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bioRxiv · 10.1101/2020.04.24.058933

Evolution and molecular characteristics of SARS-CoV-2 genome

Bai, Y.·Jiang, D.·Lon, J. R.·Chen, X.·Hu, M.·Lin, S.·Chen, Z.·Meng, Y.·Du, H.
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Abstract

ObjectivesTo 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. MethodsVarious evolution analysis methods were employed. ResultsThe 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). ConclusionsIn this study, the evolution and molecular characteristics of more than 16000 genomic sequences provided a new perspective for revealing epidemiology of SARS-CoV-2.

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Bai, Y., Jiang, D., Lon, J. R., Chen, X., Hu, M., Lin, S., Chen, Z., Meng, Y., Du, H.. 2020-04-24. Evolution and molecular characteristics of SARS-CoV-2 genome. https://doi.org/10.1101/2020.04.24.058933

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