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Volume 40 Issue 4
August 2025

    . doi: 10.1016/j.virs.2025.06.004
    Citation: Yiwei Shi, Letian Fang, Cixiu Li, Peng Li, Jiluo Liu, Yifan Chen, Yue Zhao, Zishuai Li, Shuqi Liu, Yibo Ding, Xinyu Zhou, Dongming Jiang, Jiaying Shen, Zihan Zhang, Junheng Lyu, Rui Pu, Xiaojie Tan, Jianhua Yin, Weifeng Shi, Guangwen Cao. Virome diversity in small mammals from south China: Insights into virus evolution, transmission, and ecology .VIROLOGICA SINICA, 2025, 40(4) : 520-534.  http://dx.doi.org/10.1016/j.virs.2025.06.004
    shu

    中国南部地区野生哺乳动物的病毒组多样性：病毒进化、传播、生态机制

    • a 海军军医大学流行病学教研室;

    • b海军军医大学生物安全防御教育部重点实验室;

    • c 海军军医大学上海市医学生物防护重点实验室;

    • d 山东第一医科大学(山东省医学科学院)山东省高校新发传染病重点实验室;

    • e 山东第一医科大学(山东省医学科学院)临床与基础医学院;

    • f 山东第一医科大学(山东省医学科学院)公共卫生学院;

    • g 上海交通大学医学院附属瑞金医院感染科;

    • h 上海交通大学医学院上海市病毒研究院

    • 哺乳动物是人类传染病的重要储存宿主，其病毒溢出风险与气候条件密切相关。本研究对2018至2024年间采集自中国南方8个城市的20种哺乳动物（包括蝙蝠、啮齿类、刺猬和鼩鼱）共226份样本进行宏转录组测序，样本类型涵盖内脏器官、口咽/肛门拭子及粪便。共鉴定出63种脊椎动物相关病毒，其中34种为新发现病毒。系统发育分析显示，6种病毒与已知人类或家畜病原体具有近缘关系，存在潜在感染风险。研究发现14.3%（9/63）的病毒存在跨物种传播现象（至少感染两种宿主），其中蝙蝠（尤其是菊头蝠属和蹄蝠属）是病毒传播及人畜共患溢出的关键枢纽。病毒组构成呈现显著的物种间和地理差异（adonis R2=0.50，P=0.001）。广义线性模型量化显示：宿主分类学地位（目级水平）是驱动病毒多样性的首要因素（解释偏差25.70%），其次为生态型（解释偏差10.27%）。基于本研究获得的β冠状病毒序列，以及2013年7月至2024年3月中国境内2.0×104只蝙蝠的β冠状病毒序列进行的系统发育分析表明，目前尚未发现比已知毒株（如RaTG13）与SARS-CoV-2亲缘关系更近的冠状病毒。该研究为理解病毒进化、传播规律及生态决定因素提供了关键科学依据，对新发传染病的防控具有重要意义。

    Virome diversity in small mammals from south China: Insights into virus evolution, transmission, and ecology

    • a. Department of Epidemiology, Naval Medical University, Shanghai, 200433, China;

    • b. Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai, 200433, China;

    • c. Shanghai Key Laboratory of Medical Bioprotection, Naval Medical University, Shanghai, 200433, China;

    • d. Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, 250117, China;

    • e. School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, 250117, China;

    • f. School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, 250117, China;

    • g. Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China;

    • h. Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China

    • Mammals are critical reservoirs of human infectious diseases and the spillover of viruses is related to climate conditions. We conducted meta-transcriptomic sequencing of 226 mammals (bats, rodents, hedgehogs, and shrews) representing 20 species collected across eight cities in south China between 2018 and 2024. Samples included internal organs, oropharyngeal and anal swabs, and feces. We identified 63 vertebrate-associated viruses, including 34 novel viruses. Phylogenetic analysis revealed six viruses with potential infection risks to humans or domestic animals due to their close phylogenetic relationships with known pathogens. Cross-species transmission was observed in 14.3% (9/63) of viruses, shared by at least two host species, with bats, particularly Rhinolophus and Hipposideros, serving as key hubs for viral circulation and zoonotic spillover. Virome composition varied substantially among mammalian species and geographic regions (adonis test, R2 = 0.50, P = 0.001). Generalized linear models quantified the roles of host taxonomy, ecotypes, and meteorological factors in shaping viral diversity, demonstrating host taxonomy (at the order level) as a predominant role (25.70% deviance explained), followed by ecotypes (10.27% deviance explained). Phylogenetic analysis conducted using our betacoronavirus sequences, as well as betacoronavirus sequences derived from 2.0 × 104 bats sampled in China between July 2013 and March 2024, revealed that no betacoronaviruses exhibited closer phylogenetic relationships to SARS-CoV-2 than the known strains (e.g., RaTG13). These findings provide critical insights into virus evolution, transmission, and ecological determinants, which are essential for the prevention of emerging infectious diseases.
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      1. Allen, T., Murray, K. A., Zambrana-Torrelio, C., Morse, S. S., Rondinini, C., Di Marco, M., Breit, N., Olival, K. J., Daszak, P. 2017. Global hotspots and correlates of emerging zoonotic diseases. Nat. Commun., 8, 1124.

