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A global-scale assessment of zoonotic virus diversity and spillover potential in urban-adapted mammal species

Nature Microbiology (2026)Cite this article

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Abstract

The repeated emergence of pandemic viruses underscores the linkages between land-use change and wildlife disease, and urban-adapted wildlife are of special interest due to their close proximity to humans. However, viral diversity within urban-adapted species and their zoonotic potential remain largely unexplored. Here we compiled a dataset of documented records spanning from 1574 to 2023 on red foxes, raccoons, raccoon dogs, masked palm civets, European hedgehogs, European shrews, wild boars and their viruses, covering 116 countries. These urban-adapted mammals host 286 virus species spanning 24 orders and 38 families, 14 of which are potentially high risk for human infection. Raccoon dogs had increased viral positivity in urban habitats compared to raccoons, wild boars and red foxes. Many viruses in urban-adapted species were phylogenetically related to those found in humans, and our data suggest possible viral spillback. These results highlight zoonotic risks associated with urban-adapted species and suggest enhanced surveillance to mitigate future outbreaks.

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Fig. 1: Workflow for data extraction and curation from the literature.
Fig. 2: Temporal trends and geographic distribution of seven emerging priority urban-adapted mammal species and their associated viruses.
Fig. 3: Overview of viruses harboured by seven urban-adapted mammal species.
Fig. 4: Positivity of viruses in seven urban-adapted mammal species.
Fig. 5: Virus positivity in urban and natural areas within urban-adapted species.
Fig. 6: Phylogenetic trees of ‘human-associated viruses’ in seven urban-adapted mammal species.

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Data availability

The primary dataset is available on GitHub at https://github.com/Viraldata-host/Virus (ref. 80). The sequences of seven urban-adapted mammal species associated viruses analysed in this study are available in GenBank (https://www.ncbi.nlm.nih.gov/nuccore/) under accession numbers shown in Source Data Fig. 6. All animal silhouette images used in Figs. 1, 2, 4, Extended Data Fig. 4 and Supplementary Figs. 4 and 15 were sourced from the public-domain database Phylopic (https://www.phylopic.org/). These images are made available under either the CC0 1.0 Universal Public Domain Dedication or the Public Domain Mark 1.0, which permits unrestricted use, sharing and adaptation. Phylogenetic tree data for Fig. 6 and Extended Data Figs. 1–3 are available in Source Data Fig. 6 and Source Data Extended Data Figs. 1–3. Host–virus associations were compiled from PubMed, China National Knowledge Infrastructure (CNKI), EID2, VIRION and GenBank, with detailed information available in Source Data Fig. 3. Geographic distributions of seven urban-adapted mammal species and associated viruses were compiled from PubMed, CNKI and GBIF (https://www.gbif.org/), with further details provided in Source Data Fig. 2. All source data needed to fully replicate and evaluate the analyses are provided as Source Data Figs. 2–6 and Source Data Extended Data Figs. 1–4. Source data are provided with this paper.

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Acknowledgements

This study was supported by the National Natural Science Foundation of China (32470561, Y.X.; 32271605, Z.Y.X.H.) and Taishan Scholars Project (tsqn202306003, Y.X.). D.J.B. was supported by the National Science Foundation (BII 2213854). The funders had no role in the conceptualization and design of the study, data collection, analysis, decision to publish or preparation of this manuscript.

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Author notes

  1. These authors contributed equally: Xuemin Wei, Hongfeng Li, Zheng Y. X. Huang.

Authors and Affiliations

  1. Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China

    Xuemin Wei  (韦雪敏), Hongfeng Li  (李红凤), Shuo Li  (李硕), Yuhao Wang  (王玉昊), Jie Lan  (兰洁), Li Hu  (胡莉) & Yifei Xu  (许一菲)

  2. Department of Zoology, School of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu, China

    Zheng Y. X. Huang  (黄峥)

  3. CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China

    Yang Li  (李杨) & Fuwen Wei  (魏辅文)

