cord-010155-g5fk567p	2008	As our group is interested in the epidemiology of newly discovered viruses such as HMPV, human Bocavirus, and newly discovered Coronaviruses, in the cohort of hospitalized pediatric and adult high risk patients (2-5) we have screened 225 nasopharyngeal washes that were previously RT-PCR tested for RSV, HMPV, human Coronaviruses (NL63, OC43, 229E, HKU1, and SARS), and human Bocavirus (detailed protocols available on request and previously published in: 2-5) for the presence of Melaka-virus RNA. Although the lack of a Melakavirus RNA positive sample does not imply that it is absent in our clinical samples since it could have been below the detection limit of the RT-PCR assay, we can still conclude that Melaka-virus plays no or only a minor role in hospitalized European pediatric patients. We finally conclude that Melaka-virus testing should preferably be carried out in populations with suspected contact to the virus such as inhabitants of the endemic regions or air travellers with symptoms of respiratory disease (Luna et al., 2007) .
cord-010160-wk8k2igu	2012	2, 3 The xTAG Respiratory Virus Panel (RVP, Luminex Molecular Diagnostics, Toronto, Canada) is a US Food and Drug Administration (US FDA) cleared multiplex nucleic acid amplification test for the detection of respiratory viruses including adenovirus (ADV), human metapneumovirus (hMPV), influenza A (influA with subtyping of seasonal H1 and seasonal H3), influenza B (influB), parainfluenza types 1 (PIV-1), 2 (PIV-2) and 3 (PIV-3), respiratory syncytial virus (RSV) A and B, and HRV. A multicenter study demonstrated that RVP can detect culture isolates of HRV serotypes 39 and 54 and HRV strains of phylogenetic groups A, B, C, E and F from clinical samples. Nucleic acids derived from 3 clinical samples that contained HRV species C tested positive with RVP, LDTHRV and negative with EVA. All samples positive for HRV/EV by RVP were detected by LDTHRV and were negative by EVA.
cord-026099-97luq10a	2020	title: Response to correspondence received on our paper:Interpret with caution: an evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus We reported that the sensitivity, specificity, positive predictive value (PPV) and negative predictive value of the AusDiagnostics RUO assay was 100%, 92.16%, 55.56% and 100%, respectively when compared to our RT-PCR assay. Even if the specificity of the AusDiagnostics RUO assay was 99% (i.e. a 1% false positive rate), given the current prevalence of COVID-19 infection in NSW of 0.84%, the calculated PPV of the assay would be 54.15%, which is concordant with our findings. Cohen et al also estimated false positive rates of up to 7% in commercial diagnostics assays detecting SARS-CoV-2 [Cohen] . Furthermore, false positive RT-PCR results have also been reported from commercial kits that have been contaminated with SARS-CoV-2 sequences [Bustin] . Interpret with caution: An evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus
cord-027649-6xn9swsq	2020	title: Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates Sequence reads were trimmed using Trimommatic v0.38 (5) , aligned to the SARS-CoV-2 reference genome (NC_045512.2) using BBMap (https://sourceforge.net/projects/bbmap/), trimmed of synthetic PCR primers using Primerclip (https://github.com/swiftbiosciences/primerclip) if appropriate, and visualized in Geneious v11.1.4 (6) . Interestingly, ORF6 of SARS-CoV-2 interacts with the mRNA export proteins NUP98 and RAE1, and may inhibit cellular translation (10) . We predict global sequencing projects may yield additional clinical SARS-CoV-2 isolates with deletions in ORF6 or ORF7a, but not both. Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization An 81 nucleotide deletion in SARS-CoV Structure and intracellular targeting of the SARS-coronavirus Orf7a accessory protein A SARS-CoV-2 protein interaction map reveals targets for drug repurposing A 227-nucleotide deletion beginning at nt 27,524 was identified in b) WA-UW-5812 and resulted in the fusion of ORF7a and ORF7b.
cord-253148-3t4o27xp	2008	STUDY DESIGN: From October 2005 through October 2006, we screened respiratory samples from children and adults negative for common respiratory pathogens for HBoV by PCR. CONCLUSIONS: HBoV circulates in Cleveland, OH, in children and adults with similar frequencies, and can warrant hospitalization and intensive care. We sought to further define the clinical and epidemiologic characteristics of HBoV in adult and pediatric patients in Cleveland, OH. Isolates positive for HBoV were screened for common respiratory viruses by RT-PCR with published primer sets. Forty samples (2.2%) tested positive for HBoV by PCR: 36 (90%) pediatric patients and 4 (10%) adult patients. Of pediatric patients who screened positive for HBoV, 27 (84.4%) were admitted to the hospital, including 9 (28.1%) who required intensive care. However, this report suggests that clinical disease associated with HBoV alone may be severe enough to require admission to the hospital in both adults and children and to the intensive care unit in children.
cord-253333-cwunxhyw	2018	Diagnosis with FilmArray-RP was associated with significant changes in medical management including withholding antibiotic prescriptions (OR:15.52, 95%CI:1.99–120.83 in adults and OR:12.23, 95%CI:1.56–96.09 in children), and reduction in complementary studies in children (OR:9.64, 95%CI:2.13–43.63) compared to IFA. CONCLUSIONS: The high respiratory viruses'' detection rate and availability of results within two hours when using FilmArray-RP were associated with decreases in antibiotic prescriptions and complementary studies and more accurate use of oseltamivir. The aim of this study was to determine if timely etiological diagnosis could have an impact on medical management in relation to antibiotic and antiviral prescription, and use of complementary studies, when patients were tested by either FimArray-RP or IFA. This study demonstrated that significant changes in medical management occurred in both children and adults when the results of a multiplex molecular respiratory panel were rapidly available to physicians in the ED compared to patient management using conventional testing (IFA).
cord-256699-d2tf2g7f	2020	Using 168 samples from patients hospitalized for COVID-19, non-hospitalized patients but infected with SARS-CoV-2, patients participating in screening campaigns, and samples from patients with a history of other seasonal coronavirus infections, we evaluated the clinical performance of 5 serological assays widely used worldwide (WANTAI®, BIORAD®, EUROIMMUN®, ABBOTT® and LIAISON®). Thus, we evaluated five commercial serological tests widely used worldwide on samples from patients hospitalized for COVID-19, non-hospitalized patients but infected with SARS-CoV-2, patients participating in screening campaigns, and samples from patients with a history of other seasonal coronavirus infections. The assays were validated using serum samples from (i) patients hospitalized for COVID-19 (n=20), non-hospitalized patients but PCR confirmed with SARS-CoV-2 (n= 58), patients participating in screening campaigns (n= 62), and samples from patients with a history of other seasonal coronavirus infections (n= 28). For the first group, with 20 patients hospitalized for COVID-19 with a positive nasopharyngeal SARS-CoV-2 PCR, all samples were positive with these serological assays evaluated ( Figure 1A ).
cord-259558-remrzrq1	2020	Low viral loads are known to occur in the early and late stages of COVID-19 illness [4] [5] [6] [11] [12] [13] [14] [15] [16] [17] [18] [19] , and false negative results can arise from differences in analytical sensitivity between methods (Table S1 ) [20, 21] , the variability in specimen collection, or factors influencing specimen stability or recovery of SARS-CoV-2 RNA during specimen transport, storage or processing. [4, 13] For example, three different SARS-CoV-2 targets were detected between the various PCR methods used for testing of J o u r n a l P r e -p r o o f specimens from patient 1, yet high Ct values were observed for these targets (Table 1) .
cord-259798-fnm1im98	2018	CONCLUSIONS: Rapid molecular testing positively impacts patient management of ARTIs. Adopting assays with a shorter turn-around-time improves decision making by decreasing empirical antibiotic use and duration, decreasing chest x-rays, increasing timely oseltamivir administration, and reducing length of stay. While research has demonstrated that MRPs may have a positive impact on patient outcomes such as decreasing empiric antibiotic exposures, length of hospital stay (LOS), and improving timely oseltamivir treatment for influenza patients [9] [10] [11] [12] [13] [14] , there is a dearth of information on whether this clinical impact is conditional on the turn-around-time (TAT) of the MRP assay. We hypothesized that the rapid detection of respiratory pathogens by RP compared to RVP would be positively associated with changes in antibiotic treatment, initiation of oseltamivir and LOS on pediatric patients < 18 years old.
cord-260267-nau9kayk	2011	title: Human parainfluenza virus type 4 infection in Chinese children with lower respiratory tract infections: A comparison study Background: Human parainfluenza viruses (HPIVs) are a leading cause of acute respiratory tract infections (ARTIs). Background: Human parainfluenza viruses (HPIVs) are a leading cause of acute respiratory tract infections (ARTIs). Objectives: To characterize the role of HPIV-4 and its clinical features in children with acute lower respiratory tract infections (ALRTIs) in Beijing, China. Objectives: To characterize the role of HPIV-4 and its clinical features in children with acute lower respiratory tract infections (ALRTIs) in Beijing, China. Human parainfluenza viruses (HPIVs) are a leading cause of acute respiratory tract infections (ARTIs). [10] [11] [12] [13] [14] However, the prevalence and clinical characteristics of HPIV-4 in Chinese paediatric patients with acute lower respiratory tract infections (ALRTIs) have not been addressed fully.
