On the origin and continuing evolution of SARS-CoV-2

Xiaolu Tang; Changcheng Wu; Xiang Li; Yuhe Song; Xinmin Yao; Xinkai Wu; Yuange Duan; Hong Zhang; Yirong Wang; Zhaohui Qian; Jie Cui; Jian Lu

doi:10.1093/nsr/nwaa036

On the origin and continuing evolution of SARS-CoV-2

Natl Sci Rev. 2020 Jun;7(6):1012-1023. doi: 10.1093/nsr/nwaa036. Epub 2020 Mar 3.

Authors

Xiaolu Tang¹, Changcheng Wu¹, Xiang Li², Yuhe Song², Xinmin Yao¹, Xinkai Wu¹, Yuange Duan¹, Hong Zhang¹, Yirong Wang¹, Zhaohui Qian³, Jie Cui², Jian Lu¹

Affiliations

¹ State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
² CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.
³ NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.

Abstract

The SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China, and has since impacted a large portion of China and raised major global concern. Herein, we investigated the extent of molecular divergence between SARS-CoV-2 and other related coronaviruses. Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated. Our results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by natural selection besides recombination. Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses had two major lineages (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. We found that L lineage was more prevalent than the S lineage within the limited patient samples we examined. The implication of these evolutionary changes on disease etiology remains unclear. These findings strongly underscores the urgent need for further comprehensive studies that combine viral genomic data, with epidemiological studies of coronavirus disease 2019 (COVID-19).

Keywords: SARS-CoV-2; molecular evolution; population genetics; virus.