SARS-CoV-2 viral variants can rapidly be identified for clinical decision making and population surveillance using a high-throughput digital droplet PCR assay

• Published in: Scientific reports Vol. 13; no. 1; pp. 7612 - 11
• Main Authors: 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, Kovacs, Andrea A Z
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 10.05.2023; Nature Publishing Group UK; Nature Portfolio
• Subjects: Clinical Decision-Making; COVID-19; COVID-19 - diagnosis; COVID-19 - epidemiology; COVID-19 Testing; Decision making; Disease; Epidemics; Epidemiology; Genomes; Health care; Humans; Laboratories; Mutation; Pandemics; Polymerase Chain Reaction; Population Surveillance; Preventive medicine; Public health; Saliva; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Vaccine efficacy; Vaccines; Whole genome sequencing
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-023-34188-7

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.