# pos

id: cord-263279-afdmegq0
pos: NFP
token:
  https://www.fda.gov/medical-devices/emergencysituations-medical-devices/emergency-use-authorizations

lemma:
  https://www.fda.gov/medical-devices/emergencysituations-medical-devices/emergency-use-authorizations


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

lemma:
  https://altonadiagnostics.com/en/products/reagents-140/reagents/realstar-realtime-pcr-reagents/realstar-sars-cov-2-rt-pcr-kit-ruo.html


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

lemma:
  https://www.who.int/docs/defaultsource/coronaviruse/whoinhouseassays.pdf?sfvrsn=de3a76aa_2&download=true


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

lemma:
  https://www.fda.gov/emergencypreparedness-and-response/mcm-legal-regulatory-and-policy-framework/emergency-use-authorization


# ent

id: cord-027649-6xn9swsq
type: GGP
entity:
  p38 Mitogen Activated Protein Kinase WA UW 4570 and resulted in the fusion of ORF7a and ORF8 A 227 nucleotide deletion


id: cord-253333-cwunxhyw
type: ORG
entity:
  Draft Resources Writing Review Editing Alejandro Seoane Investigation Writing Review Editing Martin Ypas Investigation Writing Review


id: cord-277909-rn1dow26
type: DISEASE
entity:
  Pneumocystis jiroveci varicella zoster virus VZV herpes simplex virus HSV 1 and 2 cytomegalovirus CMV Epstien Barr virus EBV HHV 6 HHV 7 norovirus adenovirus rotavirus astrovirus sapovirus erythrovirus B19 mumps Chlamydia trachomatis


id: cord-277909-rn1dow26
type: DISEASE
entity:
  influenza B viruses respiratory syncytial virus and parainfluenza viruses 1 2 3 and 4 Molecular beacons


id: cord-253148-3t4o27xp
type: DISEASE
entity:
  diseases of the respiratory system 2 In the United States the annual burden to society for respiratory infections


id: cord-285018-l26px1bc
type: CHEMICAL
entity:
  N gene target detection date 2020 09 07 journal J Clin Virol DOI 10 1016 j jcv 2020 104632 sha 84d1c42207592375cac4dc3d2306cfc12be0c243


id: cord-260267-nau9kayk
type: PROTEIN
entity:
  HPIV 3 X 2 7 854 P 0 005 Table 2 Respiratory Syncitial Virus RSV 65 cases and rhinovirus 64 cases were co detected with


id: cord-295189-bz3gi15h
type: DISEASE
entity:
  influenza A H1N1 virus via global airline transportation Transmission of pandemic A H1N1 2009 influenza on passenger aircraft retrospective cohort study Transmission of influenza on international flights Pandemic influenza A H1N1 outbreak


id: cord-269407-6i66zf0e
type: DISEASE
entity:
  respiratory syncytial virus RSV IFV A IFV B human adenovirus HAdV human parainfluenza hPIV 1 2 and 3 CPE positive but HAI


id: cord-268830-8li6xhbu
type: GGP
entity:
  Rhinovirus n 3 human metapneumovirus n 2 parainfluenza virus 4 n 1 respiratory syncytial virus n 2 Bacterial


id: cord-263279-afdmegq0
type: CELL_LINE
entity:
  CDC COVID 19 RT PCR tests The analytical sensitivity of the three assays was compared using the same quantified genomic materials which offered a side by side comparison of their lower limits of detection The overall accuracy of the three assays was compared using patient clinical specimens and the reproducibility was studied using contrived specimens Johns Hopkins Hospital The study was approved by the Johns Hopkins University School of Medicine IRB IRB00246024 Genomic viral RNA


id: cord-301254-093yih5n
type: DISEASE
entity:
  influenza B viruses respiratory syncytial virus and parainfluenza viruses 1 2 3 and 4 Respiratory viral infections


id: cord-290352-0pc5eji4
type: DISEASE
entity:
  influenza A virus infected lung epithelial cells the role of the nonstructural NS1 protein in the evasion of the host innate defense


id: cord-268567-2xoubkxb
type: DISEASE
entity:
  viral encephalitis Herpes simplex virus Japanese encephalitis West Nile virus have neurological and or neurocognitive sequelae 3 4 5


id: cord-296847-r752bcsu
type: DNA
entity:
  primer pair hRSV AB1 10 M and hRSV AB2 10 M Ebola specific primers ArmEBOFor 10 M and ArmEBORev 10 M Sanchez


id: cord-291029-oldket3n
type: DISEASE
entity:
  herpes simplex virus HSV Epstein Barr virus EBV varicella zoster virus VZV influenza A virus or enteroviruses


id: cord-295957-s17z2ccf
type: PROTEIN
entity:
  Simplexa COVID 19 Direct assay Moreover to evaluate the performance of the test in a different clinical specimen a total of 33 Broncho Alveolar Lavage BAL


id: cord-295957-s17z2ccf
type: PROTEIN
entity:
  Simplexa COVID 19 Direct assay and Corman s method For these samples the Abbot m2000 extraction platform


id: cord-264676-k531q3ir
type: CHEMICAL
entity:
  MgCl 2 pH 9 5 Subsequently the substrate nitroblue tetrazolium chloride 5 bromo 3 chloro 3indolyl phosphate NBT


id: cord-310140-h7uwl0pb
type: DISEASE
entity:
  influenza B viruses respiratory syncytial virus and parainfluenza viruses 1 2 3 and 4 van den Hoogen BG


id: cord-302864-2xnq1oq7
type: WORK_OF_ART
entity:
  A Single Centered Retrospective Observational Study Clinical Characteristics of Coronavirus Disease 2019


id: cord-302864-2xnq1oq7
type: WORK_OF_ART
entity:
  Airway Memory CD4 T Cells Mediate Protective Immunity against Emerging Respiratory Coronaviruses Microvascular COVID 19


id: cord-295873-kykyubdq
type: GGP
entity:
  adenoviruses n 86 16 8 of all samples and human metapneumovirus n 68 13 3 Influenza virus types A and B


id: cord-289139-5ljqnc39
type: DISEASE
entity:
  influenza respiratory syncytial virus and human metapneumovirus among infants and young children Spectrum and frequency of illness


id: cord-313375-rs3jjiuj
type: TAXON
entity:
  adenovirus n 1 respiratory syncytial virus A n 8 respiratory syncytial virus B n 2 human coronaviruses OC43 n 2 229E n 2


id: cord-311275-ysr9nqun
type: DISEASE
entity:
  respiratory syncytial virus ARI acute respiratory illness COPD chronic obstructive pulmonary disease


id: cord-318012-bg9y2nsp
type: TAXON
entity:
  adenovirus respiratory syncytial virus human metapneumovirus bocavirus rhinovirus enterovirus coronavirus


id: cord-279570-lgbqpfh5
type: GGP
entity:
  HGH 2613 18 2 2020 and was conducted according to the Outbreak Reports and Intervention studies Of Nosocomial infection ORION reporting guidelines 9


id: cord-313749-f2ct57em
type: DISEASE
entity:
  influenza B viruses respiratory syncytial virus and parainfluenza viruses 1 2 3 and 4 Design and performance testing of quantitative real time PCR


id: cord-331707-kfja1i6s
type: GGP
entity:
  herpangina 2 EV A71 and 1 CV A10 and 6 25 24 with exanthema 5 EV A71 and 1 EV C109 Only one patient developed permanent neurologic disabilities due to cardiorespiratory failure and hypoxic ischemic encephalopathy in addition to one AFP case


id: cord-331707-kfja1i6s
type: ORG
entity:
  Switzerland Rapid Risk Assesment Outbreak of Enterovirus A71 With Severe Neurologycal Symptoms Among Children


id: cord-331707-kfja1i6s
type: ORG
entity:
  Control Rapid Risk Assessment Enterovirus Detections Associated With Severe Neurological Symptoms in Children and Adults


id: cord-319864-t6ql9hz2
type: PROTEIN
entity:
  QIAstat Dx Respiratory SARS CoV 2 Panel J o u r n a l P r e p r o o f the First Rapid Multiplex PCR Commercial Assay for SARS CoV 2


id: cord-335208-xv2evahh
type: WORK_OF_ART
entity:
  Influenza Other Respir Viruses Frequency and Duration of Rhinovirus Infections in Children With Cystic Fibrosis and


id: cord-335208-xv2evahh
type: WORK_OF_ART
entity:
  RNA Transcripts of Enterovirus Species A to D Rhinovirus Species A to C and Human Parechovirus Assessment of Assay Sensitivity and Specificity of Real Time Screening and Typing Methods


id: cord-349485-iomk99lv
type: CELL_LINE
entity:
  Freiburg containing 4x10 4 copies ml J o u r n a l P r e p r o o f 3 2x10 7 copies ml 1 6x10 7 copies


id: cord-336237-hmczy0am
type: WORK_OF_ART
entity:
  Manual for the Detection of Pathogen 2019 nCoV Ver 2 6 Development of Reverse Transcription Loopmediated Isothermal Amplification RT LAMP Assays


id: cord-337799-mc1oqhf4
type: CELL_LINE
entity:
  Hong Kong COVID 19 patient hCoV 19 Hong Kong VM20030475 2020 To minimize the number of freezethaw cycle the three kits


id: cord-337799-mc1oqhf4
type: PROTEIN
entity:
  BIOCREDIT COVID 19 Ag RapdGEN Inc Korea kit was also tested as a reference method simultaneously Virus concentrations in each dilution were estimated from cycle threshold Ct value as described 3 J o u r n a l P r e p r o o f


id: cord-337799-mc1oqhf4
type: EVENT
entity:
  Rethinking Covid 19 Test Sensitivity A Strategy for Containment Predicting Infectious Severe Acute Respiratory Syndrome Coronavirus 2


id: cord-299664-nexq5ntj
type: DISEASE
entity:
  influenza and respiratory syncytial virus in the United States Respiratory syncytial virus infection


id: cord-325120-jlrievxl
type: ORG
entity:
  Development of a Panel of Recombinase Polymerase Amplification Assays for Detection of Respiratory Viruses


id: cord-307261-0a3iztns
type: DISEASE
entity:
  rhinovirus 4 coronavirus HKU1 2 RSV 2 adenovirus 1 Bocavirus 1 coronavirus OC43 1 and enterovirus 1 Analysis


id: cord-287206-ois4gnqx
type: CHEMICAL
entity:
  N Breuckmann N P Eberhardt C S title Multi Stage Group Testing Improves Efficiency of Large Scale COVID


id: cord-307602-2cmgu7rf
type: DISEASE
entity:
  human rhinoviruses paramyxoviruses coronaviruses and bocavirus during acute respiratory tract infections


# url

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


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


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


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


# bib

id: cord-010155-g5fk567p
title: Absence of Melaka-virus in European children with respiratory disease
author: Schildgen, Verena
date: 2008-03-24
txt: ./txt/cord-010155-g5fk567p.txt
cache: ./cache/cord-010155-g5fk567p.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172096/
doi: 10.1016/j.jcv.2008.02.003
abstract: nan
summary:
  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) .


id: cord-010160-wk8k2igu
author: Chandrasekaran, Alamelu
date: 2012-01-04
txt: ./txt/cord-010160-wk8k2igu.txt
cache: ./cache/cord-010160-wk8k2igu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172171/
doi: 10.1016/j.jcv.2011.12.006
abstract: nan
summary:
  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.

title:
  Broad reactivity of the Luminex xTAG Respiratory Virus Panel (RVP) assay for the detection of human rhinoviruses


id: cord-026099-97luq10a
author: Kok, J
date: 2020-06-05
txt: ./txt/cord-026099-97luq10a.txt
cache: ./cache/cord-026099-97luq10a.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7273136/
doi: 10.1016/j.jcv.2020.104484
abstract: nan
summary:
  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

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


id: cord-027649-6xn9swsq
author: Addetia, Amin
date: 2020-06-23
txt: ./txt/cord-027649-6xn9swsq.txt
cache: ./cache/cord-027649-6xn9swsq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7309833/
doi: 10.1016/j.jcv.2020.104523
abstract: nan
summary:
  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.

title:
  Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates


id: cord-253148-3t4o27xp
title: Evidence of human bocavirus circulating in children and adults, Cleveland, Ohio
author: Chow, Brian D.W.
date: 2008-09-19
txt: ./txt/cord-253148-3t4o27xp.txt
cache: ./cache/cord-253148-3t4o27xp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/18805051/
doi: 10.1016/j.jcv.2008.07.009
summary:
  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.

abstract:
  BACKGROUND: Viral respiratory illness is a major cause of morbidity and mortality. The human bocavirus (HBoV) is a recently recognized parvovirus isolated from human respiratory secretions. OBJECTIVES: To define the clinical and epidemiologic characteristics in adult and pediatric patients with evidence of HBoV. STUDY DESIGN: From October 2005 through October 2006, we screened respiratory samples from children and adults negative for common respiratory pathogens for HBoV by PCR. Demographic and clinical characteristics were obtained from medical records of HBoV positive individuals. RESULTS: Of 2075 samples screened, 1826 (88.0%) represented distinct respiratory events: 1539 (84.3%) were pediatric (<18 years), and 273 (15.0%) adult (≥18 years). Forty (2.2%) patients had HBoV: 36 (2.3%) children and 4 (1.5%) adults. HBoV positive children had history of prematurity (31.3%) and cardiac disease (18.8%). Adults had underlying pulmonary (100%) and cardiac (50%) disease. Twenty-seven children (84.4%) were hospitalized; 9 (28.1%) required intensive care. All adults were hospitalized; none required intensive care. Nosocomial acquisition likely occurred in 3 patients. CONCLUSIONS: HBoV circulates in Cleveland, OH, in children and adults with similar frequencies, and can warrant hospitalization and intensive care. Further study would clarify our understanding of this newly recognized human pathogen.


id: cord-253333-cwunxhyw
author: Echavarría, M.
date: 2018-09-14
txt: ./txt/cord-253333-cwunxhyw.txt
cache: ./cache/cord-253333-cwunxhyw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30267999/
doi: 10.1016/j.jcv.2018.09.009
summary:
  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).

title:
  Clinical impact of rapid molecular detection of respiratory pathogens in patients with acute respiratory infection

abstract:
  BACKGROUND: Acute respiratory infections (ARI) are a leading cause of morbidity and mortality worldwide. There is a need to demonstrate the clinical impact of using the new, rapid and sensitive molecular assays in prospectively designed studies. OBJECTIVES: To study the impact on medical management of a rapid molecular assay in patients with respiratory infections. STUDY DESIGN: A prospective, randomized, non-blinded study was performed in patients presenting to the Emergency Department during two respiratory seasons (2016–2017). Diagnosis was performed by FilmArray Respiratory Panel (FilmArray-RP) or by immunofluorescence assay (IFA). RESULTS: A total of 432 patients (156 children and 276 adults) were analyzed. 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. Decrease in oseltamivir prescriptions was significantly higher in adults in the FilmArray-RP group (p = 0.042; OR:1.19, 95%CI:0.51-2.79) compared to adults managed with IFA. Diagnostic yield was significantly higher by FilmArray-RP (81%) than by IFA (31%)(p < 0.001). The median time from sample collection to reporting was 1 h 52 min by FilmArray-RP and 26 h by IFA (p < 0.001). 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.


id: cord-256699-d2tf2g7f
title: Comparison of different serological assays for SARS-CoV-2 in real life
author: Brochot, Etienne
date: 2020-08-02
txt: ./txt/cord-256699-d2tf2g7f.txt
cache: ./cache/cord-256699-d2tf2g7f.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653220303115?v=s5
doi: 10.1016/j.jcv.2020.104569
summary:
  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 ).

abstract:
  BACKGROUND: The emergence of the global SARS-CoV-2 pandemic required the rapid and large-scale deployment of PCR and serological tests in different formats. OBJECTIVES: Real-life evaluation of these tests is needed. 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®). RESULTS: For hospitalized patients, all these assays showed a sensitivity of 100 % from day 9 after the symptoms onset. On the other hand, sensitivity was much lower for patients who did not require hospitalization for COVID-19 confirmed by PCR (from 91.6 % for WANTAI® to 69 % for LIAISON®). These differences do not seem to be due to the antigens chosen by the manufacturers but more to the test formats (IgG detection versus total antibodies). In addition, more than 50 days after a positive PCR for CoV-2-SARS the proportion of positive patients seem to decrease. We did not observe any significant cross-reactions for these techniques with the four other seasonal coronaviruses. CONCLUSION: In conclusion, the evaluation and knowledge of the serological tests used is important and should require an optimized strategy adaptation of the analysis laboratories to best meet patient’s expectations in the face of this health crisis.


id: cord-259558-remrzrq1
author: LeBlanc, Jason J.
date: 2020-05-16
txt: ./txt/cord-259558-remrzrq1.txt
cache: ./cache/cord-259558-remrzrq1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32425660/
doi: 10.1016/j.jcv.2020.104442
summary:
  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) .

title:
  A combined oropharyngeal/nares swab is a suitable alternative to nasopharyngeal swabs for the detection of SARS-CoV-2

abstract:
  Given the global shortage of nasopharyngeal (NP) swabs typically used for respiratory virus detection, alternative collection methods were evaluated during the COVID-19 pandemic. This study showed that a combined oropharyngeal/nares swab is a suitable alternative to NP swabs for the detection of SARS-CoV-2, with sensitivities of 91.7% and 94.4%, respectively.


id: cord-259798-fnm1im98
author: Lee, Brian R.
date: 2018-11-23
txt: ./txt/cord-259798-fnm1im98.txt
cache: ./cache/cord-259798-fnm1im98.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S138665321830283X
doi: 10.1016/j.jcv.2018.11.006
summary:
  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.

title:
  Impact of multiplex molecular assay turn-around-time on antibiotic utilization and clinical management of hospitalized children with acute respiratory tract infections

abstract:
  BACKGROUND: Empiric antibiotic treatment is common among children with acute respiratory tract infections (ARTI), despite infections being predominately viral. The use of molecular respiratory panel assays has become increasingly common for medical care of patients with ARTIs. STUDY DESIGN: This was a 6-year retrospective, single-centered study of pediatric inpatients who tested positive for an ARTI respiratory pathogen. We examined the relationship between clinical outcomes and whether the patient was tested using the Luminex Respiratory Viral Panel ([RVP]; in-use: Dec. 2009 – Jul. 2012) or Biofire Respiratory Pathogen Panel ([RP]; in-use Aug. 2012 – Jun. 2016). The prevalence and duration of pre-test empiric antibiotics, post-test oseltamivir administration to influenza patients, chest x-rays and length of stay between the two assays was compared. RESULTS: A total of 5142 patients (1264 RVP; 3878 RP) were included. The median laboratory turn-around-time for RP was significantly shorter than RVP (1.4 vs. 27.1 h, respectively; p < .001). Patients tested with RP were less likely to receive empiric antibiotics (OR: 0.45; p < .001; 95% CI: 0.39, 0.52) and had a shorter duration of empiric broad-spectrum antibiotics (6.4 h vs. 32.9 h; p < .001) compared to RVP patients. RP influenza patients had increased oseltamivir use post- test compared to RVP influenza patients (OR: 13.56; p < .001; 95% CI: 7.29, 25.20). 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.


id: cord-260267-nau9kayk
author: Ren, Lili
date: 2011-06-01
txt: ./txt/cord-260267-nau9kayk.txt
cache: ./cache/cord-260267-nau9kayk.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653211001739
doi: 10.1016/j.jcv.2011.05.001
summary:
  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.

title:
  Human parainfluenza virus type 4 infection in Chinese children with lower respiratory tract infections: A comparison study

abstract:
  BACKGROUND: Human parainfluenza viruses (HPIVs) are a leading cause of acute respiratory tract infections (ARTIs). Although HPIV-4 has been associated with mild ARTIs for years, recent investigations have also associated HPIV-4 infection with severe respiratory syndromes and with outbreaks of ARTIs in children. OBJECTIVES: To characterize the role of HPIV-4 and its clinical features in children with acute lower respiratory tract infections (ALRTIs) in Beijing, China. STUDY DESIGN: Nasopharyngeal aspirates were collected from 2009 hospitalized children with ALRTIs between March 2007 and April 2010. RT-PCR and PCR analyses were used to identify HPIV types and other known respiratory viruses. RESULTS: HPIVs were detected in 246 (12.2%) patients, of whom 25 (10.2%) were positive for HPIV-4, 11 (4.5%) for HPIV-2, 51 (20.7%) for HPIV-1, 151 (61.4%) for HPIV-3, and 8 (3.3%) were co-detected with different types of HPIVs. Like HPIV-3, HPIV-4 was detected in spring, summer, and late fall over the study period. Seasonal incidence varied for HPIV-1 and -2. The median patient age was 20 months for HPIV-4 infections and 7–11 months for HPIV-1, -2, and -3 infections, but the clinical manifestations did not differ significantly between HPIV-1, -2, -3, and -4 infections. Moreover, co-detection of HPIV-4 (44%) with other respiratory viruses was lower than that of HPIV-1 (62.7%), HPIV-2 (63.6%), and HPIV-3 (72.7%). CONCLUSIONS: HPIV-4 plays an important role in Chinese paediatric ALRTIs. The epidemiological and clinical characteristics reported here improve our understanding of the pathogenesis associated with HPIV-4.


