2024

• Sadiq, S., Harvey, E., Mifsud, J., Minasny, B., McBratney, A., Pozza, L., Mahar, J., Holmes, E. (2024). Australian terrestrial environments harbour extensive RNA virus diversity. Virology, 593, 110007. [More Information]
• Dong, X., Qin, J., Nauwynck, H., Holmes, E., Sorgeloos, P., Sui, L., Huang, J., Shi, W., Li, C., Wang, Y., et al (2024). Diversity and connectedness of brine shrimp viruses in global hypersaline ecosystems. Science in China. Series C: Life Sciences, 67(1), 188-203. [More Information]
• Costa, V., Ronco, F., Mifsud, J., Harvey, E., Salzburger, W., Holmes, E. (2024). Host adaptive radiation is associated with rapid virus diversification and cross-species transmission in African cichlid fishes. Current Biology. [More Information]
• Zhou, H., Tian, R., Wang, X., Yang, J., Wang, Y., Zhao, M., Zhang, X., Ma, Y., Lv, L., Holmes, E., et al (2024). Identification of novel mammalian viruses in tree shrews (Tupaia belangeri chinensis). Zoological Research, 45(2), 429-438. [More Information]
• Pan, Y., Zhao, H., Gou, Q., Shi, P., Tian, J., Feng, Y., Li, K., Yang, W., Wu, D., Tang, G., Holmes, E., et al (2024). Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity. Nature Ecology and Evolution, 8(5), 947-959. [More Information]
• Xie, L., Zhao, W., Chen, Y., Hou, W., Sun, Y., Guo, D., Yang, Z., Li, J., Holmes, E., Li, Y., et al (2024). The clinical outcome of COVID-19 is strongly associated with microbiome dynamics in the upper respiratory tract. Journal of Infection, 88(3), 106118. [More Information]
• Waller, S., Tortosa, P., Thurley, T., O’Donnell, C., Jackson, R., Dennis, G., Grimwood, R., Holmes, E., McInnes, K., Geoghegan, J. (2024). Virome analysis of New Zealand’s bats reveals cross-species viral transmission among the Coronaviridae. Virus Evolution, 10(1). [More Information]

2023

• Long, G., Fornaciari, A., Fornaciari, G., Holmes, E., Golding, G., Poinar, H., Hider, J., Duggan, A., Klunk, J., Eaton, K., et al (2023). A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade. PLoS Pathogens, 19(7), e1011538. [More Information]
• Wierenga, J., Morgan, K., Hunter, S., Taylor, H., Argilla, L., Webster, T., Dubrulle, J., Jorge, F., Bostina, M., Burga, L., Holmes, E., et al (2023). A novel gyrovirus is abundant in yellow-eyed penguin (Megadyptes antipodes) chicks with a fatal respiratory disease. Virology, 579, 75-83. [More Information]
• Chen, P., Jin, Z., Peng, L., Zheng, Z., Cheung, Y., Guan, J., Chen, L., Huang, Y., Fan, X., Zhang, Z., Holmes, E., et al (2023). Characterization of an Emergent Chicken H3N8 Influenza Virus in Southern China: a Potential Threat to Public Health. Journal of Virology, 97(6), e0043423. [More Information]
• Harvey, E., Mifsud, J., Holmes, E., Mahar, J. (2023). Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids). Virus Evolution, 9(2). [More Information]
• Eaton, K., Sidhu, R., Klunk, J., Gamble, J., Boldsen, J., Carmichael, A., Varlık, N., Duchene, S., Featherstone, L., Grimes, V., Holmes, E., et al (2023). Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark. Current Biology, 33(6), 1147-1152.e5. [More Information]
• Brito, B., Frost, M., Anantanawat, K., Jaya, F., Batterham, T., Djordjevic, S., Chang, W., Holmes, E., Darling, A., Kirkland, P. (2023). Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics. Microbiome, 11(1). [More Information]
• French, R., Anderson, S., Cain, K., Greene, T., Minor, M., Miskelly, C., Montoya, J., Wille, M., Muller, C., Taylor, M., Holmes, E., et al (2023). Host phylogeny shapes viral transmission networks in an island ecosystem. Nature Ecology and Evolution, 7(11), 1834-1843. [More Information]
• Grimwood, R., Fortune-Kelly, G., Holmes, E., Ingram, T., Geoghegan, J. (2023). Host specificity shapes fish viromes across lakes on an isolated remote island. Virology, 587. [More Information]
• Chen, Y., Hu, S., Lin, X., Tian, J., Lv, J., Wang, M., Luo, X., Pei, Y., Hu, R., Song, Z., Holmes, E., et al (2023). Host traits shape virome composition and virus transmission in wild small mammals. Cell, 186(21), 4662-4675.e12. [More Information]
• Wang, J., Pan, Y., Yang, L., Yang, W., Lv, K., Luo, C., Wang, J., Kuang, G., Wu, W., Gou, Q., Holmes, E., et al (2023). Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential. Nature Communications, 14(1). [More Information]
• Li, C., Liu, S., Zhou, H., Zhu, W., Cui, M., Li, J., Wang, J., Liu, J., Zhu, J., Li, W., Holmes, E., et al (2023). Metatranscriptomic Sequencing Reveals Host Species as an Important Factor Shaping the Mosquito Virome. Microbiology Spectrum, 11(2). [More Information]
• Li, N., Li, C., Hu, T., Li, J., Zhou, H., Ji, J., Wu, J., Kang, W., Holmes, E., Shi, W., et al (2023). Nationwide genomic surveillance reveals the prevalence and evolution of honeybee viruses in China. Microbiome, 11(1). [More Information]
• He, W., Li, D., Baele, G., Zhao, J., Jiang, Z., Ji, X., Veit, M., Suchard, M., Holmes, E., Lemey, P., et al (2023). Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype. Virus Evolution, 9(2). [More Information]
• Petrone, M., Lucas, C., Menasche, B., Breban, M., Yildirim, I., Campbell, M., Omer, S., Holmes, E., Ko, A., Grubaugh, N., et al (2023). Nonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants. Genome Biology and Evolution, 15(4). [More Information]
• Liang, X., Chen, X., Zhai, J., Li, X., Zhang, X., Zhang, Z., Zhang, P., Wang, X., Cui, X., Wang, H., Holmes, E., et al (2023). Pathogenicity, tissue tropism and potential vertical transmission of SARSr-CoV-2 in Malayan pangolins. PLoS Pathogens, 19(5), e1011384. [More Information]
• Eaton, K., Featherstone, L., Duchene, S., Carmichael, A., Varlık, N., Golding, G., Holmes, E., Poinar, H. (2023). Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis. Communications Biology, 6(1). [More Information]
• Giovanetti, M., Vazquez, C., Lima, M., Castro, E., Rojas, A., de la Fuente, A., Aquino, C., Cantero, C., Fleitas, F., Torales, J., Holmes, E., et al (2023). Rapid Epidemic Expansion of Chikungunya Virus East/Central/ South African Lineage, Paraguay. Emerging Infectious Diseases, 29(9), 1859-1863. [More Information]
• Wille, M., Lisovski, S., Roshier, D., Ferenczi, M., Hoye, B., Leen, T., Warner, S., Fouchier, R., Hurt, A., Holmes, E., et al (2023). Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds. Proceedings of the Royal Society B: Biological Sciences, 290(1991). [More Information]
• Ortiz-Baez, A., Jaenson, T., Holmes, E., Pettersson, J., Wilhelmsson, P. (2023). Substantial viral and bacterial diversity at the bat–tick interface. Microbial Genomics, 9(3). [More Information]