cord-260338-or4faju7	2007	BACKGROUND: Human Bocavirus (HBoV), a new species of the genus parvovirus newly detected in 2005, seems to be a worldwide distributed pathogen among children with respiratory tract infection (prevalence 2%–18%). Unlike patients with RSV-infection (Ogra, 2004; Simon et al., 2006) , and similar to those with HMPV-associated respiratory tract infection , children older than 6 months seem to be most at risk (Kesebir et al., 2006; Manning et al., 2006; Weissbrich et al., 2006) . This report discusses the prospectively documented viral RTIs in hospitalized pediatric patients in the 2005-2006 winter season and focuses on the HBoV infections detected. The most common clinical diagnoses of HBoV-positive patients included upper respiratory tract infection, bronchitis, bronchiolitis, pneumonia and exacerbation of asthma bronchiale. Human Bocavirus DNA detected by quantitative real-time PCR in two children hospitalized for lower respiratory tract infection
cord-262045-r2iqpmmc	2014	RESULTS: A reverse-transcription PCR assay for MERS-CoV targeting a 615 bp spike fragment provides a phylogenetic clustering of MERS-CoV variants comparable to that of full-length genomes. In addition, the MERS-CoV variant typing assay was performed on camel samples from a slaughterhouse in Qatar [13] and sequences for 14 MERS-CoV positive animals with cycle threshold values ranging from 12.9 to 32.2 as determined by UpE real time RT-PCR [17, 18] were obtained (Fig. 2) . Subsequent analyses revealed a region in the open reading frame that encodes the spike protein with a number of positions in which nucleotide variation occurs between MERS-CoV variants with a strong phylogenetic signal regarding previously identified clusters of viruses based on full-length MERS-CoV genomes. 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
cord-263118-6sf41rsj	2008	STUDY DESIGN: Binax NOW, cytospin-enhanced direct immunofluoroescence (DFA), and influenza A and B multiplex TaqMan RT-PCR were performed on 237 clinical samples. RESULTS: Binax NOW detected 70 (53.0%), cytospin-DFA detected 127 (96.2%), and TaqMan RT-PCR detected 132 (100%) influenza-positive samples. CONCLUSIONS: The accuracy of real-time RT-PCR should greatly improve the diagnosis of influenza in hospitals using simple rapid flu tests, but may have a more modest impact in hospitals with expertise in cytospin-DFA. In our hospital, cytospin-enhanced direct immunofluorescence (DFA) is performed on respiratory samples when Virology is open, and a rapid influenza test, Binax NOW, is used in the Core Laboratory when Virology is closed (Landry and Ferguson, 2000; Landry et al., 2004) . During the study period, reflex cultures were performed on 683 DFA-negative samples, but only three influenza A positives were detected.
cord-263279-afdmegq0	2020	Of the first assays that were available for validations were the CDC COVID-19 RT-PCR panel assay (IDT, Coralville, IA) as well as the RealStar® SARS-CoV-2 RT-PCR (Altona Diagnostics, Hamburg, Germany), and both were initially validated for clinical use at the Johns Hopkins Hospital Medical Microbiology laboratory. To compare the analytical performance of the three assays, positive and negative SARS-CoV-2 clinical specimens (using the RealStar® SARS-CoV-2 as the reference method as this assay was the first to be offered in house for clinical diagnosis) were tested by the CDC COVID-19 RT-PCR and/ or the ePlex® SARS-CoV-2 assays. Comparing the performance of the CDC COVID-19 RT-PCR to the RealStar® SARS-CoV-2 included testing 20 positive and 48 negative clinical NP specimens. In this study, we compared the analytical performance of three different molecular assays for the detection of SARS-CoV-2; the RealStar® SARS-CoV-2 RT-PCR, ePlex® SARS-CoV-2, and the CDC COVID-19 RT-PCR tests.
cord-263389-m6x9gxwe	2017	title: Diagnostic yield and clinical impact of routine cell culture for respiratory viruses among children with a negative multiplex RT-PCR result Respiratory samples from hospitalized or immunocompromised patients <18 years old were routinely inoculated on traditional tube cell culture monolayers if they tested negative by a PCR assay for 12 respiratory viruses. Still, some authors suggest performing viral culture in a backup role in respiratory specimens from high-risk populations to detect viruses that are not part of the RT-PCR assay or whose genomes have mutations that may lead to false-negative RT-PCR results [5, 6] . We performed a single-center retrospective cohort study at the Montreal Children'' population included all patients < 18 years old with a viral culture performed on a respiratory specimen that had tested negative by multiplex PCR. However, in our clinical laboratory, routine viral cultures from PCR-negative respiratory specimens had minimal impact on patient care.
cord-264360-eroqjkoh	2010	STUDY DESIGN: 878 stool specimens from children with acute gastroenteritis and 112 from control children were tested by RT-PCR to detect HCoV groups 1B, 2A and SARS. On the basis of this study, the significance of coronaviruses as gastrointestinal pathogens in children appears minor, since most of the coronavirus findings were co-infections with known gastroenteritis viruses. Our study shows that human coronaviruses OC43, HKU1, 229E and NL63 can be found in stool samples of children with acute gastroenteritis. 10 In our study one of the 36 healthy control patients had coronavirus detected in stool specimen and thus, there was no difference in the HCoV detection rate between the cases of acute gastroenteritis and control children. Future studies should investigate such mild cases for HCoVs. In conclusion, non-SARS human coronaviruses can be found in stool samples of children with acute gastroenteritis.
cord-264406-s5c0grz0	2016	Bacterial infections are very frequent in children with cystic fibrosis, but because rapid Methods: for screening for the wide variety of potentially involved viruses were unavailable until recently, the frequency of viral presence is unknown. Bacterial infections are very frequent in children with cystic fibrosis, but because rapid Methods: for screening for the wide variety of potentially involved viruses were unavailable until recently, the frequency of viral presence is unknown. Study design: In this 2-year prospective study, we obtained paired nasopharyngeal-swab and sputum specimens from children with cystic fibrosis during clinical respiratory examinations separated by at least 14 days. Study design: In this 2-year prospective study, we obtained paired nasopharyngeal-swab and sputum specimens from children with cystic fibrosis during clinical respiratory examinations separated by at least 14 days. This study aimed to evaluate the frequency viruses and bacteria in respiratory specimens and to clarify the incidence and characteristics (seasonality and age of patients) of different viruses in children with cystic fibrosis.
cord-264676-k531q3ir	2009	title: In situ reverse-transcription loop-mediated isothermal amplification (in situ RT-LAMP) for detection of Japanese encephalitis viral RNA in host cells In this study, we aimed to establish a new approach, named as in situ reverse-transcription loop-mediated isothermal amplification (in situ RT-LAMP), in order to detect JE virus infection in cultured cells and in PBMCs isolated from infected mice. When the in situ RT-LAMP was run with the DIG-labeled primer, no positive reaction was shown in either JE virus-infected (Fig. 5A ) or uninfected (Fig. 5B ) BHK-21 cells. Detection of Japanese encephalitis virus in mouse peripheral blood mononuclear cells using an in situ reverse transcriptase polymerase chain reaction Rapid detection and quantification of Japanese encephalitis virus by real-time reverse transcription loop-mediated isothermal amplification Rapid detection and differentiation of Dengue virus serotypes by real-time reverse transcription loop-mediated isothermal amplification assay Development and evaluation of reverse transcription-loop-mediated isothermal amplification assay for rapid and real-time detection of Japanese encephalitis virus
cord-264713-38dlh3wg	2004	Viral load and antiviral resistance or subtyping assays are now part of the biological monitoring of patients chronically infected by human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV) and CMV. The most striking illustration of the power of molecular techniques concerns blood transmitted viruses-human immunodeficiency virus (HIV), hepatitis B virus (HBV) and hepatitis C virus (HCV) for which spectacular progresses in the detection and treatment of viral diseases have been made following the introduction of qualitative and quantitative nucleic acid tests (NAT). For example, we have observed, using a DNA-microarray assay (see below), that the analytical sensitivity of multiplex RT-PCR detection of six viruses, i.e. influenza A, influenza B, RSV A/B, parainfluenza 1, 2 and 3 is reduced by a factor of <1-2 logs compared to single detections, depending on the virus.
cord-265760-ch4pcy21	2020	The study aimed to delve into the relationships between initial nucleic acid testing and early lung CT changes in patients with COVID-19. The initial nucleic acid test was negative, whereas at this time characteristic lung changes appeared, by repeated nucleic acid tests, it was positive, as a result, a considerable number of early patients have been missed. If with the positivity of initial nucleic acid acts as the gold standard, the sensitivity of characteristic lung CT changes will be only 12 %, which will cause huge interference or even misleading to clinical work; as a result, diagnosis and treatment will be delayed, and even the potential patient will not be isolated in time, thereby causing the spread of the virus. In conclusion, there is poor consistency between the positive rate of initial nucleic acid test and the changes of lung CT in patients with COVID-19, and initial nucleic acid test exhibits low sensitivity.
cord-266359-uf1ao1x1	2015	BACKGROUND: Compared to other respiratory viruses, relatively little is known about the clinical impact of coronavirus (CoV) infection after hematopoietic stem cell transplant (HSCT) or in patients with hematologic malignancies. CONCLUSIONS: CoV is frequently detected in HSCT and hematologic malignancy patients in whom suspicion for a respiratory viral infection exists, but is less likely to progress to lower respiratory tract disease than most other respiratory viruses. The clinical significance of respiratory viruses such as influenza, respiratory syncytial virus (RSV), parainfluenza viruses (PIVs), human metapneumovirus (hMPV), rhinovirus (RhV), and adenovirus (AdV) in patients with hematologic malignancies or recipients of autologous or allogeneic hematopoietic stem cell transplant (HSCT) is well described [1] [2] [3] [4] [5] [6] [7] [8] . In conclusion, we found that CoV is detected frequently in patients with hematologic malignancies and HSCT recipients in whom suspicion for a respiratory viral infection exists, but is associated with less LRTD than other respiratory viruses except RhV/EnV.
cord-267928-dflkggjt	2009	STUDY DESIGN: Altogether 1390 samples from immunocompetent or immunocompromised patients, including (i) tonsillar tissues and sera from tonsillectomy patients; (ii) nasopharyngeal aspirates (NPAs) and sera from wheezing children and (iii) nasal swabs, sera and stools from febrile leukemic children were studied for MCPyV. RESULTS: MCPyV DNA was detected in 14 samples altogether; 8 of 229 (3.5%) tonsillar tissues, 3 of 140 (2.1%) NPAs, 2 of 106 (1.9%) nasal swabs and 1 of 840 (0.1%) sera. In this study MCPyV DNA was detected in clinical samples of many different types: nasal swabs and nasopharyngeal aspirates, tumor-free tonsillar tissues and sera. Among immunocompetent children, the absence of MCPyV from the 496 serum samples tested is in accordance with our recent study (in submission) in which the two other polyomaviruses KIPyV and WUPyV were absent from all of these sera.
cord-268093-ta6k0uyz	2013	The presence of the new HRV-C strain in severe respiratory disease has further instilled research interest in the clinical impact, molecular biology and epidemiology of HRVs. As research of HRV is limited [8] , especially in Asian developing countries, this study aims to examine the molecular epidemiology, the demographic characteristics and clinical features including the newly discovered HRV-C species, among hospitalized children less than 5 years of age with ALRTI in Malaysia. HRV infected patients were admitted earlier compared to RSV and influenza; children with HRV presented to the hospital after a mean duration of 1.9 days (ranged 1-9 days) as compared with HRV (4.0 days, p = <0.001) and IFV-A (4.8 days, p = 0.002). Our study revealed that HRV infected children were hospitalized earlier in the course of their disease and were less febrile on presentation as compared to RSV and IFV-A infections.
