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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).
Pierri, Biancamaria; Mancusi, Andrea; Proroga, Yolande T R; Capuano, Federico; Cerino, Pellegrino; Girardi, Santa; Vassallo, Lucia; Lo Conte, Gabriella; Tafuro, Maria; Cuomo, Maria Concetta; Di Concilio, Denise; Vicenza, Teresa; Cozzi, Loredana; Di Pasquale, Simona; La Rosa, Giuseppina; Beikpour, Farzad; Suffredini, Elisabetta.
  • 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.
J Virol Methods ; 300: 114420, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1654871
ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Reverse Transcriptase Polymerase Chain Reaction / Real-Time Polymerase Chain Reaction / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study Limits: Humans Language: English Journal: J Virol Methods Year: 2022 Document Type: Article Affiliation country: J.jviromet.2021.114420

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Reverse Transcriptase Polymerase Chain Reaction / Real-Time Polymerase Chain Reaction / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study Limits: Humans Language: English Journal: J Virol Methods Year: 2022 Document Type: Article Affiliation country: J.jviromet.2021.114420