• Petrone, M., Holmes, E., Harvey, E. (2023). Through an ecological lens : An ecosystem-based approach to zoonotic risk assessment. EMBO Reports, 24(2). [More Information]
• Wierenga, J., Jorge, F., Bostina, M., Burga, L., Swindells-Wallace, P., Holmes, E., McInnes, K., Morgan, K., Geoghegan, J., Grimwood, R., et al (2023). Total infectome investigation of diphtheritic stomatitis in yellow-eyed penguins (Megadyptes antipodes) reveals a novel and abundant megrivirus. Veterinary Microbiology, 286, 109895. [More Information]
• Mifsud, J., Costa, V., Petrone, M., Marzinelli, E., Holmes, E., Harvey, E. (2023). Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians. Virus Evolution, 9(1). [More Information]
• Wasik, B., Rothschild, E., Voorhees, I., Reedy, S., Murcia, P., Pusterla, N., Chambers, T., Goodman, L., Holmes, E., Kile, J., et al (2023). Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses. Virus Evolution, 9(2). [More Information]
• López-Astacio, R., Adu, O., Goetschius, D., Lee, H., Weichert, W., Wasik, B., Frueh, S., Alford, B., Voorhees, I., Flint, J., Holmes, E., et al (2023). Viral Capsid, Antibody, and Receptor Interactions: Experimental Analysis of the Antibody Escape Evolution of Canine Parvovirus. Journal of Virology, 97(6), e0009023. [More Information]

2022

• Feng, Y., Gou, Q., Yang, W., Wu, W., Wang, J., Holmes, E., Liang, G., Mang, S. (2022). A time-series meta-transcriptomics analysis reveals the seasonal, host, and gender structure of mosquito viromes. Virus Evolution, 8(1), 1-14. [More Information]
• Huang, X., Wu, W., Tian, X., Hou, X., Cui, X., Xiao, Y., Jiao, Q., Zhou, P., Liu, L., Shi, W., Holmes, E., et al (2022). A total infectome approach to understand the etiology of infectious disease in pigs. Microbiome, 10(73). [More Information]
• Duchene, S., Featherstone, L., De Blasio, B., Holmes, E., Bohlin, J., Petterson, J. (2022). Assessment of COVID-19 intervention strategies in the Nordic countries using genomic epidemiology. Open Forum Infectious Diseases, 9(3), 1-6. [More Information]
• Wille, M., Grillo, V., Ban de Gouvea Pedroso, S., Burgess, G., Crawley, A., Dickason, C., Hansbro, P., Ahasanul Hoque, M., Horwood, P., Kirkland, P., Holmes, E., et al (2022). Australia as a global sink for the genetic diversity of avian influenza A virus. PLoS Pathogens, 18(5). [More Information]
• Jia, T., Chang, W., Marcelino, V., Zhao, S., Liu, X., You, Y., Holmes, E., Shi, M., Zhang, C. (2022). Characterization of the Gut Microbiome and Resistomes of Wild and Zoo-Captive Macaques. Frontiers in Veterinary Science, 8, 1-10. [More Information]
• Waller, S., Lamar, S., Perry, B., Grimwood, R., Holmes, E., Geoghegan, J., Geoghegan, J. (2022). Cloacal virome of an ancient host lineage – The tuatara (Sphenodon punctatus) – Reveals abundant and diverse diet-related viruses. Virology, 575, 43-53. [More Information]
• Chen, L., Shen, L., Wu, W., Guan, W., Zhou, J., Luo, G., Chen, Q., Zhou, H., Deng, Z., Chen, Y., Holmes, E., et al (2022). Co-infecting pathogens can contribute to inflammatory responses and severe symptoms in COVID-19. Journal of Thoracic Disease, 14(2), 355-370. [More Information]
• Rockett, R., Draper, J., Gall, M., Sim, E., Arnott, A., Agius, J., Johnson-Mackinnon, J., Fong, W., Martinez, E., Drew, A., Ginn, A., Wang, Q., Holmes, E., O'Sullivan, M., Chen, S., Kok, J., Dwyer, D., Sintchenko, V., et al (2022). Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance. Nature Communications, 13(2745). [More Information]
• Holmes, E. (2022). COVID-19—lessons for zoonotic disease. Science, 375(6585), 1114-1115. [More Information]
• Li, C., Burrell, R., Dale, R., Kesson, A., Blyth, C., Clark, J., Crawford, N., Jones, C., Britton, P., Holmes, E. (2022). Diagnosis and analysis of unexplained cases of childhood encephalitis in Australia using metatranscriptomic sequencing. Journal of General Virology, 103(4). [More Information]
• Kerr, P., Cattadori, I., Sim, D., Liu, J., Holmes, E., Read, A. (2022). Divergent Evolutionary Pathways of Myxoma Virus in Australia: Virulence Phenotypes in Susceptible and Partially Resistant Rabbits Indicate Possible Selection for Transmissibility. Journal of Virology, 96(20), e0088622. [More Information]
• Charon, J., Kahlke, T., Larsson, M., Abbriano, R., Commault, A., Burke, J., Ralph, P., Holmes, E. (2022). Diverse RNA Viruses Associated with Diatom, Eustigmatophyte, Dinoflagellate, and Rhodophyte Microalgae Cultures. Journal of Virology, 96(20), 1-18. [More Information]
• Harvey, E., Holmes, E. (2022). Diversity and evolution of the animal virome. Nature Reviews Microbiology, 20, 321-344. [More Information]
• Sghaier, S., Sailleau, C., Marcacci, M., Thabet, S., Curini, V., Ben Hassine, T., Teodori, L., Portanti, O., Hammami, S., Jurisic, L., Holmes, E., et al (2022). Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021. Viruses, 15(1). [More Information]
• Van Brussel, K., Mahar, J., Ortiz-Baez, A., Carrai, M., Spielman, D., Boardman, W., Baker, M., Beatty, J., Geoghegan, J., Barrs, V., Holmes, E. (2022). Faecal virome of the Australian grey-headed flying fox from urban / suburban environments contains novel coronaviruses, retroviruses and sapoviruses. Virology, 576(Nov22), 42-51. [More Information]
• Costa, V., Geoghegan, J., Holmes, E., Harvey, E. (2022). Genetic Reassortment between Endemic and Introduced Macrobrachium rosenbergii Nodaviruses in the Murray-Darling Basin, Australia. Viruses, 14(2186). [More Information]
• Giovanetti, M., Slavov, S., Fonseca, V., Wilkinson, E., Tegally, H., Patane, J., Viala, V., San, E., Rodrigues, E., Santos, E., Holmes, E., et al (2022). Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil. Nature Microbiology. [More Information]
• French, R., Charon, J., Le Lay, C., Muller, C., Holmes, E. (2022). Human land use impacts viral diversity and abundance in a New Zealand river. Virus Evolution, 8(1). [More Information]
• Zhang, Z., Zhou, H., Cao, H., Ji, J., Zhang, R., Li, W., Guo, H., Chen, L., Ma, C., Cui, M., Holmes, E., et al (2022). Human-to-human transmission of Chlamydia psittaci in China, 2020: an epidemiological and aetiological investigation. The Lancet Microbe, 3(7), e512-e520. [More Information]
• Wang, X., Carrai, M., Van Brussel, K., Feng, S., Beatty, J., Shi, M., Holmes, E., Li, J., Barrs, V. (2022). Low intrahost and interhost genetic diversity of Carnivore protoparvovirus 1 in during a feline panleukopenia outbreak. Viruses, 14(1412). [More Information]
• Ortiz-Baez, A., Holmes, E., Charon, J., Petterson, J., Hesson, J. (2022). Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites. Virus Evolution, 8(2), 1-13. [More Information]
