concepts of autoimmunity applied to idiopathic dilated cardiomyopathy Progressive interstitial collagen deposition in Coxsackievirus B3-induced murine myocarditis Myocardial remodeling in viral heart disease: Possible interactions between inflammatory mediators and MMP-TIMP system Prevention of encephalomyocarditis virus myocarditis in mice by inactivated virus vaccine Treatment of viral myocarditis with ribavirin in an animal preparation Ribavirin treatment of murine coxsackievirus B3 myocarditis with analysis of lymphocyte subsets Prevention of viral myocarditis with recombinant human leukocyte interferon alpha A/D in a murine model Modification of viral myocarditis in mice by interleukin-6 Effects of intranasal administration of recombinant murine interferon-gamma on murine acute myocarditis caused by encephalomyocarditis virus Effects of prednisolone on acute viral myocarditis in mice A nonsteroid anti-inflammatory drug exacerbates Coxsackie B3 murine myocarditis Coxsackievirus B3 murine myocarditis: deleterious effects of nonsteroidal anti-inflammatory agents Immunosuppression with high doses of cyclophosphamide reduces the severity of myocarditis but increases the mortality in murine Coxsackievirus B3 myocarditis Effect of delayed captopril therapy on left ventricular mass and myonecrosis during acute coxsackievirus murine myocarditis Impact of FK 506 on myocarditis in the enteroviral murine model Synergistic effects of tacrolimus and human interferon-alpha A/D in murine viral myocarditis Therapeutic effect of anti-tumor necrosis factor-alpha on the murine model of viral myocarditis induced by encephalomyocarditis virus Treatment of virus-induced myocardial injury with a novel immunomodulating agent, vesnarinone. Viral myocarditis is a triphasic process. keywords: abnormalities; acute; biopsy; cardiac; cardiomyopathy; cases; cell; cell myocarditis; chagas; chronic; dcm; death; diagnosis; disease; dysfunction; evidence; failure; giant; heart; heart disease; heart failure; incidence; infection; involvement; myocardial; myocarditis; myocyte; patients; phase; study; therapy; treatment; ventricular; virus cache: cord-018430-u3k8pds6.txt plain text: cord-018430-u3k8pds6.txt item: #22 of 145 id: cord-018526-rz7id5mt author: Braun, Serge title: Non-viral Vector for Muscle-Mediated Gene Therapy date: 2018-12-14 words: 5186 flesch: 27 summary: Nevertheless, muscle gene therapy using systemic administration of non-viral vectors retains major hurdles that need to be overcome before any human applications. The efficiency of plasmid gene transfer into skeletal muscle (and other tissues) by direct injection is low (~1% of cell nuclei) and remains confined at the injection site (along the needle track) across species keywords: delivery; dna; expression; gene; limb; muscle; phase; plasmid; safety; therapy; trial; vaccine; vectors cache: cord-018526-rz7id5mt.txt plain text: cord-018526-rz7id5mt.txt item: #23 of 145 id: cord-020235-stcrozdw author: None title: Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981 date: 2012-03-15 words: 13511 flesch: 54 summary: 2. the number of virus producing cells is not cor related with the appe arance of slgM or sIgG. 3. virus yields seem to be influenced by the cell cycle: the number of chick emb ryo fibro blasts producing plaques in infectious center assays is increased after synchro nisa tion of the cells before infection. Recent studies on protein kinases from a number of tumor viruses have raised the possibility that the phosphorylation of cell proteins is involved in the processes leading to cell transformation. keywords: acid; activity; analysis; antibodies; antigen; cells; cultures; disease; dna; fragments; genome; glycoproteins; hsv; human; infection; influenza; inst; mice; particles; positive; protein; restriction; results; rna; sera; sites; specific; strains; test; type; univ; virus; viruses cache: cord-020235-stcrozdw.txt plain text: cord-020235-stcrozdw.txt item: #24 of 145 id: cord-021146-wdnnjlcw author: Jandrić, Petar title: Postdigital Research in the Time of Covid-19 date: 2020-03-21 words: 2397 flesch: 49 summary: Over the centuries, viral pandemics such as the 1918 Spanish flu have been major biological, social, and cultural events. Postdigital viral modernity is equally about biology, culture, and society; in the long run, humanity cannot defend itself from Covid-19 and create a better future without engaging all strata of the society. keywords: covid-19; life; pandemic; postdigital; research; viruses cache: cord-021146-wdnnjlcw.txt plain text: cord-021146-wdnnjlcw.txt item: #25 of 145 id: cord-022156-mm8en4os author: Isaiah, Amal title: Tracheal Infections date: 2015-07-14 words: 5729 flesch: 38 summary: Tracheal infections have a signifi cantly lower incidence compared to infections of the upper respiratory tract, with 1-5 % of all children requiring outpatient evaluation for viral croup within the fi rst 3 years of life. Currently, bacterial tracheitis has three times the risk of respiratory failure associated with it than epiglottitis and viral croup combined [ 4 ] . Acute laryngotracheitis, considered to be the most common cause for croup, is almost exclusively caused by viral organisms. keywords: airway; children; clinical; croup; infections; infl; intubation; parainfl; tracheal; tracheitis; treatment; uenza cache: cord-022156-mm8en4os.txt plain text: cord-022156-mm8en4os.txt item: #26 of 145 id: cord-022196-1tionxun author: FENNER, FRANK title: The Nature and Classification of Animal Viruses date: 2013-11-17 words: 9589 flesch: 42 summary: In viruses whose genome consists of single-stranded nucleic acid, the viral nucleic acid is either the positive strand (in RNA viruses, equivalent to messenger RNA) or the negative (complementary) strand. The diameters of the nucleocapsids of several viruses have been measured, but in only a few cases is the length or the pitch of the helix known. keywords: acid; animal; capsomers; classification; dna; envelope; genome; genus; protein; rna; type; units; virion; viruses cache: cord-022196-1tionxun.txt plain text: cord-022196-1tionxun.txt item: #27 of 145 id: cord-022349-z8w1wkm8 author: Beeler, Judy A. title: Human and Animal Viruses date: 2007-09-02 words: 4589 flesch: 43 summary: Viruses held to a low number of passages in animals or cell cultures represent a viral population that is similar to that found in nature, and freezing these pools guards against genetic mutations that occur during subsequent passage. The classification of viruses is based on morphological and physiochemical properties. keywords: cell; culture; drying; freeze; freezing; seed; vaccines; virus; viruses cache: cord-022349-z8w1wkm8.txt plain text: cord-022349-z8w1wkm8.txt item: #28 of 145 id: cord-022439-8wy7rpqv author: DENMAN, A.M. title: Viral Etiology of Polymyositis/Dermatomyositis date: 2013-11-17 words: 10792 flesch: 39 summary: First, antibodies If viruses induce PM/DM, the simplest mech anism by which they could induce this disease is by replicating in muscle cells, thereby serv ing as a direct target for an immune attack. Furthermore, ephemeral or latent infection of muscle cells could initiate an immune response subsequently sustained by other mechanisms. keywords: antibodies; antibody; antigens; autoantibodies; cells; coxsackievirus; diseases; evidence; human; immune; infection; lymphocytes; mice; monoclonal; muscle; myocarditis; patients; virus; viruses cache: cord-022439-8wy7rpqv.txt plain text: cord-022439-8wy7rpqv.txt item: #29 of 145 id: cord-023143-fcno330z author: None title: Molecular aspects of viral immunity date: 2004-02-19 words: 43520 flesch: 44 summary: The immunohistological analysis suggests that CD8+ T cell dependent disappearence of marginal zone macrophages of follicular dendritic cells and of virus infected cells in general correlates with immunosuppression. Our studies indicate that MHC class I resmcted CD8+ cytotoxic T lymphocytes (CTLs) are activated in response to viral antigens leading to destruction of virus infected cells and loss of transgene expression. keywords: activity; amino; analysis; animals; antibodies; antibody; antigen; b cells; binding; cd4; cd8; cell responses; challenge; class; clones; cns; ctl; ctl response; cytokines; cytotoxic t; days; different; disease; dna; epitopes; expression; gene; hiv; hla; host; human; ifn; immune; immunity; infected; infection; influenza; lcmv; levels; lymphocytes; memory; mhc; mice; model; molecules; mouse; murine; peptides; primary; production; protein; recognition; recombinant; replication; response; results; role; sequence; specific; spleen; strains; studies; t cells; type; vaccine; vaccinia; viral; virus; virus infection; viruses; vivo cache: cord-023143-fcno330z.txt plain text: cord-023143-fcno330z.txt item: #30 of 145 id: cord-023705-3q9yr6np author: FENNER, FRANK title: Viral Replication date: 2014-06-27 words: 8336 flesch: 48 summary: The eclipse period ranges from 5 to 15 hours for the various DNA viruses and from 3 to 10 hours for RNA viruses (see Table 4 -2). 4 -3 (for DNA viruses) and Fig. 4 -5 (for RNA viruses). keywords: cell; dna; fig; genome; membrane; mrna; polymerase; proteins; replication; rna; sense; synthesis; transcription; virion; viruses cache: cord-023705-3q9yr6np.txt plain text: cord-023705-3q9yr6np.txt item: #31 of 145 id: cord-023731-jqgervt7 author: FENNER, FRANK title: Laboratory Diagnosis of Viral Diseases date: 2014-06-27 words: 6996 flesch: 37 summary: On the other hand, recovery of an enterovirus from the feces, or a herpesvirus from a nasal or throat swab may not necessarily be significant, because such viruses are often associated with inapparent infections at these sites. These pro cedures (see Plate 13-5) are most useful in the rapid identification of cell culture virus isolates, as well as directly on specimens (see below). keywords: animal; antibody; antigen; cell; cultures; diagnosis; infections; isolation; laboratory; procedures; species; specific; virus; viruses cache: cord-023731-jqgervt7.txt plain text: cord-023731-jqgervt7.txt item: #32 of 145 id: cord-103460-5thh6syt author: Carlson, Colin J. title: Climate change will drive novel cross-species viral transmission date: 2020-07-14 words: 1439 flesch: 44 summary: Moving forward, the rapid range shifts already observed 532 in many bat species (see main text) could provide an empirical reference point to fit a new allo-533 metric scaling curve (after standardizing those results for the studies' many different method-534 ologies). Counter to expectations, holding warming under 2°C within the century does not reduce new viral sharing, due to greater range expansions—highlighting the need to invest in surveillance even in a low-warming future. keywords: bats; climate; dispersal; sharing; species cache: cord-103460-5thh6syt.txt plain text: cord-103460-5thh6syt.txt item: #33 of 145 id: cord-252763-gy8f1oyt author: Shetty, Mamatha title: Viral Diarrhoea in a Rural Coastal Region of Karnataka India date: 1995-10-17 words: 1355 flesch: 47 summary: Clinical picture of viral diarrhoea was characterized by a high frequency of vomiting, fever, and respiratory symptoms. Viral diarrhoea is not uncommon in India, but very few reports have been published so far. keywords: cases; cent; children; diarrhoea cache: cord-252763-gy8f1oyt.txt plain text: cord-252763-gy8f1oyt.txt item: #34 of 145 id: cord-254194-962vynwk author: Galdiero, Stefania title: Silver Nanoparticles as Potential Antiviral Agents date: 2011-10-24 words: 10043 flesch: 33 summary: Many studies have shown the antimicrobial effects of metal nanoparticles, but the effects of silver nanoparticles against fungal pathogens are mostly unknown; silver nanoparticles, indeed, showed significant antifungal activity against Penicillium citrinum The present review aims at a description of the reported antiviral activities of metal nanoparticles and their production methods, with particular regard to silver nanoparticles. keywords: activity; antiviral; cell; effect; entry; fact; gold; inhibition; interaction; membrane; metal; metal nanoparticles; nanoparticles; silver; surface; synthesis; virus; viruses cache: cord-254194-962vynwk.txt plain text: cord-254194-962vynwk.txt item: #35 of 145 id: cord-254478-scc9wee0 author: To, Kelvin Kai-Wang title: Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study date: 2020-03-23 words: 5195 flesch: 46 summary: A patient's reluctance to provide a sample can account for the paucity of timepoints in viral load studies of respiratory virus infections. Older age was correlated with higher viral load (Spearman's ρ=0·48, 95% CI 0·074–0·75; p=0·020). keywords: antibody; coronavirus; cov-2; load; onset; patients; saliva; samples; sars; specimens; study; symptom cache: cord-254478-scc9wee0.txt plain text: cord-254478-scc9wee0.txt item: #36 of 145 id: cord-258685-ayek8zbo author: Har-Noy, Michael title: Allo-priming as a universal anti-viral vaccine: protecting elderly from current COVID-19 and any future unknown viral outbreak date: 2020-05-12 words: 7339 flesch: 34 summary: The release of IFN-ϒ orchestrates the sequential activation of immune cells resulting in formation of an antiviral state, innate elimination of invading viruses and development of a viral-specific effector response and memory. These allo-specific Th1/CTL memory cells provide a functional pool of immune cells that are capable of nonspecific (by-stander) activation [40] upon encounter with virus [14, 41] resulting in immediate release of IFN-ϒ. Har-Noy and Or J Transl Med (2020) keywords: allo; cells; ctl; ifn-ϒ; immune; immunity; immunosenescence; infection; memory; priming; response; th1; vaccine; virus cache: cord-258685-ayek8zbo.txt plain text: cord-258685-ayek8zbo.txt item: #37 of 145 id: cord-259233-smmhhroe author: de Armas‐Rillo, Laura title: Membrane dynamics associated with viral infection date: 2016-01-28 words: 7119 flesch: 35 summary: ASFVs are thought to reorganize cell membranes through viral proteins that contain a KDE motif, inducing the redistribution of ERassociated proteins [88] and the viral p54 protein. Modification of intracellular membrane structures for virus replication Viruses and endosome membrane dynamics When autophagy meets viruses: a double-edged sword with functions in defense and offense Viral infection: moving through complex and dynamic cell-membrane structures How to get out: ssRNA enveloped viruses and membrane fission Neutrophil granules and secretory vesicles in inflammation A guide to viral inclusions, membrane rearrangements, factories, and viroplasm produced during virus replication. keywords: assembly; autophagy; budding; cell; complex; escrt; figure; formation; infection; membrane; proteins; replication; rna; vesicles; virus; viruses cache: cord-259233-smmhhroe.txt plain text: cord-259233-smmhhroe.txt item: #38 of 145 id: cord-260554-nao59qx4 author: Wargo, Andrew R title: Viral fitness: definitions, measurement, and current insights date: 2012-09-15 words: 2900 flesch: 33 summary: key: cord-260554-nao59qx4 authors: Wargo, Andrew R; Kurath, Gael title: Viral fitness: definitions, measurement, and current insights date: 2012-09-15 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2012.07.007 sha: doc_id: 260554 cord_uid: nao59qx4 Viral fitness is an active area of research, with recent work involving an expanded number of human, non-human vertebrate, invertebrate, plant, and bacterial viruses. Study topics include drug resistance, immune escape, viral emergence, host jumps, mutation effects, quasispecies diversity, and mathematical models of viral fitness. keywords: fitness; host; transmission; variants; virulence; virus; viruses; vivo; work cache: cord-260554-nao59qx4.txt plain text: cord-260554-nao59qx4.txt item: #39 of 145 id: cord-262585-5vjqrnwh author: Hraber, Peter title: Resources to Discover and Use Short Linear Motifs in Viral Proteins date: 2019-08-16 words: 5671 flesch: 36 summary: A fusion intermediate gp41 immunogen elicits neutralizing antibodies to HIV-1 Immunosilencing a highly immunogenic protein trimerization domain Vaccination with soluble headless hemagglutinin protects mice from challenge with divergent influenza viruses Human chemokine MIP1a increases efficiency of targeted DNA fusion vaccines Dengue E protein domain III-based DNA immunisation induces strong antibody responses to all four viral serotypes Options for synthetic DNA order screening, revisited A transatlantic perspective on 20 emerging issues in biological engineering Biodefense in the Age of Synthetic Biology Short linear motifs -ex nihilo evolution of protein regulation Convergent evolution and mimicry of protein linear motifs in host-pathogen interactions The present and the future of motif-mediated protein-protein interactions A million peptide motifs for the molecular biologist Viral proteins can modulate immunity in several ways, which include: shutdown of host macromolecular synthesis, inhibiting antigen production or apoptosis, and interference with such processes as antigen presentation by MHC, natural killer (NK) cell function, antiviral cytokines, or interferon responses. keywords: discovery; domain; elm; function; host; immune; interactions; linear; motifs; protein; sequence; slims; viralzone; virus cache: cord-262585-5vjqrnwh.txt plain text: cord-262585-5vjqrnwh.txt item: #40 of 145 id: cord-262753-jld1ygxt author: Neidermyer, William J. title: Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells date: 2019-06-21 words: 9262 flesch: 40 summary: Collectively, these studies suggest additional mechanisms may contribute to the shut-off of host cell protein synthesis. An RNA polymerase in the virion L protein requirement for in vitro RNA synthesis by vesicular stomatitis virus Transcriptional activity and mutational analysis of recombinant vesicular stomatitis virus RNA polymerase Amino acid residues within conserved domain VI of the vesicular stomatitis virus large polymerase protein essential for mRNA cap methyltransferase activity A single amino acid change in the L-polymerase protein of vesicular stomatitis virus completely abolishes viral mRNA cap methylation A unique strategy for mRNA cap methylation used by vesicular stomatitis virus Unconventional mechanism of mRNA capping by the RNA-dependent RNA polymerase of vesicular stomatitis virus A conserved motif in region v of the large polymerase proteins of nonsegmented negative-sense RNA viruses that is essential for mRNA capping Rebinding of transcriptase components (L and NS proteins) to the nucleocapsid template of vesicular stomatitis virus Location of the binding domains for the RNA polymerase L and the ribonucleocapsid template within different halves of the NS phosphoprotein of vesicular stomatitis virus Structure of the vesicular stomatitis virus nucleoprotein-RNA complex Structure of the vesicular stomatitis virus nucleocapsid in complex with the nucleocapsid-binding domain of the small polymerase cofactor Molecular architecture of the vesicular stomatitis virus RNA polymerase Critical phosphoprotein elements that regulate polymerase architecture and function in vesicular stomatitis virus Synthesis of poly(A) in vitro by purified virions of vesicular stomatitis virus In vitro synthesis of RNA that contains polyadenylate by virion-associated RNA polymerase of vesicular stomatitis virus Site on the vesicular stomatitis virus genome specifying polyadenylation and the end of the L gene mRNA Aberrant polyadenylation by a vesicular stomatitis virus mutant is due to an altered L protein cis-Acting signals involved in termination of vesicular stomatitis virus mRNA synthesis include the conserved AUAC and the U7 signal for polyadenylation Translational control of protein synthesis after infection by vesicular stomatitis virus Vesicular stomatitis virus mRNA and inhibition of translation of cellular mRNA-is there a P function in vesicular stomatitis virus? Effect of intracellular vesicular stomatitis virus mRNA concentration on the inhibition of host cell protein synthesis Complete intergenic and flanking gene sequences from the genome of vesicular stomatitis virus Complete sequences of the ribosome recognition sites in vesicular stomatitis virus keywords: associated; association; cells; cellular; eif4e; fig; gene; host; hpi; infection; mrnas; polysome; protein; reads; stomatitis; synthesis; translation; virus; vsv cache: cord-262753-jld1ygxt.txt plain text: cord-262753-jld1ygxt.txt item: #41 of 145 id: cord-262776-6k7tcgfs author: Burnouf, Thierry title: Assessment of the viral safety of antivenoms fractionated from equine plasma date: 2004-09-30 words: 8214 flesch: 39 summary: For instance, equipment for bulk in process virus inactivation, such as the acid pH incubation or the caprylic acid treatment, should ideally be fully enclosed. The duration of the first stage should be such that the majority of virus inactivation (as found during the viral validation studies) has occurred. keywords: acid; antivenoms; blood; disease; enveloped; equine; horses; human; igg; inactivation; manufacturing; plasma; production; products; safety; treatment; virus; viruses cache: cord-262776-6k7tcgfs.txt plain text: cord-262776-6k7tcgfs.txt item: #42 of 145 id: cord-265900-7lj4bfli author: Luo, Honglin title: Interplay between the virus and the ubiquitin–proteasome system: molecular mechanism of viral pathogenesis date: 2015-09-29 words: 5069 flesch: 29 summary: Viral protein degradation is either a reflection of viral clearance by host immune response or a viral strategy to maintain an optimal level of viral protein to ensure efficient viral production. The UPS serves as a double-edged sword in viral pathogenesis: on the one hand, the UPS is utilized by many viruses to maintain proper function and level of viral proteins; while on the other hand, the UPS constitutes a host defense mechanism to eliminate viral components. keywords: degradation; host; immune; isg15; modification; protein; ubiquitin; ups; virus; viruses cache: cord-265900-7lj4bfli.txt plain text: cord-265900-7lj4bfli.txt item: #43 of 145 id: cord-266147-s8rxzm0t author: Burnouf, Thierry title: Modern Plasma Fractionation date: 2007-03-28 words: 8837 flesch: 35 summary: An updated list of the major therapeutic applications of plasma protein products can be found elsewhere. Modern plasma product production technology remains largely based on the ethanol fractionation process, but much has evolved in the last few years to improve product purity, to enhance the recovery of immunoglobulin G, and to isolate new plasma proteins, such as α1-protease inhibitor, von Willebrand factor, and protein C. Because of the human origin of the starting material and the pooling of 10 000 to 50 000 donations required for industrial processing, the major risk associated to plasma products is the transmission of blood-borne infectious agents. keywords: blood; chromatography; factor; fractionation; fviii; heat; igg; inactivation; plasma; process; production; products; protein; removal; safety; steps; treatment; viruses cache: cord-266147-s8rxzm0t.txt plain text: cord-266147-s8rxzm0t.txt item: #44 of 145 id: cord-267326-355q6k6k author: Gu, Xiaoqiong title: Geospatial distribution of viromes in tropical freshwater ecosystems date: 2018-06-15 words: 8436 flesch: 35 summary: Viral communities in different reservoirs in terms of land use impact were compared and the majority of viral communities were largely conserved and stable at the family level with Myoviridae, Siphoviridae and Podoviridae as the main family level, and small differences observed in Dicistroviridae