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Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families
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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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Cites
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Capella-Gutiérrez, S., Silla-Martinez, J., & Gabaldón, T. (2009) · Bioinform. · doi:10.1093/bioinformatics/btp348 · Cited by 12,052
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
Anisimova, M., & Gascuel, O. (2006) · Systematic Biology · doi:10.1080/10635150600755453 · Cited by 2,693
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2015) · Nature · doi:10.1038/nature15697 · Cited by 1,668
Redefining the invertebrate RNA virosphere
Shī, M., Lin, X., Tian, J.-H., Chen, L., Chen, X., Li, C., Qin, X.-C., Li, J., Cao, J., Eden, J., et al. (2016) · Nature · doi:10.1038/nature20167 · Cited by 1,649
Self-citationAnisimova, M. O., Gil, M., Dufayard, J.-F., Dessimoz, C., & Gascuel, O. (2011) · Systematic Biology · doi:10.1093/sysbio/syr041 · Cited by 1,323
Sanjuán, R., Nebot, M. R., Chirico, N., Mansky, L. M., & Belshaw, R. D. (2010) · Journal of Virology · doi:10.1128/jvi.00694-10 · Cited by 1,313
Keane, T., Creevey, C. J., Pentony, M. M., Naughton, T. J., & Mclnerney, J. O. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-29 · Cited by 1,070
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2016) · Nature · doi:10.1038/nature19417 · Cited by 928 · cited 1×
“In each case the host tree topologies used were the most up-to-date available in the literature [40] [41] [42] [43] [44] .”
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The evolutionary history of vertebrate RNA viruses
Shī, M., Lin, X., Chen, X., Tian, J.-H., Chen, L., Li, K., Wang, W., Eden, J., Shen, J., Liu, L., et al. (2018) · Nature · doi:10.1038/s41586-018-0012-7 · Cited by 763
Self-citationUsing Metagenomics to Characterize an Expanding Virosphere
Zhāng, Y.-Z., Shī, M., & Holmes, E. C. (2018) · Cell · doi:10.1016/j.cell.2018.02.043 · Cited by 359
Self-citationLi, W., Hulswit, R. J. G., Kenney, S. P., Widjaja, I., Jung, K., Alhamo, M. A., van Dieren, B., van Kuppeveld, F. J. M., Saif, L. J., & Bosch, B. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1802879115 · Cited by 308
Predicting virus emergence amid evolutionary noise
Geoghegan, J. L., & Holmes, E. C. (2017) · Open Biology · doi:10.1098/rsob.170189 · Cited by 209
Self-citationEvidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans
Enard, D., & Petrov, D. A. (2018) · Cell · doi:10.1016/j.cell.2018.08.034 · Cited by 208
Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes
Babayan, S. A., Orton, R. J., & Streicker, D. G. (2018) · Science · doi:10.1126/science.aap9072 · Cited by 188
Porcine Deltacoronavirus Infection and Transmission in Poultry, United States1
Boley, P. A., Alhamo, M. A., Lossie, G., Yadav, K. K., Vasquez-Lee, M., Saif, L. J., & Kenney, S. P. (2020) · Emerging infectious diseases · doi:10.3201/eid2602.190346 · Cited by 188
Susceptibility of Chickens to Porcine Deltacoronavirus Infection
Liang, Q., Zhang, H., Li, B., Ding, Q., Wang, Y., Gao, W., Guo, D., Wei, Z., & Hu, H. (2019) · Viruses · doi:10.3390/v11060573 · Cited by 185
Viral and host heterogeneity and their effects on the viral life cycle
Jones, J. E., Sage, V. L., & Lakdawala, S. S. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-00449-9 · Cited by 173
Lauber, C., Seitz, S., Mattei, S., Suh, A., Beck, J., Herstein, J. S., Börold, J., Salzburger, W., Kaderali, L., Briggs, J. A. G., et al. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.07.019 · Cited by 177
The evolution and clinical impact of hepatitis B virus genome diversity
Revill, P. A., Tu, T., Netter, H. J., Yuen, L. K. W., LOCARNINI, S. A., & Littlejohn, M. (2020) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-0296-6 · Cited by 182
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Harvey, E., & Holmes, E. C. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00665-x · Cited by 178
Self-citationBiology, evolution, and medical importance of polyomaviruses: An update
Moens, U. L., Krumbholz, A., Ehlers, B., Zell, R., Johne, R., Calvignac‐Spencer, S., & Lauber, C. (2017) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2017.06.011 · Cited by 161
Expanding the RNA Virosphere by Unbiased Metagenomics
