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

Priya Velu, Lin Cong, Sophie Rand, Yuqing Qiu, Zhengmao Zhang, Jianxuan Zhang, Jianfen Guo, Phyllis Ruggiero, Ashley Sukhu, Kathy Fauntleroy, Eddie Imada, Claudio Zanettini, David Brundage, Lars Westblade, Luigi Marchionni, Melissa M. Cushing, Hanna Rennert

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article number115789
JournalDiagnostic Microbiology and Infectious Disease
Volume104
Issue number4
DOIs
StatePublished - Dec 2022

Keywords

  • Coronavirus disease 19 (COVID-19)
  • Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
  • TaqMan
  • Variants of concern

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases

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