cord-268335-mfcjldu3	2020	Chloé Dimeglio 1,2* , Jean-Michel Mansuy 2 , Sandrine Charpentier 3,4 , Isabelle Claudet 4,5 , and Jacques Izopet 1 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China in December 2019. As infants and young children infected with respiratory tract viruses are particularly at risk of hospitalization (3) the paucity of pediatric patients with COVID-19 has raised many questions for clinicians, epidemiologists and scientists. The study previously published by Lancet Infectious Disease has important implications for the clinical management of these patients and the social distancing needed to prevent virus transmission (4). The abovementioned study has found that children are susceptible to SARS-CoV-2 infection, but rarely display any physical signs of the disease. The most important finding emerging from this analysis is the clear evidence that children are less susceptible to SARS-CoV-2 infection than adults. While children have been regarded as facilitators of virus transmission, we now need to identify the mechanism which protects them, at least partially, against SARS-CoV-2 infection.
cord-268567-2xoubkxb	2020	In this study, we are evaluating the work up, management and outcome of 241 adults with encephalitis based on the majority of current guidelines recommendations in literature [11] [12] [13] [14] . As summarized in (Supplemental Digital Content Table 1 ), all guidelines of encephalitis management have major parts in evaluating and managing patients with encephalitis; exposure evaluation, appropriate utilization of diagnostic and neurodiagnostic studies, and proportion and timing of empirical antibiotic and antiviral therapy [11] [12] [13] [14] [15] . The Infectious Disease Society of America (IDSA), British, Australian, International consortium, and French guidelines recommend that clinicians evaluate for potential exposures and risk factors and to perform appropriate utilization of diagnostic studies in patients with suspected encephalitis. Also, most of the guidelines recommends to repeat CSF HSV PCR in 3-7 days in undiagnosed cases of encephalitis in which patients have clinical features or neuroimaging findings of HSV encephalitis [11] [12] [13] [14] .
cord-268830-8li6xhbu	2020	It has been reported that immunocompromised patients, particularly hematopoietic cell transplant recipients, are at increased risk of lower respiratory tract infections, prolonged viral shedding and mortality, often comparable to what is seen with influenza virus [3, 4] . In acute care hospitals, much of the focus in diagnostics has been placed on influenza and respiratory syncytial virus (RSV) because of the severe infection and poor outcomes of hospitalized patients, yet the burden of CoV in acute care is not well studied. The primary objective of this study was to describe the burden of CoV among patients admitted to an acute care hospital in Toronto, Canada over a six-year period, and identify the predictors of severe disease. In our cohort smoking predicted ICU admission and/or mortality, which is similar to what was reported in a prior study on patients infected with HKU1 CoV [18] The impact of gender on outcomes of CoV, as determined by our multivariate analysis is in contrast with what is reported for MERS CoV.
cord-268993-2sjh17mw	2020	BACKGROUND: Molecular assays based on reverse transcription-loop-mediated isothermal amplification (RT-LAMP) may be useful for rapid diagnosis of the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) because of the easy performance and the option to bypass RNA extraction. OBJECTIVES: This study was designed to evaluate the clinical performance of the CE-labeled variplexTM real time SARS-CoV-2 RT-LAMP assay in comparison to commercial RT-PCRs. STUDY DESIGN: RNA extracted from pharyngeal swabs was tested by variplex™ RT-LAMP and Corman''s LightMix™ E gene RT-PCR as reference. Samples of respiratory secretions from Coronavirus infection disease (COVID-19) and negative control patients were analyzed by variplex™ without RNA extraction and tested in parallel with the Allplex™ and VIASURE BD MAX RT-PCRs. RESULTS: Using isolated RNA variplex™ RT-LAMP showed a sensitivity of 75% compared to LightMix E gene RT-PCR but contrary to the latter it produced no false-positive results.
cord-269407-6i66zf0e	2017	Three hundred and twenty-four samples which were found to be negative for influenza virus after screening with real-time RT-PCR and cell-based culture techniques demonstrated the potential for viral infection with evident cytopathic effect (CPE) in several cell lines. OBJECTIVE: To assess whether whole genome next-generation sequencing (WG-NGS) together with conventional molecular assays can be used to reveal the etiology of influenza negative, but CPE positive specimens. Individual samples in the positive pools were confirmed by qRT-PCR, RT-PCR, PCR and Sanger sequencing from the CPE culture and original clinical specimens. The 310 culture supernatants that made up the 29 pools were further tested by pathogen-specific PCR, RT-PCR or rRT-PCR to validate the WG-NGS findings and to quantify the percentage of samples within each pool where viruses were present ( Table 2) . In addition, standard molecular procedures were conducted in selected samples and results validated the presence of the identified pathogens in both clinical specimens and CPE culture.
cord-269519-8hr8wyrr	2020	
cord-271445-eft2vwgb	2004	Background: Human Metapneumovirus (hMPV), has been recently isolated from children with acute respiratory tract infections (RTIs), including bronchiolitis, and classified in the Pneumovirinae subfamily within the Paramyxoviridae family. Results and conclusions: PCR revealed the presence of hMPV in 16% of bronchiolitis cases, whereas respiratory syncytial virus (RSV; 67.9%) was the most frequently encountered viral pathogen. There were no differences in disease characteristics, either clinical or laboratory, between bronchiolitis cases where hMPV was present and those caused by RSV or other viral pathogens. A new respiratory virus, human metapneumovirus (hMPV), has been recently isolated from nasopharyngeal aspirates of young children in the Netherlands (van den Hoogen et al., 2001) . We have recently reported the results of virological evaluation of a well-characterized cohort of infants admitted to hospital with acute bronchiolitis, using reverse transcription polymerase chain reaction (PCR) for 11 respiratory pathogens (Papadopoulos et al., 2002) .
cord-272734-kawim93f	2020	title: Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies The CDC designed 2019-nCoV CDC EUA kit (IDT, USA) is based on N1 and N2 probes to detect SARS-CoV-2 that have received positive evaluation on recent reports (1) (2) (3) , and and RNase P as an RNA extraction quality control. Other kit avalaible in the market is nCoV-QS (MiCo BioMed; South Corea) that include probes "ORF3a" and "N" probes for SARS-CoV-2 detection but no probe for RNA extraction quality control, with no EUA approval neither from FDA (USA) nor from Korean CDC (4,5,6). Both CoV-QS and 2019-nCoV CDC EUA kits were used at SARS-CoV-2 diagnosis laboratory "LabGal" at "Agencia de Regulación y Control de la Bioseguridad y Cuarentena para Galápagos" at Puerto Ayora in Galapagos Islands (Ecuador), where we considered this validation necessary to guarantee the sensibility of SARS-CoV-2 during the surveillance.
cord-273229-c1jws3ol	2020	MATERIALS AND METHODS: Over a period of one month, we compared the negative results obtained with the COVID-19 Ag Respi-Strip kit with those obtained from qRT-PCR performed in a laboratory qualified for the molecular diagnosis of SARS-CoV-2. RESULTS: Of 774 patients tested, 714 negative samples were sent for confirmation, and 159 were found to be positive by qRT-PCR. CONCLUSION: Using this immunochromatographic assay as a triage test did not significantly reduce the number of samples outsourced for COVID-19 confirmation by qRT-PCR. Ag Respi-Strip kit with those obtained from qRT-PCR performed in a laboratory qualified for the molecular diagnosis of SARS-CoV-2. Under routine conditions, the sensitivity of the antigen detection of SARS-CoV-2 with the immunochromatographic COVID-19 Ag Respi-Strip kit was significantly lower than that announced by the manufacturer or reported by Vandenberg [2] , although we limited ourselves to using qRT-PCR as the comparison method.
cord-273783-z71bquck	2011	The frequencies of severe HCoVs infection was determined by real time RT-PCR among 1471 hospitalized infants (<2-years old) with acute respiratory tract disease. In addition the chain of seroconversions will reveal whether immunity to one HCoV may protect against infection by one of the other HCoVs. Two distinct study groups were monitored: healthy children (newborns) and children hospitalized due to respiratory disease. Samples in this study were selected from the complete set based on the following criteria: children who were hospitalized with acute respiratory tract illness and below the age of 2 years. The characteristic frequency of infection, in the order HCoV-OC43 ≥ HCoV-NL63 > HCoV-HKU1 ≥ HCoV-229E, observed via seroconversion but also by direct detection of the virus in hospitalized children over multiple years is in contrast with some previous studies.
cord-276316-7ot9ds34	2020	Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA in respiratory tract, blood samples and digestive tract was detected and lymphocyte subsets were tested periodically. 270 patients were detected for SARS-CoV-2 RNA in anal swabs and/or blood samples, and the overall positive rate was 23.0 % (62/270), higher in severe/critical cases than in mild/moderate cases (52.0 % vs. Detectable SARS-CoV-2 RNA in anal swabs and/or blood samples, as well as higher CD4/CD8 ratio were independent risk factors of respiratory failure and ICU admission. A total of 270 patients were detected for SARS-CoV-2 RNA in anal swabs J o u r n a l P r e -p r o o f 8 / 25 and/or blood samples, and the overall positive rate was 23.0% (62/270), higher in severe/critical cases than in mild/moderate cases (52.0% vs.
cord-277909-rn1dow26	2006	In comparison to traditional gel-based PCR assays, real time PCR offers increased sensitivity and specificity in a rapid format (turn around time from sample receipt to result <5 h). Most of the published real time probe based PCR assays for viral diagnosis utilise either molecular beacons or dual labelled probes although more recent publications tend to favour the use of dual labelled probes. In real time PCR, the signal is detected early in the amplification process, and therefore the end-point variation seen in gel-based assays does not affect the result. Despite this we still perform an initial optimisation of both primer and probe concentrations to ensure we are running our real time PCR assays at their most sensitive and efficient. Some manufacturers are now producing real time reaction mixes specifically designed for use with multiplex assays, and provide guidelines on the optimal primer and probe concentrations to use.
