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).
Autor: | Pierri B; Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy; Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy., Mancusi A; Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy., Proroga YTR; Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy., Capuano F; Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy., Cerino P; Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy., Girardi S; Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy., Vassallo L; Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy., Lo Conte G; Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy., Tafuro M; Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy., Cuomo MC; Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy., Di Concilio D; Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy., Vicenza T; Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy., Cozzi L; Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy., Di Pasquale S; Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy., La Rosa G; Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy., Beikpour F; Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy; Department of Veterinary Medicine, University of Bari 'Aldo Moro', Bari, Italy., Suffredini E; Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy. Electronic address: elisabetta.suffredini@iss.it. |
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Jazyk: | angličtina |
Zdroj: | Journal of virological methods [J Virol Methods] 2022 Feb; Vol. 300, pp. 114420. Date of Electronic Publication: 2021 Dec 10. |
DOI: | 10.1016/j.jviromet.2021.114420 |
Abstrakt: | 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. (Copyright © 2021 Elsevier B.V. All rights reserved.) |
Databáze: | MEDLINE |
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