Citation: Shuangshuang Chen, Wanping Li, Lirui Fan, Conghui Xu, Sixuan Liu, Hongye Li, Peiwen Liu, Wei Zhu, Xinwei Wu, Pengzhe Qin, Juntao Li, Xiaowei Ma, Yuehong Wei. Metatranscriptomics profiling reveals rodent- and shrew-borne viral diversity and evolutionary relationships in Guangzhou, China .VIROLOGICA SINICA, 2026, 41(1) : 35-47.  http://dx.doi.org/10.1016/j.virs.2025.12.009

Metatranscriptomics profiling reveals rodent- and shrew-borne viral diversity and evolutionary relationships in Guangzhou, China

  • Corresponding author: Xiaowei Ma, gzcdc_maxw@gz.gov.cn
    Yuehong Wei, wei_yh0928@163.com
  • Received Date: 05 August 2025
    Accepted Date: 11 December 2025
    Available online: 17 December 2025

    Fund Project: This research was supported by the Guangzhou Science, Technology and Innovation Commission project (2024A03J0473), the Key Project of Medicine Discipline of Guangzhou (No. 2025-2027-11), and the Guangzhou Nansha District Science and Technology Bureau Civilian Technology Program Project (2024MS011).

  • Emerging zoonotic infectious diseases, predominantly caused by viruses, pose increasing public health threats globally. Rodents and shrews are natural hosts for a variety of zoonotic viruses. Guangzhou is one of China’s most densely populated cities and experiences frequent international and domestic population movements, making it a hotspot for infectious diseases. This study reports the metatranscriptomics virome of 208 rodents and shrews collected between June 2023 and December 2024 from four main urban areas (Tianhe, Baiyun, Liwan, Yuexiu) and five non-main urban areas (Zengcheng, Huadu, Conghua, Panyu, Nansha) in Guangzhou. Individual libraries were constructed from mixed tissue samples (liver, spleen, lung, and kidney) of each animal. Metatranscriptomics sequencing revealed diverse viral communities, identifying 24 viral strains across eight mammalian-associated viral families. Notably, we identified 17 known viruses and seven potentially novel viruses, including Seoul virus (5.2% prevalence in Rattus norvegicus from Panyu), Wenzhou mammarenavirus (13.2% in Rattus norvegicus from Conghua and Huadu), Jeilongvirus (29.4% in Rattus andamanensis from Panyu), and a divergent lineage of arteriviruses that may represent a new genus (maximum positivity rates of 2.9% in Rattus norvegicus and 5.7% in Rattus tanezumi). Phylogenetic analysis elucidated evolutionary relationships within key families such as Hantaviridae, Arenaviridae, Flaviviridae, and Parvoviridae, revealing distinct viral carriage patterns in Guangzhou City that are shaped by host species and geographical location. This is the first macro-level study of rodent and shrew viromes in Guangzhou and provides a scientific basis for strengthening surveillance of mammalian-associated viruses and preventing emerging zoonotic infectious diseases in the region.

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    Metatranscriptomics profiling reveals rodent- and shrew-borne viral diversity and evolutionary relationships in Guangzhou, China

      Corresponding author: Xiaowei Ma, gzcdc_maxw@gz.gov.cn
      Corresponding author: Yuehong Wei, wei_yh0928@163.com
    • a. School of Basic Medicine and Public Health, Jinan University, Guangzhou 510632, China;
    • b. Guangzhou Nansha District Center for Disease Control and Prevention, Guangzhou 511400, China;
    • c. Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention (Guangzhou Health Supervision Institute), Guangzhou 510440, China;
    • d. Guangzhou Center for Disease Control and Prevention (Guangzhou Health Supervision Institute), Guangzhou 510440, China;
    • e. School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
    Fund Project:  This research was supported by the Guangzhou Science, Technology and Innovation Commission project (2024A03J0473), the Key Project of Medicine Discipline of Guangzhou (No. 2025-2027-11), and the Guangzhou Nansha District Science and Technology Bureau Civilian Technology Program Project (2024MS011).

    Abstract: Emerging zoonotic infectious diseases, predominantly caused by viruses, pose increasing public health threats globally. Rodents and shrews are natural hosts for a variety of zoonotic viruses. Guangzhou is one of China’s most densely populated cities and experiences frequent international and domestic population movements, making it a hotspot for infectious diseases. This study reports the metatranscriptomics virome of 208 rodents and shrews collected between June 2023 and December 2024 from four main urban areas (Tianhe, Baiyun, Liwan, Yuexiu) and five non-main urban areas (Zengcheng, Huadu, Conghua, Panyu, Nansha) in Guangzhou. Individual libraries were constructed from mixed tissue samples (liver, spleen, lung, and kidney) of each animal. Metatranscriptomics sequencing revealed diverse viral communities, identifying 24 viral strains across eight mammalian-associated viral families. Notably, we identified 17 known viruses and seven potentially novel viruses, including Seoul virus (5.2% prevalence in Rattus norvegicus from Panyu), Wenzhou mammarenavirus (13.2% in Rattus norvegicus from Conghua and Huadu), Jeilongvirus (29.4% in Rattus andamanensis from Panyu), and a divergent lineage of arteriviruses that may represent a new genus (maximum positivity rates of 2.9% in Rattus norvegicus and 5.7% in Rattus tanezumi). Phylogenetic analysis elucidated evolutionary relationships within key families such as Hantaviridae, Arenaviridae, Flaviviridae, and Parvoviridae, revealing distinct viral carriage patterns in Guangzhou City that are shaped by host species and geographical location. This is the first macro-level study of rodent and shrew viromes in Guangzhou and provides a scientific basis for strengthening surveillance of mammalian-associated viruses and preventing emerging zoonotic infectious diseases in the region.

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