• French, R., Fillion, A., Niebuhr, C., Holmes, E. (2022). Metatranscriptomic comparison of viromes in endemic and introduced passerines in New Zealand. Viruses, 14(7), 1364. [More Information]
• Brian, I., Manuzzi, A., Dalla Rovere, G., Giussani, E., Palumbo, E., Fusaro, A., Bonfante, F., Bortolami, A., Quaranta, E., Quaranta, E., Holmes, E., et al (2022). Molecular Monitoring of SARS-CoV-2 in Different Sewage Plants in Venice and the Implications for Genetic Surveillance. ACS Environmental Science and Technology Water. [More Information]
• French, R., Stone, Z., Parker, K., Holmes, E. (2022). Novel viral and microbial species in a translocated Toutouwai (Petroica longipes) population from Aotearoa/New Zealand. One Health Outlook. [More Information]
• Eden, J., Sikazwe, C., Xie, R., Deng, Y., Sullivan, S., Michie, A., Levy, A., Cutmore, E., Blyth, C., Britton, P., Dwyer, D., Horsburgh, B., Tulloch, R., Holmes, E., et al (2022). Off-season RSV epidemics in Australia after easing of COVID-19 restrictions. Nature Communications, 13(2884). [More Information]
• Charon, J., Buchmann, J., Sadiq, S., Holmes, E. (2022). RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data. Virus Evolution, 8(2). [More Information]
• Sun, Y., Xing, J., Xu, Z., Gao, H., Xu, S., Liu, J., Zhu, D., Guo, Y., Yang, B., Chen, X., Holmes, E., et al (2022). Re-emergence of Severe Acute Diarrhea Syndrome Coronavirus (SADS-CoV) in Guangxi, China, 2021. Journal of Infection, 85, 130-131. [More Information]
• Giovanetti, M., Fonseca, V., Wilkinson, E., Tegally, H., San, E., Althaus, C., Xavier, J., Slavov, S., Viala, V., Lima, A., Holmes, E., et al (2022). Replacement of the Gamma by the Delta variant in Brazil: impact of lineage displacement on the ongoing pandemic. Virus Evolution, 8(1), 1-6. [More Information]
• Sadiq, S., Chen, Y., Zhang, Y., Holmes, E. (2022). Resolving deep evolutionary relationships within the RNA virus phylum Lenarviricota. Virus Evolution, 8(1), 1-9. [More Information]
• Chen, Y., Sadiq, S., Tian, J., Chen, X., Lin, X., Shen, J., Chen, H., Hao, Z., Wille, M., Zhou, Z., Holmes, E., et al (2022). RNA viromes from terrestrial sites across China expand environmental RNA viral diversity. Nature Microbiology, 7. [More Information]
• Wille, M., Lisovski, S., Roshier, D., Ferenczi, M., Hoye, B., Leen, T., Warner, S., Fouchier, R., Hurt, A., Holmes, E., et al (2022). Strong phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds. bioRxiv. [More Information]
• Miot, E., Worthington, B., Ng, K., de Guilhem de Lataillade, L., Pierce, M., Liao, Y., Ko, R., Shum, M., Cheung, W., Holmes, E., et al (2022). Surveillance of Rodent Pests for SARS-CoV-2 and Other Coronaviruses, Hong Kong. Emerging Infectious Diseases, 28(2), 467-470. [More Information]
• Tian, J., Hou, X., Ge, M., Xu, H., Yu, B., Liu, J., Shao, R., Holmes, E., Lei, C., Shi, M. (2022). The diversity and evolutionary relationships of ticks and tick-borne bacteria collected in China. Parasites and Vectors, 15(352), 352. [More Information]
• Holmes, E. (2022). The Ecology of Viral Emergence. Annual Review of Virology, 9(2022), 173-192. [More Information]
• Van Brussel, K., Wang, X., Shi, M., Carrai, M., Li, J., Holmes, E., Beatty, J., Barrs, V. (2022). The enteric virome of cats with feline panleukopenia differs in abundance and diversity from healthy cats. Transboundary and Emerging Diseases, , 1-15. [More Information]
• Worobey, M., Levy, J., Serrano, L., Crits-Christoph, A., Pekar, J., Goldstein, S., Rasmussen, A., Kraemer, M., Newman, C., Koopmans, M., Holmes, E., et al (2022). The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science, (377), 951-959. [More Information]
• Pekar, J., Magee, A., Parker, E., Moshiri, N., Izhikevich, K., Havens, J., Gangavarapu, K., Serrano, L., Crits-Christoph, A., Matteson, N., Holmes, E., et al (2022). The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science, 377(6609), 960-966. [More Information]
• Shi, M., Zhao, S., Yu, B., Wu, W., Hu, Y., Tian, J., Yin, W., Ni, F., Hu, H., Geng, S., Holmes, E., et al (2022). Total infectome characterization of respiratory infections in pre-COVID-19 Wuhan, China. PLoS Pathogens, 18(2), e1010259. [More Information]
• Mifsud, J., Gallagher, R., Holmes, E., Geoghegan, J. (2022). Transcriptome Mining Expands Knowledge of RNA Viruses across the Plant Kingdom. Journal of Virology, 96(24). [More Information]
• Feng, K., Brown, J., Turner, G., Holmes, E., Allison, A. (2022). Unrecognized diversity of mammalian orthoreoviruses in North American bats. Virology, 571, 1-11. [More Information]
• He, W., Hou, X., Zhao, J., Sun, J., He, H., Si, W., Wang, J., Jiang, Z., Yan, Z., Xing, G., Holmes, E., et al (2022). Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell, 185(7), 1117-1129.e8. [More Information]
• Perry, B., Darestani, M., Ara, M., Hoste, A., Jandt, J., Dutoit, L., Holmes, E., Ingram, T., Geoghegan, J. (2022). Viromes of Freshwater Fish with Lacustrine and Diadromous Life Histories Differ in Composition. Viruses, 14(2), 257. [More Information]
• Van Brussel, K., Holmes, E. (2022). Zoonotic disease and virome diversity in bats. Current Opinion in Virology, 52, 192-202. [More Information]

2021

• Neira, V., Brito, B., Aguero, B., Berrios, F., Valdes, V., Gutierrez, A., Ariyama, N., Espinoza, P., Retamal, P., Holmes, E., et al (2021). A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners. Emerging Microbes and Infections, 10(1), 376-383. [More Information]
• Grimwood, R., Holmes, E., Geoghegan, J. (2021). A Novel Rubi-Like Virus in the Pacific Electric Ray (Tetronarce californica) Reveals the Complex Evolutionary History of the Matonaviridae. Viruses, 13(4), 585. [More Information]
• Rambaut, A., Holmes, E., O'Toole, Á., Hill, V., McCrone, J., Ruis, C., du Plessis, L., Pybus, O. (2021). Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 6(3), 415. [More Information]
• Telenti, A., Arvin, A., Corey, L., Corti, D., Diamond, M., Garcia-Sastre, A., Garry, R., Holmes, E., Pang, P., Virgin, H. (2021). After the pandemic: perspectives on the future trajectory of COVID-19. Nature, 596, 495-504. [More Information]
• O'Toole, A., Scher, E., Underwood, A., Jackson, B., Hill, V., McCrone, J., Colquhoun, R., Ruis, C., Abu-Dahab, K., et al, Holmes, E. (2021). Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution, 7(2), 1-9. [More Information]
• Hu, T., Li, J., Zhou, H., Li, C., Holmes, E., Shi, W. (2021). Bioinformatics resources for SARS-CoV-2 discovery and surveillance. Briefings in Bioinformatics, 22(2), 631-641. [More Information]
