Small mammals in a biodiversity hotspot harbor viruses of emergence risk

Yun Feng; Guopeng Kuang; Yuanfei Pan; Jing Wang; Weihong Yang; Wei-Chen Wu; Hong Pan; Juan Wang; Xi Han; Lifen Yang; Gen-Yang Xin; Yong-Tao Shan; Qin-Yu Gou; Xue Liu; Deyin Guo; Guodong Liang; Edward C Holmes; Zihou Gao; Mang Shi

doi:10.1093/nsr/nwae463

Small mammals in a biodiversity hotspot harbor viruses of emergence risk

Natl Sci Rev. 2024 Dec 17;12(6):nwae463. doi: 10.1093/nsr/nwae463. eCollection 2025 Jun.

Authors

Yun Feng^{1

2}, Guopeng Kuang², Yuanfei Pan³, Jing Wang^{4

5

6}, Weihong Yang², Wei-Chen Wu^{4

5

6}, Hong Pan², Juan Wang², Xi Han², Lifen Yang², Gen-Yang Xin^{4

5

6}, Yong-Tao Shan^{4

5

6}, Qin-Yu Gou^{4

5

6}, Xue Liu^{4

5

6}, Deyin Guo⁷, Guodong Liang⁸, Edward C Holmes^{9

10}, Zihou Gao², Mang Shi^{4

5

6

11}

Affiliations

¹ State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China.
² Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Disease Control and Prevention, Dali 671000, China.
³ Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
⁴ National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
⁵ State Key Laboratory for Biocontrol, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
⁶ Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
⁷ State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 511436, China.
⁸ Department of Arbovirus, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
⁹ School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia.
¹⁰ Laboratory of Data Discovery for Health Limited, Hong Kong 999077, China.
¹¹ Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 510300, China.

Abstract

Metagenomic sequencing has transformed the understanding of viral diversity in wildlife and the potential threats these viruses pose to human health. Despite this progress, such sequencing studies often have lacked systematic and ecologically informed sampling, thereby likely missing many potential human pathogens and the drivers behind their ecology, evolution and emergence. We conducted an extensive search for viruses in the lungs, spleens and guts of 1688 mammals from 38 species across 428 sites in Yunnan Province, China-a hotspot for zoonoses emergence. We identified 162 mammalian viruses, including 102 new ones and 24 posing potential risks to humans due to their relationships with known human pathogens associated with serious diseases or their ability to cross major host species barriers. Our findings offer an in-depth view of virus organotropism, cross-host associations, host sharing patterns, and the ecological factors influencing viral evolution, all of which are critical for anticipating and mitigating future zoonotic outbreaks.

Keywords: metatranscriptomics; virus ecology; virus evolution; wildlife virome; zoonotic diseases.