      2. Blasdell, K. R., Duong, V., Eloit, M., Chretien, F., Ly, S., Hul, V., Deubel, V., Morand, S., Buchy, P. 2016. Evidence of human infection by a new mammarenavirus endemic to Southeastern Asia. eLife, 5, e13135.

      3. Buchfink, B., Xie, C., Huson, D. H. 2015. Fast and sensitive protein alignment using DIAMOND. Nat. Methods, 12, 59-60.

      4. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T. L. 2009. BLAST+: architecture and applications. BMC Bioinf., 10, 421.

      5. Capella-Gutierrez, S., Silla-Martinez, J. M., Gabaldon, T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25, 1972-1973.

      6. Carlson, C. J., Albery, G. F., Merow, C., Trisos, C. H., Zipfel, C. M., Eskew, E. A., Olival, K. J., Ross, N., Bansal, S. 2022. Climate change increases cross-species viral transmission risk. Nature, 607, 555-562.

      7. Chen, S., Zhou, Y., Chen, Y., Gu, J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34, i884-i890.

      8. Chen, Y. M., Hu, S. J., Lin, X. D., Tian, J. H., Lv, J. X., Wang, M. R., Luo, X. Q., Pei, Y. Y., Hu, R. X., Song, Z. G., Holmes, E. C., Zhang, Y. Z. 2023. Host traits shape virome composition and virus transmission in wild small mammals. Cell, 186, 4662-4675.e12.

      9. Feng, Y., Kuang, G., Pan, Y., Wang, J., Yang, W., Wu, W.-C., Pan, H., Wang, J., Han, X., Yang, L., Xin, G.-Y., Shan, Y.-T., Yu Gou, Q.-., Liu, X., Guo, D., Liang, G., Holmes, E. C., Gao, Z., Shi, M. 2024. Small mammals in a biodiversity hotspot harbor viruses of emergence risk. Natl. Sci. Rev. 12:nwae463.

      10. Geoghegan, J. L., Holmes, E. C. 2017. Predicting virus emergence amid evolutionary noise. Open Biol, 7, 170189.

      11. Goldberg, A. R., Langwig, K. E., Brown, K. L., Marano, J. M., Rai, P., King, K. M., Sharp, A. K., Ceci, A., Kailing, C. D., Kailing, M. J., Briggs, R., Urbano, M. G., Roby, C., Brown, A. M., Weger-Lucarelli, J., Finkielstein, C. V., Hoyt, J. R. 2024. Widespread exposure to SARS-CoV-2 in wildlife communities. Nat. Commun., 15, 6210.

      12. Guy, C., Ratcliffe, J. M., Mideo, N. 2020. The influence of bat ecology on viral diversity and reservoir status. Ecol. Evol., 10, 5748-5758.

      13. Han, Y., Xu, P., Wang, Y., Zhao, W., Zhang, J., Zhang, S., Wang, J., Jin, Q., Wu, Z. 2023. Panoramic analysis of coronaviruses carried by representative bat species in Southern China to better understand the coronavirus sphere. Nat. Commun., 14, 5537.

      14. Harvey, E., Holmes, E. C. 2022. Diversity and evolution of the animal virome. Nat. Rev. Microbiol., 20, 321-334.

      15. He, J., Wang, Y., Wei, X., Sun, H., Xu, Y., Yin, W., Wang, Y., Zhang, W. 2023. Spatial-temporal dynamics and time series prediction of HFRS in mainland China: a long-term retrospective study. J. Med. Virol., 95, e28269.

      16. He, W. T., Hou, X., Zhao, J., Sun, J., He, H., Si, W., Wang, J., Jiang, Z., Yan, Z., Xing, G., Lu, M., Suchard, M. A., Ji, X., Gong, W., He, B., Li, J., Lemey, P., Guo, D., Tu, C., Holmes, E. C., Shi, M., Su, S. 2022. Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell, 185, 1117-1129.e8.

      17. Hoberg, E. P., Brooks, D. R. 2015. Evolution in action: climate change, biodiversity dynamics and emerging infectious disease. Philos. Trans. R. Soc. Lond. B Biol. Sci., 370, 20130553.

