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Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses

Jing Wang, Yuan-fei Pan, Li-fen Yang, Wei-hong Yang, Chu-ming Luo, Juan Wang, Guo-peng Kuang, Wei-chen Wu, Qin-yu Gou, Gen-yang Xin, Bo Li, Huan-le Luo, Yao-qing Chen, Yue-long Shu, Deyin Guo, Zi-Hou Gao, Guodong Liang, Jun Li, Edward C. Holmes, Yun Feng, Mang Shi
doi: https://doi.org/10.1101/2022.11.23.517609
Jing Wang
1The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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Yuan-fei Pan
2Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
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Li-fen Yang
3Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
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Wei-hong Yang
3Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
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Chu-ming Luo
4School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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Juan Wang
3Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
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Guo-peng Kuang
3Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
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Wei-chen Wu
1The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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Qin-yu Gou
1The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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Gen-yang Xin
1The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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Bo Li
5Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
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Huan-le Luo
4School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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Yao-qing Chen
4School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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Yue-long Shu
4School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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Deyin Guo
1The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
6Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong Province, China
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Zi-Hou Gao
3Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
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Guodong Liang
7State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Jun Li
8Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
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Edward C. Holmes
9Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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  • For correspondence: edward.holmes@sydney.edu.au ynfy428@163.com shim23@mail.sysu.edu.cn
Yun Feng
3Department of Viral and Rickettsial Disease Control, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, China
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  • For correspondence: edward.holmes@sydney.edu.au ynfy428@163.com shim23@mail.sysu.edu.cn
Mang Shi
1The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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  • For correspondence: edward.holmes@sydney.edu.au ynfy428@163.com shim23@mail.sysu.edu.cn
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ABSTRACT

Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within bats at the level of individual animals, and hence the frequency of virus co-infection and inter-species transmission. Using an unbiased meta-transcriptomics approach we characterised the mammalian associated viruses present in 149 individual bats sampled from Yunnan province, China. This revealed a high frequency of virus co-infection and species spillover among the animals studied, with 12 viruses shared among different bat species, which in turn facilitates virus recombination and reassortment. Of note, we identified five viral species that are likely to be pathogenic to humans or livestock, including a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV-2 and SARS-CoV, with only five amino acid differences between its receptor-binding domain sequence and that of the earliest sequences of SARS-CoV-2. Functional analysis predicts that this recombinant coronavirus can utilize the human ACE2 receptor such that it is likely to be of high zoonotic risk. Our study highlights the common occurrence of inter-species transmission and co-infection of bat viruses, as well as their implications for virus emergence.

Competing Interest Statement

The authors have declared no competing interest.

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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. All rights reserved. No reuse allowed without permission.
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Posted November 23, 2022.
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Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses
Jing Wang, Yuan-fei Pan, Li-fen Yang, Wei-hong Yang, Chu-ming Luo, Juan Wang, Guo-peng Kuang, Wei-chen Wu, Qin-yu Gou, Gen-yang Xin, Bo Li, Huan-le Luo, Yao-qing Chen, Yue-long Shu, Deyin Guo, Zi-Hou Gao, Guodong Liang, Jun Li, Edward C. Holmes, Yun Feng, Mang Shi
bioRxiv 2022.11.23.517609; doi: https://doi.org/10.1101/2022.11.23.517609
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Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses
Jing Wang, Yuan-fei Pan, Li-fen Yang, Wei-hong Yang, Chu-ming Luo, Juan Wang, Guo-peng Kuang, Wei-chen Wu, Qin-yu Gou, Gen-yang Xin, Bo Li, Huan-le Luo, Yao-qing Chen, Yue-long Shu, Deyin Guo, Zi-Hou Gao, Guodong Liang, Jun Li, Edward C. Holmes, Yun Feng, Mang Shi
bioRxiv 2022.11.23.517609; doi: https://doi.org/10.1101/2022.11.23.517609

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