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Species- and variant-specific ACE2 compatibility shapes SARS-CoV-2 spillover potential in North American cervids

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Abstract

Free-ranging white-tailed deer (WTD) are established SARS-CoV-2 reservoirs, but the susceptibility of other cervid species remains unclear. Here we integrate receptor analysis, structural modeling, and field surveillance to assess SARS-CoV-2 susceptibility across North American cervids. We identify species- and variant-specific differences in ACE2–spike compatibility. Elk ACE2 exhibits weak binding to the ancestral strain (Wuhan-Hu-1) and Delta spike receptor-binding domains (RBDs), likely due to a unique K31N substitution. In contrast, it shows stronger binding to Alpha, Beta, Gamma, and Omicron RBDs containing N501Y. Biophysical assays, gel filtration chromatography, and cryo-EM confirm stable complex formation between elk ACE2 and Alpha RBD, but not RBD from the ancestral strain. Despite weak binding, elk ACE2 supports viral entry and replication in vitro. However, surveillance revealed limited evidence of infection in the United States, contrasting with widespread WTD transmissions. These findings demonstrate that ACE2 compatibility alone is insufficient to predict reservoir potential and provide a framework for assessing species susceptibility to emerging coronaviruses.

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Data availability

GeneBank accession numbers of ACE2 and SARS-CoV-2 sequences used in this study are described in Table 1. Affinity constant (KD) data are provided in Supplementary Table S1. The structural coordinates have been deposited in the Protein Data Bank (PDB) under the accession number of 9Q3U68, EMD-72207 (2026).” href=”https://www.nature.com/articles/s41467-026-71623-5#ref-CR69″ id=”ref-link-section-d93409543e595″>69, 9Q3V70, and EMD-72208 (2026).” href=”https://www.nature.com/articles/s41467-026-71623-5#ref-CR71″ id=”ref-link-section-d93409543e604″>71 for XBB1.5 spike:elk ACE2 and XBB1.5 RBD:elk ACE2 complex, respectively. In the case of White-tailed deer SARS-CoV-2 sequences, their associated strain names and GISAID accession number can be found in the Source data file. Additional data supporting the findings of this study are available in the Source Data file. Source data are provided with this paper.

References

  1. Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020).

    Google Scholar 

  2. Oude Munnink, B. B. et al. Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans. Science 371, 172–177 (2021).

    Google Scholar 

  3. Hammer, A. S. et al. SARS-CoV-2 Transmission between Mink (Neovison vison) and Humans, Denmark. Emerg. Infect. Dis. 27, 547–551 (2021).

    Google Scholar 

  4. Shriner, S. A. et al. SARS-CoV-2 Exposure in Escaped Mink, Utah, USA. Emerg. Infect. Dis. 27, 988–990 (2021).

    Google Scholar 

  5. Wang, Y. et al. SARS-CoV-2 exposure in Norwegian rats (Rattus norvegicus) from New York City. bioRxiv, (2022).

  6. Sila, T. et al. Suspected Cat-to-Human Transmission of SARS-CoV-2, Thailand, July-September 2021. Emerg. Infect. Dis. 28, 1485–1488 (2022).

    Google Scholar 

  7. Cui, S. et al. An updated review on SARS-CoV-2 infection in animals. Viruses 14, 1527 (2022).

    Google Scholar 

  8. Wang, Y. et al. SARS-CoV-2 Exposure in Norway Rats (Rattus norvegicus) from New York City. mBio 14, e0362122 (2023).

    Google Scholar 

  9. Shang, J. et al. Cell entry mechanisms of SARS-CoV-2. Proc. Natl. Acad. Sci. USA. 117, 11727–11734 (2020).

    Google Scholar 

  10. Walls, A. C. et al. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell 183, 1735 (2020).

    Google Scholar 

  11. Wang, Q. et al. Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2. Cell 181, 894–904 e899 (2020).

    Google Scholar 

  12. Wan, Y., Shang, J., Graham, R., Baric, R. S. & Li, F. Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus. J. Virol. 94. https://doi.org/10.1128/JVI.00127-20. (2020).

  13. Damas, J. et al. Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates. bioRxiv. https://doi.org/10.1101/2020.04.16.045302. (2020).

