Rapid detection of SARS-CoV-2 variants of concern by single nucleotide polymorphism genotyping using TaqMan assays.

TitleRapid detection of SARS-CoV-2 variants of concern by single nucleotide polymorphism genotyping using TaqMan assays.
Publication TypeJournal Article
Year of Publication2022
AuthorsVelu P, Cong L, Rand S, Qiu Y, Zhang Z, Zhang J, Guo J, Ruggiero P, Sukhu A, Fauntleroy K, Imada E, Zanettini C, Brundage D, Westblade L, Marchionni L, Cushing MM, Rennert H
JournalDiagn Microbiol Infect Dis
Volume104
Issue4
Pagination115789
Date Published2022 Dec
ISSN1879-0070
KeywordsCOVID-19, COVID-19 Testing, Genotype, Humans, Mutation, Polymorphism, Single Nucleotide, SARS-CoV-2
Abstract

We evaluated the performance of SARS-CoV-2 TaqMan real-time reverse-transcription PCR (RT-qPCR) assays (ThermoFisher) for detecting 2 nonsynonymous spike protein mutations, E484K and N501Y. Assay accuracy was evaluated by whole genome sequencing (WGS). Residual nasopharyngeal SARS-CoV-2 positive samples (N = 510) from a diverse patient population in New York City submitted for routine SARS-CoV-2 testing during January-April 2020 were used. We detected 91 (18%) N501Y and 101 (20%) E484K variants. Four samples (0.8%) were positive for both variants. The assay had nearly perfect concordance with WGS in the validation subset, detecting B.1.1.7 and B.1.526 variants among others. Sensitivity and specificity ranged from 0.95 to 1.00. Positive and negative predictive values were 0.98-1.00. TaqMan genotyping successfully predicted the presence of B.1.1.7, but had significantly lower sensitivity, 62% (95% CI, 0.53, 0.71), for predicting B.1.526 sub-lineages lacking E484K. This approach is rapid and accurate for detecting SARS-CoV-2 variants and can be rapidly implemented in routine clinical setting.

DOI10.1016/j.diagmicrobio.2022.115789
Alternate JournalDiagn Microbiol Infect Dis
PubMed ID36122486
PubMed Central IDPMC9392658
Related Faculty: 
Luigi Marchionni, M.D., Ph.D. Priya Velu, M.D., Ph.D. Lars Westblade, Ph.D. Melissa Cushing, M.D. Hanna Rennert, Ph.D.

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