Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential

Jing Wang, Yuan-fei Pan, Li-fen Yang, Wei-hong Yang, Kexin Lv, Chu-ming Luo, Juan Wang, Guo-peng Kuang, Wei-chen Wu, Qin-yu Gou, Gen-yang Xin, Bo Li, Huan-le Luo, Shoudeng Chen, Yue-long Shu, Deyin Guo, Zi-Hou Gao, Guodong Liang, Jun Li, Yao-qing Chen (), Edward C. Holmes (), Yun Feng () and Mang Shi ()
Additional contact information
Jing Wang: Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University
Yuan-fei Pan: Fudan University
Li-fen Yang: Yunnan Institute of Endemic Disease Control and Prevention
Wei-hong Yang: Yunnan Institute of Endemic Disease Control and Prevention
Kexin Lv: Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University
Chu-ming Luo: Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University
Juan Wang: Yunnan Institute of Endemic Disease Control and Prevention
Guo-peng Kuang: Yunnan Institute of Endemic Disease Control and Prevention
Wei-chen Wu: Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University
Qin-yu Gou: Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University
Gen-yang Xin: Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University
Bo Li: Yunnan University
Huan-le Luo: Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University
Shoudeng Chen: Sun Yat-sen University
Yue-long Shu: Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University
Deyin Guo: Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University
Zi-Hou Gao: Yunnan Institute of Endemic Disease Control and Prevention
Guodong Liang: Chinese Center for Disease Control and Prevention
Jun Li: City University of Hong Kong
Yao-qing Chen: Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University
Edward C. Holmes: The University of Sydney
Yun Feng: Yunnan Institute of Endemic Disease Control and Prevention
Mang Shi: Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within individual bats, and hence the frequency of virus co-infection and spillover among them. We characterize the mammal-associated viruses in 149 individual bats sampled from Yunnan province, China, using an unbiased meta-transcriptomics approach. This reveals a high frequency of virus co-infection (simultaneous infection of bat individuals by multiple viral species) and spillover among the animals studied, which may in turn facilitate virus recombination and reassortment. Of note, we identify five viral species that are likely to be pathogenic to humans or livestock, based on phylogenetic relatedness to known pathogens or in vitro receptor binding assays. This includes a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV and SARS-CoV-2. In vitro assays indicate that this recombinant virus can utilize the human ACE2 receptor such that it is likely to be of increased emergence risk. Our study highlights the common occurrence of co-infection and spillover of bat viruses and their implications for virus emergence.

Date: 2023
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DOI: 10.1038/s41467-023-39835-1

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