  14. Palmer, M. V. et al. Susceptibility of white-tailed deer (Odocoileus virginianus) to SARS-CoV-2. J. Virol. 95. https://doi.org/10.1128/JVI.00083-21. (2021).

  15. Cool, K. et al. Infection and transmission of ancestral SARS-CoV-2 and its alpha variant in pregnant white-tailed deer. bioRxiv. https://doi.org/10.1101/2021.08.15.456341. (2021).

  16. Chandler, J. C. et al. SARS-CoV-2 exposure in wild white-tailed deer (Odocoileus virginianus). Proc. Natl. Acad. Sci. USA. 118. https://doi.org/10.1073/pnas.2114828118. (2021).

  17. Hale, V. L. et al. SARS-CoV-2 infection in free-ranging white-tailed deer. Nature 602, 481–486 (2022).

    Google Scholar 

  18. Feng, A. et al. Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States. Nat. Commun. 14, 4078 (2023).

    Google Scholar 

  19. Cano-Terriza, D. et al. SARS-CoV-2 in Captive Nonhuman Primates, Spain, 2020-2023. Emerg. Infect. Dis. 30, 1253–1257 (2024).

    Google Scholar 

  20. Zhang, Z. et al. The molecular basis for SARS-CoV-2 binding to dog ACE2. Nat. Commun. 12, 4195 (2021).

    Google Scholar 

  21. Wu, L. et al. Broad host range of SARS-CoV-2 and the molecular basis for SARS-CoV-2 binding to cat ACE2. Cell Discov. 6, 68 (2020).

    Google Scholar 

  22. Francisco, R. et al. Experimental Susceptibility of North American Raccoons (Procyon lotor) and Striped Skunks (Mephitis mephitis) to SARS-CoV-2. Front Vet. Sci. 8, 715307 (2021).

    Google Scholar 

  23. Griffin, B. D. et al. SARS-CoV-2 infection and transmission in the North American deer mouse. Nat. Commun. 12, 3612 (2021).

    Google Scholar 

  24. Su, C. et al. Molecular Basis of Mink ACE2 Binding to SARS-CoV-2 and Its Mink-Derived Variants. J. Virol. 96, e0081422 (2022).

    Google Scholar 

  25. Liu, Y. et al. Functional and genetic analysis of viral receptor ACE2 orthologs reveals a broad potential host range of SARS-CoV-2. Proc Natl Acad Sci USA. 118, https://doi.org/10.1073/pnas.2025373118. (2021).

  26. Marques, A. D. et al. Evolution of SARS-CoV-2 in white-tailed deer in Pennsylvania 2021-2024. PLoS Pathog. 21, e1012883 (2025).

    Google Scholar 

  27. Cool, K. et al. Infection and transmission of ancestral SARS-CoV-2 and its alpha variant in pregnant white-tailed deer. Emerg. Microbes Infect. 11, 95–112 (2022).

    Google Scholar 

  28. Feldhamer, G., L. Drickamer, S. Vessey, J. Merritt, C. Krajewski. Mammalogy: Adaptation, Diversity, Ecology. Johns Hopkins University Press (2007).

  29. Kuchipudi, S. V. et al. Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer. Proc Natl Acad Sci USA. 119. https://doi.org/10.1073/pnas.2121644119.(2022)

  30. Porter, S. M. et al. Experimental SARS-CoV-2 Infection of Elk and Mule Deer. Emerg. Infect. Dis. 30, 354–357 (2024).

    Google Scholar 

  31. Boggiatto, P. M. et al. Persistence of viral RNA in North American elk experimentally infected with an ancestral strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Sci. Rep. 14, 11171 (2024).

    Google Scholar 

  32. Shang, J. et al. Structural basis of receptor recognition by SARS-CoV-2. Nature 581, 221–224 (2020).

    Google Scholar 

  33. Isobe, A. et al. ACE2 N-glycosylation modulates interactions with SARS-CoV-2 spike protein in a site-specific manner. Commun. Biol. 5, 1188 (2022).

    Google Scholar 

  34. Zhao, P. et al. Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor. Cell Host Microbe 28, 586–601 e586 (2020).

    Google Scholar 

  35. Allen, J. D., Watanabe, Y., Chawla, H., Newby, M. L. & Crispin, M. Subtle Influence of ACE2 Glycan Processing on SARS-CoV-2 Recognition. J. Mol. Biol. 433, 166762 (2021).

