Jian Yu: Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China.
Shanshan Sun: Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China.
Qianqian Tang: Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China.
Chengzhuo Wang: Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China.
Liangchen Yu: The Second Clinical Medical School, Anhui Medical University, Hefei, China.
Lulu Ren: The Second Clinical Medical School, Anhui Medical University, Hefei, China.
Jun Li: Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, The School of Pharmacy, Anhui Medical University, Hefei, China.
Zhenhua Zhang: Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China. ORCID
Coronavirus disease 2019 (COVID-19) is a severe respiratory disease caused by the highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As the COVID-19 pandemic continues, mutations of SARS-CoV-2 accumulate. These mutations may not only make the virus spread faster, but also render current vaccines less effective. In this study, we established a reference sequence for each clade defined using the GISAID typing method. Homology analysis of each reference sequence confirmed a low mutation rate for SARS-CoV-2, with the latest clade GRY having the lowest homology with other clades (99.89%-99.93%), and the homology between other clade being greater than or equal to 99.95%. Variation analyses showed that the earliest genotypes S, V, and G had 2, 3, and 3 characterizing mutations in the genome respectively. The G-derived clades GR, GH, and GV had 5, 6, and 13 characterizing mutations in the genome respectively. A total of 28 characterizing mutations existed in the genome of the latest clades GRY. In addition, we found differences in the geographic distribution of different clades. G, GH, and GR are popular in the USA, while GV and GRY are common in the UK. Our work may facilitate the custom design of antiviral strategies depending on the molecular characteristics of SARS-CoV-2.
