A Method for Variant Agnostic Detection of SARS-CoV-2, Rapid Monitoring of Circulating Variants, and Early Detection of Emergent Variants Such as Omicron

Autor: Eric Lai, Emily B. Kennedy, Jean Lozach, Kathleen Hayashibara, Jeremy Davis-Turak, David Becker, Pius Brzoska, Tyler Cassens, Evan Diamond, Manoj Gandhi, Alexander L. Greninger, Pooneh Hajian, Nicole A. Leonetti, Jason M. Nguyen, K. M. Clair O’Donovan, Troy Peck, Jimmy M. Ramirez, Pavitra Roychoudhury, Efren Sandoval, Cassandra Wesselman, Timothy Wesselman, Simon White, Stephen Williams, David Wong, Yufei Yu, Richard S. Creager
Rok vydání: 2022
Předmět:
Zdroj: Journal of Clinical Microbiology. 60
ISSN: 1098-660X
0095-1137
Popis: The rapid emergence of SARS-CoV-2 variants raised public health questions concerning the capability of diagnostic tests to detect new strains, the efficacy of vaccines, and how to map the geographical distribution of variants to understand transmission patterns and loads on healthcare resources. Next-generation sequencing (NGS) is the primary method for detecting and tracing new variants, but it is expensive, and it can take weeks before sequence data are available in public repositories. This article describes a customizable reverse transcription PCR (RT-PCR)-based genotyping approach which is significantly less expensive, accelerates reporting, and can be implemented in any lab that performs RT-PCR. Specific single-nucleotide polymorphisms (SNPs) and indels were identified which had high positive-percent agreement (PPA) and negative-percent agreement (NPA) compared to NGS for the major genotypes that circulated through September 11, 2021. Using a 48-marker panel, testing on 1,031 retrospective SARS-CoV-2 positive samples yielded a PPA and NPA ranging from 96.3 to 100% and 99.2 to 100%, respectively, for the top 10 most prevalent World Health Organization (WHO) lineages during that time. The effect of reducing the quantity of panel markers was explored, and a 16-marker panel was determined to be nearly as effective as the 48-marker panel at lineage assignment. Responding to the emergence of Omicron, a genotyping panel was developed which distinguishes Delta and Omicron using four highly specific SNPs. The results demonstrate the utility of the condensed panel to rapidly track the growing prevalence of Omicron across the US in December 2021 and January 2022.
Databáze: OpenAIRE
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