Interpret with caution: An evaluation of the commercial AusDiagnostics versus in-house developed assays for the detection of SARS-CoV-2 virus
Date
2020Author
Rahman, H.
Carter, I.
Basile, K.
Donovan, L.
Kumar, S.
Tran, T.
Ko, D.
Alderson, S.
Sivaruban, T.
Eden, J.-S.
Rockett, R.
O’Sullivan, M.V.
Sintchenko, V.
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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 "gold
standard", 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.
Palabras clave
SARS-CoV-2; NAT; Covid-19Link to resource
https://doi.org/10.1016/j.jcv.2020.104374Collections
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