    Google Scholar 

  36. Han, P. et al. Structural basis of white-tailed deer, Odocoileus virginianus, ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity. J. Virol. 97, e0050523 (2023).

    Google Scholar 

  37. Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    Google Scholar 

  38. Tian, F. et al. N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Elife 10, (2021). https://doi.org/10.7554/eLife.69091

  39. Caserta, L. C. et al. White-tailed deer (Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern. Proc. Natl. Acad. Sci. USA. 120, e2215067120 (2023).

    Google Scholar 

  40. Pickering, B. et al. Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission. Nat. Microbiol 7, 2011–2024 (2022).

    Google Scholar 

  41. Marques, A. D. et al. Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania. mBio 13, e0210122 (2022).

    Google Scholar 

  42. Ciuti, S. et al. Effects of humans on behaviour of wildlife exceed those of natural predators in a landscape of fear. PLoS One 7, e50611 (2012).

    Google Scholar 

  43. Janousek, W. M. et al. P.C. Human activities and weather drive contact rates of wintering elk. J. Appl. Ecol. 58, 667–676 (2021).

    Google Scholar 

  44. Purves, K. et al First Eurasian cases of SARS-CoV-2 seropositivity in a free-ranging urban population of wild fallow deer. bioRxiv 2023.07.07.547941 (2023).

  45. Encinas P. et al. G. SARS-CoV-2 neutralizing antibodies in free-ranging Fallow deer (Dama dama) and Red deer (Cervus elaphus) in suburban and rural areas in Spain. Transbound Emerg Dis. https://doi.org/10.1155/2023/3324790. (2023).

  46. Hsueh, F. C. et al. Structural basis for raccoon dog receptor recognition by SARS-CoV-2. PLoS Pathog. 20, e1012204 (2024).

    Google Scholar 

  47. Ou, X. et al. Host susceptibility and structural and immunological insight of S proteins of two SARS-CoV-2 closely related bat coronaviruses. Cell Discov. 9, 78 (2023).

    Google Scholar 

  48. Carossino, M. et al. ACE2 and TMPRSS2 distribution in the respiratory tract of different animal species and its correlation with SARS-CoV-2 tissue tropism. Microbiol Spectr. 12, e0327023 (2024).

    Google Scholar 

  49. Koch, J. et al. TMPRSS2 expression dictates the entry route used by SARS-CoV-2 to infect host cells. EMBO J. 40, e107821 (2021).

    Google Scholar 

  50. Kishimoto, M. et al. TMPRSS11D and TMPRSS13 Activate the SARS-CoV-2 Spike Protein. Viruses 13. https://doi.org/10.3390/v13030384.(2021).

  51. Reed, L. J. & Muench, H. A SIMPLE METHOD OF ESTIMATING FIFTY PER CENT ENDPOINTS. Am. J. Epidemiol. 27, 493–497 (1938).

    Google Scholar 

  52. Schaub, J. M. et al. Expression and characterization of SARS-CoV-2 spike proteins. Nat. Protoc. 16, 5339–5356 (2021).

    Google Scholar 

  53. Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007).

    Google Scholar 

  54. Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).

    Google Scholar 

  55. Kastenhuber, E. R. et al. Coagulation factors directly cleave SARS-CoV-2 spike and enhance viral entry. Elife 11. https://doi.org/10.7554/eLife.77444. (2022).

  56. Murtagh, F. & Legendre, P. Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion? J. Classification 31, 274–295 (2014).

    Google Scholar 

  57. Hunter, J. Matplotlib: a 2dDgraphics environment. Computing in Science & engineering, 9, 90–95 (2007).

  58. Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261–272 (2020).

    Google Scholar 

  59. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    Google Scholar 

  60. Fernandez-Leiro, R. & Scheres, S. H. W. A pipeline approach to single-particle processing in RELION. Acta Crystallogr D. Struct. Biol. 73, 496–502 (2017).

    Google Scholar 

  61. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

    Google Scholar 

  62. Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).

    Google Scholar 

  63. van Heel, M. & Schatz, M. Fourier shell correlation threshold criteria. J. Struct. Biol. 151, 250–262 (2005).