• Cobbin, J., Charon, J., Harvey, E., Holmes, E., Mahar, J. (2021). Current challenges to virus discovery by meta-transcriptomics. Virology, 51, 48-55. [More Information]
• Di Giallonardo, F., Puglia, I., Curini, V., Cammà, C., Mangone, I., Calistri, P., Cobbin, J., Holmes, E., Lorusso, A. (2021). Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy. Viruses, 13(5), 794. [More Information]
• Gräf, T., Vazquez, C., Giovanetti, M., Fernanda, D., Fonseca, V., Claro, I., de Jesus, J., Xavier, J., de Mendonça, M., Villalba, S., Holmes, E., et al (2021). Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay. Emerging Infectious Diseases, 27(5), 1393-1404. [More Information]
• Saad-Roy, C., Morris, S., Metcalf, C., Mina, M., Baker, R., Farrar, J., Holmes, E., Pybus, O., Graham, A., Levin, S., et al (2021). Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes. Science, 372(6540), 363-370. [More Information]
• Bordicchia, M., Machado Fumian, T., Van Brussel, K., Russo, A., Carrai, M., Le, S., Pesavento, P., Holmes, E., Martella, V., White, P., Beatty, J., Barrs, V., et al (2021). Feline Calicivirus Virulent Systemic Disease: Clinical Epidemiology, Analysis of Viral Isolates and In Vitro Efficacy of Novel Antivirals in Australian Outbreaks. Viruses, 13(10), 2040. [More Information]
• Adelino, T., Giovanetti, M., Fonseca, V., Xavier, J., de Abreu, Á., do Nascimento, V., Demarchi, L., Assunção Oliveira, M., da Silva, V., de Mello, A., Holmes, E., et al (2021). Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil. Nature Communications, 12(1), 2296. [More Information]
• Mahar, J., Jenckel, M., Huang, N., Smertina, E., Holmes, E., Strive, T., Hall, R. (2021). Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses. Virus Evolution, 7(2), 1-14. [More Information]
• Swadi, T., Geoghegan, J., Devine, T., McElnay, C., Sherwood, J., Shoemack, P., Ren, X., Storey, M., Jefferies, S., Smit, E., Holmes, E., et al (2021). Genomic evidence of in-flight transmission of SARS-CoV-2 despite predeparture testing. Emerging Infectious Diseases, 27(3), 687-693. [More Information]
• Benschop, K., Faria, N., Golubchik, T., Holmes, E., Kafetzopoulou, L., et al (2021). Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health, 8 January 2021. Bulletin of the World Health Organization, , 1-94.
• Mitchell, A., Li, C., Oliver, B., Holmes, E., Glanville, A. (2021). High-resolution Metatranscriptomic Characterization of the Pulmonary RNA Virome After Lung Transplantation. Transplantation, 105(12), 2546-2553. [More Information]
• Wille, M., Geoghegan, J., Holmes, E. (2021). How accurately can we assess zoonotic risk? PLoS Biology, 19(4), e3001135. [More Information]
• Zhou, H., Ji, J., Chen, X., Bi, Y., Li, J., Wang, Q., Hu, T., Song, H., Zhao, R., Chen, Y., Holmes, E., et al (2021). Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. Cell, 184, 4380-4391. [More Information]
• Featherstone, L., Di Giallonardo, F., Holmes, E., Vaughan, T., Duchene, S. (2021). Infectious disease phylodynamics with occurrence data. Methods in Ecology and Evolution, 12, 1498-1507. [More Information]
• Chang, W., Rose, K., Holmes, E. (2021). Meta-transcriptomic analysis of the virome and microbiome of the invasive Indian myna (Acridotheres tristis) in Australia. One Health, 13, 100360. [More Information]
• Porter, A., Cobbin, J., Li, C., Eden, J., Holmes, E. (2021). Metagenomic identification of viral sequences in laboratory reagents. Viruses, 13(11), 2122. [More Information]
• Costa, V., Mifsud, J., Gilligan, D., Williamson, J., Holmes, E., Geoghegan, J. (2021). Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray–Darling Basin, Australia. Virus Evolution, 7(1), veab034-1-veab034-15. [More Information]
• Yang, R., Peng, J., Zhai, J., Xiao, K., Zhang, X., Li, X., Chen, X., Chen, Z., Holmes, E., Irwin, D., et al (2021). Pathogenicity and transmissibility of a novel respirovirus isolated from a Malayan pangolin. Journal of General Virology, 102(4), 1586. [More Information]
• Saad-Roy, C., Morris, S., Metcalf, C., Mina, M., Baker, R., Farrar, J., Holmes, E., Pybus, O., Graham, A., Levin, S., et al (2021). Response. Science, 372(6540), 354-355. [More Information]
• Alfsnes, K., Lagerqvist, N., Vene, S., Bohlin, J., Verner-Carlsson, J., Ekqvist, D., Brave, A., Holmes, E., Shi, W., Pettersson, J. (2021). Retrospective meta-transcriptomic identification of severe dengue in a traveller returning from Africa to Sweden, 1990. One Health, 12, 100217. [More Information]
• Chappell, J., Tsoleridis, T., Clark, G., Berry, L., Holmes, N., Moore, C., Carlile, M., Sang, F., Debebe, B., Wright, V., Holmes, E., et al (2021). Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV- 2 in the United Kingdom. Journal of General Virology, 102(6), 1595. [More Information]
• Charon, J., Murray, S., Holmes, E. (2021). Revealing RNA virus diversity and evolution in unicellular algae transcriptomes. Virus Evolution, 7(2), 1-18. [More Information]
• Wille, M., Shi, M., Hurt, A., Klaassen, M., Holmes, E. (2021). RNA virome abundance and diversity is associated with host age in a bird species. Virology, 561, 98-106. [More Information]
• Ortiz-Baez, A., Shi, M., Hoffmann, A., Holmes, E. (2021). RNA virome diversity and Wolbachia infection in individual Drosophila simulans flies. Journal of General Virology, 102(10), 1639. [More Information]
• Di Teodoro, G., Valleriani, F., Puglia, I., Monaco, F., Di Pancrazio, C., Luciani, M., Krasteva, I., Petrini, A., Marcacci, M., D'Alterio, N., Holmes, E., et al (2021). SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Veterinary Microbiology, 252, 108933. [More Information]
• Konings, F., Perkins, M., Kuhn, J., Pallen, M., Alm, E., Archer, B., Barakat, A., Bedford, T., Bhiman, J., Holmes, E., et al (2021). SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse. Nature Microbiology, 6(7), 821-823. [More Information]
• Barnard, K., Wasik, B., Alford, B., Hayward, J., Weichert, W., Voorhees, I., Holmes, E., Parrish, C. (2021). Sequence dynamics of three influenza A virus strains grown in different MDCK cell lines, including those expressing different sialic acid receptors. Journal of Evolutionary Biology, 2021 (34), 1878-1900. [More Information]
• Miller, A., Mifsud, J., Costa, V., Grimwood, R., Kitson, J., Baker, C., Brosnahan, C., Pande, A., Holmes, E., Gemmell, N., et al (2021). Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae. Virus Evolution, 7(2), A1342. [More Information]
• Holmes, E. (2021). The discovery, origins and evolution of SARS-CoV-2 (COVID-19). Journal and Proceedings of the Royal Society of New South Wales, 154(Part 2), 161-181.