and other families (Fig. 2B) . Bacteriophage observations and evolution The marine viromes of four oceanic regions The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes Globally mobile populations and the spread of emerging pathogens Prevalence and genetic diversity of waterborne pathogenic viruses in surface waters of tropical urban catchments Prevalence and genotypes of human noroviruses in tropical urban surface waters and clinical samples in Singapore Identification of viral pathogen diversity in sewage sludge by metagenome analysis Genomic analysis of uncultured marine viral communities The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments Oxygen minimum zones harbour novel viral communities with low diversity Spatial and temporal variability across life's hierarchies in the terrestrial Antarctic Human and bovine viruses in the Milwaukee River watershed: hydrologically relevant representation and relations with environmental variables Metagenomic analysis of coastal RNA virus communities Human norovirus transmission and evolution in a changing world Bacteria-phage interactions in natural environments Functional metagenomic profiling of nine biomes Metagenomic analysis of RNA viruses in a fresh water lake Zoonotic hepatitis E virus: classification, animal reservoirs and transmission routes Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara Global consequences of land use A latitudinal diversity gradient in planktonic marine bacteria Cyclovirus CyCV-VN species distribution is not limited to Vietnam and extends to Viral metagenomics analysis of planktonic viruses in East Lake Diarrhea and enteric emerging viruses in HIV-infected patients Bacteriophages: update on application as models for viruses in water Unbiased detection of respiratory viruses by use of RNA sequencing-based metagenomics: a systematic comparison to a commercial PCR panel Enteric viruses and diarrhea in HIV-infected patients Ecology drives the worldwide distribution of human diseases Novoalign. keywords: areas; community; contigs; diversity; et al; human; land; metagenomics; pathogens; qpcr; reads; reservoirs; singapore; study; tributaries; virome; viruses; water cache: cord-267326-355q6k6k.txt plain text: cord-267326-355q6k6k.txt item: #45 of 145 id: cord-269194-b1wlr3t7 author: Engstrom-Melnyk, Julia title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 words: 12555 flesch: 22 summary: Determining a patient's HIV viral load is indicated prior to entry into care, at the initiation of ART, at 2-8 weeks after ART initiation, and then typically every 3-4 months while on treatment: (1) to establish a baseline level of HIV viral load; (2) to establish viral response to the therapy to assess the virologic efficacy of ART; and (3) to monitor for abnormalities that may be associated with antiretroviral drugs (DHHS HIV, 2014) . (A) HIV viral loads will fluctuate as patients are on treatment, and, in most instances, will remain 'undetectable' (at or below dotted line); viral 'blips' are not uncommon and will result in transient 'detectable' and even quantifiable results (above the dashed line). keywords: assays; chronic; clinical; cmv; disease; et al; fda; hcv; hiv; infection; laboratory; load; molecular; patients; pcr; results; rna; testing; tests; therapy; time; time pcr; transplant; treatment; virus cache: cord-269194-b1wlr3t7.txt plain text: cord-269194-b1wlr3t7.txt item: #46 of 145 id: cord-270205-fw555w1u author: Cillóniz, Catia title: Pure Viral Sepsis Secondary to Community-Acquired Pneumonia in Adults: Risk and Prognostic Factors date: 2019-10-01 words: 2751 flesch: 47 summary: In conclusion, in our cohort, pure viral sepsis affected 61% of patients with a diagnosis of viral CAP, supporting the importance of stratifying patient risk for viral sepsis and making a complete microbiological diagnosis in cases of CAP. key: cord-270205-fw555w1u authors: Cillóniz, Catia; Dominedò, Cristina; Magdaleno, Daniel; Ferrer, Miquel; Gabarrús, Albert; Torres, Antoni title: Pure Viral Sepsis Secondary to Community-Acquired Pneumonia in Adults: Risk and Prognostic Factors date: 2019-10-01 journal: J Infect Dis DOI: 10.1093/infdis/jiz257 sha: doc_id: 270205 cord_uid: fw555w1u We investigated the risk and prognostic factors of pure viral sepsis in adult patients with community-acquired pneumonia (CAP), using the Sepsis-3 definition. keywords: cap; diagnosis; mortality; patients; pneumonia; sepsis cache: cord-270205-fw555w1u.txt plain text: cord-270205-fw555w1u.txt item: #47 of 145 id: cord-270294-g95skuik author: Johnstone, Jennie title: Viral Infection in Adults Hospitalized With Community-Acquired Pneumonia Prevalence, Pathogens, and Presentation date: 2008-12-31 words: 4442 flesch: 33 summary: In our study, patients with pneumonia and respiratory viral infection were older and more frail than 1146 those without evidence of viral infection. Given the 15% prevalence of viral infection in adults in our study, and the indistinguishable presentation from typical bacterial pneumonia, our results suggest routine isolation (with droplet and contact precautions) of all adults with pneumonia, from the time of hospital admission until respiratory viral infection is ruled out, should be considered to help prevent the nosocomial transmission of respiratory viruses. keywords: adults; hmpv; infection; influenza; pathogens; patients; pneumonia; study; viruses cache: cord-270294-g95skuik.txt plain text: cord-270294-g95skuik.txt item: #48 of 145 id: cord-270670-cubh9jxc author: Domingo, E. title: Viruses as Quasispecies: Biological Implications date: 2006 words: 10501 flesch: 29 summary: Despite all cellular organisms being highly polymorphic genetically (in that distinct alleles from a gene are represented among individuals of one biological species), the level of heterogeneity of RNA virus populations confers a much greater adaptability than the levels of polymorphism estimated for cells. The units of selection Lethal mutagenesis of HIV by mutagenic ribonucleoside analogs Lethal mutagenesis of HIV with mutagenic nucleoside analogs Hepatitis C virus RNA-dependent RNA polymerase (NS5B) as a mediator of the antiviral activity of ribavirin Foot-and-mouth disease virus Interferon alfa-2b alone or in combination with ribavirin as initial treatment for chronic hepatitis C. Hepatitis Interventional Therapy Group Clonal interference and the evolution of RNA viruses A mutation in tomato aspermy cucumovirus that abolishes cell-to-cell movement is maintained to high levels in the viral RNA population by complementation Pol gene quasispecies of human immunodeficiency virus: mutations associated with drug resistance in virus from patients undergoing no drug therapy Contributions of vesicular stomatitis virus to the understanding of RNA virus evolution Negative effect of genetic bottlenecks on the adaptability of vesicular stomatitis virus Size of genetic bottlenecks leading to virus fitness loss is determined by mean initial population fitness Exponential fitness gains of RNA virus populations are limited by bottleneck effects Density-dependent selection in vesicular stomatitis virus keywords: cell; error; et al; evolution; fitness; genomes; memory; mutant; mutations; number; population; quasispecies; replication; rna; spectra; spectrum; virus; viruses; volume cache: cord-270670-cubh9jxc.txt plain text: cord-270670-cubh9jxc.txt item: #49 of 145 id: cord-271495-5906wju4 author: Beldomenico, Pablo M. title: Do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of COVID-19 date: 2020-05-11 words: 1995 flesch: 42 summary: Exposure to high viral loads may result in infections of high intensity, which exposes new cases to high viral loads, and so on. The severity of the disease caused by high viral loads is expected to be high. keywords: infection cache: cord-271495-5906wju4.txt plain text: cord-271495-5906wju4.txt item: #50 of 145 id: cord-272655-qeojdpez author: Remolina, Yuly Andrea title: Viral Infection in Adults with Severe Acute Respiratory Infection in Colombia date: 2015-11-17 words: 4310 flesch: 37 summary: Furthermore, current challenges in the epidemiological surveillance of viral respiratory tract infections include the early and fast identification of aetiological agents, especially at the beginnings of outbreaks, and the optimal and timely management of a large number of samples [14] . Results from a prospective, population-based study Community-Acquired Pneumonia Requiring Hospitalization among U.S. Adults Bacterial complications of respiratory tract viral illness: a comprehensive evaluation Estimates of mortality attributable to influenza and RSV in the United States during 1997-2009 by influenza type or subtype, age, cause of death, and risk status Roles of humidity and temperature in shaping influenza seasonality Epidemiology and seasonality of respiratory tract virus infections in the tropics Utilization of nucleic acid amplification assays for the detection of respiratory viruses Comparative evaluation of effectiveness of IAVchip DNA microarray in influenza A diagnosis Microorganisms in respiratory tract of patients diagnosed with atypical pneumonia: results of a research based on the use of reverse transcription polymerase chain reaction (RT-PCR) DNA microarray method and enzyme-linked immunosorbent assay The clinical utility of a near patient care rapid microarray-based diagnostic test for influenza and respiratory syncytial virus infections in the pediatric setting Multi-center evaluation of the adenovirus R-gene US assay for the detection of adenovirus in respiratory samples Antibiotic prescribing in ambulatory care settings for adults with colds, upper respiratory tract infections, and bronchitis Procalcitonin to initiate or discontinue antibiotics in acute respiratory tract infections A role for Streptococcus pneumoniae in virus-associated pneumonia keywords: cases; days; hospital; infections; influenza; patients; pneumonia; study; virus cache: cord-272655-qeojdpez.txt plain text: cord-272655-qeojdpez.txt item: #51 of 145 id: cord-273019-hbpfz8rt author: Glingston, R. Sahaya title: Organelle dynamics and viral infections: at cross roads date: 2018-06-25 words: 9525 flesch: 30 summary: Current review briefly summarizes our knowledge of the various cell organelles/compartments following virus infection. caspase-independent cell death Lysosomal cell death at a glance A zinc finger protein Tsip1 controls cucumber mosaic virus infection by interacting with the replication complex on vacuolar membranes of the tobacco plant Visualization of assembly intermediates and budding vacuoles of Singapore grouper iridovirus in grouper embryonic cells Involvement of the vacuolar H(þ)-ATPase in animal virus entry Membrane and protein interactions of a soluble form of the semliki forest virus fusion protein The entry of reovirus into L cells is dependent on vacuolar proton-ATPase activity Cellular v-ATPase is required for virion assembly compartment formation in human cytomegalovirus infection Endocytosis via caveolae Endocytosis of simian virus 40 into the endoplasmic reticulum Cellular entry of ebola virus involves uptake by a macropinocytosis-like mechanism and subsequent trafficking through early and late endosomes Membrane dynamics associated with viral infection Biogenesis of the semliki forest virus RNA replication complex Fusion of SV40-induced endocytotic vacuoles with the nuclear membrane Interaction of endocytotic vacuoles with the inner nuclear membrane in simian virus 40 entry into CV-1 cell nucleus ESCRT complexes and the biogenesis of multivesicular bodies Involvement of vacuolar protein sorting pathway in ebola virus release independent of TSG101 interaction Identification of alpha-taxilin as an essential factor for the life cycle of hepatitis B virus Divergent roles of autophagy in virus infection keywords: cells; complex; degradation; expression; formation; golgi; hepatitis; host; human; infection; lipid; membrane; nuclear; nucleus; order; organelles; protein; replication; rna; virus; viruses cache: cord-273019-hbpfz8rt.txt plain text: cord-273019-hbpfz8rt.txt item: #52 of 145 id: cord-274080-884x48on author: Rumlová, Michaela title: In vitro methods for testing antiviral drugs date: 2018-06-30 words: 18015 flesch: 26 summary: Virus-encoded methyltransferases have been identified and characterized in flaviviruses such as Zika virus Coutard et al., 2017; Duan et al., 2017; Munjal et al., 2017; Zhao et al., 2017) , West Nile virus, and dengue virus (Dong et al., 2012) ; rhabdoviruses such as vesicular stomatitis virus (VSV) (Rahmeh et al., 2009 ); coronaviruses such as SARS (Wang et al., 2015b) ; and roniviruses (Zeng et al., 2016) . Alternatively, cleavage products may be monitored by analysis of proteolytic products by mass spectrometric methods (Hu et al., 2015; Joshi et al., 2017; Lathia et al., 2011; Rumlová et al., 2003) , analytical HPLC (Teruya et al., 2016) , or electrochemical methods based on the difference in penetration of substrate and cleavage products through the membrane of a polyionselective sensor (Gemene and Meyerhoff, 2011; Han et al., 1996) . keywords: activity; assay; assembly; binding; capsid; cell; coronavirus; dna; drug; entry; envelope; et al; fluorescence; fusion; genome; hbv; hcv; helicase; hepatitis; host; human; infection; influenza; inhibitors; integrase; kinase; membrane; method; particles; polymerase; protease; protein; replication; rna; screening; specific; target; transcription; type; uncoating; viral; virus; viruses cache: cord-274080-884x48on.txt plain text: cord-274080-884x48on.txt item: #53 of 145 id: cord-274680-6pui91uu author: Gao, Chun title: Proinflammatory cytokines are associated with prolonged viral RNA shedding in COVID-19 patients date: 2020-10-14 words: 2208 flesch: 46 summary: [10] [11] Therefore, this retrospective study aimed to analyze the clinical characteristics of COVID-19 patients who experienced prolonged viral shedding and to investigate the contributing risk factors. In our study, we found that COVID-19 patients with prolonged viral shedding were older (p<0.001) and presented with a higher rate of hypertension (p<0.001). keywords: covid-19; cytokines; patients; rna; shedding cache: cord-274680-6pui91uu.txt plain text: cord-274680-6pui91uu.txt item: #54 of 145 id: cord-274749-ji91qq9q author: Lagare, Adamou title: Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger date: 2015-11-14 words: 3583 flesch: 44 summary: Submit your manuscript at www.biomedcentral.com/submit Global and regional burden of hospital admissions for severe acute lower respiratory infections in young children in 2010: a systematic analysis Estimate of worldwide distribution of child deaths from acute respiratory infections Respiratory viruses seasonality in children under five years of age in Viral etiologies of lower respiratory tract infections among Egyptian children under five years of age Respiratory viral coinfections identified by a 10-plex real-time reversetranscription polymerase chain reaction assay in patients hospitalised with severe acute respiratory illness-South Africa Viral etiology of influenza-like illness in Cameroon Clinical utility of PCR common viruses in acute respiratory illness Microbial aetiology of community-acquired pneumonia in hospitalised patients Clinico-pathological study of atypical pathogens in community-acquired pneumonia: a prospective study Epidemiology and clinical characteristics of community-acquired pneumonia in hospitalized children Carriage of Streptococcus pneumoniae and other respiratory bacterial pathogens in low and lower-middle income countries: a systematic review and meta-analysis Viral and bacterial detection in acute respiratory infection in children under five years Sentinel surveillance of influenza and other respiratory viruses, Brazil Viral infections of the lower respiratory tract: old viruses, new viruses, and the role of diagnosis Viral etiology of acute respiratory tract infection among pediatric inpatients and outpatients from 2010 to 2012 in Beijing, China Viral and atypical bacterial etiology of acute respiratory infections in children under 5 years old living in rural tropical area of Madagascar Viral etiology of respiratory infections in children under 5 years old living in tropical rural areas of Senegal: Nasopharyngeal specimens may be used to aid in the diagnosis of certain bacterial respiratory pathogens that do not tend to colonize the nasopharynx, such as M. pneumoniae and C. pneumoniae keywords: age; bacterial; children; influenza; respiratory; study; years cache: cord-274749-ji91qq9q.txt plain text: cord-274749-ji91qq9q.txt item: #55 of 145 id: cord-274780-fmnro0kw author: Hoshino, Y. title: Detection of astroviruses in feces of a cat with diarrhea date: 1981 words: 1372 flesch: 45 summary: Bridging structures between virus particles were frequently seen (Fig. t, arrowheads) . A fecal sample was submitted for EM examination for viral particles. keywords: astroviruses; diarrhea; feces; kitten; particles cache: cord-274780-fmnro0kw.txt plain text: cord-274780-fmnro0kw.txt item: #56 of 145 id: cord-275683-1qj9ri18 author: Roux, Simon title: Metagenomics in Virology date: 2019-06-12 words: 5893 flesch: 32 summary: Viromes provide a deeper description of the virus community, since most of the sequencing data will be obtained from virus genomes. While the analyses outlined above were foundational for our current understanding of virus diversity, they were limited by the short length of next-generation sequencing reads which fragmented the view of viral genomes. keywords: diversity; dna; genomes; host; metagenomics; novel; rna; sample; sequencing; time; viruses cache: cord-275683-1qj9ri18.txt plain text: cord-275683-1qj9ri18.txt item: #57 of 145 id: cord-276908-9jthjf24 author: Gupta, Akanksha title: COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date: 2020-07-06 words: 5182 flesch: 52 summary: [92] Au NPs based materials are well known for the detection of various viruses such as dengue virus, influenza virus, bovine viral diarrhea coronavirus, etc. The viral infection encountered with present‐day challenges and futuristic approaches with the help of nanotechnology to minimize the spread of infectious viruses. keywords: antiviral; coronavirus; covid-19; covs; disease; drugs; hcov; host; human; infection; protein; rna; sars; virus; viruses cache: cord-276908-9jthjf24.txt plain text: cord-276908-9jthjf24.txt item: #58 of 145 id: cord-279716-kxfc4npg author: Blachere, Francoise M. title: Bioaerosol sampling for the detection of aerosolized influenza virus date: 2007-10-22 words: 4263 flesch: 45 summary: Furthermore, we will test the bioaerosol sampler in a healthcare setting to monitor the prevalence of airborne influenza viral particles and to study the transmission of influenza via the inhalation of aerosolized viral particles. These findings would significantly contribute toward understanding the transmission of aerosolized influenza viral particles. keywords: bioaerosol; influenza; minutes; particles; sampler; size; stage; viral cache: cord-279716-kxfc4npg.txt plain text: cord-279716-kxfc4npg.txt item: #59 of 145 id: cord-280048-b4dz1lnn author: Domingo, Esteban title: Viral quasispecies date: 2019-10-17 words: 7969 flesch: 31 summary: A model for polynucleotide replication Viral replication modes in singlepeak fitness landscapes: A dynamical systems analysis Quasispecies: From Theory to Experimental Systems Nucleotide sequence heterogeneity of an RNA phage population Subclonal components of consensus fitness in an RNA virus clone Pathogenomics: Genome Analysis of Pathogenic Microbes The proportion of revertant and mutant phage in a growing population, as a function of mutation and growth rate Mutation rates among RNA viruses Correlation between mutation rate and genome size in riboviruses: mutation rate of bacteriophage Qbeta Rapid evolution of RNA genomes The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance-a review Transitions in understanding of RNA viruses: an historical perspective Viral quasispecies evolution Temporal fluctuations in HIV quasispecies in vivo are not reflected by sequential HIV isolations New insights into the HCV quasispecies and compartmentalization Mathematical Models of Quasi-Species Theory and Exact Results for the Dynamics Quasispecies: from theory to experimental systems Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase A conserved 3'5' exonuclease active site in prokaryotic and eukaryotic DNA polymerases High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants A novel 3'-end repair mechanism in an RNA virus Exonucleolytic proofreading by p53 protein Coronaviruses as DNA wannabes: a new model for the regulation of RNA virus replication fidelity Thinking Outside the Triangle: Replication Fidelity of the Largest RNA Viruses Theoretical Models of Generalized Quasispecies Alterations in cellular metabolism triggered by URA7 or GLN3 inactivation cause imbalanced dNTP pools and increased mutagenesis Deep-Sequence Identification and Role in Virus Replication of a JC Virus Quasispecies in Patients with Progressive Multifocal Leukoencephalopathy An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-Cbound viral peptides Differential Shape of Geminivirus Mutant Spectra Across Cultivated and Wild Hosts With Invariant Viral Consensus Sequences Genetic variability: the key problem in the prevention and therapy of RNA-based virus infections Quasispecies and virus Mechanisms of viral mutation Quasispecies theory and the behavior of RNA viruses Quasispecies composition and evolution of a typical Zika virus clinical isolate from Suriname Marine RNA Virus Quasispecies Are Distributed throughout the Oceans Within-Host Variations of Human Papillomavirus Reveal APOBEC Signature Mutagenesis in the Viral Genome In vivo evolution of viral virulence: switching of deformed wing virus between hosts results in virulence changes and sequence shifts PAQ: Collective behavior of viruses was documented with mutant RNA viruses resistant to nucleotide analogues. keywords: disease; evolution; fitness; genomes; host; mutant; mutation; population; quasispecies; rate; replication; rna; sequence; spectrum; virus; viruses cache: cord-280048-b4dz1lnn.txt plain text: cord-280048-b4dz1lnn.txt item: #60 of 145 id: cord-281844-c0uhcatg author: Costa, Lusmaia D.C. title: Exacerbation of asthma and airway infection: is the virus the villain? date: 2014-12-31 words: 6550 flesch: 37 summary: The impact of viral respiratory infection on the severity and recovery from an asthma exacerbation Symptomatic viral infection is associated with impaired response to treatment in children with acute asthma Newly identified respiratory viruses in children with asthma exacerbation not requiring admission to hospital Understanding the September asthma epidemic Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center Innate immunity in the pathogenesis of virus-induced asthma exacerbations Sentinel surveillance of influenza and other respiratory viruses, Brazil Variação sazonal nos atendimentos de emergência por asma em Gama Effect of seasonality on the occurrence of respiratory symptoms in a Brazilian city with a tropical climate Prevalência dos atendimentos por crises de asma nos serviços públicos do Município de Juiz de Fora (MG) Study of modifiable risk factors for asthma exacerbations: virus infection and allergen exposure increase the risk of asthma hospital admissions in children Risk factors for wheezing in a subtropical environment: Role of respiratory viruses and allergen