    Google Scholar 

  64. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D. Biol. Crystallogr 66, 213–221 (2010).

    Google Scholar 

  65. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr D. Biol. Crystallogr 60, 2126–2132 (2004).

    Google Scholar 

  66. Pettersen, E. F. et al. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).

    Google Scholar 

  67. Schrodinger, L. A. D., W. PyMOL. http://www.pymol.org/pymol. (2020).

  68. Ye, K., Tao, Y. J. & Wan, X. F. Cryo EM structure of elk ACE2 in complex with SARS-CoV-2 spike trimer. https://doi.org/10.2210/pdb9Q3U/pdb.(2026).

  69. Ye, K., Tao, Y. J. & Wan, X. F. Cryo EM structure of elk ACE2 in complex with SARS-CoV-2 spike trimer. <https://www.ebi.ac.uk/emdb/EMD-72207> (2026).

  70. Ye, K., Tao, Y. J. & Wan, X. F. Cryo EM structure of elk ACE2 in complex with XBB 1.5 spike RBD. https://doi.org/10.2210/pdb9q3v/pdb. (2026).

  71. Ye, K., Tao, Y. J. & Wan, X. F. Cryo EM structure of elk ACE2 in complex with XBB 1.5 spike RBD, <https://www.ebi.ac.uk/emdb/EMD-72208> (2026).

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Acknowledgements

This study was supported by the U.S. Department of Agriculture Animal and Plant Health Inspection Service. K.Y. and Y.J.T. were also partially supported by the Robert A. Welch Foundation (Grant C-1565 to Y.J.T.). We also acknowledge the Arizona Game and Fish Department (AZGFD) for support through PR funding (F24AF02295) and CWD grant (AP23WSNWRC00C091), and the California Department of Fish and Wildlife (CDFW) for their collaboration in elk sample collection. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the U.S. Government.

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Author notes

  1. These authors contributed equally: Constanza Espada, Kai Ye.

Authors and Affiliations

  1. NextGen Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA

    Constanza Espada, Yingyi Long, Kritika Pasai, Riley Wiese, Qiongying Yang, Mingyi Zhou & Xiu-Feng Wan

  2. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA

    Constanza Espada, Yingyi Long, Kritika Pasai, Riley Wiese, Qiongying Yang, Mingyi Zhou & Xiu-Feng Wan

  3. Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA

    Constanza Espada, Yingyi Long, Riley Wiese, Qiongying Yang, Mingyi Zhou & Xiu-Feng Wan

  4. Department of BioSciences, Rice University, Houston, TX, USA

    Kai Ye & Yizhi Jane Tao

  5. Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA

    Kritika Pasai & Xiu-Feng Wan

  6. USDA APHIS Wildlife Services, Fort Collins, CO, USA

    Thomas J. DeLiberto & Jonathon Heale

  7. USDA APHIS Wildlife Services, Wildlife Disease Diagnostic Laboratory, Fort Collins, CO, USA

    Sean Streich & Jeffrey C. Chandler

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  1. Constanza Espada
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Contributions

Conceptualization: X.F.W., J.C.C., T.J.D., and Y.J.T.; Methodology: X.F.W., Y.J.T., C.E., M.Z., K.Y.; Investigation: C.E., K.Y., L.L., K.P., S.B., J.H., R.W., Q.Y., M.Y., Y.J.T., and X.F.W.; Visualization: C.E., K.Y., K.P., Y.J.T., S.S., and X.F.W.; Funding acquisition: X.F.W., J.C.C., Y.J.T.; Project administration: X.F.W., J.C.C., Y.J.T.; Supervision: X.F.W., J.C.C., Y.J.T.; Writing, original draft: X.F.W., C.E., Y.J.T., K.Y.; Writing, review and editing: X.F.W., C.E., K.Y., Y.J.T., J.C.C., S.B., and J.H.

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Yizhi Jane Tao, Jeffrey C. Chandler or Xiu-Feng Wan.

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Espada, C., Ye, K., Long, Y. et al. Species- and variant-specific ACE2 compatibility shapes SARS-CoV-2 spillover potential in North American cervids.
Nat Commun (2026). https://doi.org/10.1038/s41467-026-71623-5

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