• Duchene, S., Featherstone, L., De Blasio, B., Holmes, E., Bohlin, J., Pettersson, J. (2021). The impact of public health interventions in the Nordic countries during the first year of SARS-CoV-2 transmission and evolution. Eurosurveillance, 26(44), 2001996. [More Information]
• Holmes, E., Goldstein, S., Rasmussen, A., Robertson, D., Crits-Christoph, A., Werthiem, J., Anthony, S., Barclay, W., Boni, M., Doherty, P., et al (2021). The origins of SARS-CoV-2: A critical review. Cell, 184(19), 4848-4856. [More Information]
• Zhou, H., Li, C., Hu, T., Liu, T., Ni, N., Chen, W., Zhao, H., Ruan, S., Li, J., Wu, H., Holmes, E., et al (2021). Total infectomes of 162 SARS-CoV-2 cases using meta-transcriptomic sequencing. Journal of Infection, 82(1), e44-e48. [More Information]
• O'Toole, Á., Kraemer, M., Hill, V., Pybus, O., Watts, A., Bogoch, I., Khan, K., Messina, J., Tegally, H., Lessells, R., Holmes, E., et al (2021). Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Research, 6, 121. [More Information]
• Chandra, S., Harvey, E., Emery, D., Holmes, E., Slapeta, J. (2021). Unbiased Characterization of the Microbiome and Virome of Questing Ticks. Frontiers in Microbiology, 12, Article number 627327-1-Article number 627327-15. [More Information]
• Holmes, E., Hurt, A., Dobbie, Z., Clinch, B., Oxford, J., Piedra, P. (2021). Understanding the Impact of Resistance to Influenza Antivirals. Clinical Microbiology Reviews, 34(2), 1-13. [More Information]
• Geoghegan, J., Douglas, J., Ren, X., Storey, M., Hadfield, J., Silander, O., Freed, N., Jelley, L., Jefferies, S., Paine, S., Holmes, E., et al (2021). Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand. Emerging Infectious Diseases, 27(5), 1317-1322. [More Information]
• Wagner, C., Saad-Roy, C., Morris, S., Baker, R., Mina, M., Farrar, J., Holmes, E., Pybus, O., Graham, A., Emanuel, E., et al (2021). Vaccine nationalism and the dynamics and control of SARS-CoV-2. Science, 373(6562), 444-450. [More Information]
• Geoghegan, J., Di Giallonardo, F., Wille, M., Ortiz-Baez, A., Costa, V., Ghaly, T., Mifsud, J., Turnbull, O., Bellwood, D., Williamson, J., Holmes, E. (2021). Virome composition in marine fish revealed by meta-transcriptomics. Virus Evolution, 7(1), veab005. [More Information]

2020

• Ortiz-Baez, A., Eden, J., Moritz, C., Holmes, E. (2020). A Divergent Articulavirus in an Australian Gecko Identified Using Meta-Transcriptomics and Protein Structure Comparisons. Viruses, 12(6), 613. [More Information]
• Rambaut, A., Holmes, E., O'Toole, A., Hill, V., McCrone, J., Ruis, C., du Plessis, L., Pybus, O. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. [More Information]
• Zhang, Y., Holmes, E. (2020). A Genomic Perspective on the Origin and Emergence of SARS-CoV-2. Cell, 181, 223-227. [More Information]
• Wu, F., Zhao, S., Yu, B., Chen, Y., Wang, W., Song, Z., Hu, Y., Tao, Z., Tian, J., Pei, Y., Holmes, E., et al (2020). A new coronavirus associated with human respiratory disease in China. Nature, 579, 1-17. [More Information]
• Zhou, H., Chen, X., Hu, T., Li, J., Song, H., Liu, Y., Wang, P., Liu, D., Yang, J., Holmes, E., et al (2020). A Novel Bat Coronavirus Closely Related to SARSCoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein. Current Biology, 30(11), 2196-2203.e3. [More Information]
• French, R., Holmes, E. (2020). An ecosystems perspective on virus evolution and emergence. Trends in Microbiology, 28(3), 165-175. [More Information]
• Eden, J., Rockett, R., Carter, I., Rahman, H., de Ligt, J., Hadfield, J., Storey, M., Ren, X., Tulloch, R., Basile, K., Sintchenko, V., Chen, S., Sorrell, T., Holmes, E., Dwyer, D., et al (2020). An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evolution, 6(1), veaa027. [More Information]
• Benfield, C., MacKenzie, F., Ritzefeld, M., Mazzon, M., Weston, S., Tate, E., Teo, B., Smith, S., Kellam, P., Holmes, E., et al (2020). Bat IFITM3 restriction depends on S-palmitoylation and a polymorphic site within the CD225 domain. Life Science Alliance, 3(1), 1-18. [More Information]
• Chen, Y., Zheng, Y., Yu, Y., Wang, Y., Huang, Q., Qian, F., Sun, L., Song, Z., Chen, Z., Feng, J., Holmes, E., et al (2020). Blood molecular markers associated with COVID-19 immunopathology and multi-organ damage. EMBO Journal, 39(24), 1-23. [More Information]
• Marcelino, V., Clausen, P., Buchmann, J., Willie, M., Iredell, J., Meyer, W., Lund, O., Sorrell, T., Holmes, E. (2020). CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data. Genome Biology, 21(1), 1-15. [More Information]
• Pettersson, J., Ellstrom, P., Ling, J., Nilsson, I., Bergstrom, S., Gonzalez-Acuna, D., Olsen, B., Holmes, E. (2020). Circumpolar diversification of the Ixodes uriae tick virome. PLoS Pathogens, 16(8), e1008759. [More Information]
• Batovska, J., Buchmann, J., Holmes, E., Lynch, S. (2020). Coding-Complete Genome Sequence of Yada Yada Virus, a Novel Alphavirus Detected in Australian Mosquitoes. Microbiology Resource Announcements, 9(2), e01476-19. [More Information]
• Buchmann, J., Holmes, E. (2020). Collecting and managing taxonomic data with NCBI-taxonomist. Bioinformatics, 36(22-23), 5548-5550. [More Information]
• Mahar, J., Shi, M., Hall, R., Strive, T., Holmes, E. (2020). Comparative Analysis of RNA Virome Composition in Rabbits and Associated Ectoparasites. Journal of Virology, 94(11), e02119-19. [More Information]
• Tsoleridis, T., Chappell, J., Monchatre-Leroy, E., Umhang, G., Shi, M., Bennett, M., Tarlinton, R., McClure, C., Holmes, E., Ball, J. (2020). Discovery and prevalence of divergent RNA viruses in European field voles and rabbits. Viruses, 12(1), 47. [More Information]
• Parry, R., Wille, M., Turnbull, O., Geoghegan, J., Holmes, E. (2020). Divergent Influenza-Like Viruses of Amphibians and Fish Support an Ancient Evolutionary Association. Viruses, 12(9), 1042. [More Information]
