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bioRxiv · 10.1101/2020.11.01.363739

Temporal patterns in the evolutionary genetic distance of SARS-CoV-2 during the COVID-19 pandemic

Lou, J.·Zhao, S.·Cao, L.·Chen, Z.·Chan, R. W.·Chong, M. K.·Zee, B. C.·Chan, P. K.·Wang, M. H.
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Abstract

BackgroundDuring the pandemic of coronavirus disease 2019 (COVID-19), the genetic mutations occurred in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cumulatively or sporadically. In this study, we employed a computational approach to identify and trace the emerging patterns of the SARS-CoV-2 mutations, and quantify accumulative genetic distance across different periods and proteins. MethodsFull-length human SARS-CoV-2 strains in United Kingdom were collected. We investigated the temporal variation in the evolutionary genetic distance defined by the Hamming distance since the start of COVID-19 pandemic. FindingsOur results showed that the SARS-CoV-2 was in the process of continuous evolution, mainly involved in spike protein (S protein), the RNA-dependent RNA polymerase (RdRp) region of open reading frame 1 (ORF1) and nucleocapsid protein (N protein). By contrast, mutations in other proteins were sporadic and genetic distance to the initial sequenced strain did not show an increasing trend.

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Lou, J., Zhao, S., Cao, L., Chen, Z., Chan, R. W., Chong, M. K., Zee, B. C., Chan, P. K., Wang, M. H.. 2020-11-02. Temporal patterns in the evolutionary genetic distance of SARS-CoV-2 during the COVID-19 pandemic. https://doi.org/10.1101/2020.11.01.363739

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