      18. Honig, V., Kamis, J., Marsikova, A., Matejkova, T., Stopka, P., Macova, A., Ruzek, D., Kvicerova, J. 2022. Orthohantaviruses in reservoir and atypical hosts in the Czech republic: spillover infection and indication of virus-specific tissue tropism. Microbiol. Spectr., 10, e0130622.

      19. Kane, Y., Tendu, A., Li, R., Chen, Y., Mastriani, E., Lan, J., Catherine Hughes, A., Berthet, N., Wong, G. 2024. Viral diversity in wild and urban rodents of Yunnan Province, China. Emerg. Microb. Infect., 13, 2290842.

      20. Katoh, K., Standley, D. M. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol., 30, 772-780.

      21. Langmead, B., Salzberg, S. L. 2012. Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.

      22. Letko, M., Seifert, S. N., Olival, K. J., Plowright, R. K., Munster, V. J. 2020. Bat-borne virus diversity, spillover and emergence. Nat. Rev. Microbiol., 18, 461-471.

      23. Li, C. X., Shi, M., Tian, J. H., Lin, X. D., Kang, Y. J., Chen, L. J., Qin, X. C., Xu, J., Holmes, E. C., Zhang, Y. Z. 2015a. Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. eLife, 4, e05378.

      24. Li, D., Liu, C. M., Luo, R., Sadakane, K., Lam, T. W. 2015b. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, 31, 1674-1676.

      25. Luo, Y., Lv, H., Yan, H., Zhu, C., Ai, L., Li, W., Yi, J., Zhang, L., Tan, W. 2022. Meteorological change and hemorrhagic fever with renal syndrome epidemic in China, 2004-2018. Sci. Rep., 12, 20037.

      26. Michalak, T. I. 2020. Diverse virus and host-dependent mechanisms influence the systemic and intrahepatic immune responses in the woodchuck model of hepatitis B. Front. Immunol., 11, 853.

      27. Morales-Castilla, I., Pappalardo, P., Farrell, M. J., Aguirre, A. A., Huang, S., Gehman, A. M., Dallas, T., Gravel, D., Davies, T. J. 2021. Forecasting parasite sharing under climate change. Philos. Trans. R. Soc. Lond. B Biol. Sci., 376, 20200360.

      28. Morales, A. E., Dong, Y., Brown, T., Baid, K., Kontopoulos, D., Gonzalez, V., Huang, Z., Ahmed, A. W., Bhuinya, A., Hilgers, L., Winkler, S., Hughes, G., Li, X., Lu, P., Yang, Y., Kirilenko, B. M., Devanna, P., Lama, T. M., Nissan, Y., Pippel, M., Davalos, L. M., Vernes, S. C., Puechmaille, S. J., Rossiter, S. J., Yovel, Y., Prescott, J. B., Kurth, A., Ray, D. A., Lim, B. K., Myers, E., Teeling, E. C., Banerjee, A., Irving, A. T., Hiller, M. 2025. Bat genomes illuminate adaptations to viral tolerance and disease resistance. Nature, 638, 449-458.

      29. Nguyen, L. T., Schmidt, H. A., VON Haeseler, A. & Minh, B. Q. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol., 32, 268-274.

      30. Ni, X. B., Pei, Y., Ye, Y. T., Shum, M. H., Cui, X. M., Wu, Y. Q., Pierce, M. P., Zhao, L., Wang, G. P., Wei, J. T., Fan, J. L., Wang, Q., Smith, D. K., Sun, Y., Du, L. F., Zhang, J., Jiang, J. F., He, P. J., Chen, X., Wei, H., Zhao, N. Q., Cao, W. C., Lam, T. T., Jia, N. 2024. Ecoclimate drivers shape virome diversity in a globally invasive tick species. ISME J., 18, wrae087.

      31. Olival, K. J., Hosseini, P. R., Zambrana-Torrelio, C., Ross, N., Bogich, T. L., Daszak, P. 2017. Host and viral traits predict zoonotic spillover from mammals. Nature, 546, 646-650.

      32. Oude Munnink, B. B., Sikkema, R. S., Nieuwenhuijse, D. F., Molenaar, R. J., Munger, E., Molenkamp, R., Van Der Spek, A., Tolsma, P., Rietveld, A., Brouwer, M., Bouwmeester-Vincken, N., Harders, F., Hakze-Van Der Honing, R., Wegdam-Blans, M. C. A., Bouwstra, R. J., Geurtsvankessel, C., Van Der Eijk, A. A., Velkers, F. C., Smit, L. A. M., Stegeman, A., Van Der Poel, W. H. M., Koopmans, M. P. G. 2021. Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans. Science, 371, 172-177.

