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Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes revealed its epidemic trend and possible origins

View ORCID ProfileYunmeng Bai, Dawei Jiang, View ORCID ProfileJerome R Lon, Xiaoshi Chen, Meiling Hu, Shudai Lin, Zixi Chen, Xiaoning Wang, Yuhuan Meng, View ORCID ProfileHongli Du
doi: https://doi.org/10.1101/2020.04.24.058933
Yunmeng Bai
1School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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Dawei Jiang
1School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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Jerome R Lon
1School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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Xiaoshi Chen
1School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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Meiling Hu
1School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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Shudai Lin
1School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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Zixi Chen
1School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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Xiaoning Wang
1School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
2State Clinic Center of Gearitic, Chinese PLA General Hospital, Beijing 100853, China
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Yuhuan Meng
3Guangzhou KingMed Transformative Medicine Institute Co., Ltd, Guangzhou 510330, China
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  • For correspondence: hldu@scut.edu.cn zb-mengyuhuan@kingmed.com.cn
Hongli Du
1School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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  • ORCID record for Hongli Du
  • For correspondence: hldu@scut.edu.cn zb-mengyuhuan@kingmed.com.cn
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Abstract

Objectives To reveal epidemic trend and possible origins of SARS-CoV-2 by exploring its evolution and molecular characteristics based on a large number of genomes since it has infected millions of people and spread quickly all over the world.

Methods Various evolution analysis methods were employed.

Results The estimated Ka/Ks ratio of SARS-CoV-2 is 1.008 or 1.094 based on 622 or 3624 SARS-CoV-2 genomes, and the time to the most recent common ancestor (tMRCA) was inferred in late September 2019. Further 9 key specific sites of highly linkage and four major haplotypes H1, H2, H3 and H4 were found. The 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 H3 and H4 might have existed for a long time, while H1 and H2 subgroups were going through a near neutral or neutral evolution and globally increased with time. Notably the frequency of H1 was generally high in Europe and correlated to death rate (r>0.37).

Conclusions In this study, the evolution and molecular characteristics of more than 16000 genomic sequences provided a new perspective for revealing epidemiology of SARS-CoV-2.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 30, 2020.
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Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes revealed its epidemic trend and possible origins
Yunmeng Bai, Dawei Jiang, Jerome R Lon, Xiaoshi Chen, Meiling Hu, Shudai Lin, Zixi Chen, Xiaoning Wang, Yuhuan Meng, Hongli Du
bioRxiv 2020.04.24.058933; doi: https://doi.org/10.1101/2020.04.24.058933
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Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes revealed its epidemic trend and possible origins
Yunmeng Bai, Dawei Jiang, Jerome R Lon, Xiaoshi Chen, Meiling Hu, Shudai Lin, Zixi Chen, Xiaoning Wang, Yuhuan Meng, Hongli Du
bioRxiv 2020.04.24.058933; doi: https://doi.org/10.1101/2020.04.24.058933

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