PLoS ONE (Jan 2022)

A RT-qPCR system using a degenerate probe for specific identification and differentiation of SARS-CoV-2 Omicron (B.1.1.529) variants of concern.

  • Randi Jessen,
  • Line Nielsen,
  • Nicolai Balle Larsen,
  • Arieh Sierra Cohen,
  • Vithiagaran Gunalan,
  • Ellinor Marving,
  • Alonzo Alfaro-Núñez,
  • Charlotta Polacek,
  • Danish COVID-19 Genome Consortium (DCGC),
  • Anders Fomsgaard,
  • Katja Spiess

DOI
https://doi.org/10.1371/journal.pone.0274889
Journal volume & issue
Vol. 17, no. 10
p. e0274889

Abstract

Read online

Fast surveillance strategies are needed to control the spread of new emerging SARS-CoV-2 variants and gain time for evaluation of their pathogenic potential. This was essential for the Omicron variant (B.1.1.529) that replaced the Delta variant (B.1.617.2) and is currently the dominant SARS-CoV-2 variant circulating worldwide. RT-qPCR strategies complement whole genome sequencing, especially in resource lean countries, but mutations in the targeting primer and probe sequences of new emerging variants can lead to a failure of the existing RT-qPCRs. Here, we introduced an RT-qPCR platform for detecting the Delta- and the Omicron variant simultaneously using a degenerate probe targeting the key ΔH69/V70 mutation in the spike protein. By inclusion of the L452R mutation into the RT-qPCR platform, we could detect not only the Delta and the Omicron variants, but also the Omicron sub-lineages BA.1, BA.2 and BA.4/BA.5. The RT-qPCR platform was validated in small- and large-scale. It can easily be incorporated for continued monitoring of Omicron sub-lineages, and offers a fast adaption strategy of existing RT-qPCRs to detect new emerging SARS-CoV-2 variants using degenerate probes.