SARS-CoV-2 Viral Variants Can Rapidly Be Identified for Clinical Decision Making and Population Surveillance Using a High-throughput Digital Droplet PCR Assay

Overview

Journal Sci Rep

Specialty Science

Date 2023 May 10

PMID 37165019

Authors

Olivier Pernet

Maia Weisenhaus

Chrysovalantis Stafylis

Christopher Williams

Mihaela Campan

Jonas Pettersson

Nicole Green

David M Lee

Paul D Thomas

Pamela Ward

Howard Hu

Jeffrey D Klausner

Andrea A Z Kovacs

Affiliations

Soon will be listed here.

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.

Citing Articles

Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR.

Pacini A, Paredes F, Heckel S, Ibarra G, Petreli M, Perez M Front Public Health. 2024; 11:1340420.

PMID: 38298257 PMC: 10829044. DOI: 10.3389/fpubh.2023.1340420.

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