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. 2022 Jun;4(1):33-37.
doi: 10.1016/j.jobb.2021.12.001. Epub 2021 Dec 31.

Origin and evolutionary analysis of the SARS-CoV-2 Omicron variant

Yamin Sun  1   2 , Wenchao Lin  2 , Wei Dong  2 , Jianguo Xu  1   3
Affiliations

Origin and evolutionary analysis of the SARS-CoV-2 Omicron variant

Yamin Sun et al. J Biosaf Biosecur. 2022 Jun.

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved rapidly into new variants throughout the pandemic. The Omicron variant has more than 50 mutations when compared with the original wild-type strain and has been identified globally in numerous countries. In this report, we analyzed the mutational profiles of several variants, including the per-site mutation rate, to determine evolutionary relationships. The Omicron variant was found to have a unique mutation profile when compared with that of other SARS-CoV-2 variants, containing mutations that are rare in clinical samples. Moreover, the presence of five mouse-adapted mutation sites suggests that Omicron may have evolved in a mouse host. Mutations in the Omicron receptor-binding domain (RBD) region, in particular, have potential implications for the ongoing pandemic.

Keywords: Mouse-adapted mutation; Omicron variant; Reverse zoonosis; SARS-CoV-2.

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Conflict of interest statement

Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Mutation profiles of the five variants of concern (VOCs) designated by the World Health Organization. Common mutations are marked in red. Many mutations in the Omicron variant are unique when compared with mutations in other VOCs.
Fig. 2
Fig. 2
Seven key mutations among 13 mouse-adapted strains and the Omicron variant of SARS-CoV-2. IA-501Y-MA-30 is a homogenate obtained from mouse lung after 30 passages of the IA-501Y strain.
Fig. 3
Fig. 3
The abundance of different SARS-Cov-2 variants by percent of new infections from a public database (A). Evolutionary analysis shows that the Omicron variant did not evolve from the Delta variant and differs from other variants (B).
See this image and copyright information in PMC

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