sensitization Associations between environmental exposures and asthma control and exacerbations in young children: a systematic review Smoke-free legislation and hospitalizations for childhood asthma Personal exposure to nitrogen dioxide (NO 2 ) and the severity of virus-induced asthma in children Health effects of indoor nitrogen dioxide and passive smoking on urban asthmatic children Environmental tobacco smoke exposure and nocturnal symptoms among inner-city children with asthma Results of a home-based environmental intervention among urban children with asthma Guidelines reduce X-ray and blood gas utilization in acute asthma Basic Research on virus-induced asthma exacerbation: inhibition of inflammatory chemokine expression by fluticasone propionate Respiratory viral infections in children with asthma: do they matter and can we prevent them? 4 Considering the possibility of a causal relationship between respiratory virus infection and the triggering of asthma attacks in children, the implications of this association, as well as the possibility of specific prophylaxis and therapy for these agents, special attention to this subject is justified. keywords: association; asthma; children; detection; exacerbations; hrv; infection; patients; pcr; studies; viruses; years cache: cord-281844-c0uhcatg.txt plain text: cord-281844-c0uhcatg.txt item: #61 of 145 id: cord-281916-v6u5mr2i author: Bonnin, Paul title: Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice date: 2016-08-09 words: 4127 flesch: 40 summary: The underrecognized burden of influenza in young children Viral epidemiology and severity of respiratory infections in infants in 2009: a prospective study Techniques actuelles de diagnostic des infections virales respiratoires en réanimation Cost analysis of multiplex PCR testing for diagnosing respiratory virus infections Superiority of reverse-transcription polymerase chain reaction to conventional viral culture in the diagnosis of acute respiratory tract infections in children Increased detection of respiratory syncytial virus, influenza viruses, parainfluenza viruses, and adenoviruses with real-time PCR in samples from patients with respiratory symptoms Quantitation of respiratory syncytial virus RNA in nasal aspirates of children by real-time RT-PCR assay Molecular diagnosis of respiratory viruses Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Comparative evaluation of six commercialized multiplex PCR kits for the diagnosis of respiratory infections Identification of respiratory viruses in adults: nasopharyngeal versus sampling Development of an efficient qRT-PCR assay for quality control and cellular quantification of respiratory samples Guideline to reference gene selection for quantitative realtime PCR Comparison of flocked and rayon swabs for collection of respiratory epithelial cells from uninfected volunteers and symptomatic patients Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control Swabbing for respiratory viral infections in older patients:a comparison of rayon and nylon flocked swabs Comparison among nasopharyngeal swab, nasal wash, and oropharyngeal swab for respiratory virus detection in adults with acute pharyngitis Improved detection of respiratory viruses in pediatric outpatients with acute respiratory illness by real-time PCR using nasopharyngeal flocked swabs Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays Evaluation of the Quidel QuickVue test for detection of influenza A and B viruses in the pediatric emergency medicine setting by use of three specimen collection methods A quantification of human cells using an ERV-3 real time PCR assay Not applicable. key: cord-281916-v6u5mr2i authors: Bonnin, Paul; Miszczak, Fabien; Kin, Nathalie; Resa, Cecile; Dina, Julia; Gouarin, Stephanie; Viron, Florent; Morello, Remy; Vabret, Astrid title: Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice date: 2016-08-09 journal: BMC Infect Dis DOI: 10.1186/s12879-016-1730-9 sha: doc_id: 281916 cord_uid: v6u5mr2i BACKGROUND: Respiratory viral diagnosis of upper respiratory tract infections has largely developed through multiplex molecular techniques. keywords: age; cellularity; detection; diagnosis; pcr; samples; study cache: cord-281916-v6u5mr2i.txt plain text: cord-281916-v6u5mr2i.txt item: #62 of 145 id: cord-286137-4cbh3u3z author: Honce, Rebekah title: They are what you eat: Shaping of viral populations through nutrition and consequences for virulence date: 2020-08-13 words: 1928 flesch: 27 summary: Barriers to replication exist within and between susceptible hosts, which restrict viral population diversity to quell infections [13] . key: cord-286137-4cbh3u3z authors: Honce, Rebekah; Schultz-Cherry, Stacey title: They are what you eat: Shaping of viral populations through nutrition and consequences for virulence date: 2020-08-13 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008711 sha: doc_id: 286137 cord_uid: 4cbh3u3z nan Humans have coexisted with viral pathogens for tens of thousands of years, influencing both their emergence and evolution. keywords: evolution; host; infection; population; virulence; virus cache: cord-286137-4cbh3u3z.txt plain text: cord-286137-4cbh3u3z.txt item: #63 of 145 id: cord-286219-qcx5ehnh author: Calistri, Arianna title: The Ubiquitin-Conjugating System: Multiple Roles in Viral Replication and Infection date: 2014-05-06 words: 10214 flesch: 35 summary: First of all, viral proteins have been described that can modify the substrate specificity of cellular Ub ligases. In addition to p53 and pRB, another protein complex involved in cell cycle control, the anaphase-promoting complex (APC) is emerging as a key target for viral proteins. keywords: budding; cells; cellular; complex; cycle; degradation; human; ligase; proteasome; protein; replication; role; tetherin; ubiquitin; ubiquitination; virus; viruses; vpr; vpu cache: cord-286219-qcx5ehnh.txt plain text: cord-286219-qcx5ehnh.txt item: #64 of 145 id: cord-286328-ap0wfjhq author: Lewis, Toby C. title: Nasal cytokine responses to natural colds in asthmatic children date: 2012-11-26 words: 4780 flesch: 41 summary: Our finding that IRF7 mRNA is elevated after respiratory viral infection in children with asthma is validated by a recent study analysing patterns of gene expression in nasal lavage samples from children experiencing picornavirus-induced asthma exacerbations Our ability to detect statistically significant changes in specific mRNAs and proteins using the current study design suggests that this is a viable approach for use in future investigations, for example, studies examining whether an early adjustment of asthma medications could abort or temper the impact of respiratory viral infections. keywords: asthma; cells; children; cytokines; ifn; infection; levels; nasal; rhinovirus; samples; symptoms cache: cord-286328-ap0wfjhq.txt plain text: cord-286328-ap0wfjhq.txt item: #65 of 145 id: cord-286337-qk90xb3a author: Hanada, Shigeo title: Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia date: 2018-11-16 words: 9815 flesch: 11 summary: The airway epithelium: soldier in the fight against respiratory viruses Influenza virus infection decreases tracheal mucociliary velocity and clearance of Streptococcus pneumoniae Ciliary dyskinesia is an early feature of respiratory syncytial virus infection Depression of monocyte and polymorphonuclear leukocyte oxidative metabolism and bactericidal capacity by influenza A virus Sustained desensitization to bacterial Toll-like receptor ligands after resolution of respiratory influenza infection Both influenza-induced neutrophil dysfunction and neutrophil-independent mechanisms contribute to increased susceptibility to a secondary Streptococcus pneumoniae infection Influenza virus-induced immune complexes suppress alveolar macrophage phagocytosis Alteration of pulmonary macrophage function by respiratory syncytial virus infection in vitro Depletion of alveolar macrophages during influenza infection facilitates bacterial superinfections Immune impairment of alveolar macrophage phagocytosis during influenza virus pneumonia Effect of virus infection on the inflammatory response. The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity Probiotic bacteria reduced duration and severity but not the incidence of common cold episodes in a double blind, randomized, controlled trial Probiotics for the prevention of respiratory tract infections: a systematic review The microbial metabolite desaminotyrosine protects from influenza through type I interferon Oral administration of heat-killed Lactobacillus plantarum L-137 enhances protection against influenza virus infection by stimulation of type I interferon production in mice Augmentation of cellular immunity and reduction of influenza virus titer in aged mice fed Lactobacillus casei strain Shirota Microbiota regulates the TLR7 signaling pathway against respiratory tract influenza keywords: bacterial; changes; colonization; gut; host; infection; influenza; mice; microbial; microbiome; patients; pneumoniae; respiratory; responses; streptococcus; tract; virus cache: cord-286337-qk90xb3a.txt plain text: cord-286337-qk90xb3a.txt item: #66 of 145 id: cord-286843-8qh1pblc author: Quah, Jessica title: Impact of microbial Aetiology on mortality in severe community-acquired pneumonia date: 2018-09-04 words: 4065 flesch: 34 summary: The immunology of influenza virusassociated bacterial pneumonia Integrated clinical, pathologic, Virologic, and transcriptomic analysis of H5N1 influenza virus-induced viral pneumonia in the rhesus macaque Kinetics of coinfection with influenza a virus and Streptococcus pneumoniae Etiology of severe communityacquired pneumonia during the 2013 hajj-part of the MERS-CoV surveillance program Clinical and molecular characterization of rhinoviruses a, B, and C in adult patients with pneumonia Human rhinoviruses and severe respiratory infections: is it possible to identify at-risk patients early? viral pneumonia and acute respiratory distress syndrome Burden of acute respiratory disease of epidemic and pandemic potential in the WHO eastern Mediterranean region: a literature review Global threat of animal influenza viruses of zoonotic concern: then and now Surviving Sepsis campaign: international guidelines for Management of Severe Sepsis and Septic Shock Global and local epidemiology of communityacquired pneumonia: the experience of the CAPNETZ network Global changes in the epidemiology of community-acquired pneumonia Community-acquired pneumonia requiring hospitalization among U.S Adults Comprehensive molecular testing for respiratory pathogens in community-acquired pneumonia Empirical use of fluoroquinolones improves the survival of critically ill patients with tuberculosis mimicking severe pneumonia Impact of antibiotic therapy in severe community-acquired pneumonia: data from the Infauci study Predictive factors of mortality in severe community-acquired pneumonia: a model with data on the first 24h of ICU admission Viral infection in patients with severe pneumonia requiring intensive care unit admission Etiology of severe pneumonia in the very elderly Assessment of prognosis in patients with community-acquired pneumonia who require mechanical ventilation The authors would like to thank the following: Ms. Carmen Kam, the resident biostatistician for verification of the study statistical analysis; nurses Ms. Wang Xi Qin, Ms. Goh Yuan Xuan, Ms. Lim Qian Ru for assistance in data collection; senior medical technologist Ms. Heng Ying Xuan, Ms. Lee Hui Zi for assistance in performance of PCR tests; Dr. Tay Tunn Ren for her tutelage in manuscript writing. Polymerase chain reaction Etiology and outcome of severe community acquired pneumonia in immunocompetent adults Etiology of community-acquired pneumonia and diagnostic yields of microbiological methods: a 3-year prospective study in Norway Epidemiology of community-acquired respiratory tract infections in adults The intensive care global study on severe acute respiratory infection (IC-GLOSSARI): a multicenter, multinational, 14-day inception cohort study Viral-bacterial coinfection affects the presentation and alters the prognosis of severe community-acquired pneumonia Molecular diagnosis of respiratory viruses The FilmArray® respiratory panel: an automated, broadly multiplexed molecular test for the rapid and accurate detection of respiratory pathogens Rapid viral diagnosis for acute febrile respiratory illness in children in the emergency department Clinical utility of on-demand multiplex respiratory pathogen testing among adult outpatients Burden of respiratory viruses in patients with acute respiratory failure Community-acquired polymicrobial pneumonia in the intensive care unit: aetiology and prognosis Clinical characteristics and outcomes in hospitalized patients with respiratory viral co-infection during the 2009 H1N1 influenza pandemic Management of severe communityacquired pneumonia: a survey on the attitudes of 468 physicians in Iberia and South America Clinical practice of respiratory virus diagnostics in critically ill patients with a suspected pneumonia: a prospective observational study Infectious Diseases Society of America/American Thoracic Society consensus guidelines on the Management of Community-Acquired Pneumonia in adults Acute management and long-term survival among subjects with severe Middle East respiratory syndrome coronavirus pneumonia and ARDS Virus-induced acute respiratory distress syndrome: epidemiology, management and outcome Influenza a (H1N1) vs non-H1N1 ARDS: analysis of clinical course A prospective one-year microbiologic survey of combined pneumonia and respiratory failure The use of polymerase chain reaction amplification for the detection of viruses and Bacteria in severe communityacquired pneumonia keywords: cap; hospital; infections; mortality; pathogens; patients; pneumonia; study; viruses cache: cord-286843-8qh1pblc.txt plain text: cord-286843-8qh1pblc.txt item: #67 of 145 id: cord-287459-k9x3z2h1 author: Abu-Farha, Mohamed title: The Role of Lipid Metabolism in COVID-19 Virus Infection and as a Drug Target date: 2020-05-17 words: 4839 flesch: 36 summary: The role lipids play in viral infection involves the fusion of the viral membrane to the host cell, viral replication, and viral endocytosis and exocytosis. Even though lipid-lowering capabilities might impact viral replication, statins can also help in mitigating the impact of viral infection through their immunomodulatory and anti-inflammatory properties [60] . keywords: cell; coronavirus; covid-19; host; infection; lipid; membrane; replication; role; sars; statins; virus cache: cord-287459-k9x3z2h1.txt plain text: cord-287459-k9x3z2h1.txt item: #68 of 145 id: cord-287711-gw8mgg4m author: Junter, Guy-Alain title: Cellulose-based virus-retentive filters: a review date: 2017-06-01 words: 11727 flesch: 24 summary: Micro filters with 0.1-0.2 lm pore size (Koenderman et al. 2012; Terpstra et al. 2007; , but also 75N (Dichtelmüller et al. 2012 ) and 35N (Chtourou et al. 2007) . Both 20N (Caballero et al. 2014; Furuya et al. 2006; Gröner 2014) and 15N (Caballero et al. 2014; Roberts et al. 2010; Terpstra et al. 2007; Planova filters and their combination (Gröner et al. 2012; Koenderman et al. 2012 ) showed effective virus removal over a wide range of viral particle sizes (Table 1) . keywords: air; cellulose; concentration; detection; efficiency; et al; fiber; filters; filtration; masks; media; membrane; methods; particles; pore; process; recovery; removal; samples; size; step; studies; table; virus; viruses; volume; water; water samples cache: cord-287711-gw8mgg4m.txt plain text: cord-287711-gw8mgg4m.txt item: #69 of 145 id: cord-287758-da11ypiy author: Mônica Vitalino de Almeida, Sinara title: COVID-19 therapy: what weapons do we bring into battle? date: 2020-09-10 words: 17493 flesch: 35 summary: More preclinical and clinical studies are required to prove whether dasatinib is really promising for COVID-19 patient treatment. SBV is also combined with other antiviral drugs, such as ledipasvir, velpatasvir and voxilaprevir. keywords: action; activity; antiviral; binding; cells; clinical; coronavirus; cov-2; covid-19; disease; drug; entry; fig; host; human; infection; inhibitor; mechanism; new; novel; patients; potential; pro; protein; receptor; replication; results; rna; sars; studies; study; syndrome; synthesis; targets; therapy; treatment cache: cord-287758-da11ypiy.txt plain text: cord-287758-da11ypiy.txt item: #70 of 145 id: cord-287770-oxfnt2n4 author: Caricati, C. P. title: Safety of snake antivenom immunoglobulins: Efficacy of viral inactivation in a complete downstream process date: 2013-06-27 words: 4788 flesch: 42 summary: We found several evidences of virus inactivation and thus of possible cross-reaction, showing for the first time that equine plasma recognizes a wide array of typical model viruses, including a substantial amount of BVDV. Available at Q5A: quality of biotechnological products: viral safety evaluation of biotechnology products derived from cell lines of human or animal origin Genomic and serological diversity of bovine viral diarrhea virus in Japan Antibodies against bovine herpesvirus (BHV) 5 may be differentiated from antibodies against BHV1 in a BHV1 glycoprotein E blocking ELISA A method for measuring specific antibodies in bovine lacteal secretions during the nonlactating period A sensitive and specific immunoassay for the measurement of the antibodies present in horse antivenoms endowed with the capacity to block the phospholipase a2-dependent hemolysis induced by snake venoms Virus safety of human immunoglobulins: efficient inactivation of hepatitis C and other human pathogenic viruses by the manufacturing procedure Turbidity of hyperimmune equine antivenom: the role of phenol and serum lipoproteins Purification of intravenous immunoglobulin G from human plasma-aspects of yield and virus safety Characterization and viral safety validation study of a pasteurized therapeutic concentrate of antithrombin III obtained through affinity chromatography Note for guidance on production and quality control of animal immunoglobulins and immunsera for human use. keywords: heat; inactivation; pepsin; phenol; plasma; process; safety; sai; samples; step; virus; viruses cache: cord-287770-oxfnt2n4.txt plain text: cord-287770-oxfnt2n4.txt item: #71 of 145 id: cord-289093-si8btsab author: Beard, Philippa M. title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date: 2014-06-05 words: 6591 flesch: 44 summary: To investigate this complex pathogen-host relationship further, a RNAi screen of druggable host targets was carried out to analyse the effect of cellular protein depletion on VACV replication, using a multi-cycle VACV infection assay that monitors all stages of virus replication including virus spread. This resulted in a Pearson product moment correlation coefficient of 0.86, confirming that fluorescence was a reliable determinant of virus replication. keywords: analysis; cells; data; figure; gene; hfs; host; infection; proteins; replication; rnai; screen; sirna; vaccinia; vacv; virus cache: cord-289093-si8btsab.txt plain text: cord-289093-si8btsab.txt item: #72 of 145 id: cord-291063-de7v4e5s author: Moens, Ugo title: Silencing Viral MicroRNA as a Novel Antiviral Therapy? date: 2009-05-28 words: 9133 flesch: 42 summary: Hence, neutralizing the action of viral miRNAs expression by complementary single-stranded oligonucleotides or so-called anti-miRNAs may represent a strategy to combat viral infections and viral-induced pathogenesis. Human polyomaviruses: molecular mechanisms for transformation and their association with cancers The role of polyomaviruses in human disease Identification of a third human polyomavirus Identification of a novel polyomavirus from patients with acute respiratory tract infections Clonal integration of a polyomavirus in human Merkel cell carcinoma Molecular biology of BK virus and clinical aspects of BK virus renal infection SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells Evolutionarily conserved function of a viral microRNA Merkel cell polyomavirus encodes a microRNA with the ability to autoregulate viral gene expression MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs Human cytomegalovirus expresses novel microRNAs during productive viral infection Identification and function of human cytomegalovirus microRNAs Identification of virus-encoded microRNAs A microRNA polycistron as a potential human oncogene Hepadnaviruses HBV-encoded microRNA candidate and its target 25 years of HIV-1 research-progress and perspectives RNA silencing and HIV: a hypothesis for the etiology of the severe combined immunodeficiency induced by the virus HIV-1 nef suppression by virally encoded microRNA Human papillomavirus genotype 31 does not express detectable microRNA levels during latent or productive virus replication Adenoviruses Structure, function and evolution of adenovirus virus-associated RNAs Suppression of RNA interference by adenovirus virus-associated RNA Adenovirus virus-associated RNA is processed to functional interfering RNAs involved in virus production Sequence-specific interference by small RNAs derived from adenovirus VAI RNA The family Herpesviridae: a brief introduction Identification of microRNAs of the herpesvirus family Epstein-Barr virus microRNAs are evolutionarily conserved and differentially expressed Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript An acutely and latently expressed herpes simplex virus 2 viral microRNA inhibits expression of ICP34.5, a viral neurovirulence factor Prediction and identification of herpes simplex virus 1-encoded microRNAs Novel less-abundant viral miRNAs encoded by herpes simplex virus 2 latencyassociated transcript and their roles in regulating ICP34.5 and ICP0 mRNAs keywords: amos; cells; ebv; expression; gene; host; hsv-1; human; infection; k12; micrornas; mir; mirna; protein; replication; silencing; target; virus; viruses cache: cord-291063-de7v4e5s.txt plain text: cord-291063-de7v4e5s.txt item: #73 of 145 id: cord-292335-al6v3b9x author: Crotty, Matthew P. title: Impact of antibacterials on subsequent resistance and clinical outcomes in adult patients with viral pneumonia: an opportunity for stewardship date: 2015-11-18 words: 4446 flesch: 29 summary: Pandemic 2009 influenza A in Argentina: a study of 337 patients on mechanical ventilation Predominant role of bacterial pneumonia as a cause of death in pandemic influenza: implications for pandemic influenza preparedness Critically ill infants and children with influenza A (H1N1) in pediatric intensive care units in Argentina Critically ill patients with 2009 influenza A (H1N1) infection in Canada Community acquired respiratory coinfection in critically ill patients with pandemic 2009 influenza A (H1N1) virus Critical illness from 2009 pandemic influenza A virus and bacterial coinfection in the United States Critical care services and 2009 H1N1 influenza in Australia and New Zealand Bacterial coinfections in lung tissue specimens from fatal cases of 2009 pandemic influenza A (H1N1)-United States Pulmonary pathologic findings of fatal 2009 pandemic influenza A/H1N1 viral infections Lung pathology in fatal novel human influenza A (H1N1)infection Epidemiology and clinical characteristics of community-acquired pneumonia in hospitalized children Viral etiology of severe pneumonia among Kenyan infants and children Incidence of respiratory pathogens in persons hospitalized with pneumonia in two provinces in Thailand A preliminary study of