cord-279563-4lu1n0s7	2020	The Hologic Aptima SARS-CoV-2 Assay utilizes TMA as a target amplification mechanism, and it has only recently received Emergency Use Authorization (EUA) by the Food and Drug Administration (FDA). CONCLUSIONS: The higher analytical sensitivity may explain the assay''s ability to ascertain for the presence of SARS-CoV-2 genome in human specimens deemed inconclusive by real-time PCR. To assess differences in analytical sensitivity between real-time PCR and TMA, we performed a limit-ofdetection (LoD) study by creating a dilution series of purified / quantified SARS-CoV-2 genomic material either in VTM or APTIMA collection matrix. Noting the sensitivity difference demonstrated by the LoD study, we sought to assess the performance of TMA on specimens previously tested by RT-PCR for SARS-CoV-2. The Hologic Panther SARS-CoV-2 transcription mediated amplification test showed higher analytical sensitivity when compared to real time PCR for the detection of SARS-CoV-2.
cord-279570-lgbqpfh5	2020	In this study we aim to describe the clinical characteristics and complications of measles infection in hospitalized adults during the recent epidemic in Greece. All adult hospitalized patients (≥18 years old) with serologically confirmed and/or clinical features compatible with measles were included. In this study, we describe our experience from the recent outbreak of measles in adult hospitalized patients in Greece [8] . One obese female patient with a Grade II hepatic involvement and pneumonitis that progressed rapidly into acute respiratory distress syndrome (ARDS) requiring mechanical ventilation, died within 6 days of her admission due to high-risk pulmonary embolism (PE) despite being treated with ribavirin. In this study we describe the clinical features and outcomes of mostly healthy and young adult hospitalized patients with measles. In summary, in this study we presented the clinical characteristics of measles infection during the recent epidemic in hospitalized adults in Greece.
cord-281495-beb164oy	2020	title: Performance evaluation of two SARS-CoV-2 IgG/IgM rapid tests (Covid-Presto and NG-Test) and one IgG automated immunoassay (Abbott) The aim of this study was to assess the analytical performances, sensitivity and specificity, of two rapid tests (CovidPresto® test rapid Covid-19 IgG/IgM and NG-Test® IgM-IgG COVID-19) and one automated immunoassay (Abbott SARS-CoV-2 IgG) for detecting antiSARS-CoV-2 antibodies. The aim of this study was to assess the analytical performances (sensitivity and specificity) and agreement of two rapid tests and one automated immunoassay for detecting antibodies against SARS-CoV-2. In the present study, we evaluated two different lateral flow tests (Covid-Presto ® and NG-Test ® ) and compared their performances to that of the automated Abbott immunoassay using the same samples panel. Sensitivity for IgG in samples collected later than 10 days after symptoms onset was excellent with the different tests being equal to 97.1%, 96.2% and 100% for Covid-Presto ® , NG-Test ® , and Abbott, respectively.
cord-282576-mcx0xq0w	2020	title: Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument METHODS: The concordance between the cobas 8800 SARS-CoV-2 and a laboratory developed (LD) reverse transcriptase-polymerase chain reaction (RT-PCR) assay was assessed on 377 combined nasopharyngeal/oropharyngeal swabs in Hanks medium. We evaluated the concordance between the two-target cobas SARS-CoV-2 test (Roche Molecular Diagnostics, Laval, Canada) on the fully automated cobas 8800 platform authorized by Health Canada and a laboratory-developed (LD) standardized RT-PCR test using widely used primer set and probe (2, 3) in samples submitted at the diagnostic laboratory for patient care at the Centre Hospitalier de l''Université de Montréal. The correlation between Ct values obtained in the LD RT-PCR test and cobas SARS CoV-2 ORF-1 target for positive samples in both assays was good (r 2 = 0.82, data not shown).
cord-283028-g2rjjq48	2010	
cord-284841-flhfagp3	2020	
cord-285018-l26px1bc	2020	title: Comparison of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the sample-to-result Platform ELITe InGenius to the national reference method: an added value of N gene target detection? OBJECTIVES: The aim of this study was to assess the diagnostic performance of the GeneFinder(TM) COVID-19 Plus RealAmp Kit on the ELITe InGenius sample-to-result platform, which is a commercial nucleic acid amplification test (NAT) targeting genes of SARS-CoV-2. RealAmp Kit on the sample-to-result InGenius® platform in comparison to the national reference standard in the Netherlands, and to determine the added value of nucleoprotein (N) gene detection to establish the diagnosis of COVID-19. Patients were sampled from the oral cavity and subsequently from the nasal cavity using the same nasopharyngeal swab, which was tested by a validated in-house NAT assay on the presence of COVID-19 envelope protein (E) gene and RNA dependent RNA polymerase (RdRp) gene according to a reference method that was established after international collaboration [5] .
cord-287206-ois4gnqx	2020	
cord-289139-5ljqnc39	2014	title: The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit BACKGROUND: The use of a multiplex molecular technique to identify the etiological pathogen of respiratory viral infections might be a support as clinical signs are not characteristic. OBJECTIVES: The aim of the study was to evaluate a multiplex molecular real-time assay for the routine diagnosis of respiratory viruses, to analyze the symptoms associated with the pathogens detected and to determine the spread of virus during the period. This assay can detect 15 viruses: influenza viruses (IV) types A and B, parainfluenza viruses 1 to 4 (PiV), respiratory syncytial viruses A and B (RSV), rhinovirus (RV), coronaviruses 229E, OC43 and NL63 (CoV), human metapneumovirus (MPV) and adenovirus (ADV). RSV and RV were the most prevalent pathogens, particularly in the youngest children, and co-infections were associated with more severe respiratory symptoms.
cord-289740-nsiycudn	2020	OBJECTIVE: This study aimed to compare two recently-authorized rapid tests, Cepheid Xpert Xpress SARS-CoV-2 and Abbott ID Now SARS-CoV-2, to the Roche cobas SARS-CoV-2 assay for samples with low, medium, and high viral concentrations. STUDY DESIGN: A total of 113 nasopharyngeal swabs from remnant patient samples were tested, including 88 positives spanning the full range of observed Ct values on the cobas assay. CONCLUSIONS: While Xpert showed high agreement with cobas across a wide range of viral concentrations, this study highlights an important limitation of ID Now for specimens collected in viral or universal transport media with low viral concentrations. Utilizing the high volume of patient testing performed at our medical center in New York City, we sought to evaluate and compare the performance of these two rapid assays across a wide range of clinical samples. Deidentified remnant patient samples that underwent routine clinical testing with the cobas SARS-CoV-2 assay on the 6800 platform (Roche Diagnostics, Indianapolis, IN) were used to evaluate the Xpert and ID Now assays.
cord-289947-z2dw2eaz	2020	title: Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract specimens (LRT) including sputum, tracheal aspirate and bronchoalveolar lavage are not validated. OBJECTIVE: Evaluate the performance of Xpert Xpress SARS-CoV-2 assay for detection of SARS-CoV-2 from DTS and LRT specimens. CONCLUSIONS: This study demonstrated with appropriate sample pre-treatment, Xpert Xpress SARS-CoV-2 assay can be used to test on non-validated specimen types including DTS & LRT specimens. The overall performance of Xpert Xpress SARS-CoV-2 assay was satisfactory when tested with DTS and LRT specimens. To our knowledge, this is the first report to evaluate the use of PBS for sample homogenization of DTS prior to testing with Xpert Xpress SARS-CoV-2 assay. These procedures can minimize the mucus and viscous substances among non-validated specimen types and broaden the testing scope of Xpert Xpress SARS-CoV-2 assay.
cord-290352-0pc5eji4	2005	Since their reemergence in 2003, highly pathogenic avian influenza A (H5N1) viruses have reached endemic levels among poultry in several southeast Asian countries and have caused a still increasing number of more than 100 reported human infections with high mortality. However, occurrences of direct bird-to-human transmission of avian influenza viruses have increasingly been reported in recent years, culminating in the ongoing outbreak of influenza A (H5N1) among poultry in several Asian countries with associated human infections. The "Asian influenza" pandemic of 1957 was caused by an H2N2 virus that had acquired three genes (H2, N2, and PB1) from avian viruses infecting wild ducks, in a backbone of the circulating H1N1 human influenza strain. Furthermore, these infections were associated with severe hemorrhagic pneumonia and the induction of high levels of macrophage-derived cytokines and chemokines, strikingly reminiscent of clinical observations in humans during the Spanish flu pandemic, as well as of recent in vitro and in vivo observations of infections with highly pathogenic avian influenza H5N1 viruses (Cheung et al., 2002; Oxford, 2000; Peiris et al., 2004; To et al., 2001) .
cord-291029-oldket3n	2005	The QIAamp MinElute Virus kit (Qiagen Inc., Valencia, CA) was compared to the two existing methods currently used in our laboratory, IsoQuick (Orca Research Inc., Bothell, WA) for DNA extraction and RNAzol B (Leedo Laboratories Inc., Houston, TX) for RNA extraction, of viral nucleic acids. In this study, we have chosen both nasopharyngeal swab (NPS) and cerebrospinal fluid (CSF) specimens submitted for influenza A virus, enterovirus and herpesvirus testing to validate the MinElute nucleic acid extraction system. Nucleic acid recovery rates between the MinElute and RNAzol B were further determined by quantitating HIV-1 or CMV viral loads in extracted RNA or DNA specimens using a real-time TaqMan PCR. The MinElute kits possessed an equivalent sensitivity in nucleic acid recovery and detection, in comparison to the IsoQuick and RNAzol B, for both DNA and RNA extraction.
cord-291553-j9nn5g70	2016	title: Human pegivirus detected in a patient with severe encephalitis using a metagenomic pan-virus array We have used a metagenomic microarray to detect genomic RNA from human pegivirus in serum and cerebrospinal fluid from a patient suffering from severe encephalitis. We report a case of severe encephalitis where the only microbe detected in the CNS was human pegivirus (HPgV), hitherto only known to cause asymptomatic infections in humans. In both cases it is uncertain if HPgV is pathogenic but it is noteworthy to detect a virus at a high viral load in the CNS. More recently, both positive and negative RNA-strands of HPgV was detected in post mortem brain tissue from a multiple sclerosis (MS) patient, implying that the virus was replicating in the brain tissue [1] . All CSF samples where negative for HPgV but one encephalitis patient was positive in serum (Ct 27.2).
