Evolutionary analysis of Omicron variant BF.7 and BA.5.2 pandemic in China

Yamin Sun; Min Wang; Wenchao Lin; Wei Dong; Jianguo Xu

doi:10.1016/j.jobb.2023.01.002

Evolutionary analysis of Omicron variant BF.7 and BA.5.2 pandemic in China

J Biosaf Biosecur. 2023 Mar;5(1):14-20. doi: 10.1016/j.jobb.2023.01.002. Epub 2023 Jan 25.

Authors

Yamin Sun^{1

2}, Min Wang^{2

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

4

5}

Affiliations

¹ Research Institute of Public Health, Nankai University, Tianjin, PR China.
² Research Center for Functional Genomics and Biochip, Tianjin, PR China.
³ TEDA Institute of Biological Sciences and Biotechnology, Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, PR China.
⁴ 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 202206, PR China.
⁵ Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.

Abstract

On December 7, 2022, China adjusted public health control measures, there have been widespread of SARS-CoV-2 infections in Chinese mainland. As the number of infected people increased, the mutation probability of SARS-CoV-2 is also raised. Therefore, it is of great importance to monitor SARS-CoV-2 variants and its mutations in China. In this current study, 665 SARS-CoV-2 genomes from China deposited in the public database were used to analyze the proportion of different variants; to determine the composition of variants in China across different provinces; and analyze specific mutation frequency, focusing on 12 immune escape residues. The results showed that no new mutations were generated on the 12 immune escape residues. The evolutionary analysis of the BF.7 variant circulating in China showed that there is an independent evolutionary branch with unique mutation sites, officially named BF.7.14 by PANGO. This variant may have been imported from Russia to Inner Mongolia at the end of September 2022 and continued its spread in China. The evolutionary analysis of BA.5.2 variant shows that the variant is composed of two sub-variants, named BA.5.2.48 and BA.5.2.49 by PANGO, respectively. This variant may have been imported from abroad to Beijing at the beginning of September 2022 and formed two sub-variants after domestic transmission. Finally, this study showed that current epidemic variants in China were already circulating in other countries, and there were no additional mutations on immune escape residues that could pose a threat to other countries.

Keywords: Evolutionary analysis; Immune escape; SARS-CoV-2.