• Chen, Y., Holmes, E., Chen, X., Tian, J., Lin, X., Qin, X., Gao, W., Liu, J., Wu, Z., Zhang, Y. (2020). Diverse and abundant transcriptional resistomes in terrestrial and aquatic vertebrates revealed by transcriptional analysis. Scientific Reports, 10(1), 18870. [More Information]
• Guo, J., Lin, X., Chen, Y., Hao, Z., Wang, Z., Yu, Z., Lu, M., Li, K., Qin, X., Wang, W., Holmes, E., et al (2020). Diversity and circulation of Jingmen tick virus in ticks and mammals. Virus Evolution, 6(2), 1-12. [More Information]
• Wang, W., Lin, X., Zhang, H., Wang, M., Guan, X., Holmes, E., Zhang, Y. (2020). Extensive genetic diversity and host range of rodent-borne coronaviruses. Virus Evolution, 6(2), veaa078. [More Information]
• Alfelali, M., Haworth, E., Barasheed, O., Badahdah, A., Bokhary, H., Tashani, M., Azeem, M., Kok, J., Taylor, J., Barnes, E., Khandaker, G., Holmes, E., Dwyer, D., Heron, L., Booy, R., Rashid, H., et al (2020). Facemask against viral respiratory infections among Hajj pilgrims: A challenging cluster-randomized trial. PloS One, 15, 1-20. [More Information]
• Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Holmes, E., et al (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet, 395, 565-574. [More Information]
• Faye, O., de Lourdes Monteiro, M., Vrancken, B., Prot, M., Lequime, S., Diarra, M., Ndiaye, O., Valdez, T., Tavarez, S., Ramos, J., Holmes, E., et al (2020). Genomic Epidemiology of 2015–2016 Zika Virus Outbreak in Cape Verde. Emerging Infectious Diseases, 26(6), 1084-1090. [More Information]
• Di Giallonardo, F., Duchêne, S., Puglia, I., Curini, V., Profeta, F., Cammà, C., Marcacci, M., Calistri, P., Holmes, E., Lorusso, A. (2020). Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy. Viruses, 12(12), 1-11. [More Information]
• Geoghegan, J., Ren, X., Storey, M., Hadfield, J., Jelley, L., Jefferies, S., Sherwood, J., Paine, S., Huang, S., Douglas, J., Holmes, E., et al (2020). Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand. Nature Communications, 11(1), 1-7. [More Information]
• Li, C., Li, W., Zhou, J., Zhang, B., Feng, Y., Xu, C., Lu, Y., Holmes, E., Shi, M. (2020). High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection. Scientific Reports, 10(1), 1-11. [More Information]
• Wille, M., Shi, M., Hurt, A., Klaassen, M., Holmes, E. (2020). Host age shapes virome abundance and diversity in birds. bioRxiv, , 2020.08.23.263103. [More Information]
• Wille, M., Geoghegan, J., Holmes, E. (2020). How accurately can we assess zoonotic risk? bioRxiv, , 2020.08.17.254961. [More Information]
• Tuddenham, R., Eden, J., Gilbey, T., Dwyer, D., Jennings, Z., Holmes, E., Branley, J. (2020). Human pegivirus in brain tissue of a patient with encephalitis. Diagnostic Microbiology and Infectious Disease, 96(2), 1-3. [More Information]
• Carrai, M., Van Brussel, K., Shi, M., Li, C., Chang, W., Munday, J., Voss, K., McLuckie, A., Taylor, D., Laws, A., Holmes, E., Barrs, V., Beatty, J. (2020). Identification of A Novel Papillomavirus Associated with Squamous Cell Carcinoma in A Domestic Cat. Viruses, 12(1), 1-9. [More Information]
• Ling, J., Vinnersten, T., Hesson, J., Bohlin, J., Roligheten, E., Holmes, E., Pettersson, J. (2020). Identification of hepatitis C virus in the common bed bug – a potential, but uncommon route for HCV infection? Emerging Microbes and Infections, 9(1), 1429-1431. [More Information]
• Van Brussel, K., Wang, X., Shi, M., Carrai, M., Li, J., Martella, V., Beatty, J., Holmes, E., Barrs, V. (2020). Identification of Novel Astroviruses in the Gastrointestinal Tract of Domestic Cats. Viruses, 12(11), 1-10. [More Information]
• Lam, T., Jia, N., Shum, M., Zhang, Y., Jiang, J., Zhu, H., Tong, Y., Shi, Y., Ni, X., Liao, Y., Holmes, E., et al (2020). Identifying SARS-CoV-2-related coronaviruses in Malayan pangolin. Nature, 583(7815), 282-285. [More Information]
• Song, Z., Chen, Y., Wu, F., Xu, L., Wang, B., Shi, L., Chen, X., Dai, F., She, J., Chen, J., Holmes, E., et al (2020). Identifying the Risk of SARS-CoV-2 Infection and Environmental Monitoring in Airborne Infectious Isolation Rooms (AIIRs). Virologica Sinica, 35(6), 785-792. [More Information]
• Hayward, J., Tachedjian, M., Khol, C., Johnson, A., Dearnley, M., Jesaveluk, B., Langer, C., Solymosi, P., Hille, G., Nitsche, A., Holmes, E., et al (2020). Infectious KoRV-related retroviruses circulating in Australian bats. Proceedings of the National Academy of Sciences of the United States of America, 117(17), 9529-9536. [More Information]
• Voorhees, I., Lee, H., Allison, A., Lopez-Astacio, R., Goodman, L., Oyesola, O., Omobowale, O., Fagbohun, O., Dubovi, E., Hafenstein, S., Holmes, E., et al (2020). Limited Intrahost Diversity and Background Evolution Accompany 40 Years of Canine Parvovirus Host Adaptation and Spread. Journal of Virology, 94(1), 1-17. [More Information]
• Ortiz-Baez, A., Cousins, K., Eden, J., Chang, W., Harvey, E., Pettersson, J., Carver, S., Polkinghorne, A., Slapeta, J., Rose, K., Holmes, E. (2020). Meta‑transcriptomic identification of Trypanosoma spp. in native wildlife species from Australia. Parasites and Vectors, 13(477), 1-10. [More Information]
• Chang, W., Eden, J., Hall, J., Shi, M., Rose, K., Holmes, E. (2020). Meta-transcriptomic analysis of virus diversity in urban wild birds with paretic disease. Journal of Virology, 94(18), 1-22. [More Information]
• Chang, W., Li, C., Hall, J., Eden, J., Hyndman, T., Holmes, E., Rose, K. (2020). Meta-transcriptomic discovery of a divergent circovirus and a chaphamaparvovirus in captive reptiles with proliferative respiratory syndrome. Viruses, 12(10), 1073. [More Information]
• Turnbull, O., Ortiz-Baez, A., Eden, J., Shi, M., Williamson, J., Gaston, T., Zhang, Y., Holmes, E., Geohegan, J. (2020). Meta-Transcriptomic Identification of Divergent Amnoonviridae in Fish. Viruses, 12(11), 1-10. [More Information]
