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PreprintCited by 1Virology and Viral DiseasesViral Infections and Outbreaks ResearchAnimal Virus Infections Studies

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Spatio-temporal dynamics of Hendra virus in Pteropus bats in Australia reveals high evolutionary diversity linked with spillover

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Munster, Vincent, Yinda, Claude Kwe, Eden, John-Sebastian, Prates, Erica, Vlot, Anna, Anzick, Sarah, Wang, Jianning, Halpin, Kim, Borremans, Benny, Lunn, Tamika, Barbian, Kent, Greene, Ben, Meade-White, Kimberly, Bushmaker, Trenton, Falvo, Caylee, Crowley, Daniel, Jones-Slobodian, Devin, Shah, Manesh, Pavicic, Mirko, Carr, William, Martens, Craig, Jacobson, Daniel, Plowright, Raina, Peel, Alison·2025·Nature Microbiology
DOI 10.21203/rs.3.rs-6263655/v1PMC PMC13056563

Preprint — published as 10.1038/s41564-025-02254-7

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Abstract

Hendra virus (HeV) was first discovered in 1994 in Australia, following an outbreak of respiratory and neurological disease in horses and humans. Limited genomic data on HeV has hindered a comprehensive understanding of HeV’s evolutionary dynamics. We conducted extensive spatiotemporal sampling and whole-genome sequencing of HeV-positive samples from bats and horses and genomic analyses revealed four distinct clades and additional cryptic clades. Each clade extended over a large spatial area, with strains from different clades co-occurring within a single roost on the same day and over multiple consecutive years. This absence of spatiotemporal genotypic structuring suggests that viral shedding events are not driven by the introduction of a single lineage into a susceptible population and then strain evolution through population level immune pressure. These findings provide crucial insights into how bats generate and maintain their extraordinary viral diversity, with direct implications for zoonotic disease emergence and pandemic threats.

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Research works printed but not linked: 57