pneumonia etiology among hospitalized children in Kenya Etiology of community-acquired pneumonia in hospitalized children in northern Taiwan Viral coinfections in children with invasive pneumococcal disease Temporal association between rhinovirus circulation in the community and invasive pneumococcal disease in children Clinical and molecular characterization of rhinoviruses A, B, and C in adult patients with pneumonia Infection with human metapneumovirus predisposes mice to severe pneumococcal pneumonia Viral enhancement of nasal colonization with Haemophilus influenzae type b in the infant rat Epidemiology and predictors of multidrug-resistant community-acquired and health care-associated pneumonia Pneumonia pathogen characterization is an independent determinant of hospital readmission Cost-effectiveness of rapid diagnosis of viral respiratory tract infections in pediatric patients The effect of rapid respiratory viral diagnostic testing on antibiotic use in a children's hospital Clinical and financial benefits of rapid detection of respiratory viruses: an outcomes study Impact of rapid detection of viral and atypical bacterial pathogens by real-time polymerase chain reaction for patients with lower respiratory tract infection Antibiotic-resistant bugs in the 21st century: a clinical super-challenge A comparison of culture-positive and culture-negative health-care-associated pneumonia Epidemiological differences between sepsis syndrome with bacteremia and culture-negative sepsis Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance A new method of classifying prognostic comorbidity in longitudinal studies: development and validation Measurement of adult antibacterial drug use in 130 US hospitals: comparison of defined daily dose and days of therapy Infectious Diseases Society of America/American Thoracic Society consensus guidelines on the management of community-acquired pneumonia in adults Strategies to prevent antimicrobial resistance in the intensive care unit Burden of Clostridium difficile infection in the United States Clostridium difficile infection The use of antimicrobial agents after diagnosis of viral respiratory tract infections in hospitalized adults: antibiotics or anxiolytics The effect of vancomycin and third-generation cephalosporins on prevalence of vancomycin-resistant enterococci in 126 U.S. adult intensive care units The problem with cephalosporins Does antibiotic exposure increase the risk of methicillin-resistant Staphylococcus aureus (MRSA) isolation? key: cord-292335-al6v3b9x authors: Crotty, Matthew P.; Meyers, Shelby; Hampton, Nicholas; Bledsoe, Stephanie; Ritchie, David J.; Buller, Richard S.; Storch, Gregory A.; Kollef, Marin H.; Micek, Scott T. title: Impact of antibacterials on subsequent resistance and clinical outcomes in adult patients with viral pneumonia: an opportunity for stewardship date: 2015-11-18 journal: Crit Care DOI: 10.1186/s13054-015-1120-5 sha: doc_id: 292335 cord_uid: al6v3b9x INTRODUCTION: keywords: antibacterials; course; days; infection; patients; pneumonia; study; therapy; virus cache: cord-292335-al6v3b9x.txt plain text: cord-292335-al6v3b9x.txt item: #74 of 145 id: cord-292416-3hhi4wps author: Sarid, Ronit title: Investigating an Emerging Virus During a Sudden Pandemic Outbreak date: 2020-07-31 words: 4872 flesch: 35 summary: Zoonotic origins of human coronaviruses Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing Cultivation of viruses from a high proportion of patients with colds A new virus isolated from the human respiratory tract Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia Association between a novel human coronavirus and Kawasaki disease Human coronavirus NL63 is not detected in the respiratory tracts of children with acute Kawasaki disease Kawasaki disease lacks association with human coronavirus NL63 and human bocavirus Epidemiology, genetic recombination, and pathogenesis of coronaviruses Update on human rhinovirus and coronavirus infections Human coronavirus infections in Israel: epidemiology, clinical symptoms and summer seasonality of HCoV-HKU1 An outbreak of human coronavirus OC43 infection and serological cross-reactivity with SARS coronavirus Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history Molecular characterization of a canine respiratory coronavirus strain detected in Italy Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARScoronavirus 2 Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target Diagnostic testing for severe acute respiratory syndromerelated coronavirus 2: a narrative review Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease Ribavirin, remdesivir, sofosbuvir, galidesivir, and tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): a molecular docking study SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective Coronaviruses -drug discovery and therapeutic options Treatment with convalescent plasma for influenza A (H5N1) infection Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection Evaluation of convalescent plasma for Ebola virus disease in Guinea Administration of brincidofovir and convalescent plasma in a patient with Ebola virus disease Feasibility, safety, clinical, and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: a study protocol Treatment of 5 critically ill patients with COVID-19 with convalescent plasma Convalescent plasma transfusion for the treatment of COVID-19: systematic review Our understanding of other viruses, in particular regarding coronaviruses, can provide guidance for understanding and control of the SARS-CoV-2 new outbreak. keywords: coronaviruses; cov-2; disease; hcov; host; human; infection; potential; rna; sars; virus cache: cord-292416-3hhi4wps.txt plain text: cord-292416-3hhi4wps.txt item: #75 of 145 id: cord-293038-pjjvfdnq author: Fontana, Juan title: The unique architecture of Bunyamwera virus factories around the Golgi complex date: 2008-06-10 words: 7398 flesch: 45 summary: Interestingly, integrity of Golgi actin and viral NSm protein is also important for viral tube structure and normal production of infectious virions. In the present work we have studied a large number of serial sections and discovered that viral tubes actually contain a tubular domain and a bigger globular domain on one of the extremities (Fig. 1L ). keywords: actin; assembly; cells; et al; fig; golgi; membranes; nsm; protein; replication; rna; sections; tubes; virus; viruses cache: cord-293038-pjjvfdnq.txt plain text: cord-293038-pjjvfdnq.txt item: #76 of 145 id: cord-294478-3ickafd3 author: Kapil, Sanjay title: Diagnostic Investigation of Emerging Viruses of Companion Animals date: 2008-05-22 words: 7330 flesch: 35 summary: Now, these molecular techniques, which are becoming mainstream applications in routine viral diagnoses, are proving their merit in facilitating the diagnosis of emerging animal viruses. Veterinarians are bound to encounter emerging viruses in their practice. keywords: animals; antibodies; antibody; clinical; diagnosis; diseases; dogs; health; laboratory; new; test; testing; veterinary; viral; virus; viruses cache: cord-294478-3ickafd3.txt plain text: cord-294478-3ickafd3.txt item: #77 of 145 id: cord-294592-zwvr57a0 author: Mukherjee, Moumita title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 date: 2020-08-11 words: 6103 flesch: 48 summary: We have also looked at the possible regulation of viral genomic RNA through binding of host RNA binding proteins (RBPs) and miR-NAs in specific sequences of the viral UTRs. We also looked at the putative host RNA binding protein (RBP) and microRNA binding sites in these regions by ‘RBPmap’ and ‘RNA22 v2’ respectively. keywords: binding; expression; genome; host; mirna; region; rna; sars; sequence; site; variants; virus cache: cord-294592-zwvr57a0.txt plain text: cord-294592-zwvr57a0.txt item: #78 of 145 id: cord-297960-4x1j0iqg author: Bösl, Korbinian title: Common Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis date: 2019-10-04 words: 5491 flesch: 37 summary: Given that the viral proteins were interacting with a large number of host proteins, we analyzed the sub-cellular location of the host proteins. We binned the localization into 11 compartments and estimated the percent of host proteins in a given compartment as compared to the total number of host proteins targeted by a given FIGURE 3 | Clusters of hvPPI involved in core cellular processes. keywords: analysis; drug; evasion; figure; host; human; hvppi; network; novel; protein; targets; viral; virus; viruses cache: cord-297960-4x1j0iqg.txt plain text: cord-297960-4x1j0iqg.txt item: #79 of 145 id: cord-298019-gf2asni1 author: Galdiero, Stefania title: gH625: A milestone in understanding the many roles of membranotropic peptides date: 2014-10-12 words: 8593 flesch: 31 summary: Selfoligomerization of membrane embedded fusion peptides has been proposed to be responsible of inhibition [52, 53] . The preference of tryptophan for membrane interfaces Use of hydrophobic moment plot methodology to aid the identification of oblique orientated α-helices Antimicrobial peptides and viral fusion peptides: how different they are? Antimicrobial peptides: promising compounds against pathogenic microorganisms Membrane fusion and fission: enveloped viruses Recent progress of cellpenetrating peptides as new carriers for intracellular cargo delivery Mechanism of membrane fusion by viral envelope proteins Viral membrane fusion Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 A resolution Retrovirus envelope domain at 1.7 angstrom resolution Crystal structure of the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain Structure of the parainfluenza virus 5 F protein in its metastable, prefusion conformation Structural basis for coronavirus-mediated membrane fusion. keywords: brain; cell; delivery; entry; fusion; fusion peptide; gh625; herpes; hydrophobic; membrane; membrane fusion; membranotropic; peptides; proteins; simplex; structure; virus cache: cord-298019-gf2asni1.txt plain text: cord-298019-gf2asni1.txt item: #80 of 145 id: cord-298033-kzdp9edn author: Domingo, Esteban title: Quasispecies dynamics in disease prevention and control date: 2019-11-08 words: 16379 flesch: 29 summary: Drug ReposER: a web server for predicting similar amino acid arrangements to know drug binding interfaces for potential drug repositioning Involvement of a joker mutation in a polymerase-independent lethal mutagenesis escape mechanism Amantadine-resistance as a genetic marker for influenza viruses HIV Nef: role in pathogenesis and viral fitness Mechanisms of HIV-1 escape from immune responses and antiretroviral drugs Estimating HIV evolutionary pathways and the genetic barrier to drug resistance Genetic basis of resistance to rimantadine emerging during treatment of influenza virus infection Influenza: The Last Great Plague; and Unfinished Story of Discovery The Vaccine Book Transmitted/founder viruses rapidly escape from CD8 þ T cell responses in acute hepatitis C virus infection Natural History of Infections Disease Epitope-specific CD8 þ T lymphocytes cross-recognize mutant simian immunodeficiency virus (SIV) sequences but fail to contain very early evolution and eventual fixation of epitope escape mutations during SIV infection Two escape mechanisms of influenza a virus to a broadly neutralizing stalk-binding antibody Development of live-attenuated arenavirus vaccines based on codon deoptimization Immunological responses following administration of a genotype 1a/1b/2/3a quadrivalent HCV VLP vaccine The poliovirus eradication initiative Viral persistence in vivo through selection of neutralizing antibody-escape variants CD4þ T-cell-epitope escape mutant virus selected in vivo Perspectives and opportunities for novel antiviral treatments targeting virus fitness Human immunodeficiency virus type 1 fitness and tropism: concept, quantification, and clinical relevance HIV-1 drug resistance and resistance testing Antigenic determinants of possible vaccine escape by porcine circovirus subtype 2b viruses Trans-dominant inhibition of RNA viral replication can slow growth of drugresistant viruses Naturally occurring NS3-protease-inhibitor resistant mutant A156T in the liver of an untreated chronic hepatitis C patient Vaccine development: from concept to early clinical testing Molecular and functional bases of selection against a mutation bias in an RNA virus Molecular epidemiology of hepatitis B virus mutants associated with vaccine escape, drug resistance and diagnosis failure Patterns of resistanceassociated substitutions in patients with chronic HCV infection following treatment with direct-acting antivirals Multiclass HCV resistance to direct-acting antiviral failure in real-life patients advocates for tailored secondline therapies RNA virus evolution and the control of viral disease Complications of RNA heterogeneity for the engineering of virus vaccines and antiviral agents Quasispecies dynamics in disease prevention and control Quasispecies and RNA Virus Evolution: Principles and Consequences Virus population dynamics, fitness variations and the control of viral disease: an update Viral quasispecies evolution. Higher levels of resistance mutations as a function of time in untreated patients is an indication that the mutations are not due to basal mutant frequencies but to the epidemiological expansion of virus mutants that originated in treated patients. keywords: antigenic; antiviral; cell; chapter; disease; drug; drug resistance; dynamics; escape; et al; fitness; frequency; hepatitis; infection; inhibitor; mutants; mutations; population; replication; resistance; resistance mutations; section; selection; treatment; vaccine; virus; viruses cache: cord-298033-kzdp9edn.txt plain text: cord-298033-kzdp9edn.txt item: #81 of 145 id: cord-302111-kg0dmgq0 author: Darden, Dijoia B. title: The Clinical Presentation and Immunology of Viral Pneumonia and Implications for Management of Coronavirus Disease 2019 date: 2020-04-29 words: 4498 flesch: 21 summary: Severe viral pneumonia can manifest as sepsis and respiratory distress requiring intensive care (11) . The most severely ill group of 12 patients demonstrated impaired expression of numerous genes participating in adaptive immune responses (e.g., diminished antigen presentation, B-cell development, T-helper cell differentiation, and apoptosis), suggesting impaired adaptive immunity in severe viral pneumonia (55) . keywords: community; coronavirus; covid-19; disease; infection; influenza; patients; pneumonia; presentation; review; sars; vaccine cache: cord-302111-kg0dmgq0.txt plain text: cord-302111-kg0dmgq0.txt item: #82 of 145 id: cord-303330-zh8wzza5 author: Magleby, Reed title: Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019 date: 2020-06-30 words: 3560 flesch: 42 summary: Identifying high viral load patients could also be helpful for allocating scare therapeutic interventions such as antiviral agents (e.g., remdesivir) Higher viral load was associated with increased age, comorbidities, smoking status, and recent chemotherapy. keywords: cov-2; covid-19; hospital; load; patients; risk; sars cache: cord-303330-zh8wzza5.txt plain text: cord-303330-zh8wzza5.txt item: #83 of 145 id: cord-304424-048xo7jn author: Greninger, Alexander L. title: A decade of RNA virus metagenomics is (not) enough date: 2018-01-15 words: 9614 flesch: 26 summary: Mining of publicly available transcriptome data has contributed greatly to the discovery of novel RNA viruses (Basler et al., 2005; Schomacker et al., 2004) . The greatest paradigm shifter in recent viral metagenomics work has been the sheer number and diversity of novel RNA viruses present in arthropods and invertebrates. keywords: analysis; bats; detection; discovery; diversity; dna; et al; evolution; genome; greninger; host; human; identification; library; metagenomics; new; novel; number; preparation; protein; rna; rna viruses; sequence; sequencing; shi et; species; viruses cache: cord-304424-048xo7jn.txt plain text: cord-304424-048xo7jn.txt item: #84 of 145 id: cord-305195-e41yfo89 author: Rainwater-Lovett, Kaitlin title: Viral Epidemiology: Tracking Viruses with Smartphones and Social Media date: 2016-02-12 words: 6164 flesch: 30 summary: Expanded access to the Internet and social media has revolutionized outbreak detection and viral disease surveillance by providing novel sources of data in real time (Chunara, 2012) . Investigation into the spatiotemporal dynamics of viral diseases at smaller spatial scales has become ProMED, the Program for Monitoring Emerging Diseases, is an Internet-based reporting system established in 1994 that compiles information on outbreaks of infectious diseases affecting humans, animals, and food plants. keywords: data; disease; dynamics; epidemiology; individuals; infection; influenza; methods; models; patterns; surveillance; transmission; virus; viruses cache: cord-305195-e41yfo89.txt plain text: cord-305195-e41yfo89.txt item: #85 of 145 id: cord-306424-gf0bglm0 author: Scutigliani, Enzo Maxim title: Interaction of the innate immune system with positive-strand RNA virus replication organelles date: 2017-06-27 words: 8337 flesch: 30 summary: Therefore, detection of viral RNA and the subsequent induction of antiviral effector mechanisms play an important part in the onset of an antiviral state in the context of RNA virus infections. ROs are therefore believed to have a dual role in +RNA virus infection and innate immune evasion, which will be elaborated on further in this review. keywords: antiviral; host; ifn; inducible; infection; innate; lc3; membrane; protein; replication; rna; role; ros; signaling; virus; viruses cache: cord-306424-gf0bglm0.txt plain text: cord-306424-gf0bglm0.txt item: #86 of 145 id: cord-306921-3afgpunj author: Owino, Collins Oduor title: Recent advances on the role of host factors during non-poliovirus enteroviral infections date: 2019-06-19 words: 11752 flesch: 33 summary: [165] EV-D68 can disrupt autophagy process downstream Promotes viral replication and egress from infected cells; promoting viral infection within the cells [166] CV-B3 viral protein 3C targets cleavage of SNARE and PLEKHM1 proteins Impairs establishment of SNARE complexes thus providing conducive environment for viral replication [170] CV-B3 viral 2A protease cleaves SQSTM1/p62 a known intermediary of selective autophagy degradation of ubiquitinated proteins Impairs NF-kB signaling and disrupts selective autophagy in infected cells to establish an efficient viral replication/infection [173] CV-B3 interacts with CALCOCO2 and SQSTM1 Targets autophagy receptors; targets mitochondrial antiviral signaling protein for degradation thus blocking establishment of antiviral state in the infected cells [177] targeting different stages of viral infections would be an alternative in targeting different stages of the enteroviral infection cycle. Interplay between viral proteins and human host proteins play a major role in the attachment, entry and internalization of viral infections. keywords: a71; autophagy; cell; colleagues; coxsackievirus; cycle; disease; enterovirus; entry; factors; host; human; infections; protein; receptor; replication; rna; study; viruses cache: cord-306921-3afgpunj.txt plain text: cord-306921-3afgpunj.txt item: #87 of 145 id: cord-307354-dkwcheu0 author: Abernathy, Emma title: Emerging roles for RNA degradation in viral replication and antiviral defense date: 2015-05-31 words: 7171 flesch: 33 summary: (A) Viral RNA of ( þ ) RNA viruses can be recognized by cellular QC pathways like NMD, in some cases due to long 3 0 UTRs which are inherent to subgenomic RNAs (sgRNA). In addition, several antiviral pathways use RNA degradation as a viral restriction mechanism, and we will summarize new findings related to how these host-encoded ribonucleases target and destroy viral RNA. keywords: cellular; cleavage; decay; degradation; et al; expression; host; infection; mrna; protein; translation; viral; virus cache: cord-307354-dkwcheu0.txt plain text: cord-307354-dkwcheu0.txt item: #88 of 145 id: cord-307813-elom30nx author: Yip, Tsz-Fung title: Advancements in Host-Based Interventions for Influenza Treatment date: 2018-07-10 words: 15110 flesch: 27 summary: Life-threatening influenza and impaired interferon amplification in human IRF7 deficiency Disease-promoting effects of type I interferons in viral, bacterial, and coinfections Protection from lethal influenza virus challenge by oral type 1 interferon Low-dose oral interferon alpha as prophylaxis against viral respiratory illness: a double-blind, parallel controlled trial during an influenza pandemic year IFNlambda is a potent anti-influenza therapeutic without the inflammatory side effects of IFNalpha treatment Pathogenic potential of interferon alphabeta in acute influenza infection The superiority of IFN-lambda as a therapeutic candidate to control acute influenza viral lung infection Type I interferon induction during influenza virus infection increases susceptibility to secondary Streptococcus pneumoniae infection by negative regulation of gammadelta T cells Interferon-lambda mediates non-redundant front-line antiviral protection against influenza virus infection without compromising host fitness RIG-I activation protects and rescues from lethal influenza virus infection and bacterial superinfection Antiviral effect of a selective COX-2 inhibitor on H5N1 infection in vitro Avian influenza A H7N9 virus induces severe pneumonia in mice without prior adaptation and responds to a combination of zanamivir and COX-2 inhibitor Role of cyclooxygenase-2 in H5N1 viral pathogenesis and the potential use of its inhibitors Targeted prostaglandin E2 inhibition enhances antiviral immunity through induction of type I interferon and apoptosis in macrophages Modified Jiu Wei Qiang Huo decoction improves dysfunctional metabolomics in influenza A pneumoniainfected mice Pattern recognition receptors and inflammation Cutting edge: There is an urgent need to search for alternative targets to treat influenza virus infections, including non-viral targets such as host cellular factors; which are promising as viruses rely on the host machinery for replication. keywords: addition; antiviral; cells; complex; drug; export; host; human; iav; immune; infected; infection; influenza; inhibitor; lung; membrane; mice; nuclear; production; protein; replication; role; treatment; type; viral; virus; viruses; vitro; vrnp cache: cord-307813-elom30nx.txt plain text: cord-307813-elom30nx.txt item: #89 of 145 id: cord-307817-2vy28i4m author: Lou, Zhiyong title: Current progress in antiviral strategies date: 2014-01-14 words: 7596 flesch: 32 summary: This review will highlight recent achievements in antiviral development and discuss various strategies for preventing virus attachment and entry into the host cell, as well as strategies for preventing virus replication and transcription within the host cell. Throughout the life cycle of a negative sense single-stranded RNA (ssRNA) virus, the genome length RNA is encapsidated by a virally encoded nucleoprotein (NP), instead of a naked RNA, and associated with RdRp (polymerase complex) to form a stable ribonucleoprotein (RNP) complex, which is responsible for virus replication, transcription, and assembly keywords: activity; binding; complex; function; fusion; hcv; hiv; host; infection; influenza; inhibitors; protein; replication; rna; structure; virus; viruses cache: cord-307817-2vy28i4m.txt plain text: cord-307817-2vy28i4m.txt item: #90 of 145 id: cord-308126-wpxhk0pf author: Jaume, Francesca title: Common Cold and Acute