Mapping Genetic Events of SARS-CoV-2 Variants

Luyao Qin; Jing Meng; Xiao Ding; Taijiao Jiang

doi:10.3389/fmicb.2022.890590

Mapping Genetic Events of SARS-CoV-2 Variants

Front Microbiol. 2022 Jul 14:13:890590. doi: 10.3389/fmicb.2022.890590. eCollection 2022.

Authors

Luyao Qin^{1

2}, Jing Meng^{1

2}, Xiao Ding^{1

2}, Taijiao Jiang^{1

2

3

4}

Affiliations

¹ Institute of Systems Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
² Suzhou Institute of Systems Medicine, Suzhou, China.
³ Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.
⁴ Guangzhou Laboratory, Guangzhou, China.

Abstract

Genetic mutation and recombination are driving the evolution of SARS-CoV-2, leaving many genetic imprints which could be utilized to track the evolutionary pathway of SARS-CoV-2 and explore the relationships among variants. Here, we constructed a complete genetic map, showing the explicit evolutionary relationship among all SARS-CoV-2 variants including 58 groups and 46 recombination types identified from 3,392,553 sequences, which enables us to keep well informed of the evolution of SARS-CoV-2 and quickly determine the parents of novel variants. We found that the 5' and 3' of the spike and nucleoprotein genes have high frequencies to form the recombination junctions and that the RBD region in S gene is always exchanged as a whole. Although these recombinants did not show advantages in community transmission, it is necessary to keep a wary eye on the novel genetic events, in particular, the mutants with mutations on spike and recombinants with exchanged moieties on spike gene.

Keywords: SARS-CoV-2; evolutionary pathway; genetic events; genetic map; mutation and recombination.