  1. Wang, J. et al. Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential. Nature Communications 14, 4079 (2023). https://doi.org/10.1038/s41467-023-39835-1 · DOI
  2. Wang, Y. et al. Unveiling bat-borne viruses: a comprehensive classification and analysis of virome evolution. Microbiome 12, 235 (2024). https://doi.org/10.1186/s40168-024-01955-1 · DOI
  3. Olival, K. J. et al. Host and viral traits predict zoonotic spillover from mammals. Nature 546, 646–650 (2017). https://doi.org/10.1038/nature22975 · DOI · Paper page
  4. Irving, A. T., Ahn, M., Goh, G., Anderson, D. E. & Wang, L.-F. Lessons from the host defences of bats, a unique viral reservoir. Nature 589, 363–370 (2021). https://doi.org/10.1038/s41586-020-03128-0 · DOI
  5. Plowright, R. K. et al. Transmission or Within-Host Dynamics Driving Pulses of Zoonotic Viruses in Reservoir–Host Populations. PLOS Neglected Tropical Diseases 10, e0004796 (2016). https://doi.org/10.1371/journal.pntd.0004796 · DOI
  6. Field, H. et al. The natural history of Hendra and Nipah viruses. Microbes and infection 3, 307–314 (2001). · DOI
  7. Field, H. et al. Hendra virus outbreak with novel clinical features, Australia. Emerging Infectious Diseases 16, 338 (2010). · DOI
  8. Playford, E. G. et al. Human Hendra virus encephalitis associated with equine outbreak, Australia, 2008. Emerging Infectious Diseases 16, 219–223 (2010). · DOI
  9. Halpin, K. et al. Pteropid bats are confirmed as the reservoir hosts of henipaviruses: a comprehensive experimental study of virus transmission. Am J Trop Med Hyg 85, 946–951 (2011). https://doi.org/10.4269/ajtmh.2011.10-0567 · DOI
  10. Eaton, B. T., Broder, C. C., Middleton, D. & Wang, L.-F. Hendra and Nipah viruses: different and dangerous. Nature Reviews Microbiology 4, 23–35 (2006). https://doi.org/10.1038/nrmicro1323 · DOI
  11. Kummer, S. & Kranz, D.-C. Henipaviruses—A constant threat to livestock and humans. PLOS Neglected Tropical Diseases 16, e0010157 (2022). https://doi.org/10.1371/journal.pntd.0010157 · DOI
  12. Murray, K. et al. A morbillivirus that caused fatal disease in horses and humans. Science 268, 94–97 (1995). https://doi.org/10.1126/science.7701348 · DOI
  13. Plowright, R. K. et al. Ecological dynamics of emerging bat virus spillover. Proceedings of the royal society B: biological sciences 282, 20142124 (2015).
  14. Eby, P. et al. Pathogen spillover driven by rapid changes in bat ecology. Nature 613, 340–344 (2023). https://doi.org/10.1038/s41586-022-05506-2 · DOI
  15. Taylor, J. et al. Novel variant Hendra virus genotype 2 infection in a horse in the greater Newcastle region, New South Wales, Australia. One Health 15, 100423 (2022). https://doi.org/10.1016/j.onehlt.2022.100423 · DOI
  16. Peel, A. J. et al. Novel Hendra Virus Variant Circulating in Black Flying Foxes and Grey-Headed Flying Foxes, Australia. Emerg Infect Dis 28, 1043–1047 (2022). https://doi.org/10.3201/eid2805.212338 · DOI
  17. Annand, E. J. et al. Novel Hendra Virus Variant Detected by Sentinel Surveillance of Horses in Australia. Emerg Infect Dis 28, 693–704 (2022). https://doi.org/10.3201/eid2803.211245 · DOI
  18. Edson, D. et al. Routes of Hendra virus excretion in naturally-infected flying-foxes: implications for viral transmission and spillover risk. PloS one 10, e0140670 (2015). · DOI
  19. Smith, I. et al. Identifying Hendra virus diversity in pteropid bats. PLoS one 6, e25275 (2011). · DOI
  20. Halpin, K., Young, P. L., Field, H. & Mackenzie, J. Isolation of Hendra virus from pteropid bats: a natural reservoir of Hendra virus. Journal of General Virology 81, 1927–1932 (2000). · DOI
  21. Plowright, R. K. et al. Urban habituation, ecological connectivity and epidemic dampening: the emergence of Hendra virus from flying foxes (Pteropus spp.). Proceedings of the Royal Society B: Biological Sciences 278, 3703–3712 (2011).
  22. Eby, P. Seasonal movements of grey-headed flying-foxes, Pteropus poliocephalus (Chiroptera: Pteropodidae), from two maternity camps in northern New South Wales. Wildlife Research 18, 547–559 (1991). · DOI
  23. Mo, M. et al. Congregations of a threatened species: mitigating impacts from Grey-headed Flying-fox Pteropus poliocephalus camps on the Batemans Bay community. Australian Zoologist 41, 124–138 (2020). https://doi.org/10.7882/az.2020.021 · DOI
  24. Plowright, R. K. et al. Ecological dynamics of emerging bat virus spillover. Proc Biol Sci 282, 20142124 (2015). https://doi.org/10.1098/rspb.2014.2124 · DOI
  25. Eby, P., Plowright, R. K., McCallum, H. & Peel, A. J. Conditions predict heightened Hendra virus spillover risk in horses this winter: actions now can change outcomes. Aust Vet J 98, 270–271 (2020). https://doi.org/10.1111/avj.12964 · DOI
  26. Becker, D. J., Eby, P., Madden, W., Peel, A. J. & Plowright, R. K. Ecological conditions predict the intensity of Hendra virus excretion over space and time from bat reservoir hosts. Ecology Letters 26, 23–36 (2023). https://doi.org/https://doi.org/10.1111/ele.14007 · DOI
  27. Lunn, T. J. et al. Periodic shifts in viral load increase risk of spillover from bats. bioRxiv, 2023.2009.2006.556454 (2023). https://doi.org/10.1101/2023.09.06.556454 · DOI