Rhinosinusitis: Up-to-Date Management in 2020 date: 2020-06-03 words: 4440 flesch: 42 summary: Bacterial ARS should be suspected at any time when the presence of three or more of the sings or symptoms related to bacterial ARS are found (especially in patients with CRS at baseline Bacterial ARS is defined by the presence of three or more of the following clinical findings: fever (≥ 38°C), severe local pain, double sickening, unilateral disease (with discolored mucus), or elevation of C-reactive protein (CRP)/erythrocyte sedimentation ratio (ESR) in blood test ( Fig. 1 ) American guidelines (ICAR) note similar definitions and symptoms but stratify to ARS, when symptoms last up to 4 weeks, and sub-acute rhinosinusitis when the duration is between 4 and 12 weeks. keywords: acute; ars; bacterial; cold; complications; nasal; patients; symptoms; viral cache: cord-308126-wpxhk0pf.txt plain text: cord-308126-wpxhk0pf.txt item: #91 of 145 id: cord-309642-wwaa6ls0 author: Potgieter, Leon N.D. title: Pathogenesis of Viral Infections date: 1986-11-30 words: 10859 flesch: 33 summary: The respiratory tract is a very common site at which virus infections are initiated, usually as the result of airborne infections. The inert superficial protective layers of the intact skin usually are impervious to virus infection. keywords: antibody; cells; disease; dna; host; immune; infection; injury; macrophages; mechanisms; oncogene; pathogenesis; receptors; replication; result; surface; tract; transformation; virus; viruses cache: cord-309642-wwaa6ls0.txt plain text: cord-309642-wwaa6ls0.txt item: #92 of 145 id: cord-310920-itqwhi6a author: Haddad, Christina title: Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date: 2020-07-02 words: 3701 flesch: 35 summary: Thus, studying viral RNA structures and their interactions with cognate RBPs are essential to understanding the pathogenesis of RNA viruses and to further assist the design of novel antivirals. It is therefore no surprise that RNA viruses use this functional diversity to their advantage to sustain chronic or lifelong infections. keywords: genome; host; interactions; protein; replication; rna; sars; structural; virus; viruses cache: cord-310920-itqwhi6a.txt plain text: cord-310920-itqwhi6a.txt item: #93 of 145 id: cord-312332-rwmuucsp author: Dicker, Kate title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date: 2020-09-10 words: 9241 flesch: 41 summary: The human RNA-Binding proteome and its dynamics during translational arrest Purification of cross-linked RNA-protein complexes by phenol-toluol extraction Comprehensive identification of RNA-Binding domains in human cells High-resolution mapping of RNA-Binding regions in the nuclear proteome of embryonic stem cells The new (dis)order in RNA regulation Two RNA polymerase complexes from vesicular stomatitis virus-infected cells that carry out transcription and replication of genome RNA Identification of cellular interaction partners of the influenza virus ribonucleoprotein complex and polymerase complex using proteomic-based approaches Comprehensive proteomic analysis of influenza virus polymerase complex reveals a novel association with mitochondrial proteins and RNA polymerase accessory factors Discovery of widespread host protein interactions with the prereplicated genome of CHIKV using VIR-CLASP Fields Virology Diverse roles of host RNA binding proteins in RNA virus replication https://doi.org/10.1016/j.semcdb.2020.08.002. Thiouracil cross-linking mass spectrometry: a cell-based method to identify host factors involved in viral amplification Identification of proteins bound to dengue viral RNA in vivo reveals new host proteins important for virus replication Identification of RNA binding proteins associated with dengue virus RNA in infected cells reveals temporally distinct host factor requirements Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry Unconventional RNA-binding proteins step into the virus-host battlefront Identification and characterization of sindbis virus RNA-Host protein interactions System-wide profiling of RNA-Binding proteins uncovers key regulators of virus infection An RNA-centric dissection of host complexes controlling flavivirus infection Viruses seen by our cells: the role of viral RNA sensors Intracellular sensing of viral genomes and viral evasion To translate, or not to translate: viral and host mRNA regulation by interferon-stimulated genes The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts Insights into RNA biology from an atlas of mammalian mRNAbinding proteins A brave new world of RNAbinding proteins Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS) keywords: assembly; binding; cell; hiv-1; host; human; infection; particles; proteins; rbps; replication; rna; role; transcription; virion; virus; viruses; vrna cache: cord-312332-rwmuucsp.txt plain text: cord-312332-rwmuucsp.txt item: #94 of 145 id: cord-314024-n6l2804j author: Gonçalves, Antonio title: Timing of antiviral treatment initiation is critical to reduce SARS-Cov-2 viral load date: 2020-04-07 words: 2092 flesch: 45 summary: Viral loads in nasopharyngeal swabs were measured by real time reverse transcriptase 77 polymerase chain reaction (RT PCR, lower limit of quantification: 38 cycles, CT) at multiple 78 time points with an observed peak of viral load at day 5 post onset of symptoms (range: 2-27 79 days). These numbers also inform us both on the time to initiate antiviral treatment, and the 158 level of efficacy that needs to be achieved to reduce viral load [6] . keywords: efficacy; medrxiv; onset; preprint; treatment cache: cord-314024-n6l2804j.txt plain text: cord-314024-n6l2804j.txt item: #95 of 145 id: cord-314560-rswa5zdn author: Manjunath, N. title: Interfering antiviral immunity: application, subversion, hope? date: 2006-06-06 words: 5889 flesch: 39 summary: In the context of RNA viruses, siRNAs can be designed to degrade not only viral mRNA Similarly, Ge et al. achieved and Polio), for which a single mRNA is used to transcribe viral proteins, targeting any part of the coding sequence should result in degradation (scissors) of viral genomic RNA and/or progeny mRNA. keywords: cells; delivery; gene; infection; interference; protein; rnai; sequence; silencing; sirna; targeting; virus; viruses cache: cord-314560-rswa5zdn.txt plain text: cord-314560-rswa5zdn.txt item: #96 of 145 id: cord-315130-8g2ih8zl author: Bax, Adriaan title: SARS-CoV-2 transmission via speech-generated respiratory droplets date: 2020-09-11 words: 1838 flesch: 46 summary: Surfing the COVID-19 scientific wave The size and the duration of air-carriage of respiratory droplets and dropletnuclei On air-borne infection -Study II Droplets and droplet nuclei Guidelines for Environmental Infection Control in Health-Care Facilities Indoor air humidity, air quality, and health -An overview Mechanisms of airborne infection via evaporating and sedimenting droplets produced by speaking The airborne lifetime of small speech droplets and their potential importance in SARS-CoV-2 transmission What Noises Cause Hearing Loss Visualizing Speech-Generated Oral Fluid Droplets with Laser Light Scattering Virological assessment of hospitalized patients with COVID-2019 Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series A schlieren optical study of the human cough with and without wearing masks for aerosol infection control Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2) WHO confirms there's 'emerging evidence' of airborne transmission of The role of particle size in aerosolised pathogen transmission: A review SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Viral RNA Load in Mildly Symptomatic and Asymptomatic Children with COVID-19 Temporal dynamics in viral shedding and transmissibility of COVID-19 Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study Physiology of airway mucus clearance Modality of human expired aerosol size distributions Size distribution and sites of origin of droplets expelled from the human respiratory tract during expiratory activities For example, we could have stated an average of 17 virions per second over a period of 25 seconds but such a number would suggest a precision higher than warranted, considering the wide variation in viral load and the fractional uncertainty in the diameter of the fully hydrated particles. keywords: droplets; load; patients; speech; transmission cache: cord-315130-8g2ih8zl.txt plain text: cord-315130-8g2ih8zl.txt item: #97 of 145 id: cord-317037-1qydcc5e author: Kumar, Asit title: Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date: 2020-08-13 words: 9424 flesch: 28 summary: Notably, EVs can enhance viral infection by: (1) mediating transfer of chemokine co-receptors or cell surface proteins to null-target cells that do not express endogenous viral co-receptors; (2) helping viruses to evade the host immune system; (3) transferring of viral components (viral proteins and RNAs) to recipient cells, which induce cytotoxic effects on infected cells, leading to progressive loss of immune cells resulting from the apoptosis of uninfected bystander cells. Notably, EVs can enhance viral infection by: (1) mediating transfer of chemokine co-receptors or cell surface proteins to null-target cells that do not express endogenous viral co-receptors; (2) helping viruses to evade the host immune system; (3) transferring of viral components (viral proteins and RNAs) to recipient cells, which induce cytotoxic effects on infected cells, leading to progressive loss of immune cells resulting from the apoptosis of uninfected bystander cells. keywords: cells; delivery; drug; evs; exosomes; extracellular; hiv; human; immune; infected; infection; isolation; membrane; plasma; proteins; replication; rna; sars; size; vesicles; virus; viruses cache: cord-317037-1qydcc5e.txt plain text: cord-317037-1qydcc5e.txt item: #98 of 145 id: cord-317277-rr9zue4l author: Cifuentes-Munoz, Nicolas title: Viral cell-to-cell spread: Conventional and non-conventional ways date: 2020-09-29 words: 13111 flesch: 30 summary: Cell-cell transmission enables HIV-1 to evade inhibition by potent CD4bs directed antibodies Extracellular vesicles: vehicles of en bloc viral transmission Casein kinase 2 regulates vaccinia virus actin tail formation The formin FHOD1 and the small GTPase Rac1 promote vaccinia virus actin-based motility Unique features of HIV-1 spread through T cell virological synapses Cell-fusion events induced by α-herpesviruses The virological synapse facilitates herpes simplex virus entry into T cells The immune control and cell-to-cell spread of human T-lymphotropic virus type 1 Engagement of specific T-cell surface molecules regulates cytoskeletal polarization in HTLV-1-infected lymphocytes Identification of host trafficking genes required for HIV-1 virological synapse formation in dendritic cells Nonlytic viral spread enhanced by autophagy components The isolation and characterization of mutants of herpes simplex virus type 1 that induce cell fusion The global phosphorylation landscape of SARS-CoV-2 infection HIV cell-to-cell spread results in earlier onset of viral gene expression by multiple infections per cell Stem cell extracellular vesicles and their potential to contribute to the repair of damaged CNS cells Neutralizing antibody-resistant hepatitis C virus cell-to-cell transmission Rapid and efficient cell-to-cell transmission of human immunodeficiency virus infection from monocyte-derived macrophages to peripheral blood lymphocytes Different requirements for scavenger receptor class B type I in hepatitis C virus cell-free versus cell-to-cell transmission Feline tetherin is characterized by a short N-terminal region and is counteracted by the feline immunodeficiency virus envelope glycoprotein A viral fusogen hijacks the actin cytoskeleton to drive cell-cell fusion F-actin dynamics transform filopodial bridges into intercellular nanotubes capable of distant cell communication Predominant mode of human immunodeficiency virus transfer between T cells is mediated by sustained Envdependent neutralization-resistant virological synapses Phosphatidylserine vesicles enable efficient en bloc transmission of enteroviruses Culturing primary and transformed neuronal cells for studying pseudorabies virus infection Hantavirus Gn and Gc envelope glycoproteins: key structural units for virus cell entry and virus assembly Varicella-zoster virus glycoprotein I is essential for growth of virus in Vero cells Membrane fusion mediated by herpesvirus glycoproteins: the paradigm of varicella-zoster virus They might be giants: does syncytium formation sink or spread HIV infection? Cell-to-cell transfer of HIV infection: implications for HIV viral persistence Actin-based motility of vaccinia virus Compartmented neuron cultures for directional infection by alpha herpesviruses A fluorescent dye is usually used to differentiate target cells from donor cells, and quantification of cell spread is determined microscopically or by flow cytometry of a reporter virus or a labeled viral antigen. keywords: actin; antibodies; cell; cell spread; cell transmission; epithelial; et al; filopodia; formation; fusion; human; infection; membrane; particles; protein; spread; target; tnts; transfer; transmission; type; virus; viruses cache: cord-317277-rr9zue4l.txt plain text: cord-317277-rr9zue4l.txt item: #99 of 145 id: cord-318495-1w74wf02 author: Vignuzzi, Marco title: Defective viral genomes are key drivers of the virus–host interaction date: 2019-06-03 words: 8880 flesch: 20 summary: Biologic role in homologous interference Viral interference by defective particles of vesicular stomatitis virus measured in individual cells Analysis of extracellular West Nile virus particles produced by cell cultures from genetically resistant and susceptible mice indicates enhanced amplification of defective interfering particles by resistant cultures Replication signals in the genome of vesicular stoma titis virus and its defective interfering particles: identification of a sequence element that enhances DI RNA replication Functional characterisation of the genomic and antigenomic promoters of Sendai virus Homologous interference by incomplete Sendai virus particles: changes in virus-specific ribonucleic acid synthesis Defective viral genomes alter how Sendai virus interacts with cellular trafficking machinery leading to heterogeneity in the production of viral particles among infected cells Replication defective viral genomes exploit a cellular pro-survival mechanism to establish paramyxovirus persistence MDA5 participates in the detection of paramyxovirus infection and is essential for the early activation of dendritic cells in response to Sendai virus defective interfering particles Sendai virus defective-interfering genomes and the activation of interferon-beta Induction of dendritic cell production of type I and type III interferons by wild-type and vaccine strains of measles virus: role of defective interfering RNAs Highly immunostimulatory RNA derived from a Sendai virus defective viral genome A novel role for viral-defective interfering particles in enhancing dendritic cell maturation Modulation of a systemic Semliki Forest virus infection in mice by defective interfering virus Identification of a natural viral RNA motif that optimizes sensing of viral RNA by RIG.-I. mBio Activation of the beta interferon promoter by unnatural Sendai virus infection requires RIG-I and is inhibited by viral C proteins PACT-and RIG-I-dependent activation of Type I interferon production by a defective interfering RNA derived from measles virus vaccine Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing TLR-independent induction of dendritic cell maturation and adaptive immunity by negative-strand RNA viruses In vivo ligands of MDA5 and RIG-I in measles virusinfected cells Nonencapsidated 5′ Copy-Back Defective Interfering Genomes Produced by Recombinant Measles Viruses Are Recognized by RIG-I and LGP2 but Not MDA5 ATPase-driven oligomerization of RIG-I on RNA allows optimal activation of type-I interferon Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses Dicer-2-dependent generation of viral DNA from defective genomes of RNA viruses modulates antiviral immunity in insects Role of defective interfering particles of Sendai virus in persistent infections Comparative study of rabies virus persistence in human and hamster cell lines Subclinical infections in mice resulting from the modulation of a lethal dose of Semliki Forest virus with defective interfering viruses: neurochemical abnormalities in the central nervous system Defective interfering particles: effects in modulating virus growth and persistence Persistence of virulent Semliki Forest virus in mouse brain following co-inoculation with defective interfering particles Defective interfering virus particles modulate virulence Continuous influenza virus production in cell culture shows a periodic accumulation of defective interfering particles Multiple-hit inhibition of infection by defective interfering particles Defective interfering particles of human parainfluenza virus type 3 are associated with persistent infection in cell culture Defective interfering influenza virus RNAs: time to reevaluate their clinical potential as broad-spectrum antivirals? Targeting expression of the leukemogenic PML-RARalpha fusion protein by lentiviral vector-mediated small interfering RNA results in leukemic cell differentiation and apoptosis Ebola virus defective interfering particles and persistent infection Defective interfering viral particles in acute dengue infections Generation of measles virus defective interfering particles and their presence in a preparation of attenuated live-virus vaccine Effects of defective interfering viruses on virus replication and pathogenesis in vitro and in vivo Defective interfering particles of respiratory syncytial virus Induction and biological properties of defective interfering particles of rabies virus Defective T particles of vesicular stomatitis virus. keywords: cells; copy; defective; dvgs; generation; genomes; infection; influenza; interfering; particles; persistent; production; replication; rna; rnas; type; virus; viruses cache: cord-318495-1w74wf02.txt plain text: cord-318495-1w74wf02.txt item: #100 of 145 id: cord-318749-k91oku7h author: Dong, Hui-Jun title: Selective regulation in ribosome biogenesis and protein production for efficient viral translation date: 2020-10-29 words: 7270 flesch: 22 summary: IRES) Host targeted antiviral (HTA): functional inhibitor compounds of scaffold protein RACK1 inhibit herpes simplex virus proliferation Arabidopsis receptor of activated C kinase1 phosphorylation by WITH NO LYSINE8 KINASE Viral ribonucleoprotein complex formation and nucleolar-cytoplasmic relocalization of nucleolin in poliovirus-infected cells RNA-binding properties of influenza A virus matrix protein M1 Ribosomal protein RPL26 is the principal target of UFMylation Cloning of mouse genomic ribosomal protein L6 gene and analysis of its promoter The association of ribosomal protein L18 (RPL18) with infectious bursal disease virus viral protein VP3 enhances viral replication UFMylation of RPL26 links translocation-associated quality control to endoplasmic reticulum protein homeostasis Interferon production and inhibition of host synthesis in cells infected with vesicular stomatitis virus Impact of RNA polymerase I inhibitor CX-5461 on viral kinase-dependent and -independent cytomegalovirus replication New mRNAs are preferentially translated during vesicular stomatitis virus infection The structure and function of the eukaryotic ribosome Hepatitis C virus 3'X region interacts with human ribosomal proteins Specialized ribosomes: a new frontier in gene regulation and organismal biology RNA regulons in Hox 5' Ribosomal protein L4 (RPL4) ) and ribosomal protein L18 were identified as interacting partners of VP3 protein and as being involved in the regulation of IBDV replication. keywords: antiviral; biogenesis; cells; et al; host; infection; ires; mrna; protein; replication; ribosomal; ribosome; rna; rps; synthesis; translation; virus; viruses cache: cord-318749-k91oku7h.txt plain text: cord-318749-k91oku7h.txt item: #101 of 145 id: cord-318751-4v2tl0gi author: Arias, Armando title: Progress towards the prevention and treatment of norovirus infections date: 2013-11-17 words: 6844 flesch: 32 summary: Preceding the initiation of viral RNA replication, VPg must be guanylated in a step carried out by the virus polymerase NS7 pol or its precursor NS6-NS7 [55] . In addition to its capacity to inhibit viral RNA replication, suramin has been found to inhibit HuNoV capsid binding to heparan sulphate [32] . keywords: activity; cell; culture; hunov; infection; inhibition; inhibitors; mnv; norovirus; protein; replication; rna; translation; use; viruses; vpg cache: cord-318751-4v2tl0gi.txt plain text: cord-318751-4v2tl0gi.txt item: #102 of 145 id: cord-318853-mxyxwkhx author: Sallie, Richard title: Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases date: 2005-08-22 words: 10548 flesch: 17 summary: Of necessity, some receptor affinity studies have used cloned viral protein ligands, an artificial situation that cannot approach the phenotypic complexity of RNA viral protein quasispecies. Viral receptor disease is a unifying hypothesis that may also explain some diseases with well-established, but multi-factorial and apparently unrelated aetiologies – like coronary artery and other vascular diseases – in addition to diseases like schizophrenia that are poorly understood and lack plausible, coherent, pathogenic explanations. keywords: cell; disease; envelope; fidelity; hcv; hepatitis; infection; leptin; patients; pol; proteins; quasispecies; receptor; replication; responses; rna; rna pol; sequence; type; variant; virus; viruses cache: cord-318853-mxyxwkhx.txt plain text: cord-318853-mxyxwkhx.txt item: #103 of 145 id: cord-319215-8tdtia5w author: Li, Iris W. title: The Natural Viral Load Profile of Patients With Pandemic 2009 Influenza A(H1N1) and the Effect of Oseltamivir Treatment date: 2010-04-30 words: 4086 flesch: 45 summary: Viral loads in clinical specimens and SARS manifestations Functional tumor necrosis factor-related apoptosis-inducing ligand production by avian influenza virus-infected macrophages Clinical fi ndings and demographic factors associated with intensive care unit admission in Utah due to novel 2009 infl uenza A(H1N1) infection Hospitalized patients with novel influenza A (H1N1) virus infection -California Prolonged infl uenza virus infection during lymphocytopenia and frequent detection of drug-resistant viruses Comparison of fl ocked and rayon swabs for collection of respiratory epithelial cells from uninfected volunteers and symptomatic patients Oseltamivir adherence and side effects among children in three London schools affected by infl uenza A(H1N1)v Assessment of neuropsychiatric adverse events in infl uenza patients treated with oseltamivir: a comprehensive review Infl uenza associated central nervous system dysfunction in Taiwanese children: clinical characteristics and outcomes with and without administration of oseltamivir Dr Cheng: contributed to collecting the clinical data and samples. A H1N1, seasonal human infl uenza A H1N1, and avian infl uenza A H5N1 viruses Use of the oral neuraminidase inhibitor oseltamivir in experimental human infl uenza: randomized controlled trials for prevention and treatment Viral shedding in children with infl uenza virus infections treated with neuraminidase inhibitors European Infl uenza