Scientific Reports (Mar 2022)

Clinical validation of a multiplex PCR-based detection assay using saliva or nasopharyngeal samples for SARS-Cov-2, influenza A and B

  • Nikhil S. Sahajpal,
  • Ashis K. Mondal,
  • Sudha Ananth,
  • Allan Njau,
  • Kimya Jones,
  • Pankaj Ahluwalia,
  • Eesha Oza,
  • Ted M. Ross,
  • Vamsi Kota,
  • Arvind Kothandaraman,
  • Sadanand Fulzele,
  • Madhuri Hegde,
  • Alka Chaubey,
  • Amyn M. Rojiani,
  • Ravindra Kolhe

DOI
https://doi.org/10.1038/s41598-022-07152-0
Journal volume & issue
Vol. 12, no. 1
pp. 1 – 7

Abstract

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Abstract The COVID-19 pandemic has resulted in significant diversion of human and material resources to COVID-19 diagnostics, to the extent that influenza viruses and co-infection in COVID-19 patients remains undocumented and pose serious public-health consequences. We optimized and validated a highly sensitive RT-PCR based multiplex-assay for the detection of SARS-CoV-2, influenza A and B viruses in a single-test. This study evaluated clinical specimens (n = 1411), 1019 saliva and 392 nasopharyngeal swab (NPS), tested using two-assays: FDA-EUA approved SARS-CoV-2 assay that targets N and ORF1ab gene, and the PKamp-RT-PCR based assay that targets SARS-CoV-2, influenza viruses A and B. Of the 1019 saliva samples, 17.0% (174/1019) tested positive for SARS-CoV-2 using either assay. The detection rate for SARS-CoV-2 was higher with the multiplex assay compared to SARS-specific assay [91.9% (160/174) vs. 87.9% (153/174)], respectively. Of the 392 NPS samples, 10.4% (41/392) tested positive for SARS-CoV-2 using either assay. The detection rate for SARS-CoV-2 was higher with the multiplex assay compared to SARS-specific assay [97.5% (40/41) vs. 92.1% (39/41)], respectively. This study presents clinical validation of a multiplex-PCR assay for testing SARS-CoV-2, influenza A and B viruses, using NPS and saliva samples, and demonstrates the feasibility of implementing the assay without disrupting the existing laboratory workflow.