id: cord-260338-or4faju7
author: Völz, Sebastian
date: 2007-09-11
txt: ./txt/cord-260338-or4faju7.txt
cache: ./cache/cord-260338-or4faju7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17851126/
doi: 10.1016/j.jcv.2007.07.017
summary:
  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

title:
  Prospective study of Human Bocavirus (HBoV) infection in a pediatric university hospital in Germany 2005/2006

abstract:
  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%). Recently published retrospective studies and one prospective birth cohort study suggest that HBoV-primary infection occurs in infants. METHODS: Prospective single center study over one winter season (November 2005–May 2006) with hospitalized children without age restriction using PCR-based diagnostic methods. RESULTS: HBoV DNA was detected in 11 (2.8%) of 389 nasopharyngeal aspirates from symptomatic hospitalized children (median age 9.0 months; range: 3–17 months). RSV, HMPV, HCoV, and Influenza B were detected in 13.9% (n = 54), 5.1% (n = 20), 2.6% (n = 10), and 1.8% (n = 7), respectively. There was no influenza A DNA detected in any of the specimens. The clinical diagnoses were acute wheezing (bronchitis) in four patients, radiologically confirmed pneumonia in six patients (55%) and croup syndrome in one patient. In five to six patients with pneumonia, HBoV was the only pathogen detected. While no patient had to be mechanically ventilated, 73% needed oxygen supplementation. In four (36.4%) patients at least one other viral pathogen was found (plus RSV n = 3; 27.3%; Norovirus n = 1; 9.1%). CONCLUSION: HBoV causes severe respiratory tract infections in infants and young children. Its role as a copathogen and many other open questions has to be defined in further prospective studies.


id: cord-262045-r2iqpmmc
title: Reliable typing of MERS-CoV variants with a small genome fragment
author: Smits, Saskia L.
date: 2014-12-15
txt: ./txt/cord-262045-r2iqpmmc.txt
cache: ./cache/cord-262045-r2iqpmmc.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653214004685
doi: 10.1016/j.jcv.2014.12.006
summary:
  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

abstract:
  BACKGROUND: Middle East Respiratory Syndrome coronavirus (MERS-CoV) is an emerging pathogen that causes lower respiratory tract infection in humans. Camels are the likely animal source for zoonotic infection, although exact transmission modes remain to be determined. Human-to-human transmission occurs sporadically. The wide geographic distribution of MERS-CoV among dromedary camels and ongoing transmissions to humans provides concern for the evolution of a MERS-CoV variant with efficient human-to-human transmission capabilities. Phylogenetic analysis of MERS-CoV has occurred by analysis of full-length genomes or multiple concatenated genome fragments, which is time-consuming, costly and limited to high viral load samples. OBJECTIVE: To develop a simple, reliable MERS-CoV variant typing assay to facilitate monitoring of MERS-CoV diversity in animals and humans. STUDY DESIGN: Phylogenetic analysis of presently known full-length MERS-CoV genomes was performed to identify genomic regions with sufficient phylogenetic content to allow reliable MERS-CoV variant typing. RT-PCR assays targeting these regions were designed and optimized. 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. The detection limit corresponds to a cycle treshold value of ∼35 with standard upE real time PCR assays on RNA isolated from MERS-CoV EMC. Nasal swabs from RT-PCR positive camels (Ct values 12.9–32.2) yielded reliable sequence information in 14 samples. CONCLUSIONS: We developed a simple, reliable MERS-CoV variant typing assay which is crucial in monitoring MERS-CoV circulation in real time with relatively little investment on location.


id: cord-263118-6sf41rsj
author: Landry, Marie L.
date: 2008-07-18
txt: ./txt/cord-263118-6sf41rsj.txt
cache: ./cache/cord-263118-6sf41rsj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/18639488/
doi: 10.1016/j.jcv.2008.06.006
summary:
  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.

title:
  Real-time PCR compared to Binax NOW and cytospin-immunofluorescence for detection of influenza in hospitalized patients

abstract:
  BACKGROUND: Rapid tests have had a significant impact on influenza diagnosis, but more accurate tests are needed for hospitalized patients who test negative by rapid methods. OBJECTIVE: We sought to determine the increased yield obtained from influenza RT-PCR in hospitalized patients compared to two rapid methods. 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. The difference in sensitivity was significant between RT-PCR and Binax NOW (p < 0.0001), but not between RT-PCR and cytospin-DFA (p = 0.0736). Two samples testing positive for influenza B by all three methods, tested falsely positive for influenza A by Binax. Eight true positive samples did not become reactive by Binax until 30 min, and thus were counted as negative. 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. Further studies are needed to determine the effect of influenza RT-PCR on patient management and costs in hospitalized patients.


id: cord-263279-afdmegq0
title: Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays
author: Uhteg, Katharine
date: 2020-04-26
txt: ./txt/cord-263279-afdmegq0.txt
cache: ./cache/cord-263279-afdmegq0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32361285/
doi: 10.1016/j.jcv.2020.104384
summary:
  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.

abstract:
  In December 2019, a novel coronavirus (SARS-CoV-2) was first isolated from Wuhan city, China and within three months, the global community was challenged with a devastating pandemic. The rapid spread of the virus challenged diagnostic laboratories to rapidly develop molecular diagnostic methods. As SARS CoV-2 assays became available for testing on existing molecular platforms, laboratories devoted unprecedented energy and resources into evaluating the analytical performance of the new tests and in some cases developed their own diagnostic assays under FDA-EUA guidance. This study compares the validation of three different molecular assays at the Johns Hopkins Molecular Virology laboratory: the RealStar® SARS-CoV-2 RT-PCR, ePlex® SARS-CoV-2, and the CDC COVID-19 RT-PCR tests. Overall, our studies indicate a comparable analytical performance of the three assays for the detection of SARS-CoV-2.


id: cord-263389-m6x9gxwe
author: AlGhounaim, M.
date: 2017-07-29
txt: ./txt/cord-263389-m6x9gxwe.txt
cache: ./cache/cord-263389-m6x9gxwe.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653217302135
doi: 10.1016/j.jcv.2017.07.015
summary:
  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.

title:
  Diagnostic yield and clinical impact of routine cell culture for respiratory viruses among children with a negative multiplex RT-PCR result

abstract:
  BACKGROUND: Polymerase chain reaction (PCR) is the reference standard for respiratory virus testing. However, cell culture may still have added value in identifying viruses not detected by PCR. OBJECTIVES: We aimed to estimate the yield and clinical impact of routine respiratory virus culture among children with a negative PCR result. STUDY DESIGN: A retrospective cohort study was performed from Jan. 2013 to Sept. 2015. 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. We studied patients with a respiratory specimen negative by PCR and positive by culture. Duplicates and samples of sold services were excluded. Data on demographics, clinical history, laboratory findings, and patient management were collected from patients’ charts. Descriptive and multivariate statistics were performed. RESULTS: Overall, 4638 PCR-negative samples were inoculated in cell culture. Of those, 196 (4.2%) were cell culture positive, and 144 met study inclusion criteria. Most subjects (81.9%) were hospitalized. Mean age was 2.4 ± 3.4 years. The viruses most frequently isolated were cytomegalovirus (33.3%) and enteroviruses (19.4%). Cell culture results prompted a change in management in 5 patients (3.5%), all of whom had acyclovir initiated for localized HSV-1 infection. Four of these had skin or mucosal lesions that could be sampled to establish a diagnosis. CONCLUSION: In children, routine viral culture on respiratory specimens that were negative by PCR has low yield and minimal clinical impact.


id: cord-264360-eroqjkoh
title: Detection of human coronaviruses in children with acute gastroenteritis
author: Risku, Minna
date: 2010-03-15
txt: ./txt/cord-264360-eroqjkoh.txt
cache: ./cache/cord-264360-eroqjkoh.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653210000855
doi: 10.1016/j.jcv.2010.02.013
summary:
  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.

abstract:
  BACKGROUND: Human coronaviruses (HCoVs) are known respiratory pathogens. Moreover, coronavirus-like particles have been seen by electron microscope in stools, and SARS-HCoV has been isolated from intestinal tissue and detected in stool samples. OBJECTIVES: To find out if HCoVs can be found in stools of children with acute gastroenteritis and to assess the significance of HCoVs in the etiology of acute gastroenteritis in children. 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. HCoVs were typed by sequencing all PCR positive samples. RESULTS: Twenty-two (2.5%) of the 878 stool specimens of children with acute gastroenteritis were positive for HCoVs. The following HCoV types were detected: OC43 (10 cases, 45.5%), HKU1 (6 cases, 27.3%), 229E (2 cases, 9.1%) and NL63 (4 cases, 18.2%). In 4 of the cases a HCoV was the only detected virus; in the remaining cases rotavirus or norovirus was found in the same sample. In control groups there were two HCoV positive samples of 112 tested. CONCLUSIONS: This study shows that all known non-SARS HCoVs can be found in stools of children with acute gastroenteritis. 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.


id: cord-264406-s5c0grz0
title: Multiplex PCR reveals that viruses are more frequent than bacteria in children with cystic fibrosis
author: Miró-Cañís, Sílvia
date: 2016-11-13
txt: ./txt/cord-264406-s5c0grz0.txt
cache: ./cache/cord-264406-s5c0grz0.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653216305893
doi: 10.1016/j.jcv.2016.11.004
summary:
  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.

abstract:
  BACKGROUND: Cystic fibrosis is a degenerative disease characterized by progressive epithelial secretory gland dysfunction associated with repeated respiratory infections. 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. Multiplex PCR enables screening for many viruses involved in respiratory infections. OBJECTIVES: This study aimed to evaluate the frequency of viruses and bacteria in respiratory specimens from children with cystic fibrosis and to clarify the incidence and characteristics (seasonality and age of patients) of different viruses detected in children with cystic fibrosis. 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. We analyzed viruses in nasopharyngeal-swab specimens with multiplex PCR and bacteria in sputum with standard methods. RESULTS: We analyzed 368 paired specimens from 33 children. We detected viruses in 154 (41.8%) and bacteria in 132 (35.9%). Bacteria were commoner in spring and summer; viruses were commoner in autumn and winter. In every season, Staphylococcus aureus was the commonest bacteria and rhinovirus was the commonest virus. Nearly all infections with Haemophilus influenzae occurred in autumn and winter. Viruses were more prevalent in children <5 years old, and bacteria were more prevalent in children ≥12 years old. CONCLUSIONS: Multiplex PCR screening for respiratory viruses is feasible in children with cystic fibrosis; the clinical implications of screening warrant further study.


id: cord-264676-k531q3ir
author: Liu, Yi
date: 2009-07-09
txt: ./txt/cord-264676-k531q3ir.txt
cache: ./cache/cord-264676-k531q3ir.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/19592299/
doi: 10.1016/j.jcv.2009.06.010
summary:
  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

title:
  In situ reverse-transcription loop-mediated isothermal amplification (in situ RT-LAMP) for detection of Japanese encephalitis viral RNA in host cells

abstract:
  BACKGROUND: Clinical diagnosis of Japanese encephalitis is usually difficult due to non-specific signs at the early and acute stages of the infection. Virus isolation from peripheral blood is also not possible because of the short period and low level of transient viremia even in the acute stage of the disease. It is thus urgent to develop a feasible and convenient method for laboratory diagnosis of the infection. OBJECTIVES: To establish a newly designed molecular approach that can be used to detect intracellular Japanese encephalitis viral RNA in host cells. STUDY DESIGN: The method was firstly established and then was carried out to test its efficacy in cultured BHK-21 cells, subsequently in peripheral blood mononuclear cells (PBMCs) isolated from mice that have been inoculated with JE virus suspension. RESULTS: In this study, in situ reverse-transcription loop-mediated isothermal amplification (in situ RT-LAMP) was established; which combines merits of recently developed loop-mediated isothermal amplification (LAMP) and in situ reverse-transcriptase polymerase chain reaction (in situ RT-PCR). CONCLUSIONS: The newly designed method can detect viral RNAs in peripheral blood mononuclear cells (PBMCs) in a short time with high sensitivity and efficiency.


id: cord-264713-38dlh3wg
title: Molecular diagnostics in virology
author: Vernet, Guy
date: 2004-08-20
txt: ./txt/cord-264713-38dlh3wg.txt
cache: ./cache/cord-264713-38dlh3wg.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653204001696
doi: 10.1016/j.jcv.2004.06.003
summary:
  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.

abstract:
  Molecular biology has significantly improved diagnosis in the field of clinical virology. Virus discovery and rapid implementation of diagnostic tests for newly discovered viruses has strongly beneficiated from the development of molecular techniques. 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. It will be important to add to this panel assays for other viruses of the herpesviridae family. Qualitative assays for the detection of blood-borne viruses have increased safety of blood donation and organ transplantation. Screening of other blood-borne viruses (parvovirus B19, HAV), multiplexing of detection and test automation to improve practicability and reduce costs will be the next steps. A major evolution in the near future will be the generalization of NAT for the diagnosis of viral etiology in patients, mostly with respiratory, CNS or gastro-intestinal diseases. Major technical improvements have been made to avoid obstacles that still limit this generalization, i.e. genetic variability of viruses, multiplex detection, contamination risk. Commercial offers already exist but menus must be extended to limit the validation and documentation work associated with home-brew assays. Real-time amplification has allowed the development of new NAT platforms but automation and integration of all steps of the reaction are still required to reduce hands-on-time, time-to-result and costs, and to increase throughput.


id: cord-265760-ch4pcy21
title: Consistency analysis of COVID-19 nucleic acid tests and the changes of lung CT
author: Zhifeng, Jiang
date: 2020-04-10
txt: ./txt/cord-265760-ch4pcy21.txt
cache: ./cache/cord-265760-ch4pcy21.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653220301013
doi: 10.1016/j.jcv.2020.104359
summary:
  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.

abstract:
  BACKGROUND: COVID-19, the latest outbreak of infectious disease, has caused huge medical challenges to China and the entire globe. No unified diagnostic standard has been formulated. The initial diagnosis remains based on the positive of nucleic acid tests. However, early nucleic acid tests were identified to be negative in some patients, whereas the patients exhibited characteristic CT changes of lung, and positive test results appeared after repeated nucleic acid tests, having caused the failure to diagnose these patients early. The study aimed to delve into the relationships between initial nucleic acid testing and early lung CT changes in patients with COVID-19. METHOD: In accordance with the latest COVID-19 diagnostic criteria, 69 patients diagnosed with COVID-19 treated in the infected V ward of Xiaogan Central Hospital from 2020/1/25 to 2020/2/6 were retrospectively analyzed. The consistency between the first COVID-19 nucleic acid test positive and lung CT changes was studied. In addition, the sensitivity and specificity of CT and initial nucleic acid were studied. RESULT: The Kappa coefficient of initial nucleic acid positive changes and lung CT changes was −1.52. With a positive nucleic acid test as the gold standard, the sensitivity of lung CT was 12.00 %, 95 % CI: 4.6–24.3; with the changes of CT as the gold standard, the sensitivity of nucleic acid positive was 30.16 %, 95 % CI: 19.2−43.0. CONCLUSION: The consistency between the initial positive nucleic acid test and the CT changes in the lungs is poor; low sensitivity was achieved for initial nucleic acid detection and CT changes.


id: cord-266359-uf1ao1x1
author: Hakki, Morgan
date: 2015-04-15
txt: ./txt/cord-266359-uf1ao1x1.txt
cache: ./cache/cord-266359-uf1ao1x1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26071326/
doi: 10.1016/j.jcv.2015.04.012
summary:
  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.

title:
  The clinical impact of coronavirus infection in patients with hematologic malignancies and hematopoietic stem cell transplant recipients

abstract:
  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. OBJECTIVES: To characterize the role of CoV in respiratory tract infections among HSCT and hematologic malignancy patients. STUDY DESIGN: We conducted a retrospective review of all cases of CoV infection documented by polymerase chain reaction, (PCR)-based testing on nasopharyngeal and bronchoalveolar lavage fluid samples between June 2010 and 2013. Cases of CoV infection occurring in HSCT and hematologic malignancy patients were identified and the clinical characteristics of these cases were compared to other respiratory viruses. RESULTS: CoV was identified in 2.6% (n = 43) of all samples analyzed (n = 1661) and in 6.8% of all samples testing positive for a respiratory virus (n = 631). 33 of 38 (86.8%) of patients in whom CoV was identified were HSCT and hematologic malignancy patients. Among these patients, CoV was detected in 9.7% of unique infection episodes, with only rhinovirus/enterovirus (RhV/EnV) infection being more common. Group I CoV subtypes accounted for 76.3% of cases, and 57% of infections were diagnosed between December and March. CoV infection was associated with upper respiratory tract symptoms in most patients, similar to other respiratory viruses. Possible and proven lower respiratory tract disease was less common compared to other respiratory viruses except RhV/EnV. 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.


id: cord-267928-dflkggjt
author: Kantola, Kalle
date: 2009-05-22
txt: ./txt/cord-267928-dflkggjt.txt
cache: ./cache/cord-267928-dflkggjt.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S138665320900167X
doi: 10.1016/j.jcv.2009.04.008
summary:
  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.

title:
  Merkel cell polyomavirus DNA in tumor-free tonsillar tissues and upper respiratory tract samples: Implications for respiratory transmission and latency

abstract:
  BACKGROUND: Merkel cell polyomavirus (MCPyV) was discovered recently. It is considered a potential causative agent of Merkel cell carcinoma, a life-threatening skin cancer. OBJECTIVES: To study the prevalence of MCPyV in a large number of clinical samples of various types. Most of the samples were examined also for the other newly found polyomaviruses KI (KIPyV) and WU (WUPyV). 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. The tonsils, nasal swabs and stools were also studied for KIPyV and WUPyV. 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. WUPyV and KIPyV were detected in 5 (2.2%) and 0 tonsils, 1 (0.9%) and 4 (3.8%) nasal swabs and 0 and 2 (2.7%) fecal samples, respectively. The patients carrying in tonsils MCPyV were of significantly higher age (median 42 years) than those carrying WUPyV (4 years, p < 0.001). CONCLUSIONS: MCPyV DNA occurs in tonsils more frequently in adults than in children. By contrast, WUPyV DNA is found preferentially in children. MCPyV occurs also in nasal swabs and NPAs, in a frequency similar to that of KIPyV and WUPyV. The tonsil may be an initial site of WUPyV infection and a site of MCPyV persistence.


id: cord-268093-ta6k0uyz
author: Etemadi, Mohammad Reza
date: 2013-08-07
txt: ./txt/cord-268093-ta6k0uyz.txt
cache: ./cache/cord-268093-ta6k0uyz.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653213001972
doi: 10.1016/j.jcv.2013.05.017
summary:
  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.

title:
  Biodiversity and clinico-demographic characteristics of human rhinoviruses from hospitalized children with acute lower respiratory tract infections in Malaysia()

abstract:
  BACKGROUND: There is accumulating evidence that human rhinovirus (HRV) causes acute lower respiratory tract infections (ALRTI). Recently, HRV-C was identified as a new species of HRV, but its spectrum of clinical disease is not well understood. OBJECTIVES: We investigated the molecular epidemiology, demographic and clinical characteristics of HRVs among hospitalized children with ALRIs. STUDY DESIGN: One hundred and sixty-five nasopharangeal aspirates taken from children <5 years hospitalized with ALRTIs in Serdang Hospital, Malaysia, were subject to reverse transcriptase-PCR for HRV. Phylogenetic analysis on VP4/VP2 and 5′-NCR regions was used to further characterize HRV. Other respiratory viruses were also investigated using semi-nested multiplex RT-PCR assay. Clinical parameters were analyzed between HRV, RSV and IFV-A mono-infections and between HRV species. RESULTS: HRV was detected in 54 (33%) patients for both single (36 samples) and multiple (18 samples) infections, 61.1% (22/36) represents HRV-A strains while the remaining 14 HRV-C. Strain P51was the first reported representative of HRV98. The majority of the single HRV cases were in the second half of infancy; HRV-C occurred among older children compared with HRV-A. HRV children were admitted significantly earlier and less febrile than RSV and IFV-A infection. HRV-C infected children were more likely to have rhonchi and vomiting as compared to HRV-A. Pneumonia was the most common discharge diagnosis followed by bronchiolitis and post-viral wheeze in HRV patients. CONCLUSION: Our study showed high prevalence of HRVs and detection of HRV-C among hospitalized children with ALRTIs in Malaysia. Analysis of clinical parameters suggested specific features associated with HRVs infections and specific HRV groups.


id: cord-268335-mfcjldu3
title: Children are protected against SARS-CoV-2 infection
author: Dimeglio, Chloé
date: 2020-05-20
txt: ./txt/cord-268335-mfcjldu3.txt
cache: ./cache/cord-268335-mfcjldu3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32454427/
doi: 10.1016/j.jcv.2020.104451
abstract: nan
summary:
  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.


id: cord-268567-2xoubkxb
title: Compliance with international guidelines in adults with encephalitis
author: Samannodi, Mohammed
date: 2020-04-14
txt: ./txt/cord-268567-2xoubkxb.txt
cache: ./cache/cord-268567-2xoubkxb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32315818/
doi: 10.1016/j.jcv.2020.104369
summary:
  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] .