Surveillance Scheme . keywords: days; infl; load; onset; oseltamivir; pandemic; patients; post; symptom; uenza cache: cord-319215-8tdtia5w.txt plain text: cord-319215-8tdtia5w.txt item: #104 of 145 id: cord-319675-mwy3t1ny author: Gu, Li title: Sustained Viremia and High Viral Load in Respiratory Tract Secretions Are Predictors for Death in Immunocompetent Adults with Adenovirus Pneumonia date: 2016-08-17 words: 3087 flesch: 52 summary: At admission (on day 5–7 after illness onset), the patients in fatal cases presented higher initial viral loads in respiratory tract secretions (8.578 ± 2.115 vs 6.263 ± 1.225 Log(10) copies/ml, p = 0.023). For those with positive AdV PCR testing, serial whole blood and respiratory tract samples were collected until death or discharge. keywords: cases; day; load; patients; samples; tract cache: cord-319675-mwy3t1ny.txt plain text: cord-319675-mwy3t1ny.txt item: #105 of 145 id: cord-319761-bu5pzbnv author: Miller, Craig S. title: Pleiotropic mechanisms of virus survival and persistence date: 2005-07-16 words: 5660 flesch: 29 summary: The origins of virology Further studies on the proliferation in vitro of single isolated tissue cells The infection of cells in tissue culture with Rous sarcoma virus The structure of DNA A plaque assay for foot-and-mouth disease virus and kinetics of virus reproduction Exotic emerging viral diseases: progress and challenges Persistent toll-like receptor signals are required for reversal of regulatory T cellemediated CD8 tolerance The many mechanisms of viral membrane fusion proteins Proteinaseactivated receptors: novel mechanisms of signaling by serine proteases Inflammatory caspases: linking an intracellular innate immune system to autoinflammatory diseases Interleukin-18 Newly identified pair of proteasomal subunits regulated reciprocally by interferon gamma Apoptosis: an innate immune response to virus infection Viruses and apoptosis Life, death, and the pursuit of apoptosis Regulation of p53-dependent apoptosis, transcriptional repression, and cell transformation by phosphorylation of the 55-kilodalton E1B protein of human adenovirus type 5 Adenovirus-mediated gene expression in vivo is enhanced by the antiapoptotic Bcl-2 gene Inhibition of DNA-dependent transcription by the leader RNA of vesicular stomatitis virus: role of specific nucleotide sequences and cell protein binding The IAP proteins: caspase inhibitors and beyond Prevention of vertebrate neuronal death by the crmA gene Neutralization of Smac/Diablo by inhibitors of apoptosis (IAPs). As a result, greater knowledge of virus replication, viral and cellular receptors, and immunologic interactions was achieved. keywords: apoptosis; cell; gene; host; human; ifn; infection; interferon; mhc; proteins; replication; response; virus; viruses cache: cord-319761-bu5pzbnv.txt plain text: cord-319761-bu5pzbnv.txt item: #106 of 145 id: cord-320015-lbr2q4qh author: Chinchar, V. Gregory title: The Molecular Biology of Frog Virus 3 and other Iridoviruses Infecting Cold-Blooded Vertebrates date: 2011-10-20 words: 9150 flesch: 36 summary: However, because the absence of a full-sized vIF-2α gene in FV3 does not adversely affect viral protein synthesis, other viral proteins may also play roles in maintaining viral protein synthesis in infected cells. As progressively larger amounts of viral proteins bind the membrane scaffold, crescent-shaped structures that resemble icosahedral vertices are formed. keywords: 18k; cells; dna; expression; frog; fv3; gene; host; infection; iridovirus; mutants; protein; ranavirus; replication; synthesis; vif-2α; virion; virus; viruses cache: cord-320015-lbr2q4qh.txt plain text: cord-320015-lbr2q4qh.txt item: #107 of 145 id: cord-320713-b37c8aye author: Roberts, Lisa O. title: Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery date: 2009-10-27 words: 20235 flesch: 41 summary: A study to understand the components of the eIF4F complex that are required for translation of viral mRNAs has recently demonstrated that influenza virus translation has no requirement for eIF4E, as viral mRNAs are translated in cells depleted of eIF4E and in cells treated with rapamycin. 48 Members of several different families of RNA viruses are able to bypass the canonical, cap-dependent, translation initiation process by employing this strategy of internal initiation of protein synthesis. keywords: binding; cells; cellular; cleavage; complex; eif4e; expression; host; host translation; human; infected; infection; ires; kinase; mechanisms; mrnas; pabp; phosphorylation; pkr; protein; protein synthesis; ribosomal; ribosome; rna; sequence; site; translation; translation initiation; virus; viruses cache: cord-320713-b37c8aye.txt plain text: cord-320713-b37c8aye.txt item: #108 of 145 id: cord-323404-3mw4q7m3 author: Bomsel, Morgane title: Entry of viruses through the epithelial barrier: pathogenic trickery date: 2003 words: 8113 flesch: 32 summary: (3) mediates rotavirus cell entry RGD and other recognition sequences for integrins Integrin α 3 β 1 (CD 49c/29) is a cellular receptor for Kaposi's sarcoma-associated herpesvirus (KSHV/HHV-8) entry into the target cells VLA-2 (α 2 β 1 ) integrin promotes rotavirus entry into cells but is not necessary for rotavirus attachment Rotavirus contains integrin ligand sequences and a disintegrin-like domain that are implicated in virus entry into cells Entry of rotaviruses is a multistep process Adenovirus endocytosis via α (v) integrins requires phosphoinositide-3-OH kinase Internalization of echovirus 1 in caveolae Viral evolution toward change in receptor usage: adaptation of a major group of human rhinovirus to grow in ICAM-1-negative cells This characterization of the cellular function of the coxsackievirus and adenovirus receptor (CAR) sheds light on the polarity of the entry of these viruses Entry of α-herpesviruses mediated by poliovirus receptor-related protein 1 and poliovirus receptor Coronavirus infection of polarized epithelial cells Quaternary structure of coronavirus spikes in complex with carcinoembryonic antigen-related cell adhesion molecule cellular receptors Assymetric budding of viruses in epithelial cells: a model system for study of epithelial polarity Interaction of the poliovirus receptor with poliovirus Endocytic traffic in polarized epithelial cells: role of the actin and microtubule cytoskeleton GPI-anchored proteins are delivered to recycling endosomes via a distinct cdc42-regulated, clathrinindependent pinocytic pathway Conversion by Peyer's patch lymphocytes of human enterocytes into M cells that transport bacteria The role of cell-to-cell transmission in HIV infection Cell-to-cell contact as an efficient mode of Epstein-Barr virus infection of diverse human epithelial cells Biological parameters of HIV-1 infection in primary intestinal lymphocytes Constitutive expression of stromal derived factor-1 by mucosal epithelia Intercellular trafficking and protein delivery by a herpesvirus structural protein Role of tight junctions of polarized epithelial MDCK cells in the replication of herpes simplex virus type 1 The spread of herpes simplex virus type 1 from trigeminal neurons to the murine cornea: an immunoelectron microscopy study Neutrophil chemotaxis induced by corneal epithelial cells after herpes simplex virus type 1 infection Human cytomegalovirus infects Caco-2 intestinal epithelial cells basolaterally regardless of the differentiation state Patterned entry and egress by Epstein-Barr virus in polarized CR2-positive epithelial cells Epstein-Barr virus gH is essential for penetration of B cells but also plays a role in attachment of virus to epithelial cells Vaccinia virus preferentially enters polarized epithelial cells through the basolateral surface Specific interaction of HIV-1 and HIV-2 surface envelope glycoproteins with monolayers of galactosylceramide and ganglioside GM3 Respiratory syncytial virus induces selective production of the chemokine RANTES by upper airway epithelial cells Respiratory syncytial virus with the fusion protein as its only viral glycoprotein is less dependent on cellular glycosaminoglycans for attachment than complete virus Immunocytochemical colocalization of specific immunoglobulin A with Sendai virus protein in infected polarized epithelium Polarized budding of measles virus is not determined by viral surface glycoproteins Measles virus matrix protein specifies apical virus release and glycoprotein sorting in epithelial cells Identification of the α 6 integrin as a candidate receptor for papillomaviruses Influenza virus assembly and lipid raft microdomains: a role for the cytoplasmic tails of the spike glycoproteins Vesicular stomatitis virus glycoprotein does not determine the site of virus release in polarized epithelial cells Rotavirus infection induces cytoskeleton disorganization in human intestinal epithelial cells: implication of an increase in intracellular calcium concentration Rotavirus infection of cultured intestinal epithelial cells induces secretion of CXC and CC chemokines Reovirus receptors and apoptosis Identification of carbohydrate-binding domains in the attachment proteins of type 1 and type 3 reoviruses Retargeting the coxsackievirus and adenovirus receptor to the apical surface of polarized epithelial cells reveals the glycocalyx as a barrier to adenovirus-mediated gene transfer Basolateral localization of fiber receptors limits adenovirus infection from the apical surface of airway epithelia Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor Inhibition of clathrin-dependent endocytosis has multiple effects on human rhinovirus serotype 2 cell entry A novel membrane protein is a mouse mammary tumor virus receptor Coronaviruses in polarized epithelial cells Infection of polarized epithelial cells with enteric and respiratory tract bovine coronaviruses and release of virus progeny Mouse hepatitis virus strain A59 is released from opposite sides of different epithelial cell types Antigenic and molecular analyses reveal that the equine rotavirus strain H-1 is closely related to porcine, but not equine, rotaviruses: interspecies transmission from pigs to horses? As such, almost all viruses interact with epithelial cells, and make use of the normal epithelial signalling and trafficking pathways of the host cell. keywords: attachment; cell; entry; epithelial; host; human; infection; integrin; membrane; protein; receptor; surface; virus; viruses cache: cord-323404-3mw4q7m3.txt plain text: cord-323404-3mw4q7m3.txt item: #109 of 145 id: cord-325230-3kg4oe4g author: Agol, Vadim I. title: Viral security proteins: counteracting host defences date: 2010-11-09 words: 8721 flesch: 30 summary: At the same time, however, there is a certain division of labour between viral proteins. The reasons for this variability are poorly understood, although receptor compatibility and effects on viral protein and RNA synthesis that are caused by differences in the availability of host factors are surely important contributors. keywords: cardiovirus; disease; host; interferon; leader; picornavirus; poliovirus; proteins; replication; rna; security; security proteins; translation; virus; viruses cache: cord-325230-3kg4oe4g.txt plain text: cord-325230-3kg4oe4g.txt item: #110 of 145 id: cord-325626-r7k7u7ro author: Yu, Xia title: SARS-CoV-2 viral load in sputum correlates with risk of COVID-19 progression date: 2020-04-23 words: 797 flesch: 48 summary: Whether there is correlation between viral load and disease severity has not been clarified. Viral load is indicated by the Ct value of RT-PCR assay. keywords: load; patients cache: cord-325626-r7k7u7ro.txt plain text: cord-325626-r7k7u7ro.txt item: #111 of 145 id: cord-325750-x7jpsnxg author: Mokili, John L title: Metagenomics and future perspectives in virus discovery date: 2012-01-20 words: 8747 flesch: 36 summary: No association of xenotropic murine leukemia virus-related viruses with prostate cancer Reliability and reproducibility issues in DNA microarray measurements Efficient isolation of genes differentially expressed on cellulose by suppression subtractive hybridization in Agaricus bisporus Virus discovery by sequenceindependent genome amplification Suppression subtraction hybridization (SSH) and macroarray techniques reveal differential gene expression profiles in brain of sea bream infected with nodavirus Suppression subtractive hybridization: a versatile method for identifying differentially expressed genes Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi's sarcoma A novel DNA virus (TTV) associated with elevated transaminase levels in posttransfusion hepatitis of unknown etiology Identification of two flavivirus-like genomes in the GB hepatitis agent STAT1-dependent innate immunity to a Norwalk-like virus Sequence-independent, single-primer amplification (SISPA) of complex DNA populations Metagenomics and the molecular identification of novel viruses Viruses in the faecal microbiota of monozygotic twins and their mothers Hepatitis E virus (HEV): the novel agent responsible for enterically transmitted non-A, non-B hepatitis The isolation and characterization of a Norwalk virus-specific cDNA Identification of a novel astrovirus (astrovirus VA1) associated with an outbreak of acute gastroenteritis Detection of a novel astrovirus in brain tissue of mink suffering from shaking mink syndrome by use of viral metagenomics A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species Laboratory procedures to generate viral metagenomes An excellent compilation of standard operating procedures to perform metagenomic analysis on different types of samples The marine viromes of four oceanic regions Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses Viral diversity and dynamics in an infant gut RNA viral community in human feces: prevalence of plant pathogenic viruses Viral communities associated with healthy and bleaching corals Metagenomic analysis of stressed coral holobionts Assembly of viral metagenomes from yellowstone hot springs Using pyrosequencing to shed light on deep mine microbial ecology Microbes and health sackler colloquium: metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity Extraction of high molecular weight genomic DNA from soils and sediments Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification Assessment of whole genome amplification-induced bias through highthroughput, massively parallel whole genome sequencing Whole transcriptome amplification for gene expression profiling and development of molecular archives Single virus genomics: a new tool for virus discovery Flow cytometric detection of viruses DNA sequencing with chainterminating inhibitors Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses Arbovirus detection in insect vectors by rapid, highthroughput pyrosequencing Isolation and characterization of Solenopsis invicta virus 3, a new positive-strand RNA virus infecting the red imported fire ant, Solenopsis invicta A new arenavirus in a cluster of fatal transplant-associated diseases Genomic and phylogenetic characterization of Merino Walk virus, a novel arenavirus isolated in South Africa Parallel tagged sequencing on the 454 platform Targeted high-throughput sequencing of tagged nucleic acid samples The history of pyrosequencing A new method of sequencing DNA The not so universal tree of life or the place of viruses in the living world Reasons to include viruses in the tree of life Viral genomes are part of the phylogenetic tree of life There is no such thing as a tree of life (and of course viruses are out!) In this article, we review virus discovery techniques with a focus on metagenomic approaches that employ high-throughput sequencing technologies to characterize novel viruses. keywords: analysis; approach; characterization; culture; discovery; disease; dna; human; identification; koch; metagenomic; methods; molecular; novel; samples; sequence; sequencing; virus discovery; viruses cache: cord-325750-x7jpsnxg.txt plain text: cord-325750-x7jpsnxg.txt item: #112 of 145 id: cord-326273-6rp12py3 author: Chow, Kuan-Chih title: Detection of Severe Acute Respiratory Syndrome–Associated Coronavirus in Pneumocytes of the Lung date: 2004-04-01 words: 3212 flesch: 36 summary: However, the target cells of SARS viral infection have not been characterized in detail. Nevertheless, the target cells of SARS viral infection and the essence of multinucleated giant cells are not well characterized. keywords: cells; hybridization; infection; lung; sars; signal; virus cache: cord-326273-6rp12py3.txt plain text: cord-326273-6rp12py3.txt item: #113 of 145 id: cord-327444-y2464gjh author: Wilson, M.R. title: Meningitis, Viral date: 2014-05-01 words: 3379 flesch: 37 summary: Older data suggest that HSV-2 accounts for 2-3% of viral meningitis cases. This article provides an overview of the pathogenesis, epidemiology, causes, clinical presentation, laboratory diagnosis, and treatment of the most common causes of viral meningitis in the United States. keywords: agents; cases; cause; csf; infection; meningitis; patients; virus cache: cord-327444-y2464gjh.txt plain text: cord-327444-y2464gjh.txt item: #114 of 145 id: cord-328259-3g4klpyg author: Guajardo-Leiva, Sergio title: Metagenomic Insights into the Sewage RNA Virosphere of a Large City date: 2020-09-21 words: 7642 flesch: 43 summary: Viral sequences can also be misannotated to homologous cellular genes [36, 39] , which relies on the low number and diversity of viral sequences in the databases. Viral sequences identified as Partitiviridae-like viruses included in the unclassified RNA viruses ShiM-2016 category in the NCBI taxonomy (~25% abundance; Figure 2B ) and Totiviriade family were also highly abundant in treated and untreated sewage samples from the EU keywords: abundance; database; family; figure; human; ncbi; proteins; rdrp; rna; rotavirus; samples; sequences; sewage; trebal; viral; viruses; wastewater cache: cord-328259-3g4klpyg.txt plain text: cord-328259-3g4klpyg.txt item: #115 of 145 id: cord-329162-6w8qcv1c author: Ayginin, Andrey A. title: The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels date: 2018-08-12 words: 4840 flesch: 44 summary: The software BLAST was then employed to first compare the representative sequences (RS) against virus-only nucleotide and protein databases that were collected by selection of virus sequences from GenBank NT and GenBank NR databases, respectively, to identify viral nucleotide candidate RS (nRS) and protein candidate RS (pRS) with E-value cutoffs of 10 -5 and 10 -3 , respectively. We also observed a considerable number of viral reads corresponding to various genera in some samples (B27, B46, B49, B58, B66, and B69), despite the absence of specific primers in the panel for their enrichment. keywords: detection; enrichment; genus; number; panel; pcr; primer; reads; samples; sequences; sequencing; viruses cache: cord-329162-6w8qcv1c.txt plain text: cord-329162-6w8qcv1c.txt item: #116 of 145 id: cord-329306-p5wmqmvj author: Kim, Kiwook title: Rhinovirus Associated Severe Respiratory Failure in Immunocompetent Adult Patient date: 2014-09-30 words: 1019 flesch: 28 summary: Although polymerase chain reaction (PCR) methods have enhanced the detection of respiratory viral infection, PCR cannot help distinguish between with patchy consolidations in the whole lung field, but pleural effusion was not present (Figure 2 ). Second, chronic alcoholic ingestion could be a major immune modulator for respiratory viral infection, apart from alcoholic liver damage. keywords: adults; infection; pneumonia; rhinovirus cache: cord-329306-p5wmqmvj.txt plain text: cord-329306-p5wmqmvj.txt item: #117 of 145 id: cord-329710-vqorb6j7 author: Kumar, Krishna title: Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment date: 2020-05-27 words: 2481 flesch: 42 summary: By discussing the current inventory of viral inhibitors, we identify molecular scaffolds that may be improved by medicinal chemistry efforts for effective therapeutics to treat current and future coronavirus-caused diseases. Given that approximately a quarter of human proteases are predicted to belong to this class, design of specific viral inhibitors remains a challenge. keywords: coronavirus; cov-2; covid-19; helicase; host; inhibitors; sars cache: cord-329710-vqorb6j7.txt plain text: cord-329710-vqorb6j7.txt item: #118 of 145 id: cord-330200-l6bnxi40 author: Huang, Jianping title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study date: 2020-04-27 words: 4480 flesch: 55 summary: In addition, the seropositive rate for anti-S and anti-RBD IgM was significantly higher in viral RNA long persistence patients. Anti-RBD IgM and IgG levels, including anti-RBD IgM levels at presentation and peak time, were significantly higher in viral RNA short persistence patients than in long persistence patients. keywords: anti; cov-2; igm; patients; preprint; rna; sars cache: cord-330200-l6bnxi40.txt plain text: cord-330200-l6bnxi40.txt item: #119 of 145 id: cord-330684-3hxau5vt author: Richard, A title: Caspase cleavage of viral proteins, another way for viruses to make the best of apoptosis date: 2012-03-08 words: 4761 flesch: 36 summary: There are clear evidences concerning the relevance of viral protein caspase cleavages in the physiology of viruses ( Figure 1) . Based on the well-described case of AMDV, we can In some cases, apoptosis induction by the host cell leads to exactly what is expected, namely viral attenuation, but surprisingly with the help of viral protein cleavages. keywords: apoptosis; caspase; cell; cleavage; infection; ns1; p35; protein; virus; viruses cache: cord-330684-3hxau5vt.txt plain text: cord-330684-3hxau5vt.txt item: #120 of 145 id: cord-331673-xv1tcugl author: Reina, Giacomo title: Hard Nanomaterials in Time of Viral Pandemics date: 2020-07-15 words: 15723 flesch: 39 summary: Different functionalized CDs were prepared to hamper host cell viral entry. Overall, graphene materials have shown a good capacity to block host cell viral entry. keywords: activity; agents; agnps; cells; drug; effect; entry; fullerene; hiv; hnms; host; host cells; immune; infection; influenza; inhibition; interaction; mechanism; nanoparticles; replication; response; silver; surface; virus; viruses; vitro cache: cord-331673-xv1tcugl.txt plain text: cord-331673-xv1tcugl.txt item: #121 of 145 id: cord-332632-u2ud0vmq author: Lussi, Carmela title: What can pestiviral endonucleases teach us about innate immunotolerance? date: 2016-03-17 words: 8710 flesch: 36 summary: The replicative intermediate molecule of bovine viral diarrhoea virus contains multiple nascent strands Characterization of RNA synthesis during a one-step growth curve and of the replication mechanism of bovine viral diarrhoea virus Properties of the bovine viral diarrhoea virus replicase in extracts of infected MDBK cells Doublestranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses Role of doublestranded RNA and N pro of classical swine fever virus in the activation of monocyte-derived dendritic cells The viral RNase E rns prevents IFN type-I triggering by pestiviral single-and doublestranded RNAs Morphogenesis of pestiviruses: new insights from ultrastructural studies of strain giraffe-1 A cellular Jdomain protein modulates polyprotein processing and cytopathogenicity of a pestivirus The double-stranded RNA-induced apoptosis pathway is involved in the cytopathogenicity of cytopathogenic Bovine viral diarrhea virus Intracellular detection of viral nucleic acids BVDV: a pestivirus inducing tolerance of the innate immune response Self and nonself manipulation of