Frontiers in Cellular and Infection Microbiology (Nov 2022)

SARS-CoV-2 variants of concern surveillance including Omicron using RT-PCR–based genotyping offers comparable performance to whole genome sequencing

  • Simone Vanoni,
  • Arnoldas Matulevicius,
  • Besard Avdiu,
  • Giada Scantamburlo,
  • Camilla Ulekleiv,
  • Pius M. Brzoska,
  • Manohar R. Furtado,
  • Jelena D. M. Feenstra,
  • Alain Rico,
  • Manoj Gandhi,
  • Elisabetta Giacobazzi,
  • Elisa Masi,
  • Markus Paulmichl,
  • Charity Nofziger

DOI
https://doi.org/10.3389/fcimb.2022.960065
Journal volume & issue
Vol. 12

Abstract

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Known SARS-CoV-2 variants of concern (VOCs) can be detected and differentiated using an RT-PCR–based genotyping approach, which offers quicker time to result, lower cost, higher flexibility, and use of the same laboratory instrumentation for detection of SARS-CoV-2 when compared with whole genome sequencing (WGS). In the current study, we demonstrate how we applied a genotyping approach for identification of all VOCs and that such technique can offer comparable performance to WGS for identification of known SARS-CoV-2 VOCs, including more recent strains, Omicron BA.1 and BA.2.

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