Retrospective quantitative detection of SARS-CoV-2 by digital PCR showing high accuracy for low viral load specimens

Abstract

Introduction: Accurate detection of severe acute respiratory syndrome coronavirus 2 is critical for diagnosis and disease status evaluation of Coronavirus disease 2019. We retrospectively evaluated the infection status and viral load of severe acute respiratory syndrome coronavirus 2 in Nantong city, China, using a quantitative digital polymerase chain reaction and reverse-transcription PCR.

Methodology: A total of 103 clinical specimens from 31 patients were collected and tested by digital PCR and reverse-transcription PCR.

Results: The overall accuracy of digital PCR was 96.8%, which was higher than the overall accuracy of 87.1% for reverse-transcription PCR. 4 (3.88%) specimens for ORF1ab and 22 (21.36%) specimens for N gene were negative by reverse-transcription PCR but positive by digital PCR. 3 (2.91%, 3/103) specimens of ORF1ab were positive by reverse-transcription PCR but negative by digital PCR. The digital PCR assay exhibited higher sensitivity to measure the N gene than the ORF1ab gene (p < 0.01).

Conclusions: Our results showed that digital PCR assay provides more reliable detection of Coronavirus disease 2019 than reverse-transcription PCR, especially for low viral load specimens.

Keywords: COVID-19; SARS-CoV-2; digital PCR; low viral load; pharyngeal; reverse-transcription PCR.