Journal
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
Volume 100, Issue -, Pages 164-173Publisher
ELSEVIER SCI LTD
DOI: 10.1016/j.ijid.2020.08.066
Keywords
SARS-CoV-2; Evolution; Classification; Haplotype
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Funding
- National Key R&D Program of China [2018YFC0910201]
- Key R&D Program of Guangdong Province [2019B020226001]
- Technology Planning Project of Guangzhou [201704020176, 2020Q-P013]
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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. (C) 2020 The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.
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