Citation: Lin Xu, Edward C. Holmes, Weifeng Shi. Hidden diversity of coronaviruses in high-altitude plateau mammals .VIROLOGICA SINICA, 2026, 41(4) : 1002-1005.  http://dx.doi.org/10.1016/j.virs.2026.07.004

Hidden diversity of coronaviruses in high-altitude plateau mammals

  • Corresponding author: Weifeng Shi, shiwf@ioz.ac.cn
  • Received Date: 11 May 2026
    Accepted Date: 10 July 2026
    Available online: 15 July 2026
  • Highlights
    1 Pikas and marmots from plateaus host divergent α- and β-CoVs, including the candidate subgenera Pibecovirus and Mabecovirus.
    2 The plateau CoVs show distinctive genomic features (relocated HE gene, variable ORFs), indicating lineage-specific evolution.
    3 High-altitude plateau ecosystems are a key yet understudied frontier of CoV evolution, warranting systematic surveillance.

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    1. Cui, X., Fan, K., Liang, X., Gong, W., Chen, W., He, B., Chen, X., Wang, H., Wang, X., Zhang, P., Lu, X., Chen, R., Lin, K., Liu, J., Zhai, J., Liu, D.X., Shan, F., Li, Y., Chen, R.A., Meng, H., Li, X., Mi, S., Jiang, J., Zhou, N., Chen, Z., Zou, J.-J., Ge, D., Yang, Q., He, K., Chen, T., Wu, Y.-J., Lu, H., Irwin, D.M., Shen, X., Hu, Y., Lu, X., Ding, C., Guan, Y., Tu, C., Shen, Y., 2023. Virus diversity, wildlife-domestic animal circulation and potential zoonotic viruses of small mammals, pangolins and zoo animals. Nat. Commun., 14, 2488.

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    3. Hu, B., Zeng, L.P., Yang, X.L., Ge, X.Y., Zhang, W., Li, B., Xie, J.Z., Shen, X.R., Zhang, Y.Z., Wang, N., Luo, D.S., Zheng, X.S., Wang, M.N., Daszak, P., Wang, L.F., Cui, J., Shi, Z.L., 2017. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog., 13, e1006698.

    4. Li, X., Wang, L., Liu, P., Li, H., Huo, S., Zong, K., Zhu, S., Guo, Y., Zhang, L., Hu, B., Lan, Y., Chmura, A., Wu, G., Daszak, P., Liu, W.J., Gao, G.F., 2021. A novel potentially recombinant rodent coronavirus with a polybasic cleavage site in the Spike protein. J. Virol., 95, e0117321.

    5. Mao, K.S., Wang, Y., Liu, J.Q., 2021. Evolutionary origin of species diversity on the Qinghai-Tibet Plateau. J. Syst. Evol., 59, 1142-1158.

    6. Smith, A.T., Foggin, J.M., 1999. The plateau pika (Ochotona curzoniae) is a keystone species for biodiversity on the Tibetan plateau. Anim. Conserv., 2, 235-240.

    7. Sarkar, P., Takpa, J., Ahmed, R., Tiwari, S.K., Pendharkar, A., Saleem-Ul-Haq, Miandad, J., Upadhyay, A., Kaul, R., 2008. Mountain Migrants: Survey of Tibetan Antelope and Wild Yak in Ladakh, Jammu & Kashmir, India. 20080707 ed. India.

    8. Wang, W., Lin, X.D., Guo, W.P., Zhou, R.H., Wang, M.R., Wang, C.Q., Ge, S., Mei, S.H., Li, M.H., Shi, M., Holmes, E.C., Zhang, Y.Z., 2015. Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China. Virology, 474, 19-27.

    9. Xu, L., Song, M., Tian, X., Sun, J., Wang, Y., Bie, M., Bi, Y., Holmes, E.C., Guan, Y., Chen, J., Li, J., Shi, W., 2024. Five-year longitudinal surveillance reveals the continual circulation of both alpha- and beta-coronaviruses in Plateau and Gansu pikas (Ochotona spp.) at Qinghai Lake, China. Emerg. Microb. Infect., 13, 2392693.

    10. Yi, L., Liang, Y., Yan, G., Cai, C., Li, Y., Zhao, Z., Qu, Y., Tu, C., He, B., 2025. Virome profiling of long-tailed marmots reveals tissue tropism and cross-species transmission of a diversity of uncharacterized mammalian viruses. Microbiome, 14, 53.

    11. Zeng, Q., Langereis, M.A., Van Vliet, A.L., Huizinga, E.G., De Groot, R.J., 2008. Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution. Proc. Natl. Acad. Sci. U. S. A., 105, 9065-9069.

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

    13. Zhou, H., Pu, J., Liu, J., Wang, Y., Hou, Q., Ma, J., Liu, Y., Wang, W., Lu, S., Ba, J., Qi, T., Yang, J., Luo, X., Xu, J., 2026. Virome diversity, evolution, transmission networks, and zoonotic potential of wildlife on the Qinghai-Tibet plateau. npj Biofilms Microbiomes.

    14. Zhu, W., Yang, J., Lu, S., Jin, D., Wu, S., Pu, J., Luo, X.L., Liu, L., Li, Z., Xu, J., 2021a. Discovery and evolution of a divergent coronavirus in the Plateau pika from China that extends the host range of alphacoronaviruses. Front. Microbiol., 12, 755599.

    15. Zhu, W., Yang, J., Lu, S., Lan, R., Jin, D., Luo, X.L., Pu, J., Wu, S., Xu, J., 2021b. Beta- and novel delta-coronaviruses are identified from wild animals in the Qinghai-Tibetan Plateau, China. Virol. Sin., 36, 402-411.

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    Hidden diversity of coronaviruses in high-altitude plateau mammals

      Corresponding author: Weifeng Shi, shiwf@ioz.ac.cn
    • a. Department of Central Lab, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China;
    • b. School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan 250117, China;
    • c. School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia;
    • d. Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
    • e. Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai 201318, China;
    • f. School of Life Sciences and Biotechnology, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China

    Abstract: Highlights
    1 Pikas and marmots from plateaus host divergent α- and β-CoVs, including the candidate subgenera Pibecovirus and Mabecovirus.
    2 The plateau CoVs show distinctive genomic features (relocated HE gene, variable ORFs), indicating lineage-specific evolution.
    3 High-altitude plateau ecosystems are a key yet understudied frontier of CoV evolution, warranting systematic surveillance.

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