abstract:
  BACKGROUND: Encephalitis is associated with significant neurological disability and mortality. Many guidelines are published for encephalitis management but compliance with them is unknown. OBJECTIVES: To evaluate the appropriate management and compliance to the current guidelines in adults with encephalitis. STUDY DESIGN: A retrospective multicenter study at 17 hospitals in the Greater Houston area from August 1, 2008 through September 30, 2017. All cases met the definition for possible or probable encephalitis as per the international encephalitis consortium guidelines. RESULTS: A total of 241 adults (age >17 years) with encephalitis were enrolled. The most common etiologies were unknown (41.9 %), viral (27.8 %) and autoimmune (21.2 %). An adverse clinical outcome was seen in 49 % with 12.4 % in hospital mortality. A high compliance with guidelines (>90 %) was only seen in obtaining a brain computerized tomography (CT) scan, blood cultures and cerebrospinal fluid (CSF) gram stain and culture. A CSF herpes virus simplex (HSV) polymerase chain reaction (PCR) was done in 84 % and only repeated in 14.2 % of patients with an initial negative result. Furthermore, only two-thirds of patients were started empirically on intravenous acyclovir and antibiotics. Evaluation for other etiologies were not uniformly performed: arboviral serologies (57.3 %), CSF anti-N-Methyl-d-Aspartate Receptor (NMDA) receptor antibody (35.7 %), and CSF varicella zoster virus (VZV) PCR (32 %). The highest yield for the tests were arboviral serologies (42 %), anti-NMDA antibodies (41.2 %) and VZV PCR (16.4 %). CONCLUSION: The management of encephalitis as per current guidelines is suboptimal leading to underutilization of currently available diagnostic tests and empirical therapy.


id: cord-268830-8li6xhbu
author: Kozak, Robert
date: 2020-03-29
txt: ./txt/cord-268830-8li6xhbu.txt
cache: ./cache/cord-268830-8li6xhbu.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653220300809
doi: 10.1016/j.jcv.2020.104338
summary:
  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.

title:
  Severity of coronavirus respiratory tract infections in adults admitted to acute care in Toronto, Ontario

abstract:
  BACKGROUND: The World Health Organization has highlighted the need for improved surveillance and understanding of the health burden imposed by non-influenza RNA respiratory viruses. Human coronaviruses (CoVs) are a major cause of respiratory and gastrointestinal tract infections with associated morbidity and mortality. OBJECTIVES: The objective of our study was to characterize the epidemiology of CoVs in our tertiary care centre, and identify clinical correlates of disease severity. STUDY DESIGN: A cross-sectional study was performed of 226 patients admitted with confirmed CoV respiratory tract infection between 2010 and 2016. Variables consistent with a severe disease burden were evaluated including symptoms, length of stay, intensive care unit (ICU) admission and mortality. RESULTS: CoVs represented 11.3% of all positive respiratory virus samples and OC43 was the most commonly identified CoV. The majority of infections were community-associated while 21.6% were considered nosocomial. The average length of stay was 11.8 days with 17.3% of patients requiring ICU admission and an all-cause mortality of 7%. In a multivariate model, female gender and smoking were associated with increased likelihood of admission to ICU or death. CONCLUSION: This study highlights the significant burden of CoVs and justifies the need for surveillance in the acute care setting.


id: cord-268993-2sjh17mw
author: Rödel, Jürgen
date: 2020-08-31
txt: ./txt/cord-268993-2sjh17mw.txt
cache: ./cache/cord-268993-2sjh17mw.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653220303589?v=s5
doi: 10.1016/j.jcv.2020.104616
summary:
  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.

title:
  Use of the variplex(TM) SARS-CoV-2 RT-LAMP as a rapid molecular assay to complement RT-PCR for COVID-19 diagnosis

abstract:
  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. For the evaluation of samples from respiratory secretions concordance analysis showed only a moderate agreement between the variplex™ RT-LAMP conducted on unprocessed samples and Allplex™ and VIASURE RT-PCRs (Cohen’s κ ranging from 0.52-0.56). Using the approach to define a sample as true-positive when at least two assays gave a positive result the clinical sensitivities were as follows: 76.3% for variplex™, 84.2% for Allplex™ and 68.4% for VIASURE. However, when results of RT-PCR and RT-LAMP were combined diagnostic sensitivity was increased to 92-100%. CONCLUSION: The variplex RT-LAMP may serve as a rapid test to be combined with a RT-PCR assay to increase the diagnostic accuracy in patients with suspected COVID-19 infection.


id: cord-269407-6i66zf0e
author: Rutvisuttinunt, Wiriya
date: 2017-07-14
txt: ./txt/cord-269407-6i66zf0e.txt
cache: ./cache/cord-269407-6i66zf0e.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653217302007
doi: 10.1016/j.jcv.2017.07.004
summary:
  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.

title:
  Retrospective use of next-generation sequencing reveals the presence of Enteroviruses in acute influenza-like illness respiratory samples collected in South/South-East Asia during 2010–2013

abstract:
  BACKGROUND: Emerging and re-emerging respiratory pathogens represent an increasing threat to public health. Etiological determination during outbreaks generally relies on clinical information, occasionally accompanied by traditional laboratory molecular or serological testing. Often, this limited testing leads to inconclusive findings. The Armed Forces Research Institute of Medical Sciences (AFRIMS) collected 12,865 nasopharyngeal specimens from acute influenza-like illness (ILI) patients in five countries in South/South East Asia during 2010–2013. 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. STUDY DESIGN: The supernatant of these CPE positive cell cultures were grouped in 32 pools containing 2–26 supernatants per pool. Three WG-NGS runs were performed on these supernatant pools. Sequence reads were used to identify positive pools containing viral pathogens. 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. RESULTS: WG-NGS was an effective way to expand pathogen identification in surveillance studies. This enabled the identification of a viral agent in 71.3% (231/324) of unidentified surveillance samples, including common respiratory pathogens (100/324; 30.9%): enterovirus (16/100; 16.0%), coxsackievirus (31/100; 31.0%), echovirus (22/100; 22.0%), human rhinovirus (3/100; 3%), enterovirus genus (2/100; 2.0%), influenza A (9/100; 9.0%), influenza B, (5/100; 5.0%), human parainfluenza (4/100; 4.0%), human adenovirus (3/100; 3.0%), human coronavirus (1/100; 1.0%), human metapneumovirus (2/100; 2.0%), and mumps virus (2/100; 2.0%), in addition to the non-respiratory pathogen herpes simplex virus type 1 (HSV-1) (172/324; 53.1%) and HSV-1 co-infection with respiratory viruses (41/324; 12.7%).


id: cord-269519-8hr8wyrr
author: Hirotsu, Yosuke
date: 2020-07-07
url: https://doi.org/10.1016/j.jcv.2020.104543
doi: 10.1016/j.jcv.2020.104543
title:
  Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan

abstract:
  BACKGROUND: Severe acute respiratory coronavirus 2 (SARS-CoV-2) has spread and caused death worldwide. Preventive measures and infection control are underway, and some areas show signs of convergence. Other viruses in addition to SARS-CoV-2 cause cold-like symptoms and spread in the winter. However, the extent to which SARS-CoV-2, influenza viruses and other causative viruses have prevailed since implementing preventive measures is unclear. OBJECTIVES: We aim to investigate the incidence of causative viruses and pathogens in patients. STUDY DESIGN: We collected 191 nasopharyngeal swabs from patients with cold-like symptoms in Japan. All samples were subjected to multiplex PCR with the FilmArray Respiratory Panel and reverse transcription PCR (RT-PCR) to detect SARS-CoV-2. RESULTS: FilmArray Respiratory Panel analysis detected at least one virus in 32 of 191 patients with cold-like symptoms (21%). Of these, we frequently identified human rhinoviruses/enteroviruses (5.8%, n=11), human metapneumovirus (3.7%, n=7), coronavirus 229E (2.1%, n=4) and coronavirus OC43 (1.6%, n=3); while no influenza viruses were detected. RT-PCR analysis detected SARS-CoV-2 (4.2%, n=8) in patients who were not infected with the aforementioned respiratory viruses. CONCLUSIONS: Co-infection with SARS-CoV-2 and other viruses was not observed. Causative viruses remain prevalent after implementing preventive measures. SARS-CoV-2 differs from influenza viruses in its infectivity.


id: cord-271445-eft2vwgb
title: Human metapneumovirus as a causative agent of acute bronchiolitis in infants
author: Xepapadaki, Paraskevi
date: 2004-05-06
txt: ./txt/cord-271445-eft2vwgb.txt
cache: ./cache/cord-271445-eft2vwgb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15135747/
doi: 10.1016/j.jcv.2003.12.012
summary:
  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) .

abstract:
  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. Objectives: Since most bronchiolitis studies fail to detect any viral pathogen in part of the samples, we sought for the presence of hMPV in a well characterized bronchiolitis cohort. Study design: Nasal washes were obtained from 56 children admitted to the hospital for acute bronchiolitis. RNA extraction and subsequent RT-PCR were used to detect hMPV, and correlated the presence of the virus with clinical characteristics of the disease. 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. hMPV was identified either as a unique viral pathogen or co-existed with RSV, with whom they shared a similar seasonal distribution. 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. These findings suggest that hMPV is a common and important causative agent in infants with bronchiolitis, with clinical characteristics similar to that of RSV.


id: cord-272734-kawim93f
author: Freire-Paspuel, Byron
date: 2020-05-22
txt: ./txt/cord-272734-kawim93f.txt
cache: ./cache/cord-272734-kawim93f.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32485473/
doi: 10.1016/j.jcv.2020.104454
summary:
  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.

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

abstract:
  BACKGROUND: Several qPCR kits are available for SARS-CoV-2 diagnosis, mostly lacking of evaluation due to covid19 emergency. OBJECTIVE: We evaluated nCoV-QS (MiCo BioMed) kit using CDC kit as gold standard. RESULTS: We found limitations for nCoV-QS: 1) lower sensitivity 2) lack of RNA quality control probe. CONCLUSIONS: Validation studies should be implemented for any SARS-CoV-2 RT-qPCR commercial kit to prevent unreliable diagnosis.


id: cord-273229-c1jws3ol
author: Blairon, Laurent
date: 2020-05-30
txt: ./txt/cord-273229-c1jws3ol.txt
cache: ./cache/cord-273229-c1jws3ol.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653220302146?v=s5
doi: 10.1016/j.jcv.2020.104472
summary:
  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.

title:
  Implementation of rapid SARS-CoV-2 antigenic testing in a laboratory without access to molecular methods: experiences of a general hospital

abstract:
  BACKGROUND: The COVID-19 Ag (Antigen) Respi-Strip assay is a new immunochromatographic diagnostic tool recently available for antigenic diagnosis of SARS-CoV-2. The proposed sensitivity is not higher than 60%, but its high specificity allows both quick decisions for the management of patients and confirmation by molecular diagnosis for only negative tests. However, from the first tests performed, we suspected that the sensitivity observed with routine use was much lower than that announced by the manufacturer. 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. All samples tested were naso-pharyngeal smears from UTM-RT medium. RESULTS: Of 774 patients tested, 714 negative samples were sent for confirmation, and 159 were found to be positive by qRT-PCR. The median positive percentage agreement was 23.9% (95% CI: 14.2%-38.2%). The Cohen’s kappa score was 0.35. 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. In addition, even if the turn-around time is short, the assay is completely manual, which is not suitable for large volumes of routine samples. The sensitivity of this rapid test is poor, and improvements are needed to enhance its performance.


id: cord-273783-z71bquck
title: The dominance of human coronavirus OC43 and NL63 infections in infants
author: Dijkman, Ronald
date: 2011-12-19
txt: ./txt/cord-273783-z71bquck.txt
cache: ./cache/cord-273783-z71bquck.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jcv.2011.11.011
doi: 10.1016/j.jcv.2011.11.011
summary:
  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.

abstract:
  BACKGROUND: It is unknown to what extent the human coronaviruses (HCoVs) OC43, HKU1, 229E and NL63 infect healthy children. Frequencies of infections are only known for hospitalized children. OBJECTIVES: Comparing infection frequencies in children who have mild infections with frequencies in children needing hospital uptake will determine whether infection by one of the four HCoVs leads to more severe disease. In addition, the sequence of seroconversions can reveal whether infection by one HCoV protects from infection by other HCoVs. STUDY DESIGN: Two distinct study groups were monitored: healthy children and children hospitalized due to respiratory infection. HCoV natural infection rates in healthy children were obtained by serology in 25 newborns (followed 0–20 months). 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. RESULTS: The majority of healthy children seroconverted for HCoV-OC43 (n = 19) and HCoV-NL63 (n = 17), less for HCoV-HKU1 (n = 9) and HCoV-229E (n = 5). Notably, HCoV-HKU1 seroconversion was absent after HCoV-OC43 infection. Also HCoV-229E infection was rarely observed after HCoV-NL63 infection (1 out of 5). In the hospital 207 (14%) out of 1471 children were HCoV positive. Again we observed most infection by HCoV-OC43 (n = 85) and HCoV-NL63 (n = 60), followed by HCoV-HKU1 (n = 47) and HCoV-229E (n = 15). CONCLUSIONS: HCoV-NL63 and HCoV-OC43 infections occur frequently in early childhood, more often than HCoV-HKU1 or HCoV-229E infections. HCoV-OC43 and HCoV-NL63 may elicit immunity that protects from subsequent HCoV-HKU1 and HCoV-229E infection, respectively, which would explain why HCoV-OC43 and HCoV-NL63 are the most frequently infecting HCoVs. There are no indications that infection by one of the HCoVs is more pathogenic than others.


id: cord-276316-7ot9ds34
author: Lei, Chunliang
date: 2020-10-14
txt: ./txt/cord-276316-7ot9ds34.txt
cache: ./cache/cord-276316-7ot9ds34.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653220304030
doi: 10.1016/j.jcv.2020.104661
summary:
  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.

title:
  Factors associated with clinical outcomes in patients with Coronavirus Disease 2019 in Guangzhou, China

abstract:
  BACKGROUND: Coronavirus Disease 2019 (COVID-19) is threatening billions of people. We described the clinical characteristics and explore virological and immunological factors associated with clinical outcomes. METHODS: 297 COVID-19 patients hospitalized in Guangzhou Eighth People's Hospital between January 20 and February 20, 2020 were included. Epidemiological, clinical and laboratory data were collected and analyzed. 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. RESULT: Among the 297 patients (median age of 48 years), 154 (51.9 %) were female, 245 (82.5 %) mild/moderate cases, and 52 (17.5 %) severe/critical cases. 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. 16.4 %, P < 0.001). The CD4/CD8 ratio on admission was significantly higher in severe/critical cases than in mild/moderate cases (1.84 vs. 1.50, P = 0.022). During a median follow-up period of 17 days, 36 (12.1 %) patients were admitted to intensive care unit (ICU), 16 (5.4 %) patients developed respiratory failure and underwent mechanical ventilation, four (1.3 %) patients needed extracorporeal membrane oxygenation (ECMO), only one (0.34 %) patients died of multiple organ failure. 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. CONCLUSIONS: Most of COVID-19 patients in Guangzhou are mild/moderate, and presence of extrapulmonary virus and higher CD4/CD8 ratio are associated with higher risk of worse outcomes.


id: cord-277909-rn1dow26
title: Practical experience of high throughput real time PCR in the routine diagnostic virology setting
author: Gunson, R.N.
date: 2006-02-07
txt: ./txt/cord-277909-rn1dow26.txt
cache: ./cache/cord-277909-rn1dow26.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653205003501
doi: 10.1016/j.jcv.2005.12.006
summary:
  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.

abstract:
  The advent of PCR has transformed the utility of the virus diagnostic laboratory. In comparison to traditional gel based PCR assays, real time PCR offers increased sensitivity and specificity in a rapid format. Over the past 4 years, we have introduced a number of qualitative and quantitative real time PCR assays into our routine testing service. During this period, we have gained substantial experience relating to the development and implementation of real-time assays. Furthermore, we have developed strategies that have allowed us to increase our sample throughput while maintaining or even reducing turn around times. The issues resulting from this experience (some of it bad) are discussed in detail with the aim of informing laboratories that are only just beginning to investigate the potential of this technology.


id: cord-279563-4lu1n0s7
author: Gorzalski, Andrew J.
date: 2020-06-10
txt: ./txt/cord-279563-4lu1n0s7.txt
cache: ./cache/cord-279563-4lu1n0s7.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653220302432?v=s5
doi: 10.1016/j.jcv.2020.104501
summary:
  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.

title:
  High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2

abstract:
  BACKGROUND: As the demand for laboratory testing for SARS-CoV-2 increases, additional varieties of testing methodologies are being considered. While real time polymerase chain reaction (RT-PCR) has performed as the main method for virus detection, other methods are becoming available, including transcription mediated amplification (TMA). 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). OBJECTIVES: We sought to compare the sensitivity and specificity of the Aptima SARS-CoV-2 Assay to RTPCR as a means of SARS-CoV-2 detection in a diagnostic setting. STUDY DESIGN: We performed a limit-of-detection study (LoD) to assess the analytical sensitivity of TMA and RT-PCR. This preceded a comparison of the methods using previously evaluated clinical specimens (nasopharyngeal swabs) using 116 human specimens tested by both methodologies. Specimens included sixty-one (61) specimens found reactive by real-time PCR, fifty-one (51) found non-reactive, and four (4) deemed inconclusive. RESULTS: The Aptima SARS-CoV-2 Assay showed a markedly higher analytical sensitivity than RT-PCR by LoD study. Evaluation of clinical specimens resulted in fewer inconclusive results by the SARS-CoV-2 assay, leading to potentially higher clinical sensitivity. 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. TMA provides an effective, highly sensitive means of detection of SARS-CoV-2 in nasopharyngeal specimens.


id: cord-279570-lgbqpfh5
author: Fragkou, Paraskevi C.
date: 2020-08-26
txt: ./txt/cord-279570-lgbqpfh5.txt
cache: ./cache/cord-279570-lgbqpfh5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32877891/
doi: 10.1016/j.jcv.2020.104608
summary:
  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.

title:
  Clinical characteristics and outcomes of measles outbreak in adults: a multicenter retrospective observational study of 93 hospitalized adults in Greece

abstract:
  OBJECTIVES: Measles outbreaks are increasingly reported among countries that were close-to-eliminate measles infection. There are few reports of clinical characteristics of adult measles in the contemporary literature. In this study we aim to describe the clinical characteristics and complications of measles infection in hospitalized adults during the recent epidemic in Greece. METHODS: A multicentre observational retrospective study was conducted in three tertiary hospitals in Greece. All adult hospitalized patients (≥18 years old) with serologically confirmed and/or clinical features compatible with measles were included. Pediatric patients and patients with missing data were excluded. RESULTS: In total, 93 patients, 40 males (43%) and 53 females (57%), mostly young patients were included. Most of them (87%) had no past medical history. Among women, 4 were pregnant. 56 (60.2%) and 25 (26.9%) patients reported either unknown or incomplete vaccination for measles. Ribavirin was administered in 8 (8.6%) patients. Pneumonitis and hepatic involvement were the most common complications, occurring in 43 (46.2%) and 75 (80.6%) patients respectively. Pneumonitis was significantly associated with male sex, older age, lower lymphocyte counts and higher C-reactive protein (CRP) on admission. One pregnant woman suffered spontaneous fetal miscarriage and one patient died due to acute respiratory distress syndrome (ARDS) and high-risk pulmonary embolism. CONCLUSION: Considerable proportions of incompletely vaccinated or unvaccinated adults have led to the re-emergence of measles in countries with reported close-to-elimination rates. Pneumonitis is a major complication among adults with measles. More studies are imperative in order to explore the role of immune paresis in measles.


id: cord-281495-beb164oy
author: Charpentier, Charlotte
date: 2020-09-03
txt: ./txt/cord-281495-beb164oy.txt
cache: ./cache/cord-281495-beb164oy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32919222/
doi: 10.1016/j.jcv.2020.104618
summary:
  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.

title:
  Performance evaluation of two SARS-CoV-2 IgG/IgM rapid tests (Covid-Presto and NG-Test) and one IgG automated immunoassay (Abbott)

abstract:
  The aim of this study was to assess the analytical performances, sensitivity and specificity, of two rapid tests (Covid- Presto® test rapid Covid-19 IgG/IgM and NG-Test® IgM-IgG COVID-19) and one automated immunoassay (Abbott SARS-CoV-2 IgG) for detecting anti- SARS-CoV-2 antibodies. This study was performed with: (i) a positive panel constituted of 88 SARS-CoV-2 specimens collected from patients with a positive SARS-CoV-2 RT-PCR, and (ii) a negative panel of 120 serum samples, all collected before November 2019, including 64 samples with a cross-reactivity panel. Sensitivity of Covid-Presto® test for IgM and IgG was 78.4% and 92.0%, respectively. Sensitivity of NG-Test® for IgM and IgG was 96.6% and 94.9%, respectively. Sensitivity of Abbott IgG assay was 96.5% showing an excellent agreement with the two rapid tests (κ = 0.947 and κ = 0.936 for NGTest ® and Covid-Presto® test, respectively). An excellent agreement was also observed between the two rapid tests (κ = 0.937). Specificity for IgM was 100% and 86.5% for Covid-Presto® test and NG-Test®, respectively. Specificity for IgG was 92.0%, 94.9% and 96.5% for Covid-Presto®, NGTest ®, and Abbott, respectively. Most of the false positive results observed with NG-Test® resulted from samples containing malarial antibodies. In conclusion, performances of these 2 rapid tests are very good and comparable to those obtained with automated immunoassay, except for IgM specificity with the NG-Test®. Thus, isolated IgM should be cautiously interpreted due to the possible false-positive reactions with this test. Finally, before their large use, the rapid tests must be reliably evaluated with adequate and large panel including early seroconversion and possible cross-reactive samples


id: cord-282576-mcx0xq0w
author: Boutin, Catherine-Audrey
date: 2020-09-04
txt: ./txt/cord-282576-mcx0xq0w.txt
cache: ./cache/cord-282576-mcx0xq0w.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jcv.2020.104615
doi: 10.1016/j.jcv.2020.104615
summary:
  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).

