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Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families
Open accessAbstract
The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families. Notably, our analysis reveals that cross-species transmission is a near universal feature of the viruses analyzed here, with virus-host co-divergence occurring less frequently and always on a subset of viruses. Despite the overall high topological incongruence among virus and host phylogenies, the Hepadnaviridae, Polyomaviridae, Poxviridae, Papillomaviridae and Adenoviridae, all of which possess double-stranded DNA genomes, exhibited more frequent co-divergence than the other virus families studied here. At the other extreme, the virus and host trees for all the RNA viruses studied here, particularly the Rhabdoviridae and the Picornaviridae, displayed high levels of topological incongruence, indicative of frequent host switching. Overall, we show that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species, and that increased sampling will likely reveal more instances of host jumping.
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“Although this may in part be due to the reliance on transcript-based viral detection, RNA viruses are in general characterised by lower host specificity than DNA viruses, reflecting an increased occurrence of cross-species transmission (Geoghegan, Duchêne, and Holmes 2017; Wells et al. 2020).”
From Red fox viromes in urban and rural landscapes (2020) · cites this paper as Geoghegan, Duchêne, and Holmes 2017
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Eliash, N., Suenaga, M., & Mikheyev, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22602613
Additional file 6 of Vector-virus interaction affects viral loads and co-occurrence
Eliash, N., Suenaga, M., & Mikheyev, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22602610
Additional file 5 of Vector-virus interaction affects viral loads and co-occurrence
Eliash, N., Suenaga, M., & Mikheyev, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22602607
Additional file 12 of Vector-virus interaction affects viral loads and co-occurrence
Eliash, N., Suenaga, M., & Mikheyev, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22602628
Additional file 2 of Vector-virus interaction affects viral loads and co-occurrence
Eliash, N., Suenaga, M., & Mikheyev, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22602598
Additional file 1 of Vector-virus interaction affects viral loads and co-occurrence
Eliash, N., Suenaga, M., & Mikheyev, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22602595
Additional file 10 of Vector-virus interaction affects viral loads and co-occurrence
Eliash, N., Suenaga, M., & Mikheyev, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22602622
Additional file 4 of Vector-virus interaction affects viral loads and co-occurrence
Eliash, N., Suenaga, M., & Mikheyev, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22602604
Additional file 9 of Vector-virus interaction affects viral loads and co-occurrence
Eliash, N., Suenaga, M., & Mikheyev, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22602619
Rivarez, M. P. S., Pecman, A., Bačnik, K., Maksimović, O., Vučurović, A., Seljak, G., Mehle, N., Gutiérrez‐Aguirre, I., Ravnikar, M., & Kutnjak, D. (2023) · Figshare · doi:10.6084/m9.figshare.22625548
Additional file 8 of Vector-virus interaction affects viral loads and co-occurrence
Eliash, N., Suenaga, M., & Mikheyev, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22602616
Rivarez, M. P. S., Pecman, A., Bačnik, K., Maksimović, O., Vučurović, A., Seljak, G., Mehle, N., Gutiérrez‐Aguirre, I., Ravnikar, M., & Kutnjak, D. (2023) · Figshare · doi:10.6084/m9.figshare.22625560
Rivarez, M. P. S., Pecman, A., Bačnik, K., Maksimović, O., Vučurović, A., Seljak, G., Mehle, N., Gutiérrez‐Aguirre, I., Ravnikar, M., & Kutnjak, D. (2023) · Figshare · doi:10.6084/m9.figshare.22625542
Additional file 3 of Vector-virus interaction affects viral loads and co-occurrence
Eliash, N., Suenaga, M., & Mikheyev, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22602601
Rivarez, M. P. S., Pecman, A., Bačnik, K., Maksimović, O., Vučurović, A., Seljak, G., Mehle, N., Gutiérrez‐Aguirre, I., Ravnikar, M., & Kutnjak, D. (2023) · Figshare · doi:10.6084/m9.figshare.22625545
Rivarez, M. P. S., Pecman, A., Bačnik, K., Maksimović, O., Vučurović, A., Seljak, G., Mehle, N., Gutiérrez‐Aguirre, I., Ravnikar, M., & Kutnjak, D. (2023) · Figshare · doi:10.6084/m9.figshare.22625563
Additional file 11 of Vector-virus interaction affects viral loads and co-occurrence
Eliash, N., Suenaga, M., & Mikheyev, A. S. (2023) · Figshare · doi:10.6084/m9.figshare.22602625
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Self-citation
Metadata
- Authors
- Geoghegan, J. L., Duchêne, S., & Holmes, E. C.
- Affiliations
- The University of Sydney (AU)
- Corresponding author
- Holmes, Edward C.
- Venue
- PLOS Pathogens
- Publisher
- Public Library of Science (PLoS)
- Published
- 2017-02-08
- Volume
- 13
- Issue
- 2
- Pages
- e1006215
- ISSN
- 1553-7366 (ISSN-L)
- 1553-7374
- PMC
- PMC5319820
- OpenAlex
- W2587475720
- Cited by
- 275
- References
- 48
- Citations by year
- 2026: 15 · 2025: 15 · 2024: 31 · 2023: 43 · 2022: 19 · 2021: 33 · 2020: 28 · 2019: 30 · 2018: 39 · 2017: 22
- FWCI
- 30.56
- Type
- journal article
- Language
- en
- Update notices
- new_version (2017-02-21)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Pathogens (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- National Health and Medical Research Council (GNT1037231)
- Topics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Zoonotic diseases and public health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- interspecies transmission, host switching, cophylogeny, phylogenetic incongruence, viral families, emerging infectious diseases, RNA viruses, DNA viruses, Hepadnaviridae, Polyomaviridae, poxvirus, papillomavirus, Adenoviridae, Rhabdoviridae, picornavirus, host-virus coevolution
- MeSH terms
- Animals, Humans, Phylogeny, Viruses, Zoonoses, Genome, Viral, Evolution, Molecular, Host Specificity
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