Author:
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.,Hernandez-Tamayo Cassidy,Van Orman Sarah,Gilliland Frank,Conti David,Ghanem-Uzqueda Angie,Yepez Daniel,Stellar Sofia,Tadanki Aditya P.,Max Jillian,Fottrell Honour,Ong Ethan,Navarro Sabrina,Moses Kaelyn,Akaolisa Michael,Hosseini Bijan,Sunesara Shaleen,Wang Yuzhu,Zaw Andrew,Strum Earl,Casagrande Yolee,Hernandez-Rodriguez Nathalie,Thomas Paul,Chu Tara,Emerson Jane,
Abstract
AbstractEpidemiologic 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.
Funder
COVID-19 Keck Research Fund
Publisher
Springer Science and Business Media LLC
Cited by
1 articles.
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