Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern

Microbiol Spectr. 2021 Oct 31;9(2):e0081621. doi: 10.1128/Spectrum.00816-21. Epub 2021 Oct 13.

Abstract

Reverse transcription-PCRs (RT-PCRs) targeting SARS-CoV-2 variant of concern (VOC) mutations have been developed to simplify their tracking. We evaluated an assay targeting E484K/N501Y to identify B.1.351/P1. Whole-genome sequencing (WGS) confirmed only 72 (59.02%) of 122 consecutive RT-PCR P.1/B.1.351 candidates. Prescreening RT-PCRs must target a wider set of mutations, updated from WGS data from emerging variants.

Keywords: COVID-19; RT-PCR; SARS-CoV-2; VOC; WGS; reverse transcriptase PCR; whole-genome sequencing.

MeSH terms

  • COVID-19 / diagnosis*
  • COVID-19 Nucleic Acid Testing*
  • Diagnostic Errors / statistics & numerical data*
  • Genome, Viral / genetics*
  • Humans
  • Reverse Transcriptase Polymerase Chain Reaction
  • SARS-CoV-2 / classification
  • SARS-CoV-2 / genetics*
  • Spike Glycoprotein, Coronavirus / genetics*
  • Whole Genome Sequencing

Substances

  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2