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

View ORCID ProfileLi-li Li, Jing-lin Wang, Xiao-hua Ma, Jin-song Li, Xiao-fei Yang, Wei-feng Shi, Zhao-jun Duan
doi: https://doi.org/10.1101/2021.03.17.435823
Li-li Li
1Key Laboratory for Medical Virology and Viral Diseases, National Health Commission of the People’s Republic of China, Beijing, China
2National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
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  • ORCID record for Li-li Li
Jing-lin Wang
3Yunnan Tropical and Subtropical Animal Viral Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, Yunnan province, China
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Xiao-hua Ma
1Key Laboratory for Medical Virology and Viral Diseases, National Health Commission of the People’s Republic of China, Beijing, China
2National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
4School of Public Health, Gansu University of Chinese Medicine, Lanzhou, China
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Jin-song Li
1Key Laboratory for Medical Virology and Viral Diseases, National Health Commission of the People’s Republic of China, Beijing, China
2National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
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Xiao-fei Yang
5National Engineering Research Center of Freshwater Fisheries, Beijing Fisheries Research Institute
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Wei-feng Shi
6Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, and Shandong Academy of Medical Sciences, Taian, China
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Zhao-jun Duan
1Key Laboratory for Medical Virology and Viral Diseases, National Health Commission of the People’s Republic of China, Beijing, China
2National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
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  • For correspondence: zhaojund@126.com
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Abstract

A novel beta-coronavirus, SARS-CoV-2, emerged in late 2019 and rapidly spread throughout the world, causing the COVID-19 pandemic. However, the origin and direct viral ancestors of SARS-CoV-2 remain elusive. Here, we discovered a new SARS-CoV-2-related virus in Yunnan province, in 2018, provisionally named PrC31, which shares 90.7% and 92.0% nucleotide identities with SARS-CoV-2 and the bat SARSr-CoV ZC45, respectively. Sequence alignment revealed that several genomic regions shared strong identity with SARS-CoV-2, phylogenetic analysis supported that PrC31 shares a common ancestor with SARS-CoV-2. The receptor binding domain of PrC31 showed only 64.2% amino acid identity with SARS-CoV-2. Recombination analysis revealed that PrC31 underwent multiple complex recombination events within the SARS-CoV and SARS-CoV-2 sub-lineages, indicating the evolution of PrC31 from yet-to-be-identified intermediate recombination strains. Combination with previous studies revealed that the beta-CoVs may possess more complicated recombination mechanism. The discovery of PrC31 supports that bats are the natural hosts of SARS-CoV-2.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Figure 2 revised

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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 March 19, 2021.
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A novel SARS-CoV-2 related virus with complex recombination isolated from bats in Yunnan province, China
Li-li Li, Jing-lin Wang, Xiao-hua Ma, Jin-song Li, Xiao-fei Yang, Wei-feng Shi, Zhao-jun Duan
bioRxiv 2021.03.17.435823; doi: https://doi.org/10.1101/2021.03.17.435823
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A novel SARS-CoV-2 related virus with complex recombination isolated from bats in Yunnan province, China
Li-li Li, Jing-lin Wang, Xiao-hua Ma, Jin-song Li, Xiao-fei Yang, Wei-feng Shi, Zhao-jun Duan
bioRxiv 2021.03.17.435823; doi: https://doi.org/10.1101/2021.03.17.435823

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