A novel SARS-CoV-2 related coronavirus with complex recombination isolated from bats in Yunnan province, China

文献类型： 外文期刊

第一作者： Li, Li-li

作者： Li, Li-li;Ma, Xiao-hua;Sun, Xiao-man;Li, Jin-song;Duan, Zhao-jun;Li, Li-li;Sun, Xiao-man;Li, Jin-song;Duan, Zhao-jun;Wang, Jing-lin;Sun, Xiao-man;Yang, Xiao-fei;Shi, Wei-feng

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关键词： SARS-CoV-2; bats; coronaviruses; recombination; evolution

期刊名称：EMERGING MICROBES & INFECTIONS （ 影响因子：7.163； 五年影响因子：7.329 ）

ISSN：

年卷期： 2021 年 10 卷 1 期

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收录情况： SCI

摘要： At the end of 2019, A new type of beta-CoV, SARS-CoV-2 emerged and triggered the COVID-19 pandemic, which spread overwhelmingly around the world in less than a year. However, the origin and direct ancestral viruses of SARS-CoV-2 remain unknown. RaTG13, a novel coronavirus found in bats in China's Yunnan Province, is the closest relative virus of the SARS-CoV-2 identified so far. In this study, a new SARS-CoV-2 related virus, provisionally named PrC31, was discovered in Yunnan province by retrospectively analyse bat next generation sequencing (NGS) data of intestinal samples collected in 2018. PrC31 shared 90.7% and 92.0% nucleotide identities to the genomes of SARS-CoV-2 and the bat SARSr-CoV ZC45, respectively. Sequence alignment of PrC31 showed that several genomic regions, especially orf1a and orf8 had the highest homology with those corresponding genomic regions of SARS-CoV-2 than any other related viruses. Phylogenetic analysis indicated that PrC31 shared a common ancestor with SARS-CoV-2 in evolutionary history. The differences between the PrC31 and SARS-CoV-2 genomes were mainly manifested in the spike genes. The amino acid homology between the receptor binding domains of PrC31 and SARS-CoV-2 was only 64.2%. Importantly, recombination analysis revealed that PrC31 underwent multiple complex recombination events (including three recombination breakpoints) involving the SARS-CoV and SARS-CoV-2 sub-lineages, indicating that PrC31 evolved from yet-to-be-identified intermediate recombination strains. Combined with previous studies, it is revealed that the beta-CoVs may possess a more complex recombination mechanism than we thought.

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