  28. Burroughs, A. L. et al. Hendra Virus Infection Dynamics in the Grey-Headed Flying Fox (Pteropus poliocephalus) at the Southern-Most Extent of Its Range: Further Evidence This Species Does Not Readily Transmit the Virus to Horses. PLoS One 11, e0155252 (2016). https://doi.org/10.1371/journal.pone.0155252 · DOI
  29. Smith, I. et al. Identifying Hendra virus diversity in pteropid bats. PLoS One 6, e25275 (2011). https://doi.org/10.1371/journal.pone.0025275 · DOI
  30. Grenfell, B. T. et al. Unifying the Epidemiological and Evolutionary Dynamics of Pathogens. Science 303, 327–332 (2004). https://doi.org/doi:10.1126/science.1090727 · DOI
  31. Lo Presti, A. et al. Origin and evolution of Nipah virus. J Med Virol 88, 380–388 (2016). https://doi.org/10.1002/jmv.24345 · DOI
  32. Cortes-Azuero, O. et al. The genetic diversity of Nipah virus across spatial scales. J Infect Dis (2024). https://doi.org/10.1093/infdis/jiae221 · DOI
  33. Streicker, D. G., Fallas González, S. L., Luconi, G., Barrientos, R. G. & Leon, B. Phylodynamics reveals extinction–recolonization dynamics underpin apparently endemic vampire bat rabies in Costa Rica. Proceedings of the Royal Society B: Biological Sciences 286, 20191527 (2019). https://doi.org/doi:10.1098/rspb.2019.1527 · DOI
  34. Hughes, G. J., Orciari, L. A. & Rupprecht, C. E. Evolutionary timescale of rabies virus adaptation to North American bats inferred from the substitution rate of the nucleoprotein gene. Journal of General Virology 86, 1467–1474 (2005). · DOI
  35. Smith, J. S., Orciari, L. A. & Yager, P. A. in Seminars in virology. 387–400 (Elsevier).
  36. Streicker, D. G. et al. Host Phylogeny Constrains Cross-Species Emergence and Establishment of Rabies Virus in Bats. Science 329, 676–679 (2010). https://doi.org/doi:10.1126/science.1188836 · DOI
  37. Velasco-Villa, A. et al. Molecular diversity of rabies viruses associated with bats in Mexico and other countries of the Americas. J Clin Microbiol 44, 1697–1710 (2006). https://doi.org/10.1128/jcm.44.5.1697-1710.2006 · DOI
  38. Holmes, E. C., Woelk, C. H., Kassis, R. & Bourhy, H. Genetic constraints and the adaptive evolution of rabies virus in nature. Virology 292, 247–257 (2002). · DOI
  39. Briese, T. et al. Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis. mBio 6, e01491-01415 (2015). https://doi.org/10.1128/mBio.01491-15 · DOI
  40. Quick, J. et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nature protocols 12, 1261–1276 (2017). https://doi.org/10.1038/nprot.2017.066 · DOI · Paper page
  41. Avanzato, V. A. et al. Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer. Cell 183, 1901–1912 e1909 (2020). https://doi.org/10.1016/j.cell.2020.10.049 · DOI
  42. Yinda, C. K. et al. A Novel Field-Deployable Method for Sequencing and Analyses of Henipavirus Genomes From Complex Samples on the MinION Platform. J Infect Dis 221, S383-s388 (2020). https://doi.org/10.1093/infdis/jiz576 · DOI
  43. Wang, J. et al. A new Hendra virus genotype found in Australian flying foxes. Virology Journal 18, 197 (2021). https://doi.org/10.1186/s12985-021-01652-7 · DOI
  44. Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30, 772–780 (2013). https://doi.org/10.1093/molbev/mst010 · DOI · Paper page
  45. Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 14, 587–589 (2017). https://doi.org/10.1038/nmeth.4285 · DOI · Paper page
  46. Minh, B. Q. et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Molecular Biology and Evolution 37, 1530–1534 (2020). https://doi.org/10.1093/molbev/msaa015 · DOI · Paper page
  47. Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol 35, 518–522 (2018). https://doi.org/10.1093/molbev/msx281 · DOI · Paper page
  48. Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M. & Barton, G. J. Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009). https://doi.org/10.1093/bioinformatics/btp033 · DOI
  49. Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J Mol Graph 14, 33–38, 27–38 (1996). https://doi.org/10.1016/0263-7855(96)00018-5 · DOI · Paper page
  50. Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7, 214 (2007). https://doi.org/10.1186/1471-2148-7-214 · DOI
  51. Shapiro, B., Rambaut, A. & Drummond, A. J. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol 23, 7–9 (2006). https://doi.org/10.1093/molbev/msj021 · DOI
  52. Minin, V. N., Bloomquist, E. W. & Suchard, M. A. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol 25, 1459–1471 (2008). https://doi.org/10.1093/molbev/msn090 · DOI
  53. Weaver, S. et al. Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes. Molecular Biology and Evolution 35, 773–777 (2018). https://doi.org/10.1093/molbev/msx335 · DOI
  54. R: A language and Environment for Statistical computing (R Foundation for Statistical Computing, 2023).
  55. Bowden, T. A. et al. Structural basis of Nipah and Hendra virus attachment to their cell-surface receptor ephrin-B2. Nat Struct Mol Biol 15, 567–572 (2008). https://doi.org/10.1038/nsmb.1435 · DOI
  56. Bowden, T. A., Crispin, M., Harvey, D. J., Jones, E. Y. & Stuart, D. I. Dimeric architecture of the Hendra virus attachment glycoprotein: evidence for a conserved mode of assembly. J Virol 84, 6208–6217 (2010). https://doi.org/10.1128/jvi.00317-10 · DOI
  57. Wang, Z. et al. Potent monoclonal antibody-mediated neutralization of a divergent Hendra virus variant. Proc Natl Acad Sci U S A 119, e2122769119 (2022). https://doi.org/10.1073/pnas.2122769119 · DOI

