Mutations, Recombination and Insertion in the Evolution of 2019-nCoV

Wu, A.; Niu, P.; Wang, L.; Zhou, H.; Zhao, X.; Wang, W.; Wang, J.; Ji, C.; Ding, X.; Wang, X.; Lu, R.; Gold, S.; Aliyari, S.; Zhang, S.; Vikram, E.; Zou, A.; Lenh, E.; Chen, J.; Ye, F.; Han, N.; Peng, Y.; Guo, H.; Wu, G.; Jiang, T.; Tan, W.; Cheng, G.

doi:10.1101/2020.02.29.971101

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bioRxiv · 10.1101/2020.02.29.971101

Mutations, Recombination and Insertion in the Evolution of 2019-nCoV

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Abstract

BackgroundThe 2019 novel coronavirus (2019-nCoV or SARS-CoV-2) has spread more rapidly than any other betacoronavirus including SARS-CoV and MERS-CoV. However, the mechanisms responsible for infection and molecular evolution of this virus remained unclear. MethodsWe collected and analyzed 120 genomic sequences of 2019-nCoV including 11 novel genomes from patients in China. Through comprehensive analysis of the available genome sequences of 2019-nCoV strains, we have tracked multiple inheritable SNPs and determined the evolution of 2019-nCoV relative to other coronaviruses. ResultsSystematic analysis of 120 genomic sequences of 2019-nCoV revealed co-circulation of two genetic subgroups with distinct SNPs markers, which can be used to trace the 2019-nCoV spreading pathways to different regions and countries. Although 2019-nCoV, human and bat SARS-CoV share high homologous in overall genome structures, they evolved into two distinct groups with different receptor entry specificities through potential recombination in the receptor binding regions. In addition, 2019-nCoV has a unique four amino acid insertion between S1 and S2 domains of the spike protein, which created a potential furin or TMPRSS2 cleavage site. ConclusionsOur studies provided comprehensive insights into the evolution and spread of the 2019-nCoV. Our results provided evidence suggesting that 2019-nCoV may increase its infectivity through the receptor binding domain recombination and a cleavage site insertion. One Sentence SummaryNovel 2019-nCoV sequences revealed the evolution and specificity of betacoronavirus with possible mechanisms of enhanced infectivity.

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Wu, A., Niu, P., Wang, L., Zhou, H., Zhao, X., Wang, W., Wang, J., Ji, C., Ding, X., Wang, X., Lu, R., Gold, S., Aliyari, S., Zhang, S., Vikram, E., Zou, A., Lenh, E., Chen, J., Ye, F., Han, N., Peng, Y., Guo, H., Wu, G., Jiang, T., Tan, W., Cheng, G.. 2020-03-02. Mutations, Recombination and Insertion in the Evolution of 2019-nCoV. https://doi.org/10.1101/2020.02.29.971101

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