• Charon, J., Marcelino, V., Wetherbee, R., Verbruggen, H., Holmes, E. (2020). Metatranscriptomic Identification of Diverse and divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. Viruses, 12(1), 29. [More Information]
• Gao, W., Lin, X., Chen, Y., Xie, C., Tan, Z., Zhou, J., Chen, S., Holmes, E., Zhang, Y. (2020). Newly identified viral genomes in pangolins with fatal disease. Virus Evolution, 6(1), 1-10. [More Information]
• Porter, A., Pettersson, J., Chang, W., Harvey, E., Rose, K., Shi, M., Eden, J., Buchmann, J., Moritz, C., Holmes, E. (2020). Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates. Virus Evolution, 6(2), 1-13. [More Information]
• Schlub, T., Holmes, E. (2020). Properties and abundance of overlapping genes in viruses. Virus Evolution, 6(1), 1-8. [More Information]
• Campbell, S., Ashley, W., Gil-Fernandez, M., Newsome, T., Di Giallonardo, F., Ortiz-Baez, A., Mahar, J., Towerton, A., Gillings, M., Holmes, E., et al (2020). Red fox viromes in urban and rural landscapes. Virus Evolution, 6(2), veaa065. [More Information]
• Duggan, A., Holmes, E., Poinar, H. (2020). Response to Brinkmann et al. “Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States”. Genome Biology, 21(1), 287. [More Information]
• Rockett, R., Arnott, A., Lam, C., Sadsad, R., Timms, V., Gray, K., Eden, J., Chang, S., Gall, M., Draper, J., O'Sullivan, M., Chen, S., Sorrell, T., Dwyer, D., Holmes, E., Kok, J., Prokopenko, M., Sintchenko, V., et al (2020). Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nature Medicine, 26(9), 1398-1404. [More Information]
• Wille, M., Harvey, E., Shi, M., Gonzalez-Acuna, D., Holmes, E., Hurt, A. (2020). Sustained RNA virome diversity in Antarctic penguins and their ticks. The ISME Journal, 14(7), 1768-1782. [More Information]
• Wille, M., Holmes, E. (2020). The ecology and evolution of influenza viruses. Cold Spring Harbor Perspectives in Medicine, 10(7), 1-19. [More Information]
• Xavier, J., Giovanetti, M., Adelino, T., Fonseca, V., Barbosa da Costa, A., Ribeiro, A., Felicio, K., Duarte, C., Ferreira Silva, M., Salgado, Á., Holmes, E., et al (2020). The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing. Emerging Microbes and Infections, 9(1), 1824-1834. [More Information]
• Duggan, A., Klunk, J., Porter, A., Dhody, A., Hicks, R., Smith, G., Humphreys, M., McCollum, A., Davidson, W., Wilkins, K., Holmes, E., et al (2020). The origins and genomic diversity of American Civil War Era smallpox vaccine strains. Genome Biology, 21(1), 1-11. [More Information]
• Andersen, K., Rambaut, A., Lipkin, W., Holmes, E., Garry, R. (2020). The proximal origin of SARS-CoV-2. Nature Medicine, 26, 450-455. [More Information]
• Duchene, S., Ho, S., Carmichael, A., Holmes, E., Poinar, H. (2020). The Recovery, Interpretation and Use of Ancient Pathogen Genomes. Current Biology, 30(19), R1215-R1231. [More Information]
• Marcelino, V., Holmes, E., Sorrell, T. (2020). The use of taxon-specific reference databases compromises metagenomic classification. BMC Genomics, 21, 1-5. [More Information]
• Le Lay, C., Shi, M., Bucek, A., Bourguignon, T., Lo, N., Holmes, E. (2020). Unmapped RNA virus diversity in termites and their symbionts. Viruses, 12(10), 1145. [More Information]
• Pollock, D., Castoe, T., Blair, W., Spyros, L., Wade, K., Robertson, D., Robertson, D., Holmes, E., Boni, M., Kosakovsky Pond, S., et al (2020). Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2. Molecular Biology and Evolution, 37(9), 2706-2710. [More Information]
• Grubaugh, N., Petrone, M., Holmes, E. (2020). We shouldn’t worry when a virus mutates during disease outbreaks. Nature Microbiology, 5, 529-530. [More Information]
• Wille, M., Holmes, E. (2020). Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses. FEMS Microbiology Reviews, 44(5), 631-644. [More Information]

2019

• Wei, X., Chen, Y., Duan, G., Holmes, E., Cui, J. (2019). A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses. Virus Evolution, 5(1), 1-5. [More Information]
• Holmes, E., Duchene, S. (2019). Can sequence phylogenies safely infer the origin of the global virome? mBio, 10(2), 1-2. [More Information]
• Shi, W., Ke, C., Fang, S., Li, J., Song, H., Li, X., Hu, T., Wu, J., Chen, T., Lina, Y., Holmes, E., et al (2019). Co-circulation and persistence of multiple A/H3N2 influenza variants in China. Emerging Microbes and Infections, 8(1), 1157-1167. [More Information]
• Bonnaud, E., Troupin, C., Dacheux, L., Holmes, E., Monchatre-Leroy, E., Tanguy, M., Bouchier, C., Cliquet, F., Barrat, J., Bourhy, H. (2019). Comparison of intra- and inter-host genetic diversity in rabies virus during experimental cross-species transmission. PLoS Pathogens, 15(6), 1-19. [More Information]
• Nie, F., Tian, J., Lin, X., Yu, B., Xing, J., Cao, J., Holmes, E., Ma, R., Zhang, Y. (2019). Discovery of a highly divergent hepadnavirus in shrews from China. Virology, 531, 162-170. [More Information]
• Van Brussel, K., Carrai, M., Lin, C., Kelman, M., Setyo, L., Aberdein, D., Brailey, J., Lawler, M., Maher, S., Plaganyi, I., Beatty, J., Holmes, E., Barrs, V., et al (2019). Distinct lineages of feline parvovirus associated with outbreaks in Australia, New Zealand and the United Arab Emirates. Viruses, 11(12), 1-19. [More Information]
• Porter, A., Shi, M., Eden, J., Zhang, Y., Holmes, E. (2019). Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics. Viruses, 11, 1-21. [More Information]
• Buchmann, J., Holmes, E. (2019). Entrezpy: A Python library to dynamically interact with the NCBI Entrez databases. Bioinformatics, 35(21), 4511-4514. [More Information]
• Lu, M., Li, F., Liao, Y., Shen, J., Xu, J., Chen, Y., Li, J., Holmes, E., Zhang, Y. (2019). Epidemiology and Diversity of Rickettsiales Bacteria in Humans and Animals in Jiangsu and Jiangxi provinces, China. Scientific Reports, 9(1), 1-9. [More Information]