Metadata

Authors
Munster, V., Yinda, C. K., Eden, J.-S., Prates, E., Vlot, A., Anzick, S., Wang, J., Halpin, K., Borremans, B., Lunn, T., Barbian, K., Greene, B., Meade-White, K., Bushmaker, T., Falvo, C., Crowley, D., Jones-Slobodian, D., Shah, M., Pavicic, M., Carr, W., Martens, C., Jacobson, D., Plowright, R., & Peel, A.
Affiliations
  • National Institutes of Health (US)
  • The University of Sydney (AU)
  • Oak Ridge National Laboratory (US)
  • Commonwealth Scientific and Industrial Research Organisation (AU)
  • Wildlife Health Ecology Research
  • University of Georgia (US)
  • National Institute of Allergy and Infectious Diseases
  • Cornell University (US)
  • Montana state University
  • University of Tennessee at Knoxville (US)
  • City University of New York (US)
  • Griffith University (AU)
Corresponding author
Munster, Vincent
ORCID
Venue
Nature Microbiology
Publisher
Springer Science and Business Media LLC
Published
2025-04-10
Volume
11
Issue
4
Pages
851-866
ISSN
2058-5276 (ISSN-L)
DOI
10.21203/rs.3.rs-6263655/v1
PMC
PMC13056563
OpenAlex
W7151224278
Cited by
1
References
1
Citations by year
2025: 1
FWCI
0.00
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Microbiology (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • Montana State University ScholarWorks (Montana State University) (submittedVersion, cc-by)
Funders
  • National Science Foundation (D18AC00031, DEAC05- 00OR22725, 2133763, 00OR22725, 1716698, 2231624)
  • U.S. Department of Energy (AC05-00OR22725, DE--AC05--00OR22725, DE-AC05?, 00OR22725)
  • U.S. Department of Health and Human Services
  • Montana State University
  • Public Health Agency of Canada
  • University of Tennessee, Knoxville
  • Australian Government
  • Commonwealth Scientific and Industrial Research Organisation
  • Public Health Agency
  • University of Sydney (DE-AC05-00OR22725)
  • Griffith University (DE190100710)
  • Queensland Government
  • National Institutes of Health (DE-AC05-00OR22725)
  • Defense Advanced Research Projects Agency (D18AC00031, DE-AC05-00OR22725)
  • Office of Science (DEAC05- 00OR22725, AC05-00OR22725)
  • College of Veterinary Medicine, Cornell University
  • National Institute of Allergy and Infectious Diseases
  • Oak Ridge National Laboratory (AC05-00OR22725, DE-AC05-00OR22725)
  • NHLBI Division of Intramural Research
Topics
  • Health Sciences › Medicine › Epidemiology › Virology and Viral Diseases
  • Health Sciences › Medicine › Infectious Diseases › Viral Infections and Outbreaks Research
  • Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
Keywords
Hendra virus, viral clades, spatiotemporal dynamics, viral shedding, antigenic variation, viral emergence, zoonotic viruses, bat roosts, viral evolution, countermeasures
MeSH terms
Animals, Australia, Chiroptera, Horse Diseases, Horses, Phylogeny, Genetic Variation, Genome, Viral, Evolution, Molecular, Hendra Virus, Henipavirus Infections, Spatio-Temporal Analysis

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