interferon defense during persistent infection: bovine viral diarrhea virus resists alpha/beta interferon without blocking antiviral activity against unrelated viruses replicating in its host cells Classical swine fever virus N pro limits type I interferon induction in plasmacytoid dendritic cells by interacting with interferon regulatory factor 7 The amino-terminal domain of bovine viral diarrhea virus N pro protein is necessary for alpha/beta interferon antagonism RNasedependent inhibition of extra-but not intracellular, dsRNA-induced IFN synthesis by E rns of pestiviruses Classical swine fever virus interferes with cellular antiviral defense: evidence for a novel function of N pro No love lost between viruses and interferons Interferons and viruses: an evolutionary arms race of molecular interactions Microbial sensing by toll-like receptors and intracellular nucleic acid sensors, Cold Spring Harbor Perspect Viral RNA detection by RIG-I-like receptors Identification of the role of RIG-I, MDA-5 and TLR3 in sensing RNA viruses in porcine epithelial cells using lentivirus-driven RNA interference Efficient sensing of infected cells in absence of virus particles by plasmacytoid dendritic cells is blocked by the viral ribonuclease E rns Fc gamma RII-dependent sensitisation of natural interferonproducing cells for viral infection and interferon-alpha responses Extracellular dsRNA: its function and mechanism of cellular uptake Autophagydependent viral recognition by plasmacytoid dendritic cells Autophagy during early stages contributes to bovine viral diarrhea virus replication in MDBK cells N pro expressed in virus infected cells is responsible for polyubiquitinylation and proteasomal degradation of the transcription factor IRF-3 in an as yet unknown manner but without requiring its proteolytic activity. keywords: acids; activation; bovine; cells; dsrna; e rns; host; ifn; infection; rna; rnase; rns; self; type; virus; viruses cache: cord-332632-u2ud0vmq.txt plain text: cord-332632-u2ud0vmq.txt item: #122 of 145 id: cord-334010-gxu0refq author: Banerjee, Nilotpal title: Viral glycoproteins: biological role and application in diagnosis date: 2016-01-18 words: 6667 flesch: 42 summary: During maturation from host cell viruses have Viral glycoproteins: biological role and application in diagnosis 7 host glycoproteins on their surface to avoid the immunity of the host. NS1) University of Texas Medical Branch at Galveston Dengue vaccines: challenges, development, current status and prospects Cellular and humoral immunity to varicella zoster virus glycoproteins in immune and susceptible human subjects Human arbovirus infections worldwide Dengue viral infections Influenza, epidemiology and prevention of vaccine-preventable diseases Carbohydrates of human immunodeficiency virus Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for Probing virus-glycan interactions using glycan microarrays Chikungunya: a bending reality Evaluation of a dengue NS1 antigen detection assay sensitivity and specificity for the diagnosis of acute dengue virus infection Glycan receptor for influenza virus Approaches for the development of rapid serological assays for surveillance and diagnosis of infections caused by zoonotic flaviviruses of the japanese encephalitis virus serocomplex Fatal cases of Chikungunya virus infection in Colombia: diagnostic and treatment challenges Development of global consensus of dengue virus envelope glycoprotein for epitopes based vaccine design Influenza Symptoms and the Role of Laboratory Diagnostics, Health Professionals, Seasonal. keywords: cell; dengue; diagnosis; ebola; envelope; glycan; glycoproteins; hiv; host; human; infection; influenza; role; virus; viruses cache: cord-334010-gxu0refq.txt plain text: cord-334010-gxu0refq.txt item: #123 of 145 id: cord-334127-wjf8t8vp author: Brister, J. Rodney title: NCBI Viral Genomes Resource date: 2015-01-28 words: 3865 flesch: 25 summary: Given the difficulty of implementing a purely well annotated representation of viral genome sequences, the viral RefSeq model has evolved into a more flexible approach that includes both reference and representative sequences. The growing cloud of viral genome sequences also poses significant barriers to the maintenance of reference genome records. keywords: data; genome; records; reference; refseq; resource; sequence; species; taxonomy; virus; viruses cache: cord-334127-wjf8t8vp.txt plain text: cord-334127-wjf8t8vp.txt item: #124 of 145 id: cord-337361-salby0fu author: Bujarski, Jozef J. title: Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives date: 2013-03-26 words: 6867 flesch: 30 summary: From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented. keywords: bmv; events; factors; genome; host; mechanisms; plant; recombination; replicase; replication; rna; rnas; sequences; viral; virus; viruses cache: cord-337361-salby0fu.txt plain text: cord-337361-salby0fu.txt item: #125 of 145 id: cord-337636-3yc0ribg author: Morehouse, Zachary P. title: A novel two-step, direct-to-PCR method for virus detection off swabs using human coronavirus 229E date: 2020-08-25 words: 2981 flesch: 43 summary: Herein, we are proposing a novel method for viral pathogen detection off swabs as an improvement or alternative to the current PCR based assays commonly used for viral detection This novel two-step, directto-PCR method for viral detection off swabs has shown a lower limit of reliable detection at 1.2 × 10 3 viral copies/mL with 96.30% sensitivity in vitro when screening for HcoV-229E. Herein, we have demonstrated the success of this methodology in vitro and propose it as a novel approach to viral detection that allows for decrease run time in comparison to traditional PCR based viral detection assay protocols, as well as a reduction in the materials needed for successful viral detection. keywords: copies; detection; methodology; pcr; swabs; virus cache: cord-337636-3yc0ribg.txt plain text: cord-337636-3yc0ribg.txt item: #126 of 145 id: cord-337673-1nau263l author: Wu, Chang-Jer title: Antiviral applications of RNAi for coronavirus date: 2006-01-24 words: 4333 flesch: 45 summary: The final structural protein, N protein, with a molecular mass of 50 -60 kDa, probably associates with viral RNA to form a long and flexible helical nucleocapsid These plasmids were also able to block viral replication, as shown by both the titre and levels of viral RNA and protein. keywords: cells; coronavirus; cov; expression; gene; protein; rna; rnai; sars; sirna; virus cache: cord-337673-1nau263l.txt plain text: cord-337673-1nau263l.txt item: #127 of 145 id: cord-338083-77re4l0w author: Bolin, Steven R. title: Origination and consequences of bovine viral diarrhea virus diversity date: 2005-03-04 words: 6749 flesch: 39 summary: The causative agent of BVD: its epidemiology and pathogenesis Thrombocytopenia and hemorrhages in veal calves infected with bovine viral diarrhea virus Thrombocytopenia associated with acute bovine virus diarrhea infection in cattle Phylogenetic, antigenic and clinical characterization of type 2 BVDV from North America Immunology of bovine viral diarrhea virus Differences in virulence between two noncytopathic bovine viral diarrhea viruses in calves The effect of different bovine viral diarrhea virus genotypes and biotypes on the metabolic activity and activation status of bovine peripheral blood mononuclear cells Relationship between degree of viremia and disease manifestation in calves with experimentally induced bovine viral diarrhea virus infection Comparative virulence of isolates of bovine viral diarrhea virus type II in experimentally inoculated sixto nine-month-old calves Role of bovine viral diarrhea virus in the bovine respiratory disease complex Experimental production of bovine respiratory tract disease with bovine viral diarrhea virus Effect of bovine viral diarrhea virus infection on the distribution of infectious bovine rhinotracheitis virus in calves Effect of concurrent experimentally induced bovine respiratory syncytial virus and bovine viral diarrhea virus infection on respiratory tract and enteric diseases in calves Comparison of the pneumopathogenicity of two strains of bovine viral diarrhea virus Differences in experimental virulence of bovine viral diarrhoea viral strains isolated from haemorrhagic syndromes Development of a fetal challenge method for the evaluation of bovine viral diarrhea virus vaccines Variation in neuropathogenicity in sheep fetuses transplacentally infected with non-cytopathogenic and cytopathogenic biotypes of bovine-virus diarrhoea virus BVDV fetal infection with selected isolates. Bovine viral diarrhea virus infections also have been associated with concurrent salmonellosis, Escherichia coli, bovine papular stomatitis, rotavirus, and coronavirus infections. keywords: bovine; bvdv; cattle; diarrhea; disease; infection; isolates; rna; type; viral; virus; viruses cache: cord-338083-77re4l0w.txt plain text: cord-338083-77re4l0w.txt item: #128 of 145 id: cord-338804-nreqluol author: Heise, M.T. title: Viral Pathogenesis date: 2014-11-28 words: 6419 flesch: 22 summary: Though there is evidence that the host immune response exacerbates virus induced disease during both Sindbis virus and VEE infection (Rowell and Griffin, 2002; Kimura and Griffin, 2003; Charles et al., 2001) , in the case of VEE, mice lacking a functional adaptive immune system still succumb to virus-induced disease (Charles et al., 2001) , suggesting the direct cell killing by the virus contributes to disease pathogenesis. These results further reinforce the idea that virus receptor interactions play a crucial role in determining whether the virus can efficiently infect the host and ultimately cause disease. keywords: cell; disease; host; immune; infection; interactions; interferon; type; virus; viruses cache: cord-338804-nreqluol.txt plain text: cord-338804-nreqluol.txt item: #129 of 145 id: cord-339288-y8woqsii author: Tews, Birke Andrea title: Self-Replicating RNA date: 2016-06-11 words: 7569 flesch: 38 summary: Due to the technical difficulties, RNA is not amenable to site specific manipulation so that reverse genetics systems for RNA viruses always rely on a cDNA intermediate The history of reverse genetic systems for positive strand RNA viruses highlights the pitfalls that may be encountered in the design of a reverse genetic system and show solutions how to circumvent these difficulties. keywords: cdna; cells; end; genome; replication; rna; sequences; strand; transcription; translation; vaccine; virus; viruses cache: cord-339288-y8woqsii.txt plain text: cord-339288-y8woqsii.txt item: #130 of 145 id: cord-340423-f8ab7413 author: Barr, J.N. title: Genetic Instability of RNA Viruses date: 2016-09-09 words: 9780 flesch: 40 summary: Sequence analysis of RNA virus genomes has revealed that they preferentially accumulate A-to-G transitions, which are characteristic hallmarks of ADAR activity. Because the majority of nucleotide changes in RNA virus genomes are either strongly deleterious or lethal, the population is perpetually refined as deleterious genomes become purged through selection, leaving only mutations with phenotypically neutral or advantageous consequences to persist [69, 70] . keywords: cell; cycle; fidelity; genome; host; infection; mutation; polymerase; rate; recombination; replication; rna; rna viruses; robustness; viruses cache: cord-340423-f8ab7413.txt plain text: cord-340423-f8ab7413.txt item: #131 of 145 id: cord-342133-khrljehj author: Principi, Nicola title: Bocavirus Infection in Otherwise Healthy Children with Respiratory Disease date: 2015-08-12 words: 5125 flesch: 44 summary: respiratory viral panel fast for diagnosis of respiratory virus infections MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods Datamonkey: 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 Adaptation to different human populations by HIV-1 revealed by codon-based analyses Detecting individual sites subject to episodic diversifying selection Seroepidemiology of human bocavirus in Hokkaido prefecture Seroepidemiology of human bocavirus infection in Jamaica Human bocavirus: a novel parvovirus epidemiologically associated with pneumonia requiring hospitalization in Thailand Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children Human bocavirus in children: mono-detection, high viral load and viraemia are associated with respiratory tract infection Human bocavirus detection in nasopharyngeal aspirates of children without clinical symptoms of respiratory infection Human bocavirus infections in hospitalized children and adults Detection of bocavirus in saliva of children with and without respiratory illness Human bocavirus 1 primary infection and shedding in infants Single detection of human bocavirus 1 with a high viral load in severe respiratory tract infections in previously healthy children Human bocavirus detection in an atopic child affected by pneumonia associated with wheezing Detection of human bocavirus in hospitalised children Human bocavirus in children suffering from acute lower respiratory tract infection in Beijing Children's Hospital Clinical characteristics of human bocavirus infections compared with other respiratory viruses in Spanish children Role of human metapneumovirus, human coronavirus NL63 and human bocavirus in infants and young children with acute wheezing Role of emerging respiratory viruses in children with severe acute wheezing Etiology of bronchiolitis in a hospitalized pediatric population: prospective multicenter study Absence of humanbocavirus in bronchoalveolar lavage fluid of lung transplant patients Neurological manifestations in acute onset of viral gastroenteritis Frequency and clinical relevance of human bocavirus infection in acute exacerbations of chronic obstructive pulmonary disease Human bocavirus in children: mono-detection, high viral load and viraemia are associated with respiratory tract infection Human bocavirus in patients with respiratory tract infection Comorbidity and high viral load linked to clinical presentation of respiratory human bocavirus infection Frequent and prolonged shedding of bocavirus in young children attending daycare Correlation between nucleotide mutation and viral loads of human bocavirus 1 in hospitalized children with respiratory tract infection Phospholipase A2-like activity of human bocavirus VP1 unique region Human bocavirus amongst an allages population hospitalised with acute lower respiratory infections in Cambodia Complete coding sequences and phylogenetic analysis of Human Bocavirus (HBoV) Human bocavirus capsid structure: insights into the structural repertoire of the parvoviridae Evolutionary relationships among parvoviruses: virus-host coevolution among autonomous primate parvoviruses and links between adeno-associated and avian parvoviruses Epidemic and molecular evolution of human bocavirus in hospitalized children with acute respiratory tract infection Rapid molecular evolution of human bocavirus revealed by Bayesian coalescent inference The study patients were classified into disease groups (i.e., acute otitis media, rhinosinusitis, pharyngitis, croup, infectious wheezing, acute bronchitis, pneumonia) on the basis of signs and/or symptoms using well-established criteria and were finally subdivided into two subgroups: upper (URTIs) and lower respiratory tract infections (LRTIs) keywords: acid; amino; bocavirus; children; disease; hbov; infection; load; samples; strains; study; tract cache: cord-342133-khrljehj.txt plain text: cord-342133-khrljehj.txt item: #132 of 145 id: cord-342660-xigv4u3f author: Benotmane, I. title: In-depth virological assessment of kidney transplant recipients with COVID-19 date: 2020-06-19 words: 2502 flesch: 49 summary: Moreover, viral loads were not related to inflammatory markers that have been previously associated with COVID-19 severity.8 Reports on the relationship between viral load and disease severity are contradictory; three studies showed no correlation between the severity of the disease and the viral load in respiratory specimens,6,7,9 However, data on viral loads and antibody kinetics in immunocompromised populations are lacking. keywords: author; funder; medrxiv; perpetuity; preprint cache: cord-342660-xigv4u3f.txt plain text: cord-342660-xigv4u3f.txt item: #133 of 145 id: cord-343377-6muareue author: Kidszun, André title: Viral Infections in Neonates with Suspected Late-Onset Bacterial Sepsis—A Prospective Cohort Study date: 2016-05-16 words: 2357 flesch: 41 summary: 27 Funding None. Prevention of nosocomial infections in the neonatal intensive care unit Development of a surveillance system for nosocomial infections: the component for neonatal intensive care units in Germany Molecular detection of lateonset neonatal sepsis in premature infants using small blood volumes: proof-of-concept Nosocomial infections in very low birthweight infants in Germany: current data from the National Surveillance System NEO-KISS Hospital-acquired viral pathogens in the neonatal intensive care unit Clinical and epidemiologic characteristics of viral infections in a neonatal intensive care unit during a 12-year period Nosocomial rhinovirus infection in preterm infants Pandemic A/H1N1(2009) influenza infections in very-low-birth-weight infants-a case series from the German Neonatal Network Human rhinovirus causes severe infection in preterm infants Respiratory viral infections are not uncommon in neonatal intensive care units Viral outbreaks in neonatal intensive care units: what we do not know Medical and economic impact of a respiratory syncytial virus outbreak in a neonatal intensive care unit The role of multiplex PCR in respiratory tract infections in children Detection of multiple respiratory pathogens during primary respiratory infection: nasal swab versus nasopharyngeal aspirate using real-time polymerase chain reaction Detection of respiratory viral infections in neonates treated for suspicion of nosocomial bacterial sepsis: a feasibility study Viral respiratory tract infections in the neonatal intensive care unit: the VIRIoN-I study Unrecognized viral respiratory tract infections in premature infants during their birth hospitalization: a prospective surveillance study in two neonatal intensive care units Validation of a multiplex reverse transcriptase PCR ELISA for the detection of 19 respiratory tract pathogens Viral respiratory tract infections in the Neonatal Intensive Care Unit Viral infections of the lower respiratory tract: old viruses, new viruses, and the role of diagnosis Predominance of rhinovirus in the nose of symptomatic and asymptomatic infants Clinical utility of PCR for common viruses in acute respiratory illness Association of respiratory picornaviruses with acute bronchiolitis in French infants Prebiotic and probiotic supplementation prevents rhinovirus infections in preterm infants: a randomized, placebo-controlled trial A host-based RT-PCR gene expression signature to identify acute respiratory viral infection Human parechovirus infection in neonatal intensive care 5ICCN_006: Viral infections in neonates with suspected nosocomial bacterial sepsis Viral Infections in Neonates Kidszun et None. Respiratory viral infections did not occur in clusters in the NICU and none of the virus-positive infants had been discharged home previously. keywords: infants; infections; sepsis; study; virus cache: cord-343377-6muareue.txt plain text: cord-343377-6muareue.txt item: #134 of 145 id: cord-343470-w215pzdc author: Tsai, Kevin title: Epigenetic and epitranscriptomic regulation of viral replication date: 2020-06-12 words: 9796 flesch: 31 summary: Whereas cellular gene expression may be either enhanced or inhibited by specific epigenetic modifications deposited on histones (in particular, histone H3), these epigenetic modifications can also repress viral gene expression, potentially functioning as a potent antiviral innate immune response in DNA virus-infected cells. By contrast, the various covalent modifications added to RNAs, termed epitranscriptomic modifications, can positively regulate mRNA translation and/or stability, and both DNA and RNA viruses have evolved to utilize epitranscriptomic modifications as a means to maximize viral gene expression. keywords: cells; chromatin; dna; expression; gene; histone; host; ifi16; infection; modifications; pml; proteins; replication; residues; rna; virus; viruses cache: cord-343470-w215pzdc.txt plain text: cord-343470-w215pzdc.txt item: #135 of 145 id: cord-345168-3w32v2fm author: To, Kelvin K.W. title: Viral load in patients infected with pandemic H1N1 2009 influenza A virus date: 2009-11-30 words: 3778 flesch: 44 summary: Comparison was made between patients with pandemic H1N1 virus and seasonal influenza virus infection regarding their demographics, underlying diseases, presenting symptoms, total white blood cell counts, absolute lymphocyte counts, and initial pre-treatment viral load in respiratory specimens on the day of diagnosis. Coughing, vomiting, diarrhea, and duration of symptoms before diagnosis were significantly different between patients with pandemic H1N1 virus and seasonal influenza virus infection (Table I) . keywords: h1n1; influenza; load; patients; symptoms; virus cache: cord-345168-3w32v2fm.txt plain text: cord-345168-3w32v2fm.txt item: #136 of 145 id: cord-346290-my8ow5ee author: Nelson, Philipp P. title: Respiratory Viral Pathogens date: 2020-05-28 words: 4163 flesch: 37 summary: Respiratory virus infection causes an increase in both vascular permeability mediated by vasoactive amines and glandular secretion under the influence of cholinergic reflexes and neuropeptides. Human parainfluenza viruses (HPIVs) are respiratory viruses in the family of Paramyxoviridae. keywords: et al; genome; genus; host; human; infections; influenza; protein; respiratory; viruses cache: cord-346290-my8ow5ee.txt plain text: cord-346290-my8ow5ee.txt item: #137 of 145 id: cord-346916-jj4l9ydl author: Girardi, Erika title: Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell date: 2020-08-23 words: 13150 flesch: 37 summary: genomic RNA Protein kinase r degradation is essential for rift valley fever virus infection and is regulated by SKP1-CUL1-F-box (SCF)FBXW11-NSs E3 ligase Viral encounters with 2',5'-oligoadenylate synthetase and RNase L during the interferon antiviral response New insights into the role of RNase L in innate immunity Molecular mechanisms for the adaptive switching between the OAS/RNase l and OASL/RIG-I pathways in birds and mammals Homologous 2',5'-phosphodiesterases from disparate RNA viruses antagonize antiviral innate immunity Attacked from all sides: RNA decay in antiviral defense The host nonsense-mediated mRNA decay pathway restricts Mammalian RNA virus replication Competing and noncompeting activities of miR-122 and the 5' exonuclease Xrn1 in regulation of hepatitis C virus replication Stabilization of hepatitis C virus RNA by an Ago2-miR-122 complex Zika virus produces noncoding RNAs using a multipseudoknot structure that confounds a cellular exonuclease The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA Full genome sequence and sfRNA interferon antagonist activity of zika virus from Recife, Brazil RNA structures required for production of subgenomic flavivirus RNA Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity An RNA pseudoknot is required for production of yellow fever virus subgenomic RNA by the host nuclease XRN1 Zika virus noncoding RNA suppresses apoptosis and is required for virus transmission by mosquitoes Noncoding flavivirus RNA displays RNA