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

abstract:
  OBJECTIVE: Although several assays have been developed to detect SARS-CoV-2 RNA in clinical specimens, their relative performance is unknown. 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. RESULTS: The positive and negative agreement between these assays were 99.3 % (95 % CI, 97.3–99.9) and 77.1 % (95 % CI, 67.7–84.4), respectively, for an overall agreement of 93.6 % (95 % CI, 90.7–95.7) beyond random chance (kappa of 0.82, 95 % CI, 0.75−0.85). Of the 22 samples positive by cobas SARS-CoV-2 only, 9 were positive only for ORF-1 gene and had Cycle thresholds (Ct) > 35.1, 8 were positive only for the E gene with Ct > 35.5 and 5 were positive for both targets with Ct > 33.9. Samples positive only with the cobas assay were more often positive with only one gene target (77.3 %) than samples positive in both assays (16.9 %, p < 0.0001). Ct values in the cobas SARS-CoV-2 assay were significantly higher in the 279 samples testing positive in both assays (32.9 %, 95 % CI 32.3–33.6) compared to the 22 samples with discordant results (36.6 %, 95 % CI 36.2–37.1; p = 0.0009). An excellent correlation (r(2) = 0.98) was obtained between Ct values of the ORF-1 and E targets in the cobas assays and a good correlation was obtained between LD RT-PCR test and cobas SARS CoV-2 ORF-1 target (r(2) = 0.82). CONCLUSION: Our study demonstrated an excellent concordance between a LD RT-PCR and the cobas SARS-CoV-2 tests on the 8800 platform.


id: cord-283028-g2rjjq48
author: Christensen, Andreas
date: 2010-09-15
url: https://api.elsevier.com/content/article/pii/S1386653210003057
doi: 10.1016/j.jcv.2010.07.016
title:
  Human bocavirus in children: Mono-detection, high viral load and viraemia are associated with respiratory tract infection

abstract:
  BACKGROUND AND OBJECTIVES: Human bocavirus 1 (HBoV1) has recently been detected in children with respiratory tract infections (RTI). In order to study whether HBoV1 can cause RTI, we investigated its presence in children with upper RTI (URTI), lower RTI (LRTI) and a control group of children without RTI. STUDY DESIGN: Nasopharyngeal aspirates (NPA) and blood samples were collected from children admitted to hospital with RTI from 6 June 2007 to 28 February 2009 (n = 1154), and from children admitted for elective surgery who had no RTI (n = 162). Using polymerase chain reaction (PCR), the NPAs were examined for 17 infectious agents including HBoV1. Blood samples were tested with HBoV1-PCR only. RESULTS: HBoV1 was detected in NPAs from 10% of patients and 17% of controls. Adjusted for age, gender and the presence of other viruses, HBoV1 was not associated with RTI. In the HBoV1-positive NPAs, at least one other virus was detected in 75% and the virus appeared alone in 25%. Adjusted for age and gender, the detection of HBoV1 as the sole virus was associated with RTI, but not with LRTI. Viraemia was found only in children with RTI. The study showed that it was associated with RTI and LRTI. A high HBoV1-load was associated with LRTI, but not with RTI. No interactions between HBoV1 and other infectious agents were found. CONCLUSIONS: Our data support the hypothesis that HBoV1 causes RTI in children, because detection of HBoV1 alone, viraemia and high viral load are associated with RTI and/or LRTI in this age group. However, HBoV1 is common in healthy children.


id: cord-284841-flhfagp3
author: Nicol, Thomas
date: 2020-06-15
url: https://doi.org/10.1016/j.jcv.2020.104511
doi: 10.1016/j.jcv.2020.104511
title:
  Assessment of SARS-CoV-2 serological tests for the diagnosis of COVID-19 through the evaluation of three immunoassays: two automated immunoassays (Euroimmun and Abbott) and one rapid lateral flow immunoassay (NG Biotech)

abstract:
  BACKGROUND: The emergence of new SARS-CoV-2 has promoted the development of new serological tests that could be complementary to RT-PCR. Nevertheless, the assessment of clinical performances of available tests is urgently required as their use has just been initiated for diagnose. OBJECTIVES: The aim of this study was to assess the performance of three immunoassays for the detection of SARS-CoV-2 antibodies. METHODS: Two automated immunoassays (Abbott SARS-CoV-2 CLIA IgG and Euroimmun Anti-SARS-CoV-2 ELISA IgG/IgA assays) and one lateral flow immunoassay (LFIA NG-Test® IgG-IgM COVID-19) were tested. 293 specimens were analyzed from patients with a positive RT-PCR response, from patients with symptoms consistent with COVID-19 but exhibiting a negative response to the RT-PCR detection test, and from control group specimens. Days since symptoms onset were collected from clinical information sheet associated with respiratory tract samples. RESULTS: Overall sensitivity for IgG was equivalent (around 80%) for CLIA, ELISA and LFIA. Sensitivity for IgG detection, >14 days after onset of symptoms, was 100.0% for all assays. Overall specificity for IgG was greater for CLIA and LFIA (more than 98%) compared to ELISA (95.8%). Specificity was significantly different between IgA ELISA (78.9%) and IgM LFIA (95.8%) (p < 0.05). The best agreement was observed between CLIA and LFIA assays (97%; k = 0.936). CONCLUSION: Excellent sensitivity for IgG detection was obtained >14 days after onset of symptoms for all immunoassays. Specificity was also excellent for IgG CLIA and IgG LFIA. Our study shows that NG-Test® is reliable and accurate for routine use in clinical laboratories.


id: cord-285018-l26px1bc
author: Ong, David S.Y.
date: 2020-09-07
txt: ./txt/cord-285018-l26px1bc.txt
cache: ./cache/cord-285018-l26px1bc.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653220303747
doi: 10.1016/j.jcv.2020.104632
summary:
  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] .

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?

abstract:
  BACKGROUND: Due to the emergence of the coronavirus disease 2019 (COVID-19) pandemic there is an urgent need for rapid and accurate testing on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 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. STUDY DESIGN: Patients were eligible between March 18 and May 27, 2020, when they had respiratory symptoms that were suspected for COVID-19. The InGenius platform was compared to routine in-house NAT that was validated according to the national reference. RESULTS: Of 128 randomly selected patients, 58 (45%) tested positive and 55 (43%) tested negative in both platforms. Sensitivity of the InGenius platform was 100% (95% confidence interval 94-100). In the remaining 15 (12%) cases E and RdRp genes were not detected in both platforms but the nucleoprotein (N) gene was tested positive by the InGenius platform. All solitary N gene positive cases were confirmed by a N-gene specific in-house validated NAT, and most of these patients could also be considered positive based on other recently available COVID-19 positive respiratory samples or highly suspected radiological findings. CONCLUSION: The InGenius platform for SARS-CoV-2 detection has excellent sensitivity, is easy to use and provides fast results. The inclusion of the N gene as a third gene target may further increase sensitivity for the diagnosis of COVID-19 in comparison to the national reference method.


id: cord-287206-ois4gnqx
title: Multi-Stage Group Testing Improves Efficiency of Large-Scale COVID-19 Screening
author: Eberhardt, J.N.
date: 2020-04-23
url: https://doi.org/10.1016/j.jcv.2020.104382
doi: 10.1016/j.jcv.2020.104382
abstract:
  BACKGROUND: SARS-CoV-2 test kits are in critical shortage in many countries. This limits large-scale population testing and hinders the effort to identify and isolate infected individuals. OBJECTIVE: Herein, we developed and evaluated multi-stage group testing schemes that test samples in groups of various pool sizes in multiple stages. Through this approach, groups of negative samples can be eliminated with a single test, avoiding the need for individual testing and achieving considerable savings of resources. STUDY DESIGN: We designed and parameterized various multi-stage testing schemes and compared their efficiency at different prevalence rates using computer simulations. RESULTS: We found that three-stage testing schemes with pool sizes of maximum 16 samples can test up to three and seven times as many individuals with the same number of test kits for prevalence rates of around 5% and 1%, respectively. We propose an adaptive approach, where the optimal testing scheme is selected based on the expected prevalence rate. CONCLUSION: These group testing schemes could lead to a major reduction in the number of testing kits required and help improve large-scale population testing in general and in the context of the current COVID-19 pandemic.


id: cord-289139-5ljqnc39
author: Mengelle, C.
date: 2014-09-03
txt: ./txt/cord-289139-5ljqnc39.txt
cache: ./cache/cord-289139-5ljqnc39.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jcv.2014.08.023
doi: 10.1016/j.jcv.2014.08.023
summary:
  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.

title:
  The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit

abstract:
  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. STUDY DESIGN: Respiratory samples were collected from children presenting with respiratory symptoms and attending the emergency unit during the 2010–2011 winter seasons. Samples were tested with the multiplex RespiFinder(®) 15 assay (PathoFinder™) which potentially detects 15 viruses. RESULTS: 857 (88.7%) of the 966 samples collected from 914 children were positive for one (683 samples) or multiple viruses (174 samples). The most prevalent were the respiratory syncytial virus (39.5%) and the rhinovirus (24.4%). Influenza viruses were detected in 139 (14.4%) samples. Adenovirus was detected in 93 (9.6%) samples, coronaviruses in 88 (9.1%), metapneumovirus in 51 (5.3%) and parainfluenzae in 47 (4.9%). Rhinovirus (40%) was the most prevalent pathogen in upper respiratory tract infections while respiratory syncytial virus (49.9%) was the most prevalent in lower respiratory tract infections. Co-infections were associated with severe respiratory symptoms. CONCLUSION: The multiplex assay detected clinically important viruses in a single genomic test and thus will be useful for detecting several viruses causing respiratory tract disorders.


id: cord-289740-nsiycudn
author: Smithgall, Marie C.
date: 2020-05-13
txt: ./txt/cord-289740-nsiycudn.txt
cache: ./cache/cord-289740-nsiycudn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32434706/
doi: 10.1016/j.jcv.2020.104428
summary:
  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.

title:
  Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2

abstract:
  BACKGROUND: The SARS-CoV-2 pandemic has created an urgent and unprecedented need for rapid large-scale diagnostic testing to inform timely patient management. However, robust data are lacking on the relative performance of available rapid molecular tests across a full range of viral concentrations. 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. RESULTS: Compared to cobas, the overall positive agreement was 73.9% with ID Now and 98.9% with Xpert. Negative agreement was 100% and 92.0% for ID Now and Xpert, respectively. Both ID Now and Xpert showed 100% positive agreement for medium and high viral concentrations (Ct value <30). However, for Ct values >30, positive agreement was 34.3% for ID Now and 97.1% for Xpert. 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. Further studies are needed to evaluate the performance of ID Now for direct swabs


id: cord-289947-z2dw2eaz
author: Wong, River Chun-Wai
date: 2020-08-16
txt: ./txt/cord-289947-z2dw2eaz.txt
cache: ./cache/cord-289947-z2dw2eaz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32823131/
doi: 10.1016/j.jcv.2020.104593
summary:
  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.

title:
  Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay

abstract:
  BACKGROUND: Xpert® Xpress SARS-CoV-2 assay is only validated on nasopharyngeal specimens for detection of SARS-CoV-2. 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. These non-validated specimen types, however, do have significant diagnostic value. OBJECTIVE: Evaluate the performance of Xpert Xpress SARS-CoV-2 assay for detection of SARS-CoV-2 from DTS and LRT specimens. METHODS: 162 specimens from 158 patients with suspected COVID-19 disease were tested with Xpert Xpress SARS-CoV-2 assay. These included 120 DTS and 42 LRT specimens i.e. 35 sputum, 6 tracheal aspirate and one bronchoalveolar lavage. Results were compared to those by the TIB-Molbiol LightMix® SarbecoV E-gene assay. RESULTS: Xpert Xpress SARS-CoV-2 assay has satisfactory performance when compared with reference method. The positive percent agreement (PPA) of DTS and LRT specimens were 98.86% & 100% respectively while the negative percent agreement (NPA) was 100% for both 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.


id: cord-290352-0pc5eji4
title: Avian influenza A (H5N1)
author: de Jong, Menno D.
date: 2005-10-06
txt: ./txt/cord-290352-0pc5eji4.txt
cache: ./cache/cord-290352-0pc5eji4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16213784/
doi: 10.1016/j.jcv.2005.09.002
summary:
  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) .

abstract:
  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. These developments have ignited global fears of an imminent influenza pandemic. The current knowledge of the virology, clinical spectrum, diagnosis and treatment of human influenza H5N1 virus infections is reviewed herein.


id: cord-291029-oldket3n
author: Sefers, Susan E.
date: 2005-07-21
txt: ./txt/cord-291029-oldket3n.txt
cache: ./cache/cord-291029-oldket3n.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653205001526
doi: 10.1016/j.jcv.2005.05.011
summary:
  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.

title:
  QIAamp MinElute Virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs()

abstract:
  BACKGROUND: Nucleic acid preparation from a variety of clinical specimens requires efficient target recovery and amplification inhibitor removal and is critical for successful molecular diagnosis. 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. STUDY DESIGN: A total of 150 clinical specimens, including cerebrospinal fluid (CSF) and nasopharyngeal swabs (NPS), were used to determine the extraction efficiency of the MinElute compared to the other two methods. Nucleic acid recovery, hands-on time, turn-around-time and cost were compared across all kits. RESULTS: There was complete concordance between the MinElute and IsoQuick/RNAzol kits when herpes simplex virus (HSV), Epstein–Barr virus (EBV), varicella-zoster virus (VZV), influenza A virus or enteroviruses were detected using a colorimetric microtiter plate PCR system. The kits were equivalent in their ability to detect either DNA or RNA with superior ability to recover a high quality and quantity of RNA. With the potential to process larger specimen volumes, the MinElute kit can significantly shorten processing time from 2 h to 50–55 min. CONCLUSIONS: Although relatively high test kit costs were noted, the MinElute kit provides another rapid and user-friendly specimen processing tool in the diagnostic molecular microbiology laboratory.


id: cord-291553-j9nn5g70
title: Human pegivirus detected in a patient with severe encephalitis using a metagenomic pan-virus array
author: Fridholm, Helena
date: 2016-01-29
txt: ./txt/cord-291553-j9nn5g70.txt
cache: ./cache/cord-291553-j9nn5g70.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653216000366
doi: 10.1016/j.jcv.2016.01.013
summary:
  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).

abstract:
  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. No other pathogen was detected. HPgV in cerebrospinal fluid during encephalitis has never been reported before and its prevalence in cerebrospinal fluid needs further investigation.


id: cord-291930-n7wq09rq
author: Arden, K.E.
date: 2010-01-27
url: https://doi.org/10.1016/j.jcv.2010.01.001
doi: 10.1016/j.jcv.2010.01.001
title:
  Molecular characterization and distinguishing features of a novel human rhinovirus (HRV) C, HRVC-QCE, detected in children with fever, cough and wheeze during 2003

abstract:
  BACKGROUND: Human rhinoviruses (HRVs) are associated with more acute respiratory tract infections than any other viral group yet we know little about viral diversity, epidemiology or clinical outcome resulting from infection by strains, in particular the recently identified HRVs. OBJECTIVES: To determine whether HRVC-QCE was a distinct HRV-C strain, by determining its genome and prevalence, by cataloguing genomic features for strain discrimination and by observing clinical features in positive patients. STUDY DESIGN: Novel real-time RT-PCRs and retrospective chart reviews were used to investigate a well-defined population of 1247 specimen extracts to observe the prevalence and the clinical features of each HRV-QCE positive case from an in- and out-patient pediatric, hospital-based population during 2003. An objective illness severity score was determined for each HRVC-QCE positive patient. RESULTS: Differences in overall polyprotein and VP1 binding pocket residues and the predicted presence of a cis-acting replication element in 1B defined HRVC-QCE as a novel HRV-C strain. Twelve additional HRVC-QCE detections (1.0% prevalence) occurred among infants and toddlers (1–24 months) suffering mild to moderate illness, including fever and cough, who were often hospitalized. HRVC-QCE was frequently detected in the absence of another virus and was the only virus detected in three (23% of HRVC-QCE positives) children with asthma exacerbation and in two (15%) toddlers with febrile convulsion. CONCLUSIONS: HRVC-QCE is a newly identified, genetically distinct HRV strain detected in hospitalized children with a range of clinical features. HRV strains should be independently considered to ensure we do not overestimate the HRVs in asymptomatic illness.


id: cord-292578-co5essuw
author: Johnson, Marina
date: 2020-08-02
txt: ./txt/cord-292578-co5essuw.txt
cache: ./cache/cord-292578-co5essuw.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653220303140
doi: 10.1016/j.jcv.2020.104572
summary:
  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.

title:
  Evaluation of a novel multiplexed assay for determining IgG levels and functional activity to SARS-CoV-2

abstract:
  BACKGROUND: The emergence of SARS-CoV-2 has led to the development of serological assays that could aid in an understanding of the burden of COVID-19 disease. Many available tests lack rigorous evaluation and therefore results may be misleading. 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). Sensitivity was evaluated with a total of 196 COVID-19 serum samples (169 confirmed PCR positive and 27 anti-nucleocapsid IgG positive) from individuals with mild symptomatic or asymptomatic disease. Specificity was evaluated with 194 control serum samples collected from adults prior to December 2019. RESULTS: The specificity and sensitivity of the binding IgG assay was highest for S protein with a specificity of 97.4 % and sensitivity of 96.2 % for samples taken 14 days and 97.9 % for samples taken 21 days following the onset of symptoms. IgG concentration to S and RBD correlated strongly with percentage inhibition measured by the 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.


id: cord-293890-thfros7x
title: Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness
author: Carbo, Ellen C.
date: 2020-08-21
url: https://api.elsevier.com/content/article/pii/S138665322030336X
doi: 10.1016/j.jcv.2020.104594
abstract:
  INTRODUCTION: The SARS-CoV-2 pandemic of 2020 is a prime example of the omnipresent threat of emerging viruses that can infect humans. A protocol for the identification of novel coronaviruses by viral metagenomic sequencing in diagnostic laboratories may contribute to pandemic preparedness. AIM: The aim of this study is to validate a metagenomic virus discovery protocol as a tool for coronavirus pandemic preparedness. METHODS: The performance of a viral metagenomic protocol in a clinical setting for the identification of novel coronaviruses was tested using clinical samples containing SARS-CoV-2, SARS-CoV, and MERS-CoV, in combination with databases generated to contain only viruses of before the discovery dates of these coronaviruses, to mimic virus discovery. RESULTS: Classification of NGS reads using Centrifuge and Genome Detective resulted in assignment of the reads to the closest relatives of the emerging coronaviruses. Low nucleotide and amino acid identity (81% and 84%, respectively, for SARS-CoV-2) in combination with up to 98% genome coverage were indicative for a related, novel coronavirus. Capture probes targeting vertebrate viruses, designed in 2015, enhanced both sequencing depth and coverage of the SARS-CoV-2 genome, the latter increasing from 71 to 98%. CONCLUSION: The model used for simulation of virus discovery enabled validation of the metagenomic sequencing protocol. The metagenomic protocol with virus probes designed before the pandemic, can assist the detection and identification of novel coronaviruses directly in clinical samples.


id: cord-294155-94skyx5f
title: Human bocavirus detection in an atopic child affected by pneumonia associated with wheezing
author: Terrosi, Chiara
date: 2007-08-07
url: https://www.ncbi.nlm.nih.gov/pubmed/17686654/
doi: 10.1016/j.jcv.2007.06.011
abstract:
  BACKGROUND: Human bocavirus (HBoV) is a newly discovered human parvovirus. HBoV was detected in respiratory samples by PCR, but its aetiologic role in the pathogenesis of acute respiratory infectious diseases is still unclear. RESULTS: In this report, we describe an atopic child affected by pneumonia, with a past history of wheezing. A panel of bacteria and respiratory viruses were searched in the nasopharyngeal swab, only human bocavirus was detected by PCR. CONCLUSIONS: Detection of HboV, as the only microbial agent, in samples from children with wheezing and acute respiratory diseases supports the assumption that this emerging virus could have an aetiologic role in the pathogenesis of respiratory diseases.


id: cord-295189-bz3gi15h
author: Jennings, Lance C.
date: 2015-03-14
txt: ./txt/cord-295189-bz3gi15h.txt
cache: ./cache/cord-295189-bz3gi15h.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25959149/
doi: 10.1016/j.jcv.2015.03.011
summary:
  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.

