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: Classification; Evolution; Haplotype; SARS-CoV-2.
【저자키워드】 Evolution, SARS-CoV-2, classification, Haplotype, 【초록키워드】 Treatment, SARS-CoV-2, coronavirus, Europe, Epidemiology, Genome, haplotypes, classification, severe acute respiratory syndrome Coronavirus, Characteristics, SARS-CoV-2 genome, genomes, molecular, respiratory, pathogenicity, change, Haplotype, Ka/Ks, Frequency, Analysis, Non-synonymous, Neutral, Population size, Phylogenetic, death rate, subgroup, acute respiratory syndrome, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, SARS-CoV-2 genomes, whole genome, synonymous, indicated, nine, correlated, major haplotype, 【제목키워드】 Epidemic, Characteristics, SARS-CoV-2 genome, molecular, Comprehensive,