interference suppressor activity in insect and mammalian cells Viruses: overturning RNA turnover Stem-loop recognition by DDX17 facilitates miRNA processing and antiviral defense The zinc-finger antiviral protein recruits the RNA processing exosome to degrade the target mRNA CG dinucleotide suppression enables antiviral defence targeting non-self RNA KHNYN is essential for the zinc finger antiviral protein (ZAP) to restrict HIV-1 containing clustered CpG dinucleotides ZAP's stress granule localization is correlated with its antiviral activity and induced by virus replication RNA-binding activity of TRIM25 is mediated by its PRY/ SPRY domain and is required for ubiquitination TRIM25 enhances the antiviral action of zinc-finger antiviral protein (ZAP) MCPIP1 ribonuclease exhibits broad-spectrum antiviral effects through viral RNA binding and degradation MCPIP1 suppresses hepatitis C virus replication and negatively regulates virus-induced proinflammatory cytokine responses RNase L releases a small RNA from HCV RNA that refolds into a potent PAMP Activation and evasion of the antiviral 2'-5' oligoadenylate synthetase/ribonuclease L pathway by hepatitis C virus mRNA Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila Cross-species comparative analysis of Dicer proteins during Sindbis virus infection RNA interference functions as an antiviral immunity mechanism in mammals Antiviral RNA interference in mammalian cells Flavivirus induces and antagonizes antiviral RNA interference in both mammals and mosquitoes The evolution of antiviral defense systems Human virus-derived small RNAs can confer antiviral immunity in mammals Induction and suppression of antiviral RNA interference by influenza A virus in mammalian cells Viruses and RNA interference: issues and controversies No evidence for viral small RNA production and antiviral function of Argonaute 2 in human cells RNase III nucleases from diverse kingdoms serve as antiviral effectors Making the mark: the role of adenosine modifications in the life cycle of RNA viruses Innate immune restriction and antagonism of viral RNA lacking 2‫-׳‬O methylation RNA modifications: what have we learned and where are we headed? Host factors in positive-strand RNA virus genome replication Human host factors required for influenza virus replication Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens Diverse roles of host RNA binding proteins in RNA virus replication CRISPR-Cas immunity in prokaryotes Antiviral immunity directed by small RNAs Combating emerging viral threats The global distribution and burden of dengue Virus: new clinical syndromes and its emergence in the western hemisphere Emergence of a novel human coronavirus threatening human health Sensing of RNA viruses: a review of innate immune receptors involved in recognizing RNA virus invasion The innate antiviral response in animals: an evolutionary perspective from flagellates to humans Discriminating self from non-self in nucleic acid sensing Toll-like receptor control of the adaptive immune responses Toll-like receptors in antiviral innate immunity Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8 Toll-like receptor 3 is an essential component of the innate stress response in virus-induced cardiac injury Human TLR3 recognizes dengue virus and modulates viral replication in vitro Zika virus depletes neural progenitors in human cerebral organoids through activation of the innate immune receptor TLR3 Toll-like receptor 3 in viral pathogenesis: friend or foe? RIG-I-like receptors: their regulation and roles in RNA sensing 5'-Triphosphate RNA is the ligand for RIG-I RIG-I-mediated antiviral responses to single-stranded RNA bearing 5'-phosphates Recognition of 5' triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus 5'-triphosphate RNA requires base-paired structures to activate antiviral signaling via RIG-I Processing of genome 5' termini as a strategy of negative-strand RNA viruses to avoid RIG-I-dependent interferon induction Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses Cell type-specific involvement of RIG-I in antiviral response RIG-I recognizes the 5' region of dengue and Zika virus genomes Balancing act: MDA5 in Antiviral Immunity and Autoinflammation MDA5 assembles into a polar helical filament on dsRNA Enterovirus 2Apro targets MDA5 and MAVS in infected cells MDA5 detects the double-stranded RNA replicative form in picornavirus-infected cells How flaviviruses activate and suppress the interferon response MDA5 is critical to host defense during infection with murine coronavirus LGP2 is a positive regulator of RIG-I-and MDA5-mediated antiviral responses The RNA helicase Lgp2 inhibits TLR-independent sensing of viral replication by retinoic acid-inducible gene-I Loss of DExD/H box RNA helicase LGP2 manifests disparate antiviral responses The RIG-I-like receptor LGP2 inhibits Dicer-dependent processing of long double-stranded RNA and blocks RNA interference in mammalian cells DEAD-box helicases: sensors, regulators, and effectors for antiviral defense Type 1 interferons and the virus-host relationship: a lesson in détente Interferon-inducible antiviral effectors Involvement of the interferon-regulated antiviral proteins PKR and RNase L in reovirus-induced shutoff of cellular translation Doublestranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses RNA dimerization promotes PKR dimerization and activation Viral double-stranded RNAs from vaccinia virus early or intermediate gene transcripts possess PKR activating function, resulting in NF-kappaB activation, when the K1 protein is absent or mutated Regulation of innate immunity through RNA structure and the protein kinase PKR Translational control in virus-infected cells A cap-to-Tail guide to mRNA translation strategies in virus-infected cells Viral noncoding RNAs: more surprises Inhibition of the protein kinase PKR by the internal ribosome entry site of hepatitis C virus keywords: antiviral; binding; cap; cells; cellular; dsrna; factors; fig; host; infection; initiation; interactions; mrna; pkr; protein; rbps; replication; ribosome; rig; rna; rnas; translation; viral; virus; viruses; vrna cache: cord-346916-jj4l9ydl.txt plain text: cord-346916-jj4l9ydl.txt item: #138 of 145 id: cord-347731-eqxn6auk author: Garcia‐Cremades, Maria title: Optimizing Hydroxychloroquine Dosing for Patients With COVID‐19: An Integrative Modeling Approach for Effective Drug Repurposing date: 2020-05-12 words: 5438 flesch: 45 summary: 3, 9, 10 Viral kinetics were estimated from in vitro replication rate of severe acute respiratory syndrome-coronavirus (SARS-CoV)-1 and unbound drug concentration in plasma and lungs were simulated with HCQ PK model. ARTICLE Viral response to treatment was significantly associated (P < 0.001) to HCQ PK concentrations using a linear effect model ( Figure 1 and Table S1 ). keywords: data; drug; hcq; load; model; patients; qtc; treatment; viral; vitro cache: cord-347731-eqxn6auk.txt plain text: cord-347731-eqxn6auk.txt item: #139 of 145 id: cord-349358-leicos9j author: Ketzinel‐Gilad, Mali title: RNA interference for antiviral therapy date: 2006-06-16 words: 12748 flesch: 38 summary: siRNAs targeting the SARS-CoV RNA polymerase gene inhibited viral RNA replication, protein synthesis and reduced the viral cytopathic effects on Vero cells [36] . A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1 RNA interference of HIV replication Lentivirus-mediated RNA interference of DC-SIGN expression inhibits human immunodeficiency virus transmission from dendritic cells to T cells Modulating HIV-1 replication by RNA interference directed against human transcription elongation factor SPT5 Inhibition of respiratory viruses by nasally administered siRNA The promise of siRNAs for the treatment of influenza Inhibition of coxsackievirus B3 replication by small interfering RNAs requires perfect sequence match in the central region of the viral positive strand Inhibition of SARS-CoV replication by siRNA Actively replicating West Nile virus is resistant to cytoplasmic delivery of siRNA Use of RNA interference to prevent lethal murine West Nile virus infection An siRNA-based microbicide protects mice from lethal herpes simplex virus 2 infection Small interfering RNA inhibits hepatitis B virus replication in mice Short interfering RNA-directed inhibition of hepatitis B virus replication Inhibition of HBV replication by siRNA in a stable HBV-producing cell line Inhibition of hepatitis B virus expression and replication by RNA interference Inhibition of hepatitis B virus in mice by RNA interference Effective inhibition of HBV replication in vivo by anti-HBx short hairpin RNAs Knock-down of hepatitis B virus X protein reduces the tumorigenicity of hepatocellular carcinoma cells Genomic analysis of anti-hepatitis B virus (HBV) activity by small interfering RNA and lamivudine in stable HBV-producing cells Small hairpin RNAs efficiently inhibit hepatitis C IRES-mediated gene expression in human tissue culture cells and a mouse model Inhibition of hepatitis C virus translation and subgenomic replication by siRNAs directed against highly conserved HCV sequence and cellular HCV cofactors Lentiviral delivery of short hairpin RNAs protects CD4 T cells from multiple clades and primary isolates of HIV HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome Evidence that HIV-1 encodes an siRNA and a suppressor of RNA silencing HIV-1 nef suppression by virally encoded microRNA Regulation of human immunodeficiency virus 1 transcription by nef microRNA Lentiviral siRNAs targeting multiple highly conserved RNA sequences of human immunodeficiency virus type 1 Identification of cellular deoxyhypusine synthase as a novel target for antiretroviral therapy Computational design of antiviral RNA interference strategies that resist human immunodeficiency virus escape RNAi induction and activation in mammalian muscle cells where Dicer and eIF2C translation initiation factors are barely expressed RNA silencing as a plant immune system against viruses Induction and suppression of RNA silencing by an animal virus Nucleic acid-based immune system: the antiviral potential of mammalian RNA silencing Adenosine kinase inhibition and suppression of RNA silencing by geminivirus AL2 and L2 proteins Effects and side-effects of viral RNA silencing suppressors on short RNAs The coat protein of turnip crinkle virus suppresses posttranscriptional gene silencing at an early initiation step A viral protein inhibits the long range signaling activity of the gene silencing signal A viral protein suppresses RNA silencing and binds silencing-generated, 21-to 25-nucleotide double-stranded RNAs Virus-encoded suppressor of posttranscriptional gene silencing targets a maintenance step in the silencing pathway P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction Suppression of posttranscriptional gene silencing by a plant viral protein localized in the nucleus Interferon antagonist proteins of influenza and vaccinia viruses are suppressors of RNA silencing A virus-encoded inhibitor that blocks RNA interference in mammalian cells Adenovirus VA1 noncoding RNA can inhibit small interfering RNA and MicroRNA biogenesis Suppression of RNA interference by adenovirus virus-associated RNA Human immunodeficiency virus type 1 escapes from RNA interferencemediated inhibition Human immunodeficiency virus type 1 escape from RNA interference Hepatitis C virus replicons escape RNA interference induced by a short interfering RNA directed against the NS5b coding region Inhibition of hepatitis B virus gene expression by single and dual small interfering RNA treatment Expression profiling reveals off-target gene regulation by RNAi Activation of the interferon system by short-interfering RNAs Cationic liposome-mediated delivery of siRNAs in adult mice Small interfering RNAs mediate sequence-independent gene suppression and induce immune activation by signaling through toll-like receptor 3 Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA A system for stable expression of short interfering RNAs in mammalian cells Determinants of interferon-stimulated gene induction by RNAi vectors An enhanced U6 promoter for synthesis of short hairpin RNA Short hairpin type of dsRNAs that are controlled by tRNA(Val) promoter significantly induce RNAimediated gene silencing in the cytoplasm of human cells Promoter choice affects the potency of HIV-1 specific RNA interference Development and application of siRNA expression vector Conditional suppression of cellular genes: lentivirus vector-mediated drug-inducible RNA interference Short-term cytotoxic effects and longterm instability of RNAi delivered using lentiviral vectors Efficient delivery of siRNA for inhibition of gene expression in postnatal mice RNA interference in mammalian cells by chemically-modified RNA RNA interference targeting Fas protects mice from fulminant hepatitis In vivo activity of nuclease-resistant siRNAs Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate siRNA function in RNAi: a chemical modification analysis Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference Challenges for RNAi in vivo Activity of stabilized short interfering RNA in a mouse model of hepatitis B virus replication siRNA relieves chronic neuropathic pain Potent and persistent in vivo anti-HBV activity of chemically modified siRNAs Inhibition of influenza virus production in virus-infected mice by RNA interference Protection against lethal influenza virus challenge by RNA interference in vivo Atelocollagenmediated synthetic small interfering RNA delivery for effective gene silencing in vitro and in vivo Intravenous RNA interference gene therapy targeting the human epidermal growth factor receptor prolongs survival in intracranial brain cancer Recombinant viral capsids as an efficient vehicle of oligonucleotide delivery into cells Adenovirus vectormediated doxycycline-inducible RNA interference Conditionally replicating adenoviruses expressing short hairpin RNAs silence the expression of a target gene in cancer cells Inducible, reversible, and stable RNA interference in mammalian cells Cre-lox-regulated conditional RNA interference from transgenes CRE recombinase-inducible RNA interference mediated by lentiviral vectors Lentiviral vector-mediated delivery of short hairpin RNA results in persistent knockdown of gene expression in mouse brain RNAi suppresses polyglutamine-induced neurodegeneration in a model of spinocerebellar ataxia First Parkinson gene therapy trial launches Optimization of an siRNA-expression system with an improved hairpin and its significant suppressive effects in mammalian cells Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide Antisense oligonucleotides: promise and reality LNA: a versatile tool for therapeutics and genomics Rational siRNA design for RNA interference Asymmetry in the assembly of the RNAi enzyme complex Functional siRNAs and miRNAs exhibit strand bias Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNAdependent RNA polymerase Silencing SARS-CoV Spike protein expression in cultured cells by RNA interference Using siRNA in prophylactic and therapeutic regimens against SARS coronavirus in Rhesus macaque RNA interference targeting VP1 inhibits foot-and-mouth disease virus replication in BHK-21 cells and suckling mice Small interfering RNA molecules as potential anti-human rhinovirus agents: in vitro potency, specificity, and mechanism Susceptibility of human hepatitis delta virus RNAs to small interfering RNA action RNA interference against enterovirus 71 infection Inhibition of porcine endogenous retroviruses by RNA interference: increasing the safety of xenotransplantation Enhanced gene silencing of HIV-1 specific siRNA using microRNA designed hairpins Expression of small hairpin RNA by lentivirus-based vector confers efficient and stable gene-suppression of HIV-1 on human cells including primary non-dividing cells Inhibition of HIV-1 by lentiviral vector-transduced siRNAs in T lymphocytes differentiated in SCID-hu mice and CD34+ progenitor cellderived macrophages Efficient gene transfer of HIV-1-specific short hairpin RNA into human lymphocytic cells using recombinant adeno-associated virus vectors Inhibition of virus production in JC virus-infected cells by postinfection RNA interference Inhibition of the Epstein-Barr virus lytic cycle by Zta-targeted RNA interference Selective inhibition of hepatitis B virus replication by RNA interference Clearance of hepatitis B virus from the liver of transgenic mice by short hairpin RNAs Short interfering RNA-mediated inhibition of herpes simplex virus type 1 gene expression and function during infection of human keratinocytes keywords: cells; delivery; effect; expression; gene; hcv; hepatitis; hiv; human; infection; inhibition; interference; replication; rna; rna interference; rnai; silencing; sirna; specific; targeting; virus; viruses; vitro cache: cord-349358-leicos9j.txt plain text: cord-349358-leicos9j.txt item: #140 of 145 id: cord-353297-jizitnfl author: Meyer, R.F. title: Viruses and Bioterrorism date: 2008-07-30 words: 3819 flesch: 40 summary: between virus names and species names would be to change the current names of virus species into nonlatinized binomial names. Given that the common names of viruses are used repeatedly in scientific texts there is a need for abbreviating them and the ICTV has published several lists of recommended acronyms for virus names. keywords: agents; cell; disease; dna; host; names; smallpox; species; virus; viruses cache: cord-353297-jizitnfl.txt plain text: cord-353297-jizitnfl.txt item: #141 of 145 id: cord-353554-98uzivsk author: Zhang, Zheng title: Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors date: 2018-03-08 words: 2191 flesch: 55 summary: Thus, during the 408 process of searching for protein receptors, the protein with high level of glycosylation 409 could provide a basal attachment ability for the virus, and should be the preferred 410 receptor for the virus. Further correlation analysis between viral receptors and the tissue and host specificity of the virus shows that the virus receptor similarity was a significant predictor for mammalian virus cross-species. keywords: host; proteins; receptor; species; virus cache: cord-353554-98uzivsk.txt plain text: cord-353554-98uzivsk.txt item: #142 of 145 id: cord-353609-no3mbg5d author: Vandegrift, Kurt J. title: An Ecological and Conservation Perspective on Advances in the Applied Virology of Zoonoses date: 2011-04-15 words: 6927 flesch: 39 summary: Recently, it has been demonstrated that the pathogens of host populations might also be useful to this end. Unfortunately, the very characteristics that make viruses useful for estimating host population structure and demography may also impede the analyses. keywords: conservation; disease; dynamics; ecology; host; human; molecular; pathogens; population; rabies; risk; species; transmission; vaccination; viruses; wildlife cache: cord-353609-no3mbg5d.txt plain text: cord-353609-no3mbg5d.txt item: #143 of 145 id: cord-353810-mf753ae9 author: Tan, Cedric Chih Shen title: A novel method for the capture-based purification of whole viral native RNA genomes date: 2019-04-08 words: 5950 flesch: 49 summary: key: cord-353810-mf753ae9 authors: Tan, Cedric Chih Shen; Maurer-Stroh, Sebastian; Wan, Yue; Sessions, October Michael; de Sessions, Paola Florez title: A novel method for the capture-based purification of whole viral native RNA genomes date: 2019-04-08 journal: AMB Express DOI: 10.1186/s13568-019-0772-y sha: doc_id: 353810 cord_uid: mf753ae9 Current technologies for targeted characterization and manipulation of viral RNA primarily involve amplification or ultracentrifugation with isopycnic gradients of viral particles to decrease host RNA background. We report that this protocol was able to successfully purify viral RNA by 561- to 791-fold. keywords: capture; denv1; direct; host; method; pcr; post; purification; rna; sequencing; strategy; viral cache: cord-353810-mf753ae9.txt plain text: cord-353810-mf753ae9.txt item: #144 of 145 id: cord-355872-z6vsjmxn author: Colón-López, Daisy D. title: Emerging viral infections date: 2019-08-15 words: 3710 flesch: 29 summary: Vector Borne Zoonotic Dis Major emerging vector-borne zoonotic diseases of public health importance in Canada Climate change and range expansion of the Asian tiger mosquito (Aedes albopictus) in Northeastern USA: implications for public health practitioners Emerging virus diseases: can we ever expect the unexpected? SARS-CoV and emergent coronaviruses: viral determinants of interspecies transmission Comprehensive panel of real-time TaqMan polymerase chain reaction assays for detection and absolute quantification of filoviruses, arenaviruses, and new world hantaviruses Yellow fever: 100 years of discovery The etiology of yellow fever: an additional note Actionable diagnosis of neuroleptospirosis by next-generation sequencing A novel rhabdovirus associated with acute hemorrhagic fever in central Africa Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa Author correction: the discovery of Bombali virus adds further support for bats as hosts of ebolaviruses A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa Consensus statement: virus taxonomy in the age of metagenomics A strategy to estimate unknown viral diversity in mammals Public health threat of new, reemerging, and neglected zoonoses in the industrialized world Viral metagenomics on animals as a tool for the detection of zoonoses prior to human infection? Redefining the invertebrate RNA virosphere A Wolbachia symbiont in Aedes aegypti limits infection with dengue, Chikungunya, and Plasmodium The endosymbiotic bacterium Wolbachia induces resistance to dengue virus in Aedes aegypti Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation 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 Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4 Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak Molecular evidence of sexual transmission of Ebola virus Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases Possible sexual transmission of Ebola virus-Liberia Implementation of a National semen testing and counseling program for male Ebola survivors-Liberia Importation and containment of Ebola virus disease-Senegal Ebola virus disease outbreak-Nigeria Laboratory response to 2014 Ebola virus outbreak in Mali Second Ebola patient is treated in UK Molecular characterization of the first Ebola virus isolated in Italy First secondary case of Ebola outside Africa: epidemiological characteristics and contact monitoring Second US nurse with Ebola had traveled by plane Ebola and compliance with infection prevention measures in Nigeria Transmission dynamics and control of Ebola virus disease outbreak in Nigeria Zika virus. keywords: discovery; ebola; host; human; infection; outbreak; pathogen; sequencing; transmission; virus; viruses cache: cord-355872-z6vsjmxn.txt plain text: cord-355872-z6vsjmxn.txt item: #145 of 145 id: cord-355913-fhvt1ht1 author: Burrell, Christopher J. title: Virus Replication date: 2016-11-11 words: 9867 flesch: 41 summary: The situation is quite different for RNA viruses as these are unique having genetic information coded as RNA. For RNA viruses, the regulation of transcription is, on the whole, not as complex as is the case for DNA viruses. keywords: acid; cell; dna; example; genes; genome; host; membrane; mrna; particles; proteins; replication; rna; rna viruses; synthesis; transcription; viruses cache: cord-355913-fhvt1ht1.txt plain text: cord-355913-fhvt1ht1.txt