SARS-CoV-2 detection in nasopharyngeal swabs: Performance characteristics of a real-time RT-qPCR and a droplet digital RT-PCR assay based on the exonuclease region (ORF1b, nsp 14).
Droplet digital RT-PCR
Polymerase chain reaction
Real-time RT-qPCR
SARS-CoV-2
Swab
nsp14
Journal
Journal of virological methods
ISSN: 1879-0984
Titre abrégé: J Virol Methods
Pays: Netherlands
ID NLM: 8005839
Informations de publication
Date de publication:
Feb 2022
Feb 2022
Historique:
received:
27
06
2021
revised:
07
11
2021
accepted:
08
12
2021
pubmed:
14
12
2021
medline:
8
1
2022
entrez:
13
12
2021
Statut:
ppublish
Résumé
The emergence and spread of SARS-CoV-2 has led to a compelling request for accurate diagnostic tests. The aim of this study was assessing the performance of a real-time RT-qPCR (rt RT-qPCR) assay and of a droplet digital RT-PCR (dd RT-PCR) targeting the nsp14 genome region for the detection of SARS-CoV-2 in nasopharyngeal swabs. A total of 258 nasopharyngeal swabs were analyzed with the nsp14 assays and, for comparison, with a reference assay targeting the RdRp and E genes. Conflicting results were further investigated by two additional protocols, the Centers for Disease Control and Prevention (CDC) real-time targeting N1/N2, and a nested RT-PCR for the spike region. Agreement of results was achieved on 226 samples (156 positive and 70 negative), 8 samples were positive in the reference assay and in the nsp14 rt RT-qPCR but negative with the dd RT-PCR, and 24 samples provided different combinations of results with the three assays. Sensitivity, specificity and accuracy (95 %C.I.) of the nsp14 assays were: 100.0 % (97.4-100.0), 98.7 % (92.1-100.0), and 99.6 % (97.5-100.0) for the rt RT-qPCR; 92.4 % (87.4-95.6), 100.0 % (94.2-100.0), and 94.7 % (91.1-97.0) for the dd RT-PCR. The results of the study support the use of the nsp14 real-time RT-qPCR and ddPCR for the detection of SARS-CoV-2 in nasopharyngeal swabs.
Identifiants
pubmed: 34902456
pii: S0166-0934(21)00359-1
doi: 10.1016/j.jviromet.2021.114420
pmc: PMC8660663
pii:
doi:
Substances chimiques
RNA, Viral
0
Exonucleases
EC 3.1.-
Types de publication
Evaluation Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
114420Informations de copyright
Copyright © 2021 Elsevier B.V. All rights reserved.
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