cord-291930-n7wq09rq	2010	
cord-292578-co5essuw	2020	OBJECTIVES: The aim of this study was to assess the performance of a novel multiplexed immunoassay for the simultaneous detection of antibodies against SARS-CoV-2 trimeric spike (S), spike receptor binding domain (RBD), spike N terminal domain and nucleocapsid antigen and a novel pseudo-neutralisation assay. METHODS: A multiplexed solid-phase chemiluminescence assay (Meso Scale Discovery) was evaluated for the simultaneous detection of IgG binding to four SARS-CoV-2 antigens and the quantification of antibody-induced ACE-2 binding inhibition (pseudo-neutralisation assay). CONCLUSION: Excellent sensitivity for IgG detection was obtained over 14 days since onset of symptoms for three SARS-CoV-2 antigens (S, RBD and N) in this multiplexed assay which can also measure antibody functionality. In summary, the MSD multiplexed coronavirus panel assay evaluated in this study is highly reproducible, specific and sensitive for the detection of anti-SARS-CoV-2 antibody over 14 days since the onset of COVID-19 symptoms.
cord-293890-thfros7x	2020	
cord-294155-94skyx5f	2007	
cord-295189-bz3gi15h	2015	STUDY DESIGN: Data were collected from travellers arriving at Christchurch International Airport, New Zealand, during the winter 2008, via a symptom questionnaire, temperature testing, and respiratory sampling. CONCLUSIONS: The high prevalence of respiratory virus infections caused by viruses other than influenza in this study, many with overlapping symptotology to influenza, has important implications for any screening strategies for the prediction of influenza in airline travellers. In a 2008 study, we sought to assess the prevalence of influenza infection in symptomatic and asymptomatic arriving international airline travellers and whether using a symptom-screening questionnaire and temperature measurement could reliably predict seasonal influenza infection [16] . The high prevalence of respiratory virus infections caused by viruses other than influenza in this study, many with overlapping symptoms to influenza, has important implications for any screening strategy for the prediction of influenza in airline travellers.
cord-295600-xe3ruu9a	2015	OBJECTIVES: To analyze the kinetics of T-lymphocyte subsets in LTR and the association between nadir CD4 T-cell count and viral infections after transplantation. STUDY DESIGN: Serial measurements of peripheral blood CD4 and CD8 T-cell counts obtained during the first year post-transplantation from 83 consecutive LTR and their correlation with both viral OI and community-acquired infections post-transplantation were retrospectively analyzed. To analyze the kinetics of CD4 and CD8 T-cell counts in peripheral blood obtained from LTR during the first year after transplantation and evaluated the association between nadir CD4 T-cell count with the development of viral infections posttransplantation. The present study provides a detailed analysis of T-cell subsets in peripheral blood during the first 12 months after lung transplantation and correlates these immunological data with infectious complications. Although the study has limitations, our findings reveal an association between nadir CD4 T-cell count and incidence of infectious episodes in LTR, suggesting that, particularly in patients with low CD4 T-cell numbers, monitoring of infections should be intensified to improve early detection and treatment.
cord-295873-kykyubdq	2015	
cord-295957-s17z2ccf	2020	BACKGROUND: So far, one of the major drawbacks of the available molecular assays for the diagnosis of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) is the need for viral nucleic acid extraction from clinical specimens. CONCLUSIONS: The high sensitivity and specificity of this new assay indicate that it is promising for laboratory diagnosis, enabling highspeed detection in just over one hour, which is significantly faster than the up to five hours currently required by traditional extraction followed by amplification technologies, thus allowing prompt decision making regarding isolation of infected patients. Moreover, to evaluate the performance of the test in a different clinical specimen, a total of 33 Broncho-Alveolar Lavage (BAL) collected for COVID-19 diagnosis between 20 March and 03 April 2020 were also analysed in parallel with the Simplexa™ COVID-19 Direct assay and the routine laboratory method, based on the WHO protocols (7, 8) , using the Abbot m2000 extraction platform.
cord-296847-r752bcsu	2007	In the present study, we quantified the hRSV RNA load (both subgroups A and B) in NPAs from hRSV-infected infants by quantitative RT-PCR to investigate the possibility of defining the etiologic role of hRSV in the current ARTI episode from a series of infants admitted to the hospital either with a single hRSV infection or with two or three simultaneous or sequential viral infections including hRSV. NPAs from a series of 253 infants aged less than 1 year and admitted to the hospital in the period November 2005-May 2006 with a diagnosis of ARTI were examined for hRSV as well as other respiratory viruses by DFA, CC, and qualitative RT-PCR, as reported (Rovida et al., 2005) . In addition, 14 infants with multiple simultaneous (coinfections) or sequential (within 30 days) infections in the respiratory tract (including hRSV) were examined prospectively in order to identify the virus responsible for the current ARTI episode.
cord-297365-11es4w0u	2020	METHODS: We retrospectively summarized the characteristics, treatment and outcomes of pediatric cases in Wuhan children''s hospital which was the only designated hospital for children with COVID-19 in Hubei Province. In December 2019, a cluster of cases caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in Wuhan, Hubei The observed cases were pediatric patients who were discharged from the Wuhan Children''s Hospital from December 8, 2019 to February 29, 2020 and diagnosed with COVID-19. Chinese Center for Disease Control and Prevention has analyzed the illness severity of 44415 adult and pediatric patients, and found that severe and critical cases accounted for nearly 20% [9] . A epidemiological study in Chinese children with COVID-19 (n=2143) showed that severe and critical illness accounted for J o u r n a l P r e -p r o o f 5.8% [10, 11] . Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study
cord-299388-okiqmy6e	2017	STUDY DESIGN: Cohorts: 142 (2004) and 172 (2014) infants at ages zero to 12 months; clinical diagnosis of AVB; medical care in hospital and genetic screening of nasopharyngeal secretion for respiratory viruses. AVB seems to be correlated with seasonality, gender, gestational birth age, birth weight, breastfeeding, tobacco exposure, crowding, maternal education and viral etiology [7] [8] [9] [10] . In this study, epidemiologic risk factors, clinical features and viral identification in nasopharyngeal secretion by polymerase chain reaction (PCR) were evaluated and compared in two cohorts (2004 [11] and 2014) with 314 infants with AVB. Epidemiologic data [gender, age at attendance, seasonality, gestational age, birth weight, breastfeeding, tobacco exposure, crowding (more than 5 people at home) and maternal education] were analyzed. Risk factors for respiratory syncytial virus associated with acute lower respiratory infection in children under five years: systematic review and meta-analysis
cord-299537-lbx1plqx	2010	
cord-299664-nexq5ntj	2014	OBJECTIVES AND STUDY DESIGN: The performance of the FilmArray Respiratory Panel (RP) and Verigene RV+ (RV+) were compared in a retrospective analysis of 89 clinical specimens previously determined to be positive for the following viruses by our test of record, Prodesse (Pro): influenza A (29, FluA), influenza B (13, FluB), respiratory syncytial virus (12, RSV), human metapneumovirus (10, hMPV), parainfluenza (14, PIV), and adenovirus (10, AdV). More recently, less complex sample-toresult molecular platforms such as Xpert Flu Assay (Cepheid), RP (BioFire Diagnostics), RV+ (Nanosphere), eSensor Respiratory Viral Panel (GenMark Diagnostic) and Liat Influenza A/B (Iquum) have been introduced into the marketplace which have the potential to Specimens, collected between January 2008 and February 2012 and stored at −80 • C, were selected based on results from original testing.
cord-300018-3uzau7if	2020	authors: Mak, Gannon C.K.; Lau, Angela W.L.; Chan, Andy M.Y.; Chan, Desmond Y.W.; Tsang, Dominic N.C. title: The D614G substitution in the S gene and clinical information for patients with COVID-19 detected in Hong Kong In an attempt to understand the relevance of D614G substitution among COVID-19 patients in Hong Kong, full length S gene sequences from severe and non-severe cases were examined. Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 The SARS-CoV-2 Spike Protein D614G
cord-300316-r54ksiy3	2016	
cord-301254-093yih5n	2010	OBJECTIVES: The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. CONCLUSIONS: Duration of symptoms significantly affects the detection rate of respiratory pathogens by multiplex real-time PCR in nasopharyngeal swab samples from adult patients with respiratory infections. The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. All patients still positive for the same agent on follow-up had a higher Ct-value (corresponding to a lower Table 2 Follow-up (10 ± 2 days after initial visit) test result from analysis with real-time PCR of nasopharyngeal/throat swab specimens.
cord-302125-96w0nh9q	2020	title: Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris Sequential SARS-CoV-2 IgG assays as confirmatory strategy to confirm equivocal results: Hospital-wide antibody screening in 3,569 staff health care workers in Paris Running title: Sequential SARS-CoV-2 serology testing in health-workers Hélène Péré 1,2,3 , Maxime Wack 4 , Benoit Védie 5 , Nathalie Demory Guinet 6 , Kassis Chikani Najiby 7 , Laurence Janot 6 , Laurent Bélec 1,2,3 , David Veyer 1, 8 surface protein, with the high-throughput UniCel DxI 800 Access Immunoassay System (Beckman Coulter), to increase hospital productivity in SARS-CoV-2 IgG serology testing. SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients The authors are also grateful to Beckman Coulter, France, for providing the ACCESS SARS-CoV-2 IgG kits for the study.J o u r n a l P r e -p r o o f
cord-302528-wmxw9e0c	2020	• ID NOW EUA SARS-CoV-2 assay had an overall agreement of 78.7% when compared to the standard of care reference methods. While most of the SARS-CoV-2 EUA assays for molecular detection must be performed in moderate-to high-complexity clinical laboratories, a few are authorized as point-of-care devices, such as the Abbott ID NOW. In addition to clinical laboratories, this assay can be performed by trained non-laboratory personnel in patient care settings such an Emergency Departments, physician''s offices or pharmacies, potentially bringing diagnostic testing for SARS-CoV-2 closer to the patient (1). Among the marketing information for this new assay, potential advantages include its reported sensitivity (stated limit of detection (LOD) of 125 genome equivalents/ml) and run time (detection of SARS-CoV-2 RNA as early as five minutes and a negative result in thirteen minutes). Residual positive and negative nasopharyngeal patient samples collected in VTM were tested using the ID NOW EUA assay.
