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Sci Rep
. 2022 Mar 3;12(1):3480.
doi: 10.1038/s41598-022-07152-0.
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 1 , Ashis K Mondal 1 , Sudha Ananth 1 , Allan Njau 2 , Kimya Jones 1 , Pankaj Ahluwalia 1 , Eesha Oza 1 , Ted M Ross 3 , Vamsi Kota 4 , Arvind Kothandaraman 5 , Sadanand Fulzele 6 , Madhuri Hegde 5 , Alka Chaubey 1 7 , Amyn M Rojiani 8 , Ravindra Kolhe 9
Affiliations
- PMID: 35241679
- DOI: 10.1038/s41598-022-07152-0
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.