title:
  Respiratory viruses in airline travellers with influenza symptoms: Results of an airport screening study

abstract:
  BACKGROUND: There is very little known about the prevalence and distribution of respiratory viruses, other than influenza, in international air travellers and whether symptom screening would aid in the prediction of which travellers are more likely to be infected with specific respiratory viruses. OBJECTIVES: In this study, we investigate whether, the use of a respiratory symptom screening tool at the border would aid in predicting which travellers are more likely to be infected with specific respiratory viruses. 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. RESULTS: Respiratory viruses were detected in 342 (26.0%) of 1313 samples obtained from 2714 symptomatic travellers. The most frequently identified viruses were rhinoviruses (128), enteroviruses (77) and influenza B (48). The most frequently reported symptoms were stuffy or runny nose (60%), cough (47%), sore throat (27%) and sneezing (24%). Influenza B infections were associated with the highest number of symptoms (mean of 3.4) followed by rhinoviruses (mean of 2.2) and enteroviruses (mean of 1.9). The positive predictive value (PPV) of any symptom for any respiratory virus infection was low at 26%. 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.


id: cord-295600-xe3ruu9a
author: Calarota, Sandra A.
date: 2015-06-17
txt: ./txt/cord-295600-xe3ruu9a.txt
cache: ./cache/cord-295600-xe3ruu9a.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653215002632
doi: 10.1016/j.jcv.2015.06.078
summary:
  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.

title:
  T-lymphocyte subsets in lung transplant recipients: association between nadir CD4 T-cell count and viral infections after transplantation

abstract:
  BACKGROUND: Little is known about the kinetics of T-cell subsets in lung transplant recipients (LTR) and their association with the occurrence of opportunistic infections (OI). 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. RESULTS: LTR with a nadir CD4 T-cell count <200 cells/μl had consistently lower CD4 and CD8 T-cell counts than LTR with a nadir CD4 T-cell count >200 cells/μl (p < 0.001). In LTR with a nadir CD4 T-cell count <200 cells/μl, the cumulative incidence of viral infections detected in peripheral blood and in bronchoalveolar lavage (BAL) samples was higher than in LTR with a nadir CD4 T-cell count >200 cells/μl (p = 0.0012 and p = 0.0058, respectively). A nadir CD4 T-cell count <200 cells/μl within the first three months post-transplantation predicted a higher frequency of viral infectious episodes in BAL samples within the subsequent six month period (p = 0.0066). CONCLUSIONS: Stratification of patients according to nadir CD4 T-cell count may represent a new and simple approach for early identification of patients at risk for subsequent virus infections.


id: cord-295873-kykyubdq
title: Seasonal variations of respiratory viruses and etiology of human rhinovirus infection in children
author: Morikawa, Saeko
date: 2015-10-22
url: https://www.ncbi.nlm.nih.gov/pubmed/26521224/
doi: 10.1016/j.jcv.2015.10.001
abstract:
  BACKGROUND: Using the polymerase chain reaction (PCR) method it is possible to detect uncultivable viruses and discover multiple viral infections. However, the clinical importance of these findings in relation to symptoms is not known. OBJECTIVES: The seasonal fluctuations of respiratory viruses and the clinical outcomes of single infections and dual infections were investigated. STUDY DESIGN: Nasal aspirate samples were obtained from outpatients and inpatients of a children’s hospital and these samples were subjected to real-time PCR to detect 16 respiratory viruses. Seasonal variations of the 16 viruses and the clinical outcomes such as wheezing, the need for oxygenation and prolonged hospitalization of patients with single viral infections and multiple infections were determined for the 5 most often detected viruses. RESULTS: Among 512 specimens analyzed, one or more viruses were detected in 424 (83%) specimens. Two or more viruses were detected in 160 samples (31% of all samples). The epidemic peaks of the viruses did not coincide with each other. Rhinoviruses were the most frequently detected viruses and their coinfection rates were also higher. However, the disease severity in the lower respiratory tract did not differ in most respiratory viral infections regardless of whether there was single infection or dual infection with a rhinovirus and other respiratory virus. CONCLUSIONS: Seasonal distribution was seen for each virus. There were no significant differences in clinical symptoms in the children studied. Because the infection of rhinoviruses is the common occurrence in children, it is hypothesized that the factors related to disease severity are mainly the underlying conditions of the children.


id: cord-295957-s17z2ccf
title: Rapid and sensitive detection of SARS-CoV-2 RNA using the Simplexa™ COVID-19 direct assay
author: Bordi, Licia
date: 2020-05-04
txt: ./txt/cord-295957-s17z2ccf.txt
cache: ./cache/cord-295957-s17z2ccf.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S138665322030158X?v=s5
doi: 10.1016/j.jcv.2020.104416
summary:
  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.

abstract:
  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. OBJECTIVE: The aim of this study was to evaluate the performances of a newly designed real-time RT-PCR (Simplexa™ COVID-19 Direct assay), that is established with an all-in-one reagent mix and no separate extraction required. RESULTS: The lower limit of detection (LOD) for both target genes resulted the same: 3.2 (CI: 2.9–3.8) log10 cp/mL and 0.40 (CI: 0.2–1.5) TCID50/mL for S gene while 3.2 log10 (CI: 2.9–3.7) log10 cp/mL and 0.4 (CI: 0.2–1.3) TCID50/mL for ORF1ab. The LOD obtained with extracted viral RNA for both S gene or ORF1ab was 2.7 log10 cp/mL. Crossreactive analysis performed in 20 nasopharyngeal swabs confirmed a 100% of clinical specificity of the assay. Clinical performances of Simplexa™ COVID-19 Direct assay were assessed in 278 nasopharyngeal swabs tested in parallel with Corman's method. Concordance analysis showed an "almost perfect" agreement in SARS-CoV-2 RNA detection between the two assays, being κ = 0.938; SE = 0.021; 95% CI = 0.896-0.980. 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.


id: cord-296847-r752bcsu
author: Campanini, Giulia
date: 2007-04-23
txt: ./txt/cord-296847-r752bcsu.txt
cache: ./cache/cord-296847-r752bcsu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17452001/
doi: 10.1016/j.jcv.2007.03.009
summary:
  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.

title:
  Human respiratory syncytial virus (hRSV) RNA quantification in nasopharyngeal secretions identifies the hRSV etiologic role in acute respiratory tract infections of hospitalized infants

abstract:
  BACKGROUND: Human respiratory syncytial virus (hRSV) detection in nasopharyngeal aspirates (NPAs) from infants with acute respiratory tract infection (ARTI) does not prove the hRSV etiology of the current ARTI episode. HRSV RNA quantification may help in affording this issue. OBJECTIVES: hRSV was detected by quantitative reverse transcription-PCR in NPAs taken upon admission to hospital and, whenever possible, at discharge and subsequent medical visits. STUDY DESIGN: Prospective study, including 63 infants affected by either hRSV upper or lower ARTI. RESULTS: Based on the kinetics of viral load, hRSV etiology was identified in 25 infants in whom hRSV load dropped from 2.5 × 10(6) upon admission (presence of respiratory symptoms) to 7.5 × 10(2) RNA copies/ml NPA upon discharge (absence of symptoms) after a median time of 5 days, and in 19 infants, in whom hRSV load was determined at admission only, in association with clinical symptoms (2.4 × 10(6) copies/ml). Furthermore, low levels of hRSV RNA (<1 × 10(5) copies/ml NPA) identified 14 patients with non-hRSV ARTI. Finally, in 14 infants with hRSV coinfections or sequential infections, hRSV quantification defined the hRSV role in the current ARTI episode. CONCLUSIONS: hRSV RNA quantification is critical in defining the hRSV role in respiratory infections.


id: cord-297365-11es4w0u
title: Coronavirus Disease 2019 in Children: Characteristics, Antimicrobial Treatment, and Outcomes
author: Peng, Hui
date: 2020-05-07
txt: ./txt/cord-297365-11es4w0u.txt
cache: ./cache/cord-297365-11es4w0u.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32446167/
doi: 10.1016/j.jcv.2020.104425
summary:
  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

abstract:
  BACKGROUND: At present, coronavirus disease 2019 (COVID-19) has spread in many countries. We conducted this study to help paediatricians To help pediatricians understand the conditions of COVID-19 in children, we conducted this study. 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. A Cox proportional hazards regression analysis was used to evaluate factors associated with clinical outcomes. RESULTS: As of February 29, 75 children had been discharged, of which only one was has severe pneumonia and one was critical cases. Children younger than 2 years were more susceptible to COVID-19. All patients have received interferon-α nebulization, and eight cases including the severe and critical cases were co-administrated ribavirin. Five patients with mild pneumonia were given arbidol. Twenty-three patients were given traditional Chinese medicine (TCM). The average length of stay (LOS) and the time of SARS-CoV-2 clearance were 10.57 and 6.39 days, respectively. None of the factors was associated with LOS or time of SARS-CoV-2 clearance. CONCLUSIONS: The severity of COVID-19 in pediatric cases were milder than adults. The efficacy of the antiviral therapy in children with COVID-19 remains to be evaluated.


id: cord-299388-okiqmy6e
title: Respiratory syncytial virus in Brazilian infants – Ten years, two cohorts
author: Wollmeister, Elinara
date: 2017-12-06
txt: ./txt/cord-299388-okiqmy6e.txt
cache: ./cache/cord-299388-okiqmy6e.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S138665321730330X
doi: 10.1016/j.jcv.2017.12.002
summary:
  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

abstract:
  BACKGROUND: Each year, a considerable amount of children will experience at least one episode of acute viral bronchiolitis (AVB) during their first year of life. About 10% of them will be hospitalized, with significant physical and economic burdens. OBJECTIVES: To compare two cohorts of infants with AVB, from same region, in a ten-year interval, regarding epidemiologic factors and viral etiology. 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. RESULTS: The comparative analysis showed a difference in the percentage of respiratory syncytial virus (RSV) positive patients [2004 (33.1%); 2014 (70.3%)] (p < 0.01). No differences were noted regarding gender, breastfeeding, tobacco exposure, crowding and maternal education. There was a difference as to the month of incidence (seasonality) of AVB (higher in April 2014). There was a higher age at attendance in the first cohort, and lower birth weight and gestational age ratios in the second cohort (p < 0.05). There were no differences in hospitalization time, need of mechanical ventilation and number of deaths, however a difference regarding co-morbidities was noted (higher in 2004) (p < 0.001). CONCLUSION: None of the analyzed variables had an impact on severity features. Virology and immunology must be considered in this kind of situation, by studying genetic variants and the maturation of the immune system in AVB by RSV or other viruses.


id: cord-299537-lbx1plqx
author: Wang, Wei
date: 2010-09-19
url: https://www.ncbi.nlm.nih.gov/pubmed/20855230/
doi: 10.1016/j.jcv.2010.08.005
title:
  Molecular monitoring of causative viruses in child acute respiratory infection in endemo-epidemic situations in Shanghai

abstract:
  BACKGROUND: Numerous viruses are responsible for respiratory infections; however, both their distribution and genetic diversity, in a limited area and a population subgroup, have been studied only rarely during a sustained period of time. METHODS: A 2-year surveillance program of children presenting with acute respiratory infections (ARIs) was carried out to characterize the viral etiology and to assess whether using gene amplification and sequencing could be a reliable approach to monitor virus introduction and spread in a population subgroup. RESULTS: Using multiplex RT-PCR, 15 different respiratory viruses were detected within the 486 nasopharyngeal positive samples collected among 817 children aged <9-year old who presented with ARI during October 2006 to September 2008. A single virus was detected in 373 patients (45.7%), and two to four viruses in 113 patients (13.8%). The most frequent causative viruses were respiratory syncytial virus (RSV) (24.7%), human bocavirus (24.5%), and human rhinovirus (HRV) (15%). RSV was more prevalent in winter and among young infants. Cases of seasonal influenza A and B viruses were reported mainly in January and August. An increase in adenovirus infection was observed during the spring of the second year of the study. Sequence analyses showed multiple introductions of different virus subtypes and identified a high prevalence of the newly defined HRV-C species. A higher viral incidence was observed during the winter of 2008, which was unusually cold. CONCLUSIONS: This study supports the usefulness of multiplex RT-PCR for virus detection and co-infection, and for implementation of a molecular monitoring system for endemic and epidemic viral respiratory infections.


id: cord-299664-nexq5ntj
title: Comparison of three commercial RT-PCR systems for the detection of respiratory viruses
author: Butt, S.A.
date: 2014-08-18
txt: ./txt/cord-299664-nexq5ntj.txt
cache: ./cache/cord-299664-nexq5ntj.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653214003102
doi: 10.1016/j.jcv.2014.08.010
summary:
  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.

abstract:
  BACKGROUND: Due to the insensitivity of rapid tests for respiratory viruses, nucleic acid amplification tests are quickly becoming the standard of care. 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). Samples positive for influenza A, B or RSV were tested by both methods, while the remainder were tested by RP only. True positives were defined as positive by two or more assays. RESULTS: Limit of detection (LOD) analyses demonstrated Pro had the lowest LOD for all FluA strains tested, PIV1, PIV2 and AdV; RV+ had the lowest LOD for FluB; and RP had the lowest LOD for RSV, PIV3 and hMPV. Of the 55 samples tested by RV+, all 54 true positive samples were positive by RV+. Of the 89 samples tested by RP, 85 of the 88 true positive samples were positive by RP. From these results, the overall sensitivities for influenza A, B and RSV were 100% and 98% for RV+ and RP, respectively. The overall sensitivity of RP for all viruses was 97%. CONCLUSIONS: In summary, these systems demonstrated excellent performance. Furthermore, each system has benefits which will ensure they will all have a niche in a clinical laboratory.


id: cord-300018-3uzau7if
author: Mak, Gannon C.K.
date: 2020-07-24
txt: ./txt/cord-300018-3uzau7if.txt
cache: ./cache/cord-300018-3uzau7if.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jcv.2020.104550
doi: 10.1016/j.jcv.2020.104550
abstract: nan
summary:
  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

title:
  The D614G substitution in the S gene and clinical information for patients with COVID-19 detected in Hong Kong


id: cord-300316-r54ksiy3
author: Moesker, F.M.
date: 2016-03-25
url: https://api.elsevier.com/content/article/pii/S1386653216300506
doi: 10.1016/j.jcv.2016.03.022
title:
  Diagnostic performance of influenza viruses and RSV rapid antigen detection tests in children in tertiary care

abstract:
  BACKGROUND: Rapid antigen detection tests (RADTs) are increasingly used to detect influenza viruses and respiratory syncytial virus (RSV). However, their sensitivity and specificity are a matter of debate, challenging their clinical usefulness. OBJECTIVES: Comparing diagnostic performances of BinaxNow Influenza AB(®) (BNI) and BinaxNow RSV(®) (BNR), to those of real-time reverse transcriptase PCR (RT-PCR), virus isolation and direct immunofluorescence (D-IF) in paediatric patients. STUDY DESIGN: Between November 2005 and September 2013, 521 nasal washings from symptomatic children (age <5 years) attending our tertiary care centre were tested, with a combination of the respective assays using RT-PCR as gold standard. RESULTS: Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of BNI were 69% (confidence interval [CI] [51–83]), 96% [94–97], 55% [39–70] and 98% [96–99] respectively. Of eleven false-negative samples, RT-PCR Ct-values were higher than all RT-PCR positive test results (27 vs 22, p = 0.012). Of twenty false-positive samples, none were culture positive and two tested positive in D-IF. Sensitivity, specificity, PPV and NPV for BNR were 79% [73–85], 98% [96–99], 97% [93–99] and 88% [84–91]. Of the 42 false-negative samples the median Ct-value was higher than that of all RT-PCR positive samples (31 vs 23, p < 0.0001). Five false-positive samples were detected. Three of these tested positive for RSV in virus isolation and D-IF. CONCLUSIONS: RADTs have a high specificity with BNR being superior to BNI. However, their relative low sensitivity limits their usefulness for clinical decision making in a tertiary care paediatric hospital.


id: cord-301254-093yih5n
author: Brittain-Long, Robin
date: 2010-01-18
txt: ./txt/cord-301254-093yih5n.txt
cache: ./cache/cord-301254-093yih5n.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/20080440/
doi: 10.1016/j.jcv.2009.12.010
summary:
  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.

title:
  Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens—Duration of symptoms significantly affects detection rate

abstract:
  BACKGROUND: Nucleic acid amplification techniques have improved the diagnostic possibilities in respiratory tract infections, although their clinical applicability is not yet fully defined. We have evaluated a multiplex real-time PCR method for the detection of 13 respiratory viruses and 2 bacteria (Mycoplasma and Chlamydophila) in a clinical setting. 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. STUDY DESIGN: Nasopharyngeal swab samples were prospectively collected from 209 adult outpatients with respiratory infections and 100 asymptomatic controls. RESULTS: An infectious agent was identified in 43% of samples from patients and 2% of asymptomatic controls. The detection rate was significantly higher in samples from patients with a duration of symptoms of 6 days or less (51%) than in samples from patients with a duration of symptoms of 7 days or more (30%, p < 0.01). For human corona viruses, and influenza virus A and B there was a correlation between the amount of virus in each patient sample as measured Ct values and duration of symptoms. 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. Our finding should be taken into account when using these tests in clinical practise.


id: cord-302125-96w0nh9q
author: Péré, Hélène
date: 2020-09-03
txt: ./txt/cord-302125-96w0nh9q.txt
cache: ./cache/cord-302125-96w0nh9q.txt
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mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653220303590
doi: 10.1016/j.jcv.2020.104617
abstract: nan
summary:
  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

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


id: cord-302528-wmxw9e0c
title: Evaluation of the COVID19 ID NOW EUA Assay
author: Mitchell, Stephanie L.
date: 2020-05-15
txt: ./txt/cord-302528-wmxw9e0c.txt
cache: ./cache/cord-302528-wmxw9e0c.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653220301712
doi: 10.1016/j.jcv.2020.104429
summary:
  • 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.

abstract:
  • ID NOW EUA SARS-CoV-2 assay had an overall agreement of 78.7% when compared to the standard of care reference methods. • ID NOW had a sensitivity of 71.7% and specificity of 100%. • All the false-negative results occurred with weakly positive samples, with reference method C(T) values ≥35.


id: cord-302864-2xnq1oq7
author: Quartuccio, Luca
date: 2020-05-15
url: https://www.sciencedirect.com/science/article/pii/S1386653220301864?v=s5
doi: 10.1016/j.jcv.2020.104444
title:
  Profiling COVID-19 pneumonia progressing into the cytokine storm syndrome: results from a single Italian Centre study on tocilizumab versus standard of care

abstract:
  OBJECTIVE: Approximately 5% of patients with coronavirus disease 2019 (COVID-19) develop a life-threatening pneumonia that often occurs in the setting of increased inflammation or “cytokine storm”. Anti-cytokine treatments are being evaluated but optimal patient selection remains unclear, and the aim of our study is to address this point. METHODS: Between February 29 to April 6, 2020, 111 consecutive hospitalized patients with COVID-19 pneumonia were evaluated in a single centre retrospective study. Patients were divided in two groups: 42 severe cases (TOCI) with adverse prognostic features including raised CRP and IL-6 levels, who underwent anti-cytokine treatments, mostly tocilizumab, and 69 standard of care patients (SOC). RESULTS: In the TOCI group, all received anti-viral therapy and 40% also received glucocorticoids. In TOCI, 62% of cases were ventilated and there were 3 deaths (17.8 ± 10.6 days, mean follow up) with 7/26 cases remaining on ventilators, without improvement, and 17/26 developed bacterial superinfection. One fatality occurred in the 15 TOCI cases treated on noninvasive ventilation and 1 serious bacterial superinfection. Of the 69 cases in SOC, there was no fatalities and no bacterial complications. The TOCI group had higher baseline CRP and IL-6 elevations (p < 0.0001 for both) and higher neutrophils and lower lymphocyte levels (p = 0.04 and p = 0.001, respectively) with the TOCI ventilated patients having higher markers than non-ventilated TOCI patients. CONCLUSION: Higher inflammatory markers, more infections and worse outcomes characterized ventilated TOCI cases compared to ward based TOCI. Despite the confounding factors, this suggests that therapy time in anti-cytokine randomized trials will be key.


id: cord-302896-3zvjyl3g
title: Phylogenetic analysis of human coronavirus NL63 circulating in Italy
author: Minosse, C.
date: 2008-07-03
txt: ./txt/cord-302896-3zvjyl3g.txt
cache: ./cache/cord-302896-3zvjyl3g.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/18602337/
doi: 10.1016/j.jcv.2008.04.015
summary:
  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

abstract:
  BACKGROUND: Five known human coronaviruses infect the human respiratory tract: HCoV-OC43, HCoV-229E, SARS-CoV, HCoV-NL63 and HCoV-HKU1. OBJECTIVES: To evaluate the prevalence of HCoV-NL63 in hospitalized adult patients and to perform molecular characterization of Italian strains. 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. Phylogenetic analysis was performed by partial sequencing of S and ORF1a. Additional S sequences from Northern Italy were included in the phylogenetic trees. RESULTS: HCoV-NL63 was detected in 10 patients (2.0%) with symptomatic respiratory diseases, mainly during winter. Phylogenetic analysis indicated a certain degree of heterogeneity in Italian isolates. The ORF1a gene clustering in phylogenetic trees did not match with that of the S gene. CONCLUSIONS: As observed by others, HCoV-NL63 is often associated with another virus. Phylogenetic characterization of HCoV-NL63 circulating in Italy indicates that this virus circulates as a mixture of variant strains, as observed in other countries.