cord-302864-2xnq1oq7	2020	
cord-302896-3zvjyl3g	2008	STUDY DESIGN: HCoV-NL63 was sought by RT-PCR in 510 consecutive lower respiratory tract (LRT) samples, collected from 433 Central-Southern Italy patients over a 1-year period. Based on phylogenetic analysis of different genome regions, several subtypes, currently co-circulating in the human population, have been identified in France, Canada, Australia, Belgium, Netherlands, Sweden, China and Korean (Arden et al., 2005; Bastien et al., 2005a; Chiu et al., 2005; Han et al., 2007; Koetz et al., 2006; Moës et al., 2005; Vabret et al., 2005; van der Hoek et al., 2004) . New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia Genetic variability of human coronavirus OC43-, 229E-, and NL63-like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients
cord-307261-0a3iztns	2012	title: Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children Samples were de-identified and assayed in parallel using two different, broadly multiplexed PCR systems: ResPlex™ II Panel v2.0 (ResPlex), Qiagen, Hilden, Germany and FilmArray(®) Respiratory Panel (FilmArray), Idaho Technology Inc., Salt Lake City, UT. Two broadly multiplexed PCR systems were compared to each other and to a panel of laboratory developed tests for the detection of respiratory viral pathogens in clinical respiratory tract specimens from pediatric immunocompromised children. FilmArray detected viral targets: adenovirus, bocavirus, coronavirus 229E, HKU1, NL63, OC43, enterovirus, hMPV, human rhinovirus, influenza virus types A and B, parainfluenza viruses 1, 2, 3 and 4, and RSV. The current study, to our knowledge, is the first reported that compares the FilmArray with the ResPlex II v2.0 for the direct detection of viral agents in clinical respiratory tract specimens from immunocompromised children.
cord-307602-2cmgu7rf	2007	BACKGROUND: Human rhinoviruses (HRVs) are some of the earliest identified and most commonly detected viruses associated with acute respiratory tract infections (ARTIs) and yet the molecular epidemiology and genomic variation of individual serotypes remains undefined. RESULTS: Phylogenetic studies of complete coding sequences defined HRV-QPM as a novel member the genus Rhinovirus residing within the previously described HRV-A2 sub-lineage. CONCLUSIONS: We present the molecular characterisation and preliminary clinical impact of a newly identified HRV along with sequences representing additional new HRVs. Acute respiratory tract infections (ARTIs) are a leading cause of human morbidity worldwide and are most frequently viral in origin. We further investigated one of these putative viruses and herein present the complete polyprotein coding sequence of a novel HRV, HRV-QPM, which was first detected in an infant with bronchiolitis.
cord-308921-lpcjhxvg	2019	
cord-309763-8eywr57j	2005	
cord-310140-h7uwl0pb	2005	STUDY DESIGN: Respiratory virus proficiency panels were produced from diluted stocks of respiratory viruses provided and tested by four reference laboratories. Laboratories performing respiratory molecular tests want to report accurate and reliable results regardless of the type of assay in use and one of the best ways to assess performance is to participate in proficiency programmes, enabling laboratories to evaluate their performance (Schirm et al., 2002; Schloss et al., 2003; Noordhoek et al., 2004; Verkooyen et al., 2003) . Laboratories who had expressed an interest to QCMD in participating in a proficiency programme for molecular detection of respiratory viruses were asked to complete a questionnaire detailing technical aspects of the assays they had applied. In this study, samples were grown in cell culture and dilutions were made so sensitivity and limited specificity of assays for these viruses could be assessed.
cord-310171-1fmsxx2s	2014	Since the sensitive molecular methods for detection of viruses are more and more common, several recent studies highlight the clinical importance of respiratory viruses especially during exacerbation of asthma, chronic obstructive pulmonary disease (COPD) or CF [3] [4] [5] [6] [7] [8] [9] . In the present study, we reported detection of respiratory viruses from adult patients with CF during either routine visit or acute pulmonary exacerbation. To conclude, we have reported a relatively high frequency of respiratory viruses in a cohort of CF adult patients from France, and demonstrated for the first time that rhinovirus detection including newly identified HRV-Ca variants are the most frequent and significantly associated with respiratory exacerbations. Respiratory viruses in children with cystic fibrosis: viral detection and clinical findings Association of respiratory viral infections with pulmonary deterioration in patients with cystic fibrosis
cord-310631-ru5f69qg	2020	
cord-310680-klywz85w	2005	
cord-311275-ysr9nqun	2019	There were a few data of adult hospitalized patients with RSV infection, with high complications, in Thailand; [3, 12, 13] however, additional clinical data are required for planning patient management and also disease prevention in this region. RSV, respiratory syncytial virus; ARI, acute respiratory illness; COPD, chronic obstructive pulmonary disease; HAP, hospital-acquired pneumonia; VAP, ventilator-associated pneumonia. The pre-existing coronary arterial disease (CAD) was the risk factor of overall cardiovascular complications in hospitalized adult patients with RSV infection with odds ratio 6.18, (95% CI 1.18-32.5), p = 0.03, adjusted for age, sex, HT, DLP, DM, pre-existing CHF, arrhythmia, and VHD. The prospective study of all adult hospitalized patients with acute respiratory illness should be conducted to determine the prevalence, clinical manifestations, and outcomes of the virus. Most of the adult hospitalized patients with RSV infections aged ≥ 50 years old and had pre-existing cardiopulmonary diseases, hematologic malignancy, immunocompromised hosts, and DM.
cord-311633-i9ret7bw	2020	We herein evaluated the analytical performances of the CE IVD-labeled Abbott SARS-CoV-2 IgG assay (Des Plaines, IL, USA) carried out with the automated Abbott Architect™ i2000 platform at Hôpital Européen Georges Pompidou, Paris, France, using serum sample panels obtained from health-workers with COVID-19 history confirmed by positive nucleic acid amplification-based diagnosis and from patients randomly selected for whom serum samples were collected before the COVID-19 epidemic. Interestingly, several inpatients hospitalized in COVID-19 free areas suffering from a wide range of unexplained clinical features including cardiac, vascular, renal, metabolic and infectious disorders, were unexpectedly found seropositive for SARS-CoV-2 IgG by systematic routine serology, suggesting possible causal involvement of SARS-CoV-2 infection. To analytically and clinically validate the Abbott SARS-CoV-2 IgG assay, we tested pre-epidemic sera, sera from pauci-symptomatic health-worker with SARS-CoV-2 positive RT-PCR and sera from hospitalized patients from both the COVID-positive area and the COVID-free area.
cord-312971-r9sggqh8	2020	
cord-313375-rs3jjiuj	2010	
cord-313749-f2ct57em	2007	title: Multiplex real-time PCR for detection of respiratory tract infections STUDY DESIGN: An assay targeting influenza virus A (IfA) and B (IfB), parainfluenza 1-3 (PIV), human metapneumovirus (MPV), respiratory syncytial virus (RSV), rhinovirus (RV), enterovirus (EV), adenovirus (AdV), human coronaviruses (229E, OC43, NL63), M. We developed a real-time PCR procedure, based on automated specimen extraction and multiplex amplification, at a relatively low cost (D 33). We believe that a combination of low cost, high accuracy and prompt result delivery is the key to achieving a wide clinical use of molecular diagnostics of respiratory infections. Further studies of respiratory infection aetiologies in different patient categories, and of the clinical utility of this and similar multiplex assays, need to be carried out. Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4
cord-313821-5f5b107l	2014	
cord-314028-sf8zt9r9	2020	From March 7 to May 3, during the lockdown phase, 61 requests of telemedicine consultation (28, 45.9%, males; mean age ± standard deviation, 4.69 ± 3.22 years) to the paediatric infectious disease specialist in the hospital by the primary care paediatricians were made. A total of 55 (90.2%) paediatric problems that without telemedicine support could have led the patient to the emergency room of the hospital were solved in the community: 30 (54.5%) children with fever of unknown origin, 20 (36.4%) with skin rash, 3 (5.5%) with suspected primary immunodeficiency and 2 (3.6%) with acrocyanosis. This experience shows that during the COVID-19 outbreak, the use of telemedicine for the management of paediatric infectious diseases permitted us to avoid hospital access J o u r n a l P r e -p r o o f in 90% of the cases, favouring reduction of the pressure on the hospitals. Our experience shows that telemedicine may be an easy and effective measure to solve many paediatric problems in the community during COVID-19 outbreak, reducing emergency room visits.
cord-314829-tmgmqtjq	2020	
cord-314888-i7nn2e3m	2020	
cord-315782-tx2vqr64	2006	
cord-316723-srenbxa7	2004	Amino acid residues 450–650 of the spike (S) glycoprotein of SARS-CoV (S450-650) contains dominant epitopes for anti-viral antibodies (Abs) in patient sera. However, so far there is no enzyme-linked immunosorbent assay (ELISA) available for easier and more sensitive detection of anti-S Abs. Our computer-assisted analysis suggested that amino acid residues 450-650 of the S glycoprotein (S450-650) of SARS-CoV is largely solvent accessible and likely to contain dominant B cell epitopes. (2004) showing that residues 441-700 of the S protein of SARS-CoV contained dominant epitope(s) for anti-S Abs in patient sera, as determined in WB assays. All patient sera were tested for anti-SARS-CoV IgG Abs using an ELISA kit produced by Huada Institute (see below). Sera from three convalescent SARS patients and two healthy individuals were serial diluted and tested in the S450-650-based ELISAs, which detected anti-S IgG Abs in a specific and sensitive manner, with the reactivity end point from 1:400 to 1:800 diluted patient sera (Fig. 2) .
cord-318012-bg9y2nsp	2014	BACKGROUND: The management of children with community-acquired pneumonia (CAP) is largely influenced by the development of new molecular diagnostic tests that allow the simultaneous detection of a wide range of pathogens. CONCLUSIONS: These findings highlight the huge proportion of CAP of viral origin, the high number of co-infection by multiple viruses and the low number of bacterial CAP, notably in children under 5 years, and address the need to re-evaluate the indications of empiric antimicrobial treatment in this age group. The aim of the present study was to document the presence of a large variety of pathogens in respiratory specimens from children attending the Pediatric Emergency Department of the University hospital of Saint-Etienne, France, during a six-month period and presenting a CAP based on clinical and radiological evidence. A single center epidemiological observational study was conducted over a six-month period (November 2012 to April 2013) on children aging from one month to 16.5 years and presenting with CAP at the Pediatric Emergency Department of the University hospital of Saint-Etienne, France.
cord-319864-t6ql9hz2	2020	In silico analysis and clinical sample testing showed that the primers/probes designed by the CDC were specific to the SARS-CoV-2 as they accurately detected all reactive samples with an assay LoD of 200 copies/ml. In this study, we sought to describe a modified CDC SARS-CoV-2 assay validation and compare its performance and workflow to that of the NeuMoDx SARS-CoV-2 and DiaSorin Simplexa Covid-19 Direct assays using respiratory specimens. The primer/probe sets used in this validation were selected from regions of the SARS-CoV-2 virus nucleocapsid (N) gene and were described in the CDC EUA protocol for COVID-19 diagnostic testing (7) . Of the 43 samples used for comparison between modified CDC SARS-CoV-2 assay and Simplexa Covid 19 Direct assay, 37 samples were run within 2 days and 6 were run within 5 days of first testing. The clinical performance comparison between NeuMoDx SARS-CoV-2 assay, Simplexa Covid-19 Direct assay, and the modified CDC SARS-CoV-2 assay showed an overall agreement of 100%.
