학술논문
SARS-CoV-2 viral variants can rapidly be identified for clinical decision making and population surveillance using a high-throughput digital droplet PCR assay.
Document Type
Article
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
Source
Subject
*SARS-CoV-2
*WHOLE genome sequencing
*DECISION making
*SARS-CoV-2 Omicron variant
*POLYMERASE chain reaction
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Language
ISSN
2045-2322
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. [ABSTRACT FROM AUTHOR]