      33. Pardo-Roa, C., Nelson, M. I., Ariyama, N., Aguayo, C., Almonacid, L. I., Gonzalez-Reiche, A. S., Munoz, G., Ulloa, M., Avila, C., Navarro, C., Reyes, R., Castillo-Torres, P. N., Mathieu, C., Vergara, R., Gonzalez, A., Gonzalez, C. G., Araya, H., Castillo, A., Torres, J. C., Covarrubias, P., Bustos, P., Van Bakel, H., Fernandez, J., Fasce, R. A., Johow, M., Neira, V., Medina, R. A. 2025. Cross-species and mammal-to-mammal transmission of clade 2.3.4.4b highly pathogenic avian influenza A/H5N1 with PB2 adaptations. Nat. Commun., 16, 2232.

      34. Shan, T., Yang, S., Wang, H., Wang, H., Zhang, J., Gong, G., Xiao, Y., Yang, J., Wang, X., Lu, J., Zhao, M., Yang, Z., Lu, X., Dai, Z., He, Y., Chen, X., Zhou, R., Yao, Y., Kong, N., Zeng, J., Ullah, K., Wang, X., Shen, Q., Deng, X., Zhang, J., Delwart, E., Tong, G., Zhang, W. 2022. Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses. Microbiome, 10, 60.

      35. Shi, M., Lin, X. D., Tian, J. H., Chen, L. J., Chen, X., Li, C. X., Qin, X. C., Li, J., Cao, J. P., Eden, J. S., Buchmann, J., Wang, W., Xu, J., Holmes, E. C., Zhang, Y. Z. 2016. Redefining the invertebrate RNA virosphere. Nature, 540, 539-543.

      36. Tian, J., Sun, J., Li, D., Wang, N., Wang, L., Zhang, C., Meng, X., Ji, X., Suchard, M. A., Zhang, X., Lai, A., Su, S., Veit, M. 2022. Emerging viruses: cross-species transmission of coronaviruses, filoviruses, henipaviruses, and rotaviruses from bats. Cell Rep., 39, 110969.

      37. Wang, D., Yang, X., Ren, Z., Hu, B., Zhao, H., Yang, K., Shi, P., Zhang, Z., Feng, Q., Nawenja, C. V., Obanda, V., Robert, K., Nalikka, B., Waruhiu, C. N., Ochola, G. O., Onyuok, S. O., Ochieng, H., Li, B., Zhu, Y., Si, H., Yin, J., Kristiansen, K., Jin, X., Xu, X., Xiao, M., Agwanda, B., Ommeh, S., Li, J., Shi, Z. L. 2024. Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation. Microbiome, 12, 72.

      38. Wang, J., Pan, Y. F., Yang, L. F., Yang, W. H., Lv, K., Luo, C. M., Wang, J., Kuang, G. P., Wu, W. C., Gou, Q. Y., Xin, G. Y., Li, B., Luo, H. L., Chen, S., Shu, Y. L., Guo, D., Gao, Z. H., Liang, G., Li, J., Chen, Y. Q., Holmes, E. C., Feng, Y., Shi, M. 2023. Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential. Nat. Commun., 14, 4079.

      39. Wang, L. F., Anderson, D. E. 2019. Viruses in bats and potential spillover to animals and humans. Curr Opin Virol, 34, 79-89.

      40. Watsa, M. 2020. Rigorous wildlife disease surveillance. Science, 369, 145-147.

      41. Wolfe, N. D., Dunavan, C. P., Diamond, J. 2007. Origins of major human infectious diseases. Nature, 447, 279-283.

      42. Wu, Z., Han, Y., Liu, B., Li, H., Zhu, G., Latinne, A., Dong, J., Sun, L., Su, H., Liu, L., Du, J., Zhou, S., Chen, M., Kritiyakan, A., Jittapalapong, S., Chaisiri, K., Buchy, P., Duong, V., Yang, J., Jiang, J., Xu, X., Zhou, H., Yang, F., Irwin, D. M., Morand, S., Daszak, P., Wang, J., Jin, Q. 2021. Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia. Microbiome, 9, 18.

      43. Wu, Z., Lu, L., Du, J., Yang, L., Ren, X., Liu, B., Jiang, J., Yang, J., Dong, J., Sun, L., Zhu, Y., Li, Y., Zheng, D., Zhang, C., Su, H., Zheng, Y., Zhou, H., Zhu, G., Li, H., Chmura, A., Yang, F., Daszak, P., Wang, J., Liu, Q., Jin, Q. 2018. Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases. Microbiome, 6, 178.