id: cord-307261-0a3iztns
author: Hayden, Randall T.
date: 2012-01-30
txt: ./txt/cord-307261-0a3iztns.txt
cache: ./cache/cord-307261-0a3iztns.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653211005531
doi: 10.1016/j.jcv.2011.12.020
summary:
  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.

title:
  Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children

abstract:
  BACKGROUND: The detection of viral respiratory tract infections has evolved greatly with the development of PCR based commercial systems capable of simultaneously detecting a wide variety of pathogens. OBJECTIVES: Evaluate the relative performance of two commercial broad range systems for the detection of viral agents in clinical respiratory tract specimens from immunocompromised children. STUDY DESIGN: A total of 176 patient samples were included in the analysis, representing only the first sample collected for each patient, and excluding failed reactions. 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. Method comparison was based upon pair-wise concordance of results according to patient age, viral target and number of targets detected. RESULTS: The two systems showed an overall concordance, by patient, of 83.8% (p = 0.0001). FilmArray detected at least one target in 68.8% of samples, while ResPlex detected at least one target in 56.8%. ResPlex failed to detect 20.7% of FilmArray positives, and FilmArray failed to detect 4% of ResPlex positives. The relative performance of each system (including which system detected a higher number of positive samples) varied when stratified by target viral pathogen. CONCLUSIONS: Broadly multiplexed PCR is an effective means of detecting large numbers of clinically relevant respiratory viral pathogens.


id: cord-307602-2cmgu7rf
author: McErlean, P.
date: 2007-05-07
txt: ./txt/cord-307602-2cmgu7rf.txt
cache: ./cache/cord-307602-2cmgu7rf.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653207001278
doi: 10.1016/j.jcv.2007.03.012
summary:
  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.

title:
  Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis

abstract:
  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. OBJECTIVES: To molecularly characterise a novel HRV and determine its prevalence and clinical impact on a predominantly paediatric population. STUDY DESIGN: Nucleotide sequencing was employed to determine the complete HRV-QPM coding sequence. Two novel real-time RT-PCR diagnostic assays were designed and employed to retrospectively screen a well-defined population of 1244 specimen extracts to identify the prevalence of HRV-QPM during 2003. 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. Investigation of the relatively short VP1 sequence suggest that the virus is resistant to Pleconaril, setting it apart from the HRV A species. Sixteen additional HRV-QPM strains were detected (1.4% of specimens) often as the sole micro-organism present among infants with suspected bronchiolitis. HRV-QPM was also detected in Europe during 2006, and a closely related virus circulated in the United States during 2004. CONCLUSIONS: We present the molecular characterisation and preliminary clinical impact of a newly identified HRV along with sequences representing additional new HRVs.


id: cord-308921-lpcjhxvg
author: Stellrecht, Kathleen A.
date: 2019-11-09
url: https://doi.org/10.1016/j.jcv.2019.104204
doi: 10.1016/j.jcv.2019.104204
title:
  Panther Fusion® Respiratory Virus Assays for the detection of influenza and other respiratory viruses()

abstract:
  BACKGROUND: Nucleic acid amplification tests (NAATs), such as PCR, are preferred for respiratory virus testing, due to superior diagnostic accuracy and faster turnaround time. Panther Fusion® Respiratory Assays (Fusion), which includes FluA/B/RSV (FFABR), Paraflu and AdV/hMPV/RV, offers a modular approach to syndromic testing on a fully automated platform while improving gene targets and expanding the test menu. OBJECTIVES AND STUDY DESIGN: We evaluated Fusion using 275 consecutive nasopharyngeal specimens previously used in an analysis of five PCRs, as well as 225 archived specimens. RESULTS: Of the combined 500 specimens, 134 were positive for influenza A (FluA), 54 for FluB, 65 for RSV, 64 for parainfluenza (PIV), 24 for adenovirus (AdV), 21 for humanmetapneumovirus (hMPV), and 40 for rhinovirus (RV) with Fusion. Of the positive samples Fusion correlated with historical results for all but one, despite multiple freeze-thaws cycles of this collection. Fusion was positive for an additional 33 samples, including 11 FluAs, 7 RSVs, 3 PIV3s, 3 AdV, 6 hMPV and 3 RVs. These samples were retested with corresponding Prodesse (Pro) assays using quadruple sample volume. This resolver test confirmed Fusion results for an additional 4 FluAs, 4 RSVs, 1 PIV3 and 3 AdVs. The sensitivity and specificity ranges of Fusion were 99–100% and 98–100%. Limit of detection (LOD) analyses were performed on a variety of Flu isolates. The LODs ranged from 2.69 to 2.99 log copies/ml and demonstrated superior LOD as compared to previously published data for some assays or to concurrent analyses with two new commercial tests.


id: cord-309763-8eywr57j
title: Detection and quantification of human metapneumovirus in pediatric specimens by real-time RT-PCR
author: Kuypers, Jane
date: 2005-02-11
url: https://www.ncbi.nlm.nih.gov/pubmed/16036180/
doi: 10.1016/j.jcv.2004.11.023
abstract:
  BACKGROUND: Human metapneumovirus (hMPV), a recently identified virus, causes respiratory illness in children. OBJECTIVES: A real-time reverse transcription-polymerase chain reaction (RT-PCR) assay was developed and used to detect and quantify hMPV in respiratory specimens. STUDY DESIGN: The quantitative RT-PCR assay amplified an approximately 70 base pair fragment from the hMPV fusion protein gene. The assay was validated and used to test respiratory specimens obtained from children seen at a hospital in Seattle, Washington, from December 2002 through May 2003. RESULTS: The assay detected 1000 hMPV copies/mL of specimen, did not detect 19 other respiratory viruses, and was able to detect and accurately quantify isolates from the four known hMPV genetic lineages in a proficiency panel of 20 previously tested samples. hMPV was detected in 52 (7.2%) of 719 pediatric respiratory specimens. The mean log 10 copies/mL of hMPV in the 52 positive specimens was 7.67 (range = 4.59–10.60). Children aged 7–12 months had a significantly higher hMPV prevalence (12.4%) than did children younger than 7 months (4.7%) (P < 0.005). Children in this age group also had significantly higher levels of hMPV in their respiratory specimens (mean log 8.43 copies/mL) than did the younger children (mean log 6.93 copies/mL) (P = 0.0025). CONCLUSIONS: The rapid real-time RT-PCR assay described here is a sensitive test for clarifying the epidemiology of and diseases associated with hMPV.


id: cord-310140-h7uwl0pb
author: Templeton, K.E.
date: 2005-07-12
txt: ./txt/cord-310140-h7uwl0pb.txt
cache: ./cache/cord-310140-h7uwl0pb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16019258/
doi: 10.1016/j.jcv.2005.05.005
summary:
  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.

title:
  A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses

abstract:
  OBJECTIVES: To assess the quality of molecular detection of respiratory viruses in clinical diagnostic laboratories. STUDY DESIGN: Respiratory virus proficiency panels were produced from diluted stocks of respiratory viruses provided and tested by four reference laboratories. The panels consisted of strong positive, positive, low positive and negative samples for influenza viruses A and B, respiratory syncytial virus, parainfluenza viruses 1 and 3, adenovirus serotypes 4 and 7, human rhinovirus serotypes 16, 72 and 90, human coronaviruses OC43 and 229E. The panels were sent to 17 participants; results and information on methodology was collected. RESULTS: All laboratories returned results, of which five submitted complete data sets. So, for analysis all results were combined. Samples were correctly identified by participants in 93.75%, 76.75% and 47.03% for the high positive, positive and low positive samples, respectively. One false positive was reported for all data sets (1.1%). The overall score for all assays using different methodologies was 78.8%. Laboratory performance was not dependant on methodology as all in-house methodologies could achieve optimal results, but dependant on careful optimisation and procedures specific to the laboratory. CONCLUSIONS: The first proficiency panel showed that in general all participants performed well. Although, it also highlights areas for improvement for all participants in order to generate robust results for use in clinical diagnostics.


id: cord-310171-1fmsxx2s
title: Virus and cystic fibrosis: Rhinoviruses are associated with exacerbations in adult patients()
author: Goffard, Anne
date: 2014-02-25
txt: ./txt/cord-310171-1fmsxx2s.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jcv.2014.02.005
doi: 10.1016/j.jcv.2014.02.005
summary:
  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

abstract:
  BACKGROUND: Few studies have suggested the potential role of respiratory viruses in cystic fibrosis (CF) exacerbation, but their real impact is probably underestimated. METHOD: Sixty-four sputum samples collected from 46 adult patients were included in the study: 33 samples were collected during exacerbation of CF, and 31 during the stable phase. After extraction, nucleic acids were tested for the presence of respiratory viruses. When rhinovirus (HRV) was detected, the 5′UTR and VP4/2 regions were sequenced, and phylogenetically analyzed. The characteristics of patients in exacerbation and stable phase were compared. RESULTS: Viruses were found in 25% of samples. The HRV viruses were the most frequently detected followed by coronaviruses. Only the HRV detection was significantly associated with the occurrence of CF pulmonary exacerbation (p < 0.027). Characterization of 5′UTR and VP4/2 regions of the HRV genome specified that HRV-A, -B, -C were detected. All HRV-C were recombinant HRV-Ca. CONCLUSIONS: HRV were the most frequently detected viruses; their detection was significantly associated with the occurrence of an exacerbation. The reality of viral recombination between HRV was demonstrated in CF patients for the first time, raising the role of viruses in lung microbiota. Further studies are now warranted to decipher virus impact in CF.


id: cord-310680-klywz85w
author: Li, Qihan
date: 2005-04-06
url: https://www.ncbi.nlm.nih.gov/pubmed/16157265/
doi: 10.1016/j.jcv.2004.12.019
title:
  The interaction of the SARS coronavirus non-structural protein 10 with the cellular oxido-reductase system causes an extensive cytopathic effect

abstract:
  The pathological mechanism of SARS-CoV infection was investigated. The gene for the SARS-CoV non-structural protein 10, which is located in the open reading frame of pp1a/pp1ab gene, was synthesized and used to screen for the specific cellular gene coding for the protein interacting with this nsp10 protein in a human embryo lung cDNA library using a yeast trap method. The results indicated that apart from the two subunits of cellular RNA polymerase complex, BTF3 and ATF5, this nsp10 protein was also able to interact specifically with the NADH 4L subunit and cytochrome oxidase II. Further study revealed that the activity of the NADH-cytochrome was altered and the inner mitochondrial membrane was depolarized in the transfected human embryo lung fibroblast by the nsp10 protein gene. The cytopathic effect of the Coronavirus 229E strain appeared more extensive in these cells than in the control cells.


id: cord-311275-ysr9nqun
author: Chuaychoo, Benjamas
date: 2019-07-03
txt: ./txt/cord-311275-ysr9nqun.txt
cache: ./cache/cord-311275-ysr9nqun.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jcv.2019.07.001
doi: 10.1016/j.jcv.2019.07.001
summary:
  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.

title:
  Clinical manifestations and outcomes of respiratory syncytial virus infection in adult hospitalized patients

abstract:
  BACKGROUND: Respiratory syncytial virus (RSV) is an important virus found in adult hospitalized patients. OBJECTIVES: To study the clinical outcomes of hospitalized patients aged ≥ 15 years and diagnosed with RSV infection. STUDY DESIGN: Both retrospective and prospective cohort studies were conducted at a university hospital between May 2014 and December 2015. Results: RSV was detected in 86 of 1562(5.5%) adult hospitalized patients suspected of respiratory viral infection. Sixty-nine patients were included in the study. RSV was detected by RT-PCR (82.6%), IFA (10.1%), and both RT-PCR and IFA (7.3%). Most patients (87.0%) were aged ≥ 50 years. Cardiovascular diseases, pulmonary diseases, immunocompromised hosts, and diabetes were the major comorbidities. The common manifestations were cough (92.8%), dyspnea (91.3%), sputum production (87.0%), tachypnea (75.4%), wheezing (73.9%), and fever (71.0%). Fifty- five patients (79.7%) were diagnosed with pneumonia. Hypoxemia (SpO2 ≤ 92%) was found in 53.6% patients. Twenty-five of 69(36.2%) patients developed respiratory failure and required ventilatory support. Cardiovascular complications were found in 24.6% of patients. Congestive heart failure, acute myocardial infarction (MI), new atrial fibrillation, and supraventricular tachycardia were found in 9(13.0%), 7(10.1%), 4(5.8%), and 3(4.3%) of 69 patients, respectively. Overall mortality was 15.9%. Pneumonia (81.8%) and acute MI (18.2%) were the major causes of death. CONCLUSIONS: Most adult hospitalized patients with RSV infection were of advanced age and had comorbidities. Cardiopulmonary complications were the major causes of death. Management and prevention of RSV infection in these vulnerable groups are necessary.


id: cord-311633-i9ret7bw
title: Unexpected diagnosis of COVID-19-associated disorders by SARS-CoV-2-specific serology
author: Péré, Hélène
date: 2020-08-04
txt: ./txt/cord-311633-i9ret7bw.txt
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mime: text/plain
url: https://doi.org/10.1016/j.jcv.2020.104568
doi: 10.1016/j.jcv.2020.104568
summary:
  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.

abstract:
  Facing the ongoing pandemic caused by SARS-CoV-2, there is an urgent need for serological assays identifying individuals with on-going infection as well as past coronavirus infectious disease 2019 (COVID-19). 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. The Abbott SARS-CoV-2 IgG assay showed sensitivity of 94% and specificity of 100%, demonstrating high analytical performances allowing convenient management of suspected on-going and past-infections. In addition, the SARS-CoV-2 IgG positivity rates were compared in COVID-19 positive and COVID-19 free areas from our hospital. Thus, the frequency of SARS-CoV-2-specific IgG was around 10-fold higher in COVID-19 areas than COVID-19 free areas (75% versus 8%; P < 0.001). 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. Taken together, these observations highlight the potential interest of SARS-CoV-2-specific serology in the context of COVID-19 epidemic, especially to assess past SARS-CoV-2 infection as well as possible unexpected COVID-19-associated disorders.


id: cord-312971-r9sggqh8
author: Mancino, Enrica
date: 2020-04-29
url: https://doi.org/10.1016/j.jcv.2020.104385
doi: 10.1016/j.jcv.2020.104385
title:
  A single centre study of viral community-acquired pneumonia in children: no evidence of SARS-CoV-2 from October 2019 to March 2020

abstract:
  Pneumonia is an important cause of morbidity and mortality in children. We described viral aetiologies, with particular interest in detecting SARS-CoV-2, in hospitalized pneumonia children. Human rhinovirus was the most frequently detected agent. No children tested positive for SARS-CoV-2. Our findings suggest that SARS-CoV-2 infection is rare in children and it was not circulating in Rome before COVID-19 outbreak.


id: cord-313375-rs3jjiuj
author: Panning, Marcus
date: 2010-11-13
url: https://www.ncbi.nlm.nih.gov/pubmed/21075679/
doi: 10.1016/j.jcv.2010.10.010
title:
  Singleplex real-time RT-PCR for detection of influenza A virus and simultaneous differentiation of A/H1N1v and evaluation of the RealStar influenza kit

abstract:
  BACKGROUND: A novel influenza A virus, subtype A/H1N1v emerged in April 2009 and caused the first influenza pandemic of the 21st century. Reliable detection and differentiation from seasonal influenza viruses is mandatory for appropriate case management as well as public health. OBJECTIVES: To develop and technically validate a novel one-step real-time RT-PCR assay which can be used for influenza A virus screening and subtyping of A/H1N1v in a singleplex fashion. To assess the clinical performance of a novel commercial influenza RT-PCR kit based on the in-house version. STUDY DESIGN: A real-time RT-PCR assay targeting the matrix gene of influenza A viruses was developed and validated using in vitro transcribed RNA derived from influenza A/H1N1v, A/H1N1 and A/H3N2 virus as well as plaque-quantified influenza A/H1N1v, A/H1N1 and A/H3N2 virus samples. After validation of the in-house version the commercial RealStar kit was used to assess the clinical performance and specificity on a panel of influenza viruses including A/H1N1v, A/H1N1, swine A/H1N1, A/H3N2, avian A/H5N1 as well as patient specimens. RESULTS: The lower limit of detection of the in-house version was 2149, 1376 and 2994 RNA copies/ml for A/H1N1v, A/H1N1 and A/H3N2, respectively. The RealStar kit displayed 100% sensitivity and specificity and could reliably discriminate influenza A viruses from A/H1N1v. No cross reaction with swine A/H1N1 and A/H1N2 was observed with the RealStar A/H1N1v specific probe. CONCLUSION: Both assays demonstrated high sensitivity and specificity and might assist in the diagnosis of suspected influenza cases.


id: cord-313749-f2ct57em
title: Multiplex real-time PCR for detection of respiratory tract infections
author: Brittain-Long, Robin
date: 2007-12-26
txt: ./txt/cord-313749-f2ct57em.txt
cache: ./cache/cord-313749-f2ct57em.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653207003940
doi: 10.1016/j.jcv.2007.10.029
summary:
  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

abstract:
  BACKGROUND: Broad diagnostics of respiratory infection by molecular assays has not yet won acceptance due to technical difficulties and high costs. OBJECTIVES: To evaluate clinical applicability of multiplex real-time PCR. 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. pneumoniae and Ch. pneumoniae was developed and run daily on consecutive clinical nasopharyngeal swab samples. RESULTS: An etiology was identified in 48% of the 954 samples, with IfA in 25%, RV in 20%, MPV in 10% and M. pneumoniae in 10% of the positive. By a rational procedure costs could be reduced and the customer price set relatively low (€33 per sample). CONCLUSION: Streamlined testing and cost limitation is achievable and probably critical for implementation of a broad molecular diagnostics of respiratory infections.


id: cord-313821-5f5b107l
author: Poelman, Randy
date: 2014-11-15
url: https://www.sciencedirect.com/science/article/pii/S1386653214004193
doi: 10.1016/j.jcv.2014.11.011
title:
  The emergence of enterovirus D68 in a Dutch University Medical Center and the necessity for routinely screening for respiratory viruses

abstract:
  BACKGROUND: Since August 2014, an increase in infections caused by enterovirus D68 (EV-D68) was reported in the USA and Canada, for the most part in children presenting with severe respiratory symptoms. OBJECTIVES: To determine whether an increase in severe EV-D68 respiratory infections was observed in our region. STUDY DESIGN: Samples from patients with respiratory symptoms were screened for viral pathogens, including rhinovirus and enterovirus. Subsequently, samples positive for rhinovirus and enterovirus were routinely sequenced for phylogenetic analysis. Furthermore, an additional method was used to detect EV-D68 specifically. RESULTS: During the first three quarters of the year 2014, 1896 respiratory samples were analyzed; 39 (2%) of them tested positive for enterovirus. Eighteen samples tested positive for EV-D68, obtained from 16 different patients admitted to our hospital. Eleven were children below the age of 18, of whom five children needed intensive care treatment. The remaining five samples were from adults, who all had an underlying disease; three were transplant patients (heart, lung and renal transplantation), the other two had an underlying lung condition (COPD, asthma). Phylogenetic analysis showed a close relationship with the strains circulating currently in the USA, all belonging to the known EV-D68 genetic subtypes. CONCLUSIONS: We observed an increase of EV-D68 infections in our population, both in children as well as in adult. In 2014 there have been 16 cases so far, compared to none in 2011 and 2013 and a single case in 2012. Phylogenetic analysis identified two similar clusters as shown in the USA and Canada.


id: cord-314028-sf8zt9r9
title: Telemedicine for management of paediatric infectious diseases during COVID-19 outbreak
author: Esposito, Susanna
date: 2020-06-23
txt: ./txt/cord-314028-sf8zt9r9.txt
cache: ./cache/cord-314028-sf8zt9r9.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S138665322030264X
doi: 10.1016/j.jcv.2020.104522
abstract: nan
summary:
  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.


id: cord-314829-tmgmqtjq
title: Low performance of rapid antigen detection test as frontline testing for COVID-19 diagnosis
author: Scohy, Anaïs
date: 2020-05-21
url: https://api.elsevier.com/content/article/pii/S1386653220301979
doi: 10.1016/j.jcv.2020.104455
abstract:
  BACKGROUND: Ensuring accurate diagnosis is essential to limit the spread of the SARS-CoV-2 and for the clinical management of COVID-19. Although real-time reverse transcription polymerase chain reaction (RT- qPCR) is the current recommended laboratory method to diagnose SARS-CoV-2 acute infection, several factors such as requirement of special equipment and skilled staff limit the use of these time-consuming molecular techniques. Recently, several easy to perform rapid antigen detection tests were developed and recommended in some countries as the first line of diagnostic. OBJECTIVES: The aim of this study was to evaluate the performances of the Coris COVID-19 Ag Respi-Strip. Study design. We performed a comparison study by testing nasopharyngeal samples with RT-qPCR and antigen rapid test. RESULTS: 148 nasopharyngeal swabs were tested. Amongst the 106 positive RT-qPCR samples, 32 were detected by the rapid antigen test, given an overall sensitivity of 30.2%. All the samples detected positive with the antigen rapid tests were also positive with RT-qPCR. CONCLUSIONS: Highest viral load is associated with better antigen detection rates. Unfortunately, the overall poor sensitivity of the COVID-19 Ag Respi-Strip does not allow using it alone as the frontline testing for COVID-19 diagnosis.


