• 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.

  • 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.

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

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

  • 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.

  • 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.

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

  • 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.

  • 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.

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

  • 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.

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

  • 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.

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

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

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

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

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

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

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

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

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

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

  • 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.

  • 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.