      44. Yan, X., Liu, Y., Hu, T., Huang, Z., Li, C., Guo, L., Liu, Y., Li, N., Zhang, H., Sun, Y., Yi, L., Wu, J., Feng, J., Zhang, F., Jiang, T., Tu, C., He, B. 2025. A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics. Nat. Microbiol., 10, 554-568.

      45. Yang, C. H., Song, A. L., Qiu, Y., Ge, X. Y. 2024. Cross-species transmission and host range genes in poxviruses. Virol. Sin., 39, 177-193.

      46. Zhang, J. T., Hu, Z. Y., Tang, F., Liu, Y. T., Tan, W. L., Ma, X. F., Zhang, Y. F., Si, G. Q., Zhang, L., Zhang, M. Q., Peng, C., Fu, B. K., Fang, L. Q., Zhang, X. A., Liu, W. 2024. Decoding the RNA viromes in shrew lungs along the eastern coast of China. NPJ Biofilms Microbiomes, 10, 68.

      47. Zhang, Y. Z., Shi, M., Holmes, E. C. 2018. Using metagenomics to characterize an expanding virosphere. Cell, 172, 1168-1172.

      48. Zhou, H., Ji, J., Chen, X., Bi, Y., Li, J., Wang, Q., Hu, T., Song, H., Zhao, R., Chen, Y., Cui, M., Zhang, Y., Hughes, A. C., Holmes, E. C., Shi, W. 2021. Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. Cell, 184, 4380-4391.e14.

      49. Zhou, X., Shen, X., Johnson, J. S., Spakowicz, D. J., Agnello, M., Zhou, W., Avina, M., Honkala, A., Chleilat, F., Chen, S. J., Cha, K., Leopold, S., Zhu, C., Chen, L., Lyu, L., Hornburg, D., Wu, S., Zhang, X., Jiang, C., Jiang, L., Jiang, L., Jian, R., Brooks, A. W., Wang, M., Contrepois, K., Gao, P., Rose, S. M. S., Tran, T. D. B., Nguyen, H., Celli, A., Hong, B. Y., Bautista, E. J., Dorsett, Y., Kavathas, P. B., Zhou, Y., Sodergren, E., Weinstock, G. M., Snyder, M. P. 2024. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe, 32, 506-526.e9.

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      Virome diversity in small mammals from south China: Insights into virus evolution, transmission, and ecology

        Corresponding author: Weifeng Shi, shiwf@ioz.ac.cn
        Corresponding author: Guangwen Cao, gcao@smmu.edu.cn
      • a. Department of Epidemiology, Naval Medical University, Shanghai, 200433, China;
      • b. Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai, 200433, China;
      • c. Shanghai Key Laboratory of Medical Bioprotection, Naval Medical University, Shanghai, 200433, China;
      • d. Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, 250117, China;
      • e. School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, 250117, China;
      • f. School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, 250117, China;
      • g. Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China;
      • h. Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
      • Received Date: 04 April 2025
      • Accepted Date: 24 June 2025

      Abstract: Mammals are critical reservoirs of human infectious diseases and the spillover of viruses is related to climate conditions. We conducted meta-transcriptomic sequencing of 226 mammals (bats, rodents, hedgehogs, and shrews) representing 20 species collected across eight cities in south China between 2018 and 2024. Samples included internal organs, oropharyngeal and anal swabs, and feces. We identified 63 vertebrate-associated viruses, including 34 novel viruses. Phylogenetic analysis revealed six viruses with potential infection risks to humans or domestic animals due to their close phylogenetic relationships with known pathogens. Cross-species transmission was observed in 14.3% (9/63) of viruses, shared by at least two host species, with bats, particularly Rhinolophus and Hipposideros, serving as key hubs for viral circulation and zoonotic spillover. Virome composition varied substantially among mammalian species and geographic regions (adonis test, R2 = 0.50, P = 0.001). Generalized linear models quantified the roles of host taxonomy, ecotypes, and meteorological factors in shaping viral diversity, demonstrating host taxonomy (at the order level) as a predominant role (25.70% deviance explained), followed by ecotypes (10.27% deviance explained). Phylogenetic analysis conducted using our betacoronavirus sequences, as well as betacoronavirus sequences derived from 2.0 × 104 bats sampled in China between July 2013 and March 2024, revealed that no betacoronaviruses exhibited closer phylogenetic relationships to SARS-CoV-2 than the known strains (e.g., RaTG13). These findings provide critical insights into virus evolution, transmission, and ecological determinants, which are essential for the prevention of emerging infectious diseases.

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