  4. School of Biological Sciences, University of Oklahoma, Norman, OK, USA

    Daniel J. Becker

  5. Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang, Jiangxi, China

    Fuwen Wei  (魏辅文)

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Contributions

Y.X. and F.W. conceptualized the initial hypothesis and conceived and designed the study. X.W., H.L., S.L., Y.W., J.L. and L.H. collected the data and conducted the data analyses. X.W., H.L. and D.J.B. performed the statistical analyses. X.W. and S.L. carried out phylogenetic analyses and interpretation. X.W., S.L. and H.L. created and prepared the figures and tables. Y.X., D.J.B., Z.Y.X.H., X.W. and H.L. wrote the first draft of the manuscript. X.W., H.L., Z.Y.X.H., S.L., Y.W., J.L., L.H., Y.L., D.J.B., F.W. and Y.X. contributed substantially to data acquisition, interpretation, and revision and editing of the manuscript.

Corresponding authors

Correspondence to Daniel J. Becker, Fuwen Wei  (魏辅文) or Yifei Xu  (许一菲).

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Extended data

Extended Data Fig. 1 Phylogenetic tree of SFTSV showing potential bidirectional transmission between urban-adapted wildlife and humans.

The trees were midpoint-rooted, with the scale bar representing the number of nucleotide substitutions per site. Only support values > 80% are shown. Virus names include GenBank accession numbers, host species, sampling location, and sampling year.

Source data

Extended Data Fig. 2 Additional phylogenetic trees illustrating clustering between viruses from urban-adapted species and human viruses.

The trees were midpoint-rooted, with the scale bar representing the number of nucleotide substitutions per site. Only support values > 80% are shown. Virus names include GenBank accession numbers, host species, sampling location, and sampling year.

Source data

Extended Data Fig. 3 Additional phylogenetic trees of viruses from urban-adapted species clustering with human and domestic animal viruses.

The trees were midpoint-rooted, with the scale bar representing the number of nucleotide substitutions per site. Only support values > 80% are shown. Virus names include GenBank accession numbers, host species, sampling location, and sampling year.

Source data

Extended Data Fig. 4 Virus transmission among seven urban-adapted mammal species, domestic animals, and humans.

a) The human-associated virus-sharing network. Node size indicates the number of ‘human-associated viruses’ carried by each urban-adapted species. The edge thickness represents the number of shared viruses between two hosts. b) Boxplot showing the number of shared ‘human-associated viruses’ between each urban-adapted species and domestic animals. The sample size for each group is n = 21. c) Boxplot showing the number of shared viruses between each domestic animal and urban-adapted species. The sample size for each group is n = 7. The lollipop chart displays the eigenvector centrality of each domestic animal species, with circle color representing the eigenvector centrality and the y-axis representing the weighted eigenvector centrality. In b and c, the boxes represent the interquartile range (IQR), which spans from the first to the third quartiles. The lines outside the boxes represent values within 1.5 times the IQR. The horizontal line within each box marks the median, while the rhombus indicates the mean.

Source data

Supplementary information

Source data

41564_2026_2311_MOESM5_ESM.zip (download ZIP )

Source Data Fig. 2 Statistical source data. Source Data Fig. 3 Statistical source data. Source Data Fig. 4 Statistical source data. Source Data Fig. 5 Statistical source data. Source Data Fig. 6 Unprocessed phylogenetic tree. Source Data Extended Data Fig. 1 Unprocessed phylogenetic tree. Source Data Extended Data Fig. 2 Unprocessed phylogenetic tree. Source Data Extended Data Fig. 3 Unprocessed phylogenetic tree. Source Data Extended Data Fig. 4 Statistical source data.

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Wei, X., Li, H., Huang, Z.Y.X. et al. A global-scale assessment of zoonotic virus diversity and spillover potential in urban-adapted mammal species. Nat Microbiol (2026). https://doi.org/10.1038/s41564-026-02311-9

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