cord-320156-xs936r6u	2014	
cord-321287-mh2j2koa	2020	
cord-322220-mlphue1r	2007	
cord-323567-1397kds0	2007	
cord-324125-wau2xq0x	2013	
cord-325120-jlrievxl	2015	title: Diagnostics-in-a-Suitcase: Development of a portable and rapid assay for the detection of the emerging avian influenza A (H7N9) virus STUDY DESIGN: A suitcase laboratory "Diagnostics-in-a-Suitcase" (56 cm × 45.5 cm × 26.5 cm) containing all reagents and devices necessary for performing a reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed. Several real-time RT-PCRs were developed for sensitive detection of avian influenza (H7N9) virus [15, 16, 19] . Development of real time RT-PCR assays for detection of type A influenza virus and for subtyping of avian H5 and H7 hemagglutinin subtypes Detection of a novel avian influenza A (H7N9) virus in humans by multiplex one-step real-time RT-PCR assay Development of a reverse transcription loop-mediated isothermal amplification assay for the rapid diagnosis of avian influenza A (H7N9) virus infection Rapid and sensitive detection of H7N9 avian influenza virus by use of reverse transcription-loop-mediated isothermal amplification
cord-326816-a7yovhvk	2018	
cord-328290-kbysppgb	2015	Community-acquired respiratory virus Isothermal PCR Turn-around time (TAT) Antigen detection Nucleic acid amplification testing (NAT) a b s t r a c t Background: Rapid diagnosis of influenza is important for controlling outbreaks and starting antiviral therapy. Objectives: To evaluate the performance of a rapid isothermal NAT and two DADs. Study design: During February-May 2014, we tested 211 consecutive patients with influenza-like illness using a commercial isothermal NAT (Alere TM Influenza A&B) as well as the DAD Sofia ® Influenza A + B and BinaxNOW ® Influenza A&B for detection of influenza-A and -B virus. Results: Compared to RespiFinder-22 ® , the isothermal NAT Alere TM Influenza A&B, and the DAD Sofia ® Influenza A + B and BinaxNOW ® Influenza A&B had sensitivities of 77.8%, 59.3% and 29.6%, and specificities of 99.5%, 98.9% and 100%, respectively, for the first 211 patient samples.
cord-329052-jan20ljs	2020	
cord-331707-kfja1i6s	2018	The main objective of this study is to describe the seasonality, the prevalence, the genetic diversity and the clinical features related to respiratory EV from the paediatric cases attended at a tertiary hospital in Barcelona (Catalonia, Spain) during the 2014-2017 seasons. From October 2014 (week 40/2014) to May 2017 (week 20/2017), upper (nasopharyngeal aspirates or swabs) and lower (bronchoalveolar lavages, bronchoaspirates and tracheal aspirates) respiratory tract specimens were collected for respiratory viruses'' laboratory-confirmation from paediatric patients (< 17 years old) with suspicion of acute respiratory tract infection (RTI) or enterovirus infection who were [29] [30] [31] [32] [33] [34] [35] attended at the emergency department or admitted to the hospital. The present study describes the epidemiology, the genetic diversity and the clinical features related to respiratory EV laboratory-confirmed infections in paediatric patients attended at a tertiary university hospital in Spain.
cord-332723-rz1iilsv	2020	Since 30% of nasopharyngeal swab specimens have a SARS CoV-2 Ct >30 and thus detection of virus in low titers is clinically relevant, a sample with a high titer was diluted and each 10 fold dilution was tested in triplicate and compared against 6 other EUA approved SARS CoV-2 assays. These data suggested that the BioFire® RP2.1 panel, along with four other SARS CoV-2 assays (Roche cobas, Cepheid Xpert Xpress, BioFire® Defense COVID19, and NECoV19), consistently detected viral RNA at the 10-7 dilution. Ten-fold serial dilutions of a natural nasopharyngeal swab specimen with known high positivity for SARS-CoV-2 RNA (E gene detected at a cycle threshold (Ct) of 16.6 by the cobas SARS-CoV-2 assay) were prepared with a diluent of pooled NPS. Comparison of SARS-CoV-2 Detection from Nasopharyngeal Swab Samples by the Roche cobas(R) 6800 SARS-CoV-2 Test and a Laboratory-Developed Real-Time RT-PCR test
cord-335067-tg66h99q	2013	The realisation that many newly discovered and/or emerging pathogens have zoonotic origins has prompted much interest in the nature of the non-human reservoirs and biological characteristics that enable pathogens to jump between host species. 1 Here, we focus on an important group of pathogens -RNA viruses -and consider how taxonomic diversity and various aspects of ecological diversity -host range, route of infection and transmissibility -are related to one another. 2 We catalogue ICTV-recognised RNA virus species for which we can find convincing evidence of natural human infection in the peer-reviewed scientific literature (see Ref. 3 for more methodological details). Our procedure reveals a total of 158 human infective RNA virus species from 47 genera and 17 families (with one genus unassigned to a family). The overlap is also illustrated in that 47 out of 60 recognised mammal virus genera contain human infective species, as do 17 out of 19 families. There are 68 species of vector-borne RNA virus that can infect humans.
cord-335208-xv2evahh	2020	Parents filled out symptom diaries and collected nasal swabs when their children were symptomatic and asymptomatic. We conducted a pilot study to examine the prevalence and clinical impact of different RV species in young children with CF and to assess the feasibility of parental home-sampling in this population. This study suggests that although RV is the most prevalent virus in young children with CF, it is not always associated with symptomatic infections. Role of respiratory viruses in pulmonary exacerbations in children with cystic fibrosis Feasibility of parental collected nasal swabs for virus detection in young children with cystic fibrosis Respiratory viruses in children with cystic fibrosis: viral detection and clinical findings. Frequency and Duration of Rhinovirus Infections in Children With Cystic Fibrosis and Healthy Controls: A Longitudinal Cohort Study Human rhinovirus species C infection in young children with acute wheeze is associated with increased acute respiratory hospital admissions
cord-335891-j78pnwgk	2020	The 180-and 111-nucleotide duplications occurred in A2c lineage G protein increased in prevalence throughout the study, in addition to short genetic changes observed in other HMPV lineages. The 180-and 111-nucleotide duplications occurred in A2c lineage G protein increased in prevalence throughout the study, in addition to short genetic changes observed in other HMPV lineages. Novel variants carrying duplications might present an evolutionary advantage due to an improved steric shielding, which would have been responsible for the reported increasing prevalence and the association to LRTI in adults. The aims of this study were to describe circulation pattern, genetic diversity and clinical impact of HMPV in paediatric and adult population attended at a tertiary university hospital in Barcelona from the 2014-2015 to the 2016-2017 seasons, focusing on the emergence and spread of variants carrying these two nucleotide duplications.
cord-336237-hmczy0am	2020	authors: Kitagawa, Yutaro; Orihara, Yuta; Kawamura, Rieko; Imai, Kazuo; Sakai, Jun; Tarumoto, Norihito; Matsuoka, Masaru; Takeuchi, Shinichi; Maesaki, Shigefumi; Maeda, Takuya title: Evaluation of rapid diagnosis of novel coronavirus disease (COVID-19) using loop-mediated isothermal amplification In this study, we evaluated the effectiveness of the Loopamp® 2019-SARSCoV-2 Detection Reagent Kit, which uses loop-mediated isothermal amplification (LAMP) technology. The RT-LAMP test kit amplified the targeted RNA of a SARS-CoV-2 isolate with a detection limit of 1.0 × 101 copies/μL, which was comparable to the detection sensitivity of quantitative reverse transcription PCR (RT-qPCR). To evaluate the analytical sensitivity of the RT-LAMP method, we used purified and quantified total RNA of SARS-CoV-2, which was provided by the National Institute of Infectious Diseases, Japan, as a standard specimen for the molecular diagnosis of COVID-19. Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay
cord-336535-r3a57m57	2020	So far, there is limited data on how recently commercially available, high-throughput immunoassays, using different recombinant SARS-CoV-2 antigens, perform with clinical samples. Five follow-up samples of three individuals were only detected in either an S and/or N protein-based assay, indicating an individual different immune response to SARS-CoV-2 and the influence of the used assay in the detection of IgG antibodies. This study aims to provide a quick overview on some of these assays (two commercially available ELISA assays, four automated immunoassays and a plaque reduction neutralization test (PRNT)) focusing on the detection and neutralization capacity of IgG antibodies in follow up serum or plasma samples of individuals with PCR-diagnosed infections with SARS-CoV-2. The commercially available assays examined in our study, generated consistent results regarding the detection of SARS-CoV-2-IgG antibodies. Interestingly, in samples of three individuals with mild clinical course of COVID-19, examined in our study (1, 2, 3 in The automated immunoassays demonstrated a higher overall sensitivity than the ELISA based assays.
cord-336636-xgfw21hk	2020	Abstract Background Redondovirus (ReDoV) is a recently discovered circular, Rep-encoding single-stranded DNA (CRESS-DNA) virus in humans. While attempting to study human virome in bronchoalveolar lavage (BAL) samples of lung transplant patients [1, 2] , Abbas and colleagues identified sequence reads that aligned with low-coverage to a poorly characterized circovirus, named porcine stool-associated circular virus-5 (PoSCV-5) [3] . These observations suggest that ReDoV is not part of the normal oral and/or respiratory microflora of humans, differently to other circular single-stranded DNA viruses [5, 15] and that its infection might be involved in clinically relevant disorders. Redondoviridae, a family of small, circular DNA viruses of the human oro-respiratory tract associated with periodontitis and critical illness Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample
cord-337799-mc1oqhf4	2020	STUDY DESIGN: Analytical sensitivity for the detection of SARS-CoV-2 virus was determined by limit of detection (LOD) using PCR as a reference method. Clinical sensitivity of RAD kits ranged from 22.9% to 71.4% for detecting specimens from COVID-19 patients. CONCLUSIONS: Although RAD kits were less sensitive than RT-PCR, understanding the clinical characteristics of different RAD kits can guide us to obtain suitable specimens for testing. Besides RT-PCR, rapid antigen detection (RAD) kits for qualitative determination of SARS-CoV-2 antigen are available. The purpose of this evaluation is to assess analytical sensitivity of the three SARS-CoV-2 RAD kits by means of limit of detection (LOD) using a set of serial tenfold dilution samples; and It means that if we set a cut off by means of ≤day X after symptom onset for performing RAD kits, we will miss another group of specimens having a similar high viral load.
