Elsevier

Virus Research

Volume 314, June 2022, 198753
Virus Research

An evolutionary insight into Severe Acute Respiratory Syndrome Coronavirus 2 Omicron variant of concern.

https://doi.org/10.1016/j.virusres.2022.198753Get rights and content

Highlights

  • A comprehensive phylogenetic analysis of SARS-CoV-2 Omicron variants was performed.

  • Codon usage in variants of concern (VOCs) Spike genes is linked to strain genotype.

  • Omicron belongs to a complete different genetic lineage from previous variants.

  • Omicron strains evolved from ancestors that existed around May 15th, 2020.

  • A rate of evolution of 5.61 × 10−4 substitutions/site/year was found for Omicron VOC.

  • Spike genes have suitable genetic information for VOCs assignment specific genotypes.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel virus that belongs to the family Coronaviridae. This virus produces a respiratory illness known as coronavirus disease 2019 (COVID-19) and is to blame for the pandemic of COVID-19. Due to its massive circulation around the world and the capacity of mutation of this virus, genomic studies are much needed in to order to reveal new variants of concern (VOCs). On November 26th, 2021, the WHO announced that a new SARS-CoV-2 VOC, named Omicron, had emerged. In order to get insight into the emergence, spread and evolution of Omicron SARS-CoV-2 variants, a comprehensive phylogenetic study was performed. The results of these studies revealed significant differences in codon usage among the S genes of SARS-CoV-2 VOCs Alfa, Beta, Gamma, Delta and Omicron, which can be linked to SARS-CoV-2 genotypes. Omicron variant did not evolve out of one of the early VOCs, but instead it belongs to a complete different genetic lineage from previous ones. Strains classified as Omicron variants evolved from ancestors that existed around May 15th, 2020, suggesting that this VOC may have been circulating undetected for a period of time until its emergence was observed in South Africa. A rate of evolution of 5.61 × 10−4 substitutions/site/year was found for Omicron strains enrolled in these analyses. The results of these studies demonstrate that S genes have suitable genetic information for clear assignment of emerging VOCs to its specific genotypes.

Keywords

Coronavirus
evolution
SARS-CoV-2
Omicron
COVID-19

Cited by (0)

View Abstract