tetano
Editor, Senior Moderator
Int J Infect Dis
. 2020 Aug 28;S1201-9712(20)30695-0.
doi: 10.1016/j.ijid.2020.08.066. Online ahead of print.
Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes reveal its epidemic trends
Yunmeng Bai[SUP] 1 [/SUP], Dawei Jiang[SUP] 1 [/SUP], Jerome R Lon[SUP] 1 [/SUP], Xiaoshi Chen[SUP] 1 [/SUP], Meiling Hu[SUP] 1 [/SUP], Shudai Lin[SUP] 1 [/SUP], Zixi Chen[SUP] 1 [/SUP], Xiaoning Wang[SUP] 2 [/SUP], Yuhuan Meng[SUP] 3 [/SUP], Hongli Du[SUP] 4 [/SUP]
Affiliations
Abstract
Objectives: To further reveal the phylogenetic evolution and molecular characteristics of the whole genome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) based on a large number of genomes and provide a basis for the prevention and treatment of SARS-CoV-2.
Methods: Various evolution analysis methods were employed.
Results: The estimated ratio of the rates of non-synonymous to synonymous changes (Ka/Ks) of SARS-CoV-2 was 1.008 or 1.094 based on 622 or 3624 SARS-CoV-2 genomes and 9 key specific sites of highly linkage and four major haplotypes H1, H2, H3 and H4 were found. The results of Ka/Ks, detected population size and development trends of each major haplotype showed H3 and H4 subgroups were going through a purify evolution and almost disappeared after detection, indicating they might have existed for a long time. H1 and H2 subgroups were going through a near neutral or neutral evolution and globally increased with time, and the frequency of H1 was generally high in Europe and correlated to death rate (r>0.37), suggesting these two haplotypes might relate to infectivity or pathogenicity of SARS-CoV-2.
Conclusions: Several key specific sites and haplotypes related to infectivity or pathogenicity of SARS-CoV-2 as well as the possible earlier origin time and place of SARS-CoV-2 were indicated based on evolution and epidemiology of 16373 SARS-CoV-2 genomes.
Keywords: SARS-CoV-2; classification; evolution; haplotype.
. 2020 Aug 28;S1201-9712(20)30695-0.
doi: 10.1016/j.ijid.2020.08.066. Online ahead of print.
Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes reveal its epidemic trends
Yunmeng Bai[SUP] 1 [/SUP], Dawei Jiang[SUP] 1 [/SUP], Jerome R Lon[SUP] 1 [/SUP], Xiaoshi Chen[SUP] 1 [/SUP], Meiling Hu[SUP] 1 [/SUP], Shudai Lin[SUP] 1 [/SUP], Zixi Chen[SUP] 1 [/SUP], Xiaoning Wang[SUP] 2 [/SUP], Yuhuan Meng[SUP] 3 [/SUP], Hongli Du[SUP] 4 [/SUP]
Affiliations
- PMID: 32866640
- DOI: 10.1016/j.ijid.2020.08.066
Abstract
Objectives: To further reveal the phylogenetic evolution and molecular characteristics of the whole genome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) based on a large number of genomes and provide a basis for the prevention and treatment of SARS-CoV-2.
Methods: Various evolution analysis methods were employed.
Results: The estimated ratio of the rates of non-synonymous to synonymous changes (Ka/Ks) of SARS-CoV-2 was 1.008 or 1.094 based on 622 or 3624 SARS-CoV-2 genomes and 9 key specific sites of highly linkage and four major haplotypes H1, H2, H3 and H4 were found. The results of Ka/Ks, detected population size and development trends of each major haplotype showed H3 and H4 subgroups were going through a purify evolution and almost disappeared after detection, indicating they might have existed for a long time. H1 and H2 subgroups were going through a near neutral or neutral evolution and globally increased with time, and the frequency of H1 was generally high in Europe and correlated to death rate (r>0.37), suggesting these two haplotypes might relate to infectivity or pathogenicity of SARS-CoV-2.
Conclusions: Several key specific sites and haplotypes related to infectivity or pathogenicity of SARS-CoV-2 as well as the possible earlier origin time and place of SARS-CoV-2 were indicated based on evolution and epidemiology of 16373 SARS-CoV-2 genomes.
Keywords: SARS-CoV-2; classification; evolution; haplotype.