About: Interpret with caution: An evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus

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About: Interpret with caution: An evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Interpret with caution: An evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus
Creator	Chen, C-A Kumar, S Kok, J Tran, T Alderson, S Basile, K Carter, I Donovan, L Dwyer, D Eden, J.-S Ko, D Maddocks, S O'sullivan, M Rahman, H Rockett, R Sintchenko, V Sivaruban, T
Source	Elsevier; Medline; PMC
abstract	INTRODUCTION: There is limited data on the analytical performance of commercial nucleic acid tests (NATs) for laboratory confirmation of COVID-19 infection. METHODS: Nasopharyngeal, combined nose and throat swabs, nasopharyngeal aspirates and sputum was collected from persons with suspected SARS-CoV-2 infection, serial dilutions of SARS-CoV-2 viral cultures and synthetic positive controls (gBlocks, Integrated DNA Technologies) were tested using i) AusDiagnostics assay (AusDiagnostics Pty Ltd); ii) in-house developed assays targeting the E and RdRp genes; iii) multiplex PCR assay targeting endemic respiratory viruses. Discrepant SARS-CoV-2 results were resolved by testing the N, ORF1b, ORF1ab and M genes. RESULTS: Of 52 clinical samples collected from 50 persons tested, respiratory viruses were detected in 22 samples (42 %), including SARS CoV-2 (n = 5), rhinovirus (n = 7), enterovirus (n = 5), influenza B (n = 4), hMPV (n = 5), influenza A (n = 2), PIV-2 (n = 1), RSV (n = 2), CoV-NL63 (n = 1) and CoV-229E (n = 1). SARS-CoV-2 was detected in four additional samples by the AusDiagnostics assay. Using the in-house assays as the %22gold standard%22, the sensitivity, specificity, positive and negative predictive values of the AusDiagnostics assay was 100 %, 92.16 %, 55.56 % and 100 % respectively. The Ct values of the real-time in-house-developed PCR assay targeting the E gene was significantly lower than the corresponding RdRp gene assay when applied to clinical samples, viral culture and positive controls (mean 21.75 vs 28.1, p = 0.0031). CONCLUSIONS: The AusDiagnostics assay is not specific for the detection SARS-CoV-2. Any positive results should be confirmed using another NAT or sequencing. The case definition used to investigate persons with suspected COVID-19 infection is not specific.
has issue date	2020-04-20(xsd:dateTime)
bibo:doi	10.1016/j.jcv.2020.104374
bibo:pmid	32361322
has license	no-cc
sha1sum (hex)	b299ca7945f2a6a41300cf6a722a35d6fea4629c
schema:url	https://doi.org/10.1016/j.jcv.2020.104374
resource representing a document's title	Interpret with caution: An evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus
has PubMed Central identifier	PMC7195305
has PubMed identifier	32361322
schema:publication	J Clin Virol
resource representing a document's body	covid:b299ca7945f2a6a41300cf6a722a35d6fea4629c#body_text
is schema:about of	named entity 'assay' named entity 'influenza A' named entity 'nucleic acid' named entity 'swabs' named entity 'tests' named entity 'assays' named entity 'SARS' named entity 'NUCLEIC ACID' named entity 'TARGETING' named entity 'INTRODUCTION' named entity 'testing' named entity 'serial dilutions' named entity 'samples' named entity 'developed' named entity 'There' named entity 'tested' named entity 'collected' named entity 'virus' named entity 'SARS-CoV-2' named entity 'SARS-CoV-2' named entity 'nasopharyngeal' named entity 'SARS CoV' named entity 'NATs' named entity 'positive controls' named entity 'RSV' named entity 'in-house' named entity 'assay' named entity 'genes' named entity 'NATs' named entity 'NAT' named entity 'viruses' named entity 'Australia' named entity 'saliva' named entity 'epidemiology' named entity 'LRT' named entity 'cough' named entity 'HKU' named entity 'nucleic acid' named entity 'Public Health' named entity 'betacoronavirus' named entity 'infection control' named entity 'nasopharyngeal' named entity 'Laboratory Services' named entity 'RT-PCR' named entity 'infection' named entity 'SARS' named entity 'Coralville' named entity 'SARS-CoV-2' named entity 'SARS-CoV-2' named entity 'LRT' named entity 'NATs' named entity 'specific testing' named entity 'Data analysis' named entity 'accounting' named entity 'RdRp' named entity 'primers' named entity 'positive and negative predictive values' named entity 'NAT' named entity 'acute respiratory infection' named entity 'Department of Health, Australia' named entity 'SARS-CoV-2' named entity 'diagnostic algorithm' named entity 'URT' named entity 'Wuhan' named entity 'fever'

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