Zhang, Y., Chen, Y., Wang, W., Qin, X.-C., & Holmes, E. C. (2019) · Annual Review of Virology · doi:10.1146/annurev-virology-092818-015851 · Cited by 164
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Viruses as vectors of horizontal transfer of genetic material in eukaryotes
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Shī, M., Zhāng, Y.-Z., & Holmes, E. C. (2017) · Virus Research · doi:10.1016/j.virusres.2017.10.016 · Cited by 134
Self-citationWang, J., Pan, Y., Yang, L., Yang, W., Lv, K., Luo, C., Wang, J., Kuang, G., Wu, W.-C., Gou, Q., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39835-1 · Cited by 119
Self-citationPrioritizing surveillance of Nipah virus in India
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Self-citationVirome heterogeneity and connectivity in waterfowl and shorebird communities
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Ross, Z. P., Klunk, J., Fornaciari, G., Giuffra, V., Duchêne, S., Duggan, A. T., Poinar, D., Douglas, M. W., Eden, J., Holmes, E. C., et al. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1006750 · Cited by 94
Self-citationThe diversity, evolution and origins of vertebrate RNA viruses
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Self-citationVirome composition in marine fish revealed by meta-transcriptomics
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Self-citationBiological species in the viral world
Bobay, L., & Ochman, H. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1717593115 · Cited by 82
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Xu, X., Zhao, H., Gong, Z. H., & Han, G. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1007072 · Cited by 83
Rivarez, M. P. S., Pecman, A., Bačnik, K., Maksimović, O., Vučurović, A., Seljak, G., Mehle, N., Gutiérrez‐Aguirre, I., Ravnikar, M., & Kutnjak, D. (2023) · Microbiome · doi:10.1186/s40168-023-01500-6 · Cited by 83
Azab, W., Dayaram, A., Greenwood, A. D., & Osterrieder, N. (2018) · Annual Review of Virology · doi:10.1146/annurev-virology-092917-043227 · Cited by 80
Leopardi, S., Holmes, E. C., Gastaldelli, M., Tassoni, L., Priori, P., Scaravelli, D., Zamperin, G., & Benedictis, P. D. (2018) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2018.01.012 · Cited by 74
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Shapiro, J. W., & Putonti, C. (2018) · mBio · doi:10.1128/mbio.01870-17 · Cited by 55
Geoghegan, J. L., & Holmes, E. C. (2018) · Genetics · doi:10.1534/genetics.118.301556 · Cited by 59
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Transmissibility of emerging viral zoonoses
Walker, J. W., Han, B. A., Ott, I. M., & Drake, J. M. (2018) · PLoS ONE · doi:10.1371/journal.pone.0206926 · Cited by 51
Zoonotic potential of Newcastle disease virus: Old and novel perspectives related to public health
Ul‐Rahman, A., Ishaq, H. M., Raza, M. A., & Shabbir, M. Z. (2021) · Reviews in Medical Virology · doi:10.1002/rmv.2246 · Cited by 51
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Kong, F., Jia, H., Xiao, Q., Fang, L., & Wang, Q. (2023) · Vaccines · doi:10.3390/vaccines12010011 · Cited by 41
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Ehlers, B., Anoh, E. A., Salem, N. B., Broll, S., Couacy‐Hymann, E., Fischer, D., Gedvilaitė, A., Ingenhütt, N., Liebmann, S., Martín, M., et al. (2019) · Viruses · doi:10.3390/v11100930 · Cited by 37
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Self-citationHurdiss, D. L., Drulyte, I., Lang, Y., Shamorkina, T. M., Pronker, M. F., van Kuppeveld, F. J. M., Snijder, J., & de Groot, R. J. (2020) · Nature Communications · doi:10.1038/s41467-020-18440-6 · Cited by 38
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Zhai, X., Wang, S., Zhu, M., He, W., Pan, Z., & Su, S. (2019) · Pathogens · doi:10.3390/pathogens8030144 · Cited by 33
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Valero, A., & Sanjuán, R. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2215600119 · Cited by 33
Laenen, L., Vergote, V., Kafetzopoulou, L. E., Wawina-Bokalanga, T., Vassou, D., Cook, J. A., Hugot, J.-P., Deboutte, W., Kang, H. J., Witkowski, P. T., et al. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx268 · Cited by 31
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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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