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

Yamin Sun; Wenchao Lin; Wei Dong; Jianguo Xu

doi:10.1016/j.jobb.2021.12.001

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

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

Authors

Yamin Sun^{1

2}, Wenchao Lin², Wei Dong², Jianguo Xu^{1

3}

Affiliations

¹ Research Institute of Public Health, Nankai University, Tianjin, PR China.
² Engineering and Research Center for Microbial Functional Genomics and Detection Technology, Ministry of Education, Nankai University.
³ State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China.

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.