Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes reveal its epidemic trends.
Int J Infect Dis
; 100: 164-173, 2020 Nov.
Article
in English
| MEDLINE | ID: covidwho-943165
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 nine key specific sites of high linkage, and four major haplotypes were found H1, H2, H3 and H4. The results of Ka/Ks, detected population size and development trends of each major haplotype showed that H3 and H4 subgroups were going through a purify evolution and almost disappeared after detection, indicating that they might have existed for a long time. The 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 with the death rate (r >0.37), suggesting that these two haplotypes might relate to the infectivity or pathogenicity of SARS-CoV-2.CONCLUSIONS:
Several key specific sites and haplotypes related to the infectivity or pathogenicity of SARS-CoV-2, and the possible earlier origin time and place of SARS-CoV-2 were indicated based on the evolution and epidemiology of 16,373 SARS-CoV-2 genomes.Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Genome, Viral
/
SARS-CoV-2
/
COVID-19
Type of study:
Observational study
/
Randomized controlled trials
Limits:
Humans
Country/Region as subject:
Europa
Language:
English
Journal:
Int J Infect Dis
Journal subject:
Communicable Diseases
Year:
2020
Document Type:
Article
Affiliation country:
J.ijid.2020.08.066
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