cord-338923-hc7gagnq	2020	We compared the performance of six commercial immunoassays for the detection of SARS-CoV-2 IgG, IgA and IgM antibodies, including four automated assays [Abbott SARS-COV-2 IgG (CE marked), Diasorin Liaison® SARS-CoV-2 S1/S2 IgG (research use only, RUO), and Euroimmun SARS-CoV-2 IgG and IgA (CE marked)], and two rapid lateral flow (immunocromatographic) tests [Acro Biotech 2019-nCoV IgG/IgM (CE marked) and Xiamen Biotime Biotechnology SARS-CoV-2 IgG/IgM (CE marked)] with a microneutralisation test (MNT). Forty-one out of 62 COVID-19 patients showed neutralising antibodies.The specificity and sensitivity values of the commercial tests against MNT, respectively, were as follows: 95.1%/80.5% (Abbott Architect SARS-CoV-2 IgG), 94.9%/43.8% (Diasorin Liaison SARS-CoV-2 IgG; RUO), 68.3%/87.8% (Euroimmun SARS-CoV-2 IgA), 86.6%/70.7% (Euroimmun SARS-CoV-2 IgG), 74.4%/56.1% (Acro 2019-nCoV IgG), 69.5%/46.3% (Acro 2019-nCoV IgM), 97.5%/71.9% (Xiamen Biotime SARS-CoV-2 IgG), and 88.8%/81.3% (Xiamen Biotime SARS-CoV-2 IgM). In this study, we assessed the specificity and sensitivity of six commercial immunoassays for the detection of SARS-CoV-2 antibodies, including two rapid lateral flow tests, in comparison with a neutralisation test.
cord-340336-u59l0taa	2020	 -Of all 356 samples tested, triplexing demonstrated 99.2% (n=353/356) assay agreement Abstract: Background -The novel respiratory virus SARS-CoV-2, responsible for over 380,000 COVID-19 related deaths, has caused significant strain on healthcare infrastructure and clinical laboratories globally. Methods -Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) -a CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. Methods -Nasopharyngeal swabs submitted to UW Virology for SARS-CoV-2 clinical testing were extracted, amplified by our laboratory developed test (LDT) -a CDC-based quantitative reverse transcriptase PCR reaction -and analyzed for agreement between the multiplexed assay. To increase throughput of SARS-CoV-2 testing in clinical laboratories, we designed a multiplexed real-time quantitative reverse transcription PCR (qRT-PCR) assay utilizing primers and probe sets from the CDC combined with an internal extraction control.
cord-343800-nbydaoac	2020	We evaluated the recently CE-approved rapid POCT SD-Biosensor for SARS-CoV-2 nucleoprotein detection in nasopharyngeal secretions from 330 patients admitted to the Emergency Room for a suspect of COVID-19 and travelers returning home from high risk countries. Point-of-care diagnostic tests (POCTs) for detecting viral antigens in clinical samples would be very helpful for the diagnosis of COVID-19 [2] either as mass-screening or first aid tests at the emergency room. To evaluate a recently CE-approved POCT, the STANDARD Q COVID-19 Ag (SD-Biosensor, RELAB, I), for the detection of SARS CoV-2 nucleoprotein in NP swabs in comparison with the gold standard RT-PCR. POCTs for the detection of SARS-CoV-2 J o u r n a l P r e -p r o o f antigens are quite promising; however, the principal concerns are the false-negative rate due to low viral loads [3] [4] [5] [6] [7] [8] . Evaluation of novel antigen-based rapid detection test for the diagnosis of SARS-CoV-2 in respiratory samples
cord-344979-ngujhhp6	2020	OBJECTIVES: To establish a rapid RT-qPCR protocol for the detection of SARS-CoV-2 without the need of RNA extraction suitable for all respiratory materials. MATERIAL AND METHODS: Different SARS-CoV-2 positive respiratory materials from our routine laboratory were used as crude material after heat inactivation in direct RT-qPCR with the PrimeDirect™ Probe RT-qPCR Mix (TaKaRa). RESULTS: The protocol for the detection of SARS-CoV-2 in crude material used a prepared frozen-PCR mix with optimized primers and 5 µl of fresh, undiluted and pre-analytically heat inactivated respiratory material. To establish a rapid RT-qPCR protocol for the detection of SARS-CoV-2 without the need of RNA extraction suitable for all respiratory materials. The protocol for the detection of SARS-CoV-2 in crude material used a prepared frozen-PCR mix with optimized primers and 5 µl of fresh, undiluted and pre-analytically heat inactivated respiratory material. Ct values of 91 SARS-CoV-2 positive samples analyzed in direct comparison by RT-qPCR using different primary materials and extracted RNA showed a significant correlation.
cord-345603-mirsz6m8	2020	Self-collected swabs in the community for SARS-CoV-2, the agent of COVID-19, and for other respiratory viruses offers potential significant benefit in the current pandemic by J o u r n a l P r e -p r o o f reducing requirement for PPE, limiting exposure of patients and staff to infection, increased convenience and access for patients and timeliness of a sample receipt. 9 Recent reports on SARS-CoV-2 in respiratory specimens indicate early high viral loads in symptomatic and asymptomatic patients in a variety of clinical specimens including nasal and throat swabs, sputum and saliva samples. The aim of this study was to compare prospectively the performance of HC with separate SC nasal (SCN) and throat swabs (SCT) and the combination of the two (SCNT) for respiratory viruses including SARS-CoV-2.
cord-349485-iomk99lv	2020	title: Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples To rapidly identify unrecognized cases in hospitals in an efficient, resource-saving and cost effective manner we propose an ad hoc laboratory-based surveillance approach for SARS-CoV-2. It is based upon minipool (MP) testing of nucleic acid preparations of respiratory samples submitted to laboratories for routine diagnostics. The workflow comprises individual nucleic acid (NA) extraction of respiratory samples, pooling of extracted NA samples in batches of 10 and SARS-CoV-2 specific real-time RT-PCR. We report a diagnostic workflow for the laboratory-based surveillance of SARS-CoV-2 in a rapid and cost effective manner. From a public health perspective an easy to establish and cost effective laboratory-based screening strategy may assist in rapid case detection, surveillance and ultimately in a better understanding of this epidemic (7) .
cord-349541-7g50vg14	2020	key: cord-349541-7g50vg14 title: SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England cord_uid: 7g50vg14 Please cite this article as: Poulikakos D, Sinha S, Kalra PA, SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England, Journal of Clinical Virology (2020), doi: https://doi.org/10.1016/j.jcv.2020.104545 Amongst the 22 (7·8%) HCW with previous SARS-Cov-2 PCR nasopharyngeal swabs, 2 were positive, 12 were negative, and 7 did not disclose the result. Positive SARS-Cov-2 IgG was detected in 17 (6%) HCW and 6 (35·3%) had been asymptomatic. All IgG positive cases were in DIPC HCW (17 out of 195; 8·7%). One IgG positive HCW did not disclose ethnicity. SARS-CoV-2-specific antibody detection in healthcare workers in Germany with direct contact to COVID-19 patients Hospital-Wide SARS-CoV-2 Antibody Screening Analytical performances of a chemiluminescence immunoassay for SARS-CoV-2 IgM/IgG and antibody kinetics First experience of COVID-19 screening of health-care workers in England
cord-349782-djzxkus2	2020	On top of this, they have dedicated their time to providing the global diagnostic community with a much needed initial comparison of commercially available COVID-19 RT-PCR kits, which was recently published in the Journal of Clinical Virology (1). Obviously, our selection of 13 SARS-CoV-2-positive clinical samples does not reflect the variation encountered in the field, especially since we specifically included several samples with relatively high Ct values. Notably, the FIND initiative protocol (3) and the presented results for PrimerDesign and other kits (4) do not provide information regarding the composition of the 50 positive samples included in the study and no information on viral loads using e.g. reference Ct values. If only samples from patients in the hospital setting that have relatively high viral loads have been selected, every kit will score a near 100% diagnostic clinical sensitivity. We have specifically sought for the clinical performance using samples that have a viral load around the LOD of the kits.
cord-349921-v1tewoi0	2020	title: Case fatality rate in patients with COVID-19 infection and its relationship with length of follow up() In their systematic review on the clinical characteristics of COVID-19, Wu and colleagues report a 3.2% case fatality rate (CFR), ranging from 2% to 4% 1 with strong heterogeneity between studies (I 2 =100%). 2 The authors suggest that higher complication and fatality rate in Wuhan could be due to the limited clinical experience in the initial phase of the epidemic. We report data from the COVID-19 information system set up in Italy by the National Institute of Health and described elsewhere, 5,6 diagnosed from February 20 to March 29 and followed up to April 5 in Emilia-Romagna region (approximately 4.5 million inhabitants). Our data show that, according to the Italian definition of COVID-related death, 5,6 the CFR can reach about 20% if we follow up patients for a long enough time to observe the vast majority of deaths. Case-Fatality Rate and Characteristics of Patients Dying in Relation to COVID-19 in Italy
cord-353640-giznbcpd	2020	RT-PCR results using the ChromaCode HDPCR™ SARS-CoV-2 were compared using the heat-RNA release method and an automated RNA extraction system (EMAG). We compared the diagnostic sensitivity of the heat-RNA release method for detection of SARS-CoV-2 using NP swabs in viral transport media (VTM) to results obtained using an automated RNA extraction system (EMAG ® , bioMerieux, Durham, NC). A total of 174 COVID-19 positive samples were used for the study comprising 87 unique COVID-19 NP including Ct values using the heat-RNA release method were compared to the results obtained using the automated RNA-extraction method with both the LDT and ChromaCode SARS-CoV-2 assays. Comparison of the heat-RNA release method to EMAG ® using the ChromaCode SARS-CoV-2 RUO alone yielded a 94% agreement (81/86 positive samples). We found that the direct detection of SARS-CoV-2 using a 65°C heat inactivation and release step for 20minutes without RNA extraction and purification performed very well compared to the use of an automated RNA extraction instrument.