id: cord-314888-i7nn2e3m
title: Human parainfluenza virus circulation, United States, 2011–2019
author: DeGroote, Nicholas P.
date: 2020-01-09
url: https://doi.org/10.1016/j.jcv.2020.104261
doi: 10.1016/j.jcv.2020.104261
abstract:
  BACKGROUND: Human parainfluenza viruses (HPIVs) cause upper and lower respiratory tract illnesses, most frequently among infants and young children, but also in the elderly. While seasonal patterns of HPIV types 1–3 have been described, less is known about national patterns of HPIV-4 circulation. OBJECTIVES: To describe patterns of HPIVs circulation in the United States (US). STUDY DESIGN: We used data from the National Respiratory and Enteric Virus Surveillance System (NREVSS), a voluntary passive laboratory-based surveillance system, to characterize the epidemiology and circulation patterns of HPIVs in the US during 2011–2019. We summarized the number of weekly aggregated HPIV detections nationally and by US census region, and used a subset of data submitted to NREVSS from public health laboratories and several clinical laboratories during 2015–2019 to analyze differences in patient demographics. RESULTS: During July 2011 - June 2019, 2,700,135 HPIV tests were reported; 122,852 (5 %) were positive for any HPIV including 22,446 for HPIV-1 (18 %), 17,474 for HPIV-2 (14 %), 67,649 for HPIV-3 (55 %), and 15,283 for HPIV-4 (13 %). HPIV testing increased substantially each year. The majority of detections occurred in children aged ≤ 2 years (36 %) with fluctuations in the distribution of age by type. CONCLUSIONS: HPIVs were detected year-round during 2011–2019, with type-specific year-to-year variations in circulation patterns. Among HPIV detections where age was known, the majority were aged ≤ 2 years. HPIV-4 exhibited an annual fall-winter seasonality, both nationally and regionally. Continued surveillance is needed to better understand national patterns of HPIV circulation.


id: cord-315782-tx2vqr64
title: Human Coronavirus-NL63 infections in Korean children, 2004–2006
author: Han, Tae Hee
date: 2006-11-29
url: https://api.elsevier.com/content/article/pii/S1386653206004070
doi: 10.1016/j.jcv.2006.10.009
abstract:
  BACKGROUND: Human coronavirus-NL63 (HCoV-NL63) has been isolated from children with respiratory tract infections and its prevalence in Korea has not been reported. OBJECTIVES: This study was designed to investigate the presence and the clinical features of HCoV-NL63 during two winter seasons. STUDY DESIGN: During April 2004–April 2006, nasopharyngeal specimens from children hospitalized with acute respiratory disease were tested for common respiratory viruses, including RSV, influenza A, influenza B, parainfluenza viruses, and adenovirus by IFA. hMPV infection was excluded by nested RT-PCR using primers for F-gene. To detect HCoV-NL63, previously described nested PCR assays for 1a and 1b were used. PCR products of the 1a gene for HCoV-NL63 were sequenced. RESULTS: Out of 872 nasopharyngeal aspirate from children aged under 16 years, 14 (1.7%) were positive for HCoV-NL63. Most of the patients had croup (64.2%) or bronchiolitis (21.4%). The peak prevalence was found in November (28.5%). Most were collected between November 2004 and February 2005. CONCLUSIONS: HCoV-NL63 may be one of the causative agents of acute respiratory tract infection, especially croup.


id: cord-316723-srenbxa7
author: Zhao, Jincun
date: 2004-11-23
txt: ./txt/cord-316723-srenbxa7.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15797360/
doi: 10.1016/j.jcv.2004.09.024
summary:
  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) .

title:
  Development and evaluation of an enzyme-linked immunosorbent assay for detection of antibodies against the spike protein of SARS-coronavirus

abstract:
  BACKGROUND: Severe acute respiratory syndrome (SARS) is caused by infection with SARS-associated coronavirus (CoV). 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. OBJECTIVES: To develop and evaluate an ELISA system for detection of anti-S Abs in patient sera. STUDY DESIGN: Express recombinant S450-650 in E. Coli and evaluate the sensitivity and specificity of an ELISA system based on the S450-650 polypeptide. RESULTS: The S450-650-based ELISA detected IgG Abs in 41 out of 51 serum samples from 22 hospitalized patients with probable SARS, a result closely correlated with that obtained with a virus-based ELISA (r = 0.75, k = 0.8). Differential anti-S IgG responses were observed amongst SARS patients. Some of them produced anti-S Abs early during their infection, while others failed to make IgG Abs against the S450-650 polypeptide. None of the serum samples from 100 healthy blood donors was positive in the S450-650-based assay. CONCLUSION: The S450-650-based ELISA can detect anti-S IgG Abs with high sensitivity and specificity.


id: cord-318012-bg9y2nsp
author: Cantais, Aymeric
date: 2014-05-22
txt: ./txt/cord-318012-bg9y2nsp.txt
cache: ./cache/cord-318012-bg9y2nsp.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653214001838
doi: 10.1016/j.jcv.2014.05.006
summary:
  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.

title:
  Epidemiology and microbiological investigations of community-acquired pneumonia in children admitted at the emergency department of a university hospital

abstract:
  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. OBJECTIVES: Evaluation of a diagnostic approach including multiplex PCR assays for revisiting the epidemiology and etiology of CAP in children at hospital. STUDY DESIGN: Children of all ages consulting at the Emergency Department of the University hospital of Saint-Etienne, France, during the 2012–2013 winter period were included. In addition to bacterial cultures, the following pathogens were detected using biplex commercially-available rt-PCR tests: adenovirus, respiratory syncytial virus, human metapneumovirus, bocavirus, rhinovirus/enterovirus, coronavirus, influenza viruses A and B, parainfluenza viruses, Mycoplasma pneumoniae and Chlamydophila pneumonia. RESULTS: From 85 patients with CAP, at least one pathogen was identified in 81 cases (95.3%), including 4 bacterial exclusive infections (4.7%), 53 viral exclusive infections (62.4%) and 24 mixed infections (28.2%). Coinfection by at least two viruses was observed in 37 cases (43.5%). Mean age was higher in the case of documented bacterial infection (P < 0.05). In the subgroup of viral exclusive infection, the mean age of severe cases was 2.0 years vs 3.8 years in mild and moderate cases (P < 0.05). 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.


id: cord-319864-t6ql9hz2
author: Lima, Amorce
date: 2020-11-11
txt: ./txt/cord-319864-t6ql9hz2.txt
cache: ./cache/cord-319864-t6ql9hz2.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653220304303
doi: 10.1016/j.jcv.2020.104688
summary:
  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%.

title:
  Validation of a Modified CDC Assay and Performance Comparison with the NeuMoDx™ and DiaSorin® automated assays for Rapid Detection of SARS-CoV-2 in Respiratory Specimens

abstract:
  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has spread rapidly around the globe since it was first identified in December of 2019 in Wuhan, China. In a race to contain the infection, researchers and healthcare officials have developed several assays to help diagnose individuals with COVID-19. To help laboratories decide what assay to bring into testing lines, factors such as assay availability, cost, throughput, and TAT should be considered. Here we validated a modified version of the CDC assay and used it as a reference to evaluate the performance of the NeuMoDxTM SARS-CoV-2 and DiaSorin SimplexaTM Covid-19 Direct assays. 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. The performance of the three assays were analyzed using 159 nasopharyngeal swabs specimen tested within 1 to 5 days after routine testing. A 100% agreement was observed between the commercial assays and the modified CDC SARS-CoV-2 assay. A deeper look at the Ct values showed no significant difference between NeuMoDx and the modified CDC SARS-CoV-2 assay, whereas DiaSorin had lower overall Ct values than the modified CDC SARS-CoV-2 assay. NeuMoDx and DiaSorin workflows were much easier to perform. NeuMoDx has the highest throughput and shortest TAT, whereas although the modified CDC SARS-CoV-2 assay has comparable throughput to DiaSorin, it has the longest hands-on time and highest TAT.


id: cord-320156-xs936r6u
title: Polyomaviruses-associated respiratory infections in HIV-infected and HIV-uninfected children
author: Nunes, Marta C.
date: 2014-10-28
url: https://api.elsevier.com/content/article/pii/S1386653214004004
doi: 10.1016/j.jcv.2014.10.013
abstract:
  BACKGROUND: Two recently discovered polyomaviruses (PyV), WU and KI, have been identified in respiratory-tract specimens from children with acute respiratory infections, although there are limited data in HIV-infected children. OBJECTIVES: To determine the prevalence and clinical manifestations of WUPyV and KIPyV-associated lower respiratory tract infections (LRTIs) hospitalization in HIV-infected and -uninfected children; and probe the role of pneumococcal co-infection. STUDY DESIGN: Nasopharyngeal aspirates were collected from a cohort of 39,836 children randomized to receive 9-valent pneumococcal conjugate vaccine (PCV9) or placebo when hospitalized for LRTIs, and were screened by PCR for WUPyV, KIPyV and other respiratory viruses. RESULTS: In placebo-recipients the prevalence of WUPyV was 6.3% (18/285) in HIV-infected and 13.9% (66/476) in HIV-uninfected children (p = 0.002). In WUPyV-positive LRTIs HIV-infected children had lower oxygen saturation at admission and a higher case fatality rate (11.1% vs. 0%; p = 0.04). KIPyV was identified in 10.2% (29/285) of HIV-infected and in 7.4% (35/476) of HIV-uninfected placebo-recipients with LRTIs (p = 0.13). HIV-infected compared to HIV-uninfected children with KIPyV-positive LRTIs had lower oxygen saturation, higher respiratory rate and longer duration of hospitalization. Co-infections with other respiratory-viruses were detected in 65.5% of WUPyV-positive LRTIs and in 75.0% of KIPyV-positive LRTIs. Among HIV-uninfected children, there was a lower incidence of hospitalization for clinical pneumonia episodes in which KIPyV (80%; 95% CI: 41, 93) and WUPyV (49%; 95% CI: 9, 71) were identified among PCV9-recipients compared to placebo-recipients. CONCLUSIONS: Polyomaviruses were commonly identified in HIV-infected and -uninfected children hospitalized for LRTIs, frequently in association with other viruses and may contribute to the pathogenesis of pneumococcal pneumonia.


id: cord-321287-mh2j2koa
author: Trémeaux, Pauline
date: 2020-07-06
url: https://api.elsevier.com/content/article/pii/S1386653220302833
doi: 10.1016/j.jcv.2020.104541
title:
  Evaluation of the Aptima™ Transcription-Mediated Amplification assay (Hologic®) for detecting SARS-CoV-2 in clinical specimens

abstract:
  BACKGROUND: The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which appeared in late 2019, has been limited by isolating infected individuals. However, identifying such individuals requires accurate diagnostic tools. OBJECTIVE: This study evaluates the capacity of the Aptima™ Transcription-Mediated Amplification (TMA) assay (Hologic® Panther System) to detect the virus in clinical samples. STUDY DESIGN: We compared the Aptima™ assay to two in-house real-time RT-PCR techniques, one running on the Panther Fusion™ module and the other on the MagNA Pure 96 and Light-Cycler 480 instruments. We included a total of 200 respiratory specimens: 100 tested prospectively and 100 retrospectively (25 -ve/75 +ve). RESULTS: The final Cohen’s kappa coefficients were: κ = 0.978 between the Aptima™ and Panther Fusion™ assays, κ = 0.945 between the Aptima™ and MagNA/LC480 assays and κ = 0.956 between the MagNA/LC480 and Panther Fusion™ assays. CONCLUSION: These findings indicate that the Aptima™ SARS-CoV-2 TMA assay data agree well with those obtained with our routine methods and that this assay can be used to diagnose coronavirus disease 2019 (COVID-19).


id: cord-323567-1397kds0
author: Bialasiewicz, S.
date: 2007-08-21
url: https://www.ncbi.nlm.nih.gov/pubmed/17714984/
doi: 10.1016/j.jcv.2007.07.015
title:
  Development and evaluation of real-time PCR assays for the detection of the newly identified KI and WU polyomaviruses

abstract:
  BACKGROUND: Recently, novel human polyomaviruses, KI (KIV) and WU (WUV) were described. Their role in human disease has not yet been determined. OBJECTIVES: The aim of this study was to develop sensitive and specific assays for the detection of KIV and WUV. STUDY: Two KIV (KI-A and KI-B) and three WUV (WU-A, WU-B and WU-C) real-time polymerase chain reaction (rtPCR) assays were developed and evaluated. Clinical sensitivities and specificities were determined by testing 200 respiratory specimens and the results compared to those for previously described conventional PCR assays. Limits of detection were determined, and the analytical specificities of the assays were investigated. RESULTS: No cross-reactivity was observed between the rtPCR methods and unrelated organisms. All five rtPCR assays could reliably detect 10 copies of genomic DNA equivalents per reaction, which was more sensitive than conventional methods. Compared to the conventional PCR assays, the sensitivity of the KI-A, KI-B, WU-A, WU-B and WU-C assays was 100%, 86.7% 95.5%, 100% and 100%, respectively. Specificity was 94.6%, 97.3%, 96.6%, 97.7% and 97.2%, respectively. CONCLUSIONS: The KI-A, WU-B and WU-C assays provide the most sensitive detection of KIV and WUV in clinical specimens and may be used for further research into these viruses.


id: cord-324125-wau2xq0x
author: Qiu, Chao
date: 2013-12-16
url: https://api.elsevier.com/content/article/pii/S1386653213005167
doi: 10.1016/j.jcv.2013.12.004
title:
  Epidemiologic report and serologic findings for household contacts of three cases of influenza A (H7N9) virus infection

abstract:
  BACKGROUND AND OBJECTIVE: We conducted epidemiologic investigations and serologic assays on household contacts that were extensively exposed to three influenza A (H7N9) virus infected case-patients before infection-control practices were implemented. STUDY DESIGN: Data on the early clinical course of each patient and the exposure history for each patient's household contacts were obtained by interviewing household members and by reviewing medical records. Viral RNA in patient samples was tested using real-time reverse transcriptase polymerase chain reaction assay. Antibodies against H7N9 virus in serum samples were tested using hemagglutination inhibition and pseudovirus based neutralization assays. RESULTS: All household contacts were extensively exposed to the case-patients without the use of measures to protect against infection. Viral RNA was detected in the specimens from case-patients for approximately 7–11 days after confirmation of infection. However, the results of the analyses of serum specimens taken from the household contacts 15–26 days post exposure revealed no evidence of transmission of H7N9 virus from the case-patients to the contacts. CONCLUSION: Despite ample unprotected exposures to case-patients during the virus shedding period, household members in this report were not infected by the H7N9 virus.


id: cord-325120-jlrievxl
author: Abd El Wahed, Ahmed
date: 2015-05-19
txt: ./txt/cord-325120-jlrievxl.txt
cache: ./cache/cord-325120-jlrievxl.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653215001493
doi: 10.1016/j.jcv.2015.05.004
summary:
  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

title:
  Diagnostics-in-a-Suitcase: Development of a portable and rapid assay for the detection of the emerging avian influenza A (H7N9) virus

abstract:
  BACKGROUND: In developing countries, equipment necessary for diagnosis is only available in few central laboratories, which are less accessible and of limited capacity to test large numbers of incoming samples. Moreover, the transport conditions of samples are inadequate, therefore leading to unreliable results. OBJECTIVES: The development of a rapid, inexpensive, and simple test would allow mobile detection of viruses. 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. As an example, two RT-RPA assays were established for the detection of hemagglutinin (H) and neuraminidase (N) genes of the novel avian influenza (H7N9) virus. RESULTS: The sensitivities of the H7 and the N9 RT-RPA assays were 10 and 100 RNA molecules, respectively. The assays were performed at a single temperature (42 °C). The results were obtained within 2–7 min. The H7N9 RT-RPA assays did not show a cross-detection either of any other respiratory viruses affecting humans and/or birds or of the human or chicken genomes. All reagents were used, stored, and transported at ambient temperature, that is, cold chain independent. In addition, the Diagnostics-in-a-Suitcase was operated by a solar-powered battery. CONCLUSIONS: The developed assay protocol and mobile setup performed well. Moreover, it can be easily implemented to perform diagnoses at airports, quarantine stations, or farms for rapid on-site viral nucleic acid detection.


id: cord-326816-a7yovhvk
author: Piralla, Antonio
date: 2018-01-12
url: https://api.elsevier.com/content/article/pii/S1386653218300052
doi: 10.1016/j.jcv.2018.01.005
title:
  Enterovirus-D68 (EV-D68) in pediatric patients with respiratory infection: The circulation of a new B3 clade in Italy

abstract:
  BACKGROUND: In recent years, several outbreaks due to Enterovirus D-68 (EV-D68) have been reported, and it was confirmed that the virus can cause upper and lower respiratory tract diseases and be associated with the development of neurological problems. OBJECTIVES: The main aim of this research was to study the genetic characteristics of EV-D68 strains that were circulating in Italy identified during an outbreak of an EV-D68 infection that occurred in Italy during the period March-October 2016. STUDY DESIGN: A retrospective study of the circulation of different types and subtypes of EV-D68 was performed. Nasopharyngeal swabs were collected from March 2016 through October 2016 in children admitted to the Emergency Room with respiratory diseases. RESULTS: Among 390 children, 22 (59.1% males; mean age 47 months) were found to be infected by EV-D68 and most of them were immunocompetent (72.7%). Pneumonia was diagnosed in 12 (54.5%) children. Phylogenetic analysis of the VP1 region showed that all the strains identified in this study belonged to clade B3. Within B3 subclade, the Italian EV-D68 strains were most closely related to strains detected in Southern China in 2015 as well as to strains detected in US and the Netherlands in 2016. CONCLUSIONS: These results showed that EV-D68 infections are a common cause of lower respiratory illness in pediatric age. The circulation of one EV-D68 lineage has been proven in Italy and in the European region during 2016. However, further studies are required to investigate whether some strains or lineages may possess a higher affinity for the lower airway or central nervous system.


id: cord-328290-kbysppgb
title: Diagnostic performance of near-patient testing for influenza
author: Beckmann, Christiane
date: 2015-03-31
txt: ./txt/cord-328290-kbysppgb.txt
cache: ./cache/cord-328290-kbysppgb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25959157/
doi: 10.1016/j.jcv.2015.03.024
summary:
  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.

abstract:
  BACKGROUND: Rapid diagnosis of influenza is important for controlling outbreaks and starting antiviral therapy. Direct antigen detection (DAD) is rapid, but lacks sensitivity, whereas nucleic acid amplification testing (NAT) is more sensitive, but also more time-consuming. 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™ 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. RespiFinder-22(®) a commercial multiplex NAT served as reference test. Serial 10-fold dilutions of influenza-A and -B cell culture supernatants were examined. Another 225 patient samples were tested during December 2014–February 2015. RESULTS: Compared to RespiFinder-22(®), the isothermal NAT Alere™ 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. Alere™ Influenza A&B showed 85.7% sensitivity and 100% specificity in the second cohort. Isothermal NAT was 10-100-fold more sensitive compared to DAD for influenza virus culture supernatants with a lower limit of detection of 5000–50,000 copies/mL. The average turn-around time (TAT) of isothermal NAT and DADs was 15 min, but increased to 110 min for Alere™ Influenza A&B, 30 min for BinaxNOW(®) Influenza A&B, and 45 min for Sofia(®) Influenza A + B, when analyzing batches of 6 samples. CONCLUSION: Simple sample processing and a TAT of 15 min render isothermal NAT Alere™ Influenza A&B suitable for sequential near-patient testing, but the TAT advantage is lost when testing of larger series.


id: cord-329052-jan20ljs
title: Persistent detection of SARS-CoV-2 RNA in patients and healthcare workers with COVID-19
author: Gombar, Saurabh
date: 2020-05-30
url: https://www.sciencedirect.com/science/article/pii/S1386653220302195?v=s5
doi: 10.1016/j.jcv.2020.104477
abstract:
  BACKGROUND: Current guidelines for returning health care workers (HCW) to service after a positive SARS-CoV-2 RT-PCR test and ceasing of transmission precautions for patients is based on two general strategies. A test-based strategy that requires negative respiratory RT-PCR tests obtained after the resolution of symptoms. Alternatively, due to the limited availability of testing, many sites employ a symptom-based strategy that recommends excluding HCW from the workforce and keeping patients on contact precautions until a fixed period of time has elapsed from symptom recovery. The underlying assumption of the symptom-based strategy is that waiting for a fixed period of time is a surrogate for negative RT-PCR testing, which itself is a surrogate for the absence of shedding infectious virus. OBJECTIVES: To better understand the appropriate length of symptom based return to work and contact precaution strategies. STUDY DESIGN: We performed an observational analysis of 150 patients and HCW that transitioned from RT-PCR SARS-CoV-2 positive to negative over the course of 2 months at a US academic medical center. RESULTS: We found that the average time to transition from RT-PCR positive to negative was 24 days after symptom onset and 10 % remained positive even 33 days after symptom onset. No difference was seen in HCW and patients. CONCLUSIONS: These findings suggest until definitive evidence of the length of infective viral shedding is obtained that the fixed length of time before returning to work or ceasing contract precautions be revised to over one-month.


id: cord-331707-kfja1i6s
author: Andrés, Cristina
date: 2018-11-30
txt: ./txt/cord-331707-kfja1i6s.txt
cache: ./cache/cord-331707-kfja1i6s.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653218302816
doi: 10.1016/j.jcv.2018.11.004
summary:
  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.

