1. SARS-CoV-2 viral variants can rapidly be identified for clinical decision making and population surveillance using a high-throughput digital droplet PCR assay
- Author
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Pernet, Olivier, Weisenhaus, Maia, Stafylis, Chrysovalantis, Williams, Christopher, Campan, Mihaela, Pettersson, Jonas, Green, Nicole, Lee, David M, Thomas, Paul D, Ward, Pamela, Hu, Howard, Klausner, Jeffrey D, and Kovacs, Andrea AZ
- Subjects
Microbiology ,Biological Sciences ,Biomedical and Clinical Sciences ,Prevention ,Genetics ,Biodefense ,Vaccine Related ,Biotechnology ,Emerging Infectious Diseases ,Infection ,Good Health and Well Being ,Humans ,SARS-CoV-2 ,COVID-19 ,Polymerase Chain Reaction ,Clinical Decision-Making ,Population Surveillance ,COVID-19 Testing ,U. S. C. Variant Study Group - Abstract
Epidemiologic surveillance of circulating SARS-CoV-2 variants is essential to assess impact on clinical outcomes and vaccine efficacy. Whole genome sequencing (WGS), the gold-standard to identify variants, requires significant infrastructure and expertise. We developed a digital droplet polymerase chain reaction (ddPCR) assay that can rapidly identify circulating variants of concern/interest (VOC/VOI) using variant-specific mutation combinations in the Spike gene. To validate the assay, 800 saliva samples known to be SARS-CoV-2 positive by RT-PCR were used. During the study (July 2020-March 2022) the assay was easily adaptable to identify not only existing circulating VAC/VOI, but all new variants as they evolved. The assay can discriminate nine variants (Alpha, Beta, Gamma, Delta, Eta, Epsilon, Lambda, Mu, and Omicron) and sub-lineages (Delta 417N, Omicron BA.1, BA.2). Sequence analyses confirmed variant type for 124/124 samples tested. This ddPCR assay is an inexpensive, sensitive, high-throughput assay that can easily be adapted as new variants are identified.
- Published
- 2023