title:
  Surveillance of enteroviruses from paediatric patients attended at a tertiary hospital in Catalonia from 2014 to 2017

abstract:
  BACKGROUND: Enterovirus (EV) infections are usually asymptomatic or mild, but symptomatic infections can evolve to severe complications. Outbreaks of EV-A71 and EV-D68 have been recently reported worldwide, sometimes related to severe clinical outcomes. OBJECTIVE: To describe EV genetic diversity and the clinical outcomes from paediatric patients attended at a tertiary university hospital in Barcelona (Catalonia, Spain) from 2014 to 2017. STUDY DESIGN: Specimens were collected from paediatric (<17 years old) cases with suspicion of respiratory tract infection or EV infection. EV laboratory-confirmation was performed by specific real-time multiplex RT-PCR assay. Partial viral VP1 protein was sequenced for genetic characterisation by phylogenetic analyses. RESULTS: A total of 376 (7%) from 5703 cases were EV laboratory-confirmed. Phylogenetic analyses of VP1 (210; 81%) sequences distinguished up to 27 different EV types distributed within EV-A (82; 40%), EV-B (90; 42%), EV-C (5; 2%), and EV-D (33; 15%), in addition to 50 (19%) rhinoviruses. The most predominant were EV-A71 (37; 45%) and EV-D68 (32; 99%). EV-A71 was highly related to neurological complications (25/39, 63%), of which 20/39 were rhombencephalitis, and most EV-D68 (28/32, 88%) were associated with lower respiratory tract infections (LRTI), and exceptionally one (3%) with acute flaccid paralysis. CONCLUSIONS: EV-A71 and EV-D68 were the most detected EV in respiratory specimens. EV-A71 was highly related to neurological disease and EV-D68 was often associated with LRTI. However, both potential relatedness to neurological diseases makes the monitoring of EV circulation obligatory.


id: cord-332723-rz1iilsv
title: Clinical evaluation of the BioFire® Respiratory Panel 2.1 and detection of SARS-CoV-2
author: Creager, Hannah M.
date: 2020-07-06
txt: ./txt/cord-332723-rz1iilsv.txt
cache: ./cache/cord-332723-rz1iilsv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jcv.2020.104538
doi: 10.1016/j.jcv.2020.104538
summary:
  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

abstract:
  We evaluated the performance of the BioFire® Respiratory Panel 2.1 (RP2.1) in the detection of SARS CoV-2 in comparison against three other SARS CoV-2 EUA assays. In these studies, the RP2.1 panel had 98% positive percent agreement (48/49) and 100% negative percent agreement (49/49). 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. Overall, these studies suggest that the BioFire® RP2.1 assay can be used to detect acute cases of SARS CoV2 in addition to patients with low viral titer later in disease presentation.


id: cord-335067-tg66h99q
title: Ecological and taxonomic variation among human RNA viruses
author: Woolhouse, Mark E.J.
date: 2013-03-19
txt: ./txt/cord-335067-tg66h99q.txt
cache: ./cache/cord-335067-tg66h99q.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653213000802
doi: 10.1016/j.jcv.2013.02.019
summary:
  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.

abstract:
  Only a minority of RNA viruses that can infect humans are capable of spreading in human populations independently of a zoonotic reservoir. This is especially true of vector-borne RNA viruses; the majority of these are not transmissible (via the vector) between humans at all. Understanding the biology underlying this observation will help us evaluate the public health risk associated with novel vector-borne RNA viruses.


id: cord-335208-xv2evahh
title: The role of rhinovirus infections in young children with cystic fibrosis
author: O Loughlin, D.W.
date: 2020-06-01
txt: ./txt/cord-335208-xv2evahh.txt
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mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653220302201
doi: 10.1016/j.jcv.2020.104478
summary:
  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

abstract:
  Rhinovirus (RV) is an important virus in children with chronic respiratory conditions such as asthma; however, little is known about its role in CF. Our aim was to examine the prevalence and clinical impact of different RV species in young children with CF. We collected clinical data and nasal swabs on patients at home and in the hospital setting. Parents filled out symptom diaries and collected nasal swabs when their children were symptomatic and asymptomatic. A novel RV typing PCR assay was used to determine the RV species present. We collected 55 nasal swab samples from ten preschool CF patients over a six month period. The quality of parent collected samples at home was sufficient for PCR analysis. RV was the most common virus detected in young children with CF. There was no difference in the frequency of RV species between symptomatic and asymptomatic subjects. However, parental home-sampling is an acceptable and feasible approach to monitoring young children with CF.


id: cord-335891-j78pnwgk
author: Piñana, Maria
date: 2020-08-11
txt: ./txt/cord-335891-j78pnwgk.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32957052/
doi: 10.1016/j.jcv.2020.104590
summary:
  The 180-and 111-nucleotide duplications occurred in A2c lineage G protein increased in prevalence throughout the study, in addition to short genetic changes observed in other HMPV lineages. The 180-and 111-nucleotide duplications occurred in A2c lineage G protein increased in prevalence throughout the study, in addition to short genetic changes observed in other HMPV lineages. 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.

title:
  Insights into immune evasion of human metapneumovirus: novel 180- and 111-nucleotide duplications within viral G gene throughout 2014-2017 seasons in Barcelona, Spain

abstract:
  BACKGROUND: Human metapneumovirus (HMPV) is an important etiologic agent of respiratory tract infection (RTI). This study aimed to describe its genetic diversity and clinical impact in patients attended at a tertiary university hospital in Barcelona from the 2014-2015 to the 2016-2017 seasons, focusing on the emerging duplications in G gene and their structural properties. METHODS: Laboratory-confirmed HMPV were characterized based on partialcoding F and G gene sequences with MEGA.v6.0. Computational analysis of disorder propensity, aggregation propensity and glycosylation sites in viral G predicted protein sequence were carried out. Clinical data was retrospectively reviewed and further associated to virological features. RESULTS: HMPV prevalence was 3%. 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 A2c G protein without duplications was calculated to protrude over F protein in 23% of cases and increased to a 39% and a 46% with the 111- and 180-nucleotide duplications, respectively. Children did not seem to be more affected by these mutant viruses, but there was a strong association of these variants to LRTI in adults. DISCUSSION: HMPV presents a high genetic diversity in all 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.


id: cord-336237-hmczy0am
author: Kitagawa, Yutaro
date: 2020-05-21
txt: ./txt/cord-336237-hmczy0am.txt
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url: https://www.sciencedirect.com/science/article/pii/S1386653220301888?v=s5
doi: 10.1016/j.jcv.2020.104446
summary:
  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

title:
  Evaluation of rapid diagnosis of novel coronavirus disease (COVID-19) using loop-mediated isothermal amplification

abstract:
  With the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is an urgent need for more rapid and simple detection technologies at the forefront of medical care worldwide. In this study, we evaluated the effectiveness of the Loopamp® 2019-SARSCoV-2 Detection Reagent Kit, which uses loop-mediated isothermal amplification (LAMP) technology. In this protocol, cDNA is synthesized from SARS-CoV-2 RNA using reverse transcriptase, followed by DNA amplification under isothermal conditions in one step. 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). Comparison with the results of RT-qPCR for 76 nasopharyngeal swab samples from patients with suspected COVID-19 showed a sensitivity of 100% and a specificity of 97.6%. In the 24 RNA specimens derived from febrile Japanese patients with or without influenza A, no amplification was observed using RT-LAMP. RT-LAMP could be a simple and easy-to-use diagnostic tool for the detection of SARS-CoV-2.


id: cord-336535-r3a57m57
title: Brief clinical evaluation of six high-throughput SARS-CoV-2 IgG antibody assays
author: Kohmer, Niko
date: 2020-06-01
txt: ./txt/cord-336535-r3a57m57.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32505777/
doi: 10.1016/j.jcv.2020.104480
summary:
  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.

abstract:
  Serological SARS-CoV-2 assays are urgently needed for diagnosis, contact tracing and for epidemiological studies. 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. Focusing on IgG and total antibodies, we demonstrate the performance of four automated immunoassays (Abbott Architect™ i2000 (N protein-based)), Roche cobas™ e 411 analyzer (N protein-based, not differentiating between IgA, IgM or IgG antibodies), LIAISON®XL platform (S1 and S2 protein-based), VIRCLIA® automation system (S1 and N protein-based) in comparison two ELISA assays (Euroimmun SARS-CoV-2 IgG (S1 protein-based) and Virotech SARS-CoV-2 IgG ELISA (N protein-based)) and an in-house developed plaque reduction neutralization test (PRNT). We tested follow up serum/plasma samples of individuals PCR-diagnosed with COVID-19. When calculating the overall sensitivity, in a time frame of 49 days after first PCR-positivity, the PRNT as gold standard, showed the highest sensitivity with 93.3% followed by the dual-target assay for the VIRCLIA® automation system with 89%. The overall sensitivity in the group of N protein-based assays ranged from 66.7 to 77.8% and in the S protein-based-assays from 71.1 to 75.6%. 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 should be further analysed. The specificity of the examined assays was ≥ 97%. However, because of the low or unknown prevalence of SARS-CoV-2, the examined assays in this study are currently primarily eligible for epidemiological investigations, as they have limited information in individual testing.


id: cord-336636-xgfw21hk
title: Redondovirus DNA in human respiratory samples
author: Spezia, Pietro Giorgio
date: 2020-08-15
txt: ./txt/cord-336636-xgfw21hk.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32841923/
doi: 10.1016/j.jcv.2020.104586
summary:
  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

abstract:
  Abstract Background Redondovirus (ReDoV) is a recently discovered circular, Rep-encoding single-stranded DNA (CRESS-DNA) virus in humans. Its pathogenesis and clinical associations are still completely unknown. Methods The presence of ReDoV DNA was investigated in biological specimens of 543 Italian subjects by in-house developed PCR assays. Results The overall ReDoV prevalence was about 4% (23 of 543 samples). The virus was detected in 22 of 209 (11 %) respiratory samples. One stool sample was also ReDoV positive. Viral DNA was not found in blood samples from immunocompetent and immunosuppressed subjects and cerebrospinal fluids from patients with neurological diseases. Genomic nucleotide differences were detected among the ReDoV isolates by sequencing a 582-nucleotide fragment of the capsid gene of the viral genome. Conclusions The results demonstrate that ReDoV is mainly present in the respiratory tract of infected people. Further investigations are needed to reveal possible clinical implications of this new CRESS-DNA virus in humans.


id: cord-337799-mc1oqhf4
author: Mak, Gannon CK
date: 2020-10-29
txt: ./txt/cord-337799-mc1oqhf4.txt
cache: ./cache/cord-337799-mc1oqhf4.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jcv.2020.104684
doi: 10.1016/j.jcv.2020.104684
summary:
  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.

title:
  Analytical sensitivity and clinical sensitivity of the three rapid antigen detection kits for detection of SARS-CoV-2 virus

abstract:
  BACKGROUND: Numerous rapid antigen detection (RAD) kits for diagnosing COVID-19 patients are available in the market recently. OBJECTIVE: To compare analytical sensitivity and clinical sensitivity for the three commercially available RAD kits. 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 was evaluated by using respiratory specimens collected from confirmed COVID-19 patients. RESULTS: The LOD results showed that the three RAD kits varied 102 to 105 fold less sensitive than RT-PCR. 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. The likelihood of positive results for RAD kits will be higher.


id: cord-338923-hc7gagnq
title: Performance of six SARS-CoV-2 immunoassays in comparison with microneutralisation
author: Jääskeläinen, AJ
date: 2020-06-15
txt: ./txt/cord-338923-hc7gagnq.txt
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mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653220302547?v=s5
doi: 10.1016/j.jcv.2020.104512
summary:
  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.

abstract:
  There is an urgent need for reliable high-throughput serological assays for the management of the ongoing COVID-19 pandemic. Preferably, the performance of serological tests for a novel virus should be determined with clinical specimens against a gold standard, i.e. virus neutralisation. 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). Two specimen panels from serum samples sent to Helsinki University Hospital Laboratory (HUSLAB) were compiled: the patient panel (N=70) included sera from PCR confirmed COVID-19 patients, and the negative panel (N=81) included sera sent for screening of autoimmune diseases and respiratory virus antibodies in 2018 and 2019. The MNT was carried out for all COVID-19 samples (70 serum samples, 62 individuals) and for 53 samples from the negative panel. 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). This study shows variable performance values. Laboratories should carefully consider their testing process, such as a two-tier approach, in order to optimize the overall performance of SARS- CoV-2 serodiagnostics.


id: cord-340336-u59l0taa
title: Multiplexing primer/probe sets for detection of SARS-CoV-2 by qRT-PCR
author: Perchetti, Garrett A.
date: 2020-06-08
txt: ./txt/cord-340336-u59l0taa.txt
cache: ./cache/cord-340336-u59l0taa.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653220302419?v=s5
doi: 10.1016/j.jcv.2020.104499
summary:
   -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.

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. The pandemic's initial challenges include broad diagnostic testing, consistent reagent supply lines, and access to laboratory instruments and equipment. In early 2020, primer/probe sets distributed by the CDC utilized the same fluorophore for molecular detection - requiring multiple assays to be run in parallel - consuming valuable and limited resources. 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. Laboratory- confirmed respiratory infection samples were included to evaluate assay cross-reaction specificity. RESULTS: Triplexing correctly identified SARS-CoV-2 in 98.4% of confirmed positive or inconclusive patient samples by single-plex LDT (n = 183/186). All 170 SARS-CoV-2 negative samples tested by single-plex LDT were negative by triplexing. Other laboratory-confirmed respiratory infections did not amplify for SARS-CoV-2 in the triplex reaction. CONCLUSIONS: Multiplexing two virus-specific gene targets and an extraction control was found to be comparable to running parallel assays independently, while significantly improving assay throughput.


id: cord-343800-nbydaoac
author: Cerutti, Francesco
date: 2020-09-29
txt: ./txt/cord-343800-nbydaoac.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jcv.2020.104654
doi: 10.1016/j.jcv.2020.104654
summary:
  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

title:
  Urgent need of rapid tests for SARS CoV-2 antigen detection: evaluation of the SD-Biosensor antigen test for SARS-CoV-2

abstract:
  At the time of writing, FIND has listed four CE-marked SARSCoV-2 antigen tests. 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. Sensitivity, specificity, accuracy, negative and predictive values were consistent with the use of the test to mass-screening for SARS-CoV-2 surveillance.


id: cord-344979-ngujhhp6
author: Lübke, Nadine
date: 2020-08-05
txt: ./txt/cord-344979-ngujhhp6.txt
cache: ./cache/cord-344979-ngujhhp6.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653220303218?v=s5
doi: 10.1016/j.jcv.2020.104579
summary:
  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.

title:
  Extraction-free SARS-CoV-2 detection by rapid RT-qPCR universal for all primary respiratory materials

abstract:
  BACKGROUND: Fast and reliable detection of SARS-CoV-2 is crucial for efficient control of the COVID-19 pandemic. Due to the high demand for SARS-CoV-2 testing there is a worldwide shortage of RNA extraction reagents. Therefore, extraction-free RT-qPCR protocols are urgently needed. 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). SARS-CoV-2 was detected using novel primers targeted to the E-gene. 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. For validation, 91 respiratory samples were analyzed in direct comparison to classical RNA-based RT-qPCR. Overall 81.3% of the samples were detected in both assays with a strong correlation between both Ct values (r = 0.8492, p < 0.0001). The SARS-CoV-2 detection rate by direct RT-qPCR was 95.8% for Ct values <35. All negative samples were characterized by low viral loads (Ct >35) and/or long storage times before sample processing. CONCLUSION: Direct RT-qPCR is a suitable alternative to classical RNA RT-qPCR, provided that only fresh samples (storage <1 week) are used. RNA extraction should be considered if samples have longer storage times or if PCR inhibition is observed. In summary, this protocol is fast, inexpensive and suitable for all respiratory materials.


id: cord-345603-mirsz6m8
title: Self-collection: an appropriate alternative during the SARS-CoV-2 pandemic
author: Wehrhahn, Michael C.
date: 2020-05-04
txt: ./txt/cord-345603-mirsz6m8.txt
cache: ./cache/cord-345603-mirsz6m8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32403007/
doi: 10.1016/j.jcv.2020.104417
summary:
  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.

abstract:
  OBJECTIVES: To evaluate the reliability of self-collection for SARS-CoV-2 and other respiratory viruses because swab collections for SARS-CoV-2 put health workers at risk of infection and require use of personal protective equipment (PPE). METHODS: In a prospective study, patients from two states in Australia attending dedicated COVID-19 collection clinics were offered the option to first self-collect (SC) throat and nasal swabs (SCNT) prior to health worker collect (HC) using throat and nasal swabs (Site 1) or throat and nasopharyngeal swabs (Site 2). Samples were analysed for SARS-CoV-2 as well as common respiratory viruses. Concordance of results between methods was assessed using Cohen's kappa (κ) and Cycle threshold (Ct) values were recorded for all positive results as a surrogate measure for viral load. RESULTS: Of 236 patients sampled by HC and SC, 25 had SARS-CoV-2 (24 by HC and 25 by SC) and 63 had other respiratory viruses (56 by HC and 58 y SC). SC was highly concordant with HC (κ = 0.890) for all viruses including SARS-CoV-2 and more concordant than HC to positive results by any method (κ = 0.959 vs 0.933). Mean SARS-CoV-2 E-gene and N-gene, rhinovirus and parainfluenza Ct values did not differ between HC and SCNT. CONCLUSIONS: Self-collection of throat and nasal swabs offers a reliable alternative to health worker collection for the diagnosis of SARS-CoV-2 and other respiratory viruses and provides patients with easier access to testing, reduces exposure of the community and health workers to those being tested and reduces requirement for PPE.


id: cord-349485-iomk99lv
author: Eis-Hübinger, Anna M.
date: 2020-04-22
txt: ./txt/cord-349485-iomk99lv.txt
cache: ./cache/cord-349485-iomk99lv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jcv.2020.104381
doi: 10.1016/j.jcv.2020.104381
summary:
  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) .

title:
  Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples

abstract:
  BACKGROUND: A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in China in late 2019 and subsequently caused a pandemic. Surveillance is important to better appreciate this evolving pandemic and to longitudinally monitor the effectiveness of public health measures. OBJECTIVES: We aimed to provide a rapid, easy to establish and costeffective laboratory-based surveillance tool for SARS-CoV-2. Study design: We used minipools of RNA prepared from nucleic acid extractions of routine respiratory samples. We technically validated the assay and distributed the protocol within an informal network of five German university laboratories. RESULTS: We tested a total of 70 minipools resembling 700 samples shortly before the upsurge of cases in Germany from 17.02.2020- 10.03.2020. One minipool reacted positive and after resolution one individual sample tested SARS-COV-2 positive. This sample was from a hospitalized patient not suspected of having contracted SARS-CoV-2. CONCLUSIONS: Our approach of a laboratory-based surveillance for SARSCoV-2 using minipools proved its concept is easily adaptable and resource-saving. It might assist not only public health laboratories in SARS-CoV-2 surveillance.


id: cord-349541-7g50vg14
title: SARS-CoV-2 antibody screening in healthcare workers in a tertiary centre in North West England
author: Poulikakos, Dimitrios
date: 2020-07-07
txt: ./txt/cord-349541-7g50vg14.txt
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mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1386653220302870?v=s5
doi: 10.1016/j.jcv.2020.104545
abstract: nan
summary:
  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


id: cord-349782-djzxkus2
title: Response to letter of concern by Oladimeji and Pickford of PrimerDesign
author: van Kasteren, Puck B.
date: 2020-06-29
txt: ./txt/cord-349782-djzxkus2.txt
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mime: text/plain
url: https://doi.org/10.1016/j.jcv.2020.104526
doi: 10.1016/j.jcv.2020.104526
abstract: nan
summary:
  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.


id: cord-349921-v1tewoi0
author: Giorgi Rossi, Paolo
date: 2020-05-05
txt: ./txt/cord-349921-v1tewoi0.txt
cache: ./cache/cord-349921-v1tewoi0.txt
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mime: text/plain
url: https://doi.org/10.1016/j.jcv.2020.104415
doi: 10.1016/j.jcv.2020.104415
abstract: nan
summary:
  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

title:
  Case fatality rate in patients with COVID-19 infection and its relationship with length of follow up()


id: cord-353640-giznbcpd
author: Barza, Ruby
date: 2020-08-11
txt: ./txt/cord-353640-giznbcpd.txt
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mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1386653220303292
doi: 10.1016/j.jcv.2020.104587
summary:
  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.

title:
  Use of a Simplified Sample Processing step without RNA Extraction for direct SARS-CoV-2 RT-PCR Detection

abstract:
  The severe acute respiratory syndrome coronavirus (SARS-CoV-2) pandemic has resulted in significant shortages of RT-PCR testing supplies including RNA extraction kits. The goal of our study was to determine if a simplified heat-RNA release method would provide comparable detection of SARS-CoV-2 without the need for nucleic acid extraction. 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). The heat-RNA release method correctly identified 94% (81/86 nasopharyngeal samples) that were positive for SARS-CoV-2. Five samples that were missed by heat-RNA release method had a mean Ct value: 35 using the automated extraction instrument, indicating a very low viral load. Our findings show that a simple heat-RNA release method is a reasonable alternative for the majority of COVID-19 positive patients and can help overcome the cost and availability issues of RNA extraction reagents.