• Bucek, A., Sobotnik, J., He, S., Mang, S., McMahon, D., Holmes, E., Roisin, Y., Lo, N., Bourguignon, T. (2019). Evolution of Termite Symbiosis Informed by Transcriptome-Based Phylogenies. Current Biology, 29(21), 3728-3734.e4. [More Information]
• Wang, J., Firth, C., Amos-Ritchie, R., Davis, S., Yin, H., Holmes, E., Blasdell, K., Walker, P. (2019). Evolutionary history of Simbu serogroup orthobunyaviruses in the Australian episystem. Virology, 535, 32-44. [More Information]
• Holmes, E., Duchene, S. (2019). Evolutionary stasis of viruses? Nature Reviews Microbiology, 17(5), 329-329. [More Information]
• Zhang, Y., Chen, Y., Wang, W., Qin, X., Holmes, E. (2019). Expanding the RNA Virosphere by Unbiased Metagenomics. Annual Review of Virology, 6(1), 119-139. [More Information]
• Harvey, E., Rose, K., Eden, J., Lo, N., Abeyasuriya, T., Shi, M., Doggett, S., Holmes, E. (2019). Extensive Diversity of RNA Viruses in Australian Ticks. Journal of Virology, 93(3), 1-15. [More Information]
• Chong, R., Shi, M., Grueber, C., Holmes, E., Hogg, C., Belov, K., Barrs, V. (2019). Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics. Journal of Virology, 93(11), 1-18. [More Information]
• Nelson, M., Lloyd-Smith, J., Simonsen, L., Rambaut, A., Holmes, E., Chowell, G., Miller, M., Spiro, D., Grenfell, B., Viboud, C. (2019). Fogarty International Center collaborative networks in infectious disease modeling: lessons learnt in research and capacity building. Epidemics, 26, 116-127. [More Information]
• Dehhaghi, M., Shariat Panahi, H., Holmes, E., Hudson, B., Schloeffel, R., Guillemin, G. (2019). Human Tick-Borne Diseases in Australia. Frontiers in Cellular and Infection Microbiology, 9, 1-17. [More Information]
• Chen, Y., Wei, X., Zhang, G., Holmes, E., Cui, J. (2019). Identification and evolution of avian endogenous foamy viruses. Virus Evolution, 5(2), 1-6. [More Information]
• Li, C., Chang, W., Mitsakos, K., Rodger, J., Holmes, E., Hudson, B. (2019). Identification of a Novel Equine Papillomavirus in Semen from a Thoroughbred Stallion with a Penile Lesion. Viruses, 11, 1-7. [More Information]
• Harvey, E., Madden, D., Polkinghorne, A., Holmes, E. (2019). Identification of A Novel Picorna-Like Virus, Burpengary Virus, that is Negatively Associated with Chlamydial Disease in the Koala. Viruses, 11(3), 1-9. [More Information]
• Harvey, E., Rose, K., Eden, J., Lawrence, A., Doggett, S., Holmes, E. (2019). Identification of diverse arthropod associated viruses in native Australian fleas. Virology, 535, 189-199. [More Information]
• Wasik, B., Voorhees, I., Barnard, K., Alford-Lawrence, B., Weichert, W., Hood, G., Nogales, A., Martinez-Sobrido, L., Holmes, E., Parrish, C. (2019). Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation. Journal of Virology, 93(23), 1-17. [More Information]
• Novelo, M., Hall, M., Pak, D., Young, P., Holmes, E., McGraw, E. (2019). Intra-host growth kinetics of dengue virus in the mosquito Aedes aegypti. PLoS Pathogens, 15(12), 1-19. [More Information]
• Di Giallonardo, F., Pinto, A., Keen, P., Shaik, A., Carrera, A., Salem, H., Telfer, B., Cooper, C., Price, K., Lee, F., Dwyer, D., Holmes, E., et al (2019). Limited sustained local transmission of HIV-1 CRF01_AE in New South Wales, Australia. Viruses, 11(5), 1-9. [More Information]
• Pettersson, J., Shi, M., Eden, J., Holmes, E., Hesson, J. (2019). Meta-transcriptomic comparison of the RNA Viromes of the mosquito vectors culex pipiens and culex torrentium in Northern Europe. Viruses, 11, 1-20. [More Information]
• Pettersson, J., Piorkowski, G., Mayxay, M., Rattanavong, S., Vongsouvath, M., Davong, V., Alfsnes, K., Eldholm, V., de Lamballerie, X., Holmes, E., et al (2019). Meta-transcriptomic identification of hepatitis B virus in cerebrospinal fluid in patients with central nervous system disease. Diagnostic Microbiology and Infectious Disease, 95(4), 1-4. [More Information]
• Marcelino, V., Wille, M., Hurt, A., Gonzalez-Acuna, D., Klaassen, M., Schlub, T., Eden, J., Shi, M., Iredell, J., Sorrell, T., Holmes, E. (2019). Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes. BMC Biology, 17(1), 1-11. [More Information]
• Marcelino, V., Irinyi, L., Eden, J., Meyer, W., Holmes, E., Sorrell, T. (2019). Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities – a proof of concept under laboratory conditions. IMA Fungus, 10(1), 1-10. [More Information]
• Chang, W., Pettersson, J., Le Lay, C., Shi, M., Lo, N., Wille, M., Eden, J., Holmes, E. (2019). Novel hepatitis D-like agents in vertebrates and invertebrates. Virus Evolution, 5(2), 1-10. [More Information]
• Charon, J., Grigg, M., Eden, J., Piera, K., Rana, H., William, T., Rose, K., Davenport, M., Anstey, N., Holmes, E. (2019). Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease. PLoS Pathogens, 15(12), 1-26. [More Information]
• dos Passos Cunha, M., Duarte-Neto, A., Pour, S., Ortiz-Baez, A., Cerny, J., de Souza Pereira, B., Torres Braconi, C., Ho, Y., Perondi, B., Sztajnbok, J., Holmes, E., et al (2019). Origin of the São Paulo Yellow Fever epidemic of 2017-2018 revealed through molecular epidemiological analysis of fatal cases. Scientific Reports, 9, 1-10. [More Information]
• Kerr, P., Eden, J., Di Giallonardo, F., Peacock, D., Liu, J., Strive, T., Read, A., Holmes, E. (2019). Punctuated Evolution of Myxoma Virus: Rapid and Disjunct Evolution of a Recent Viral Lineage in Australia. Journal of Virology, 93(8), 1-18. [More Information]
• Holmes, E. (2019). Reagent contamination in viromics: all that glitters is not gold. Clinical Microbiology and Infection, 25(10), 1277-1285. [More Information]
• Poon, L., Song, T., Wentworth, D., Holmes, E., Greenbaum, B., Peiris, J., Cowling, B., Ghedin, E. (2019). Reply to ‘Reconciling disparate estimates of viral genetic diversity during human influenza infections’. Nature Genetics, 51(9), 1301-1303. [More Information]
• Tsoleridis, T., Chappell, J., Onianwa, O., Marston, D., Fooks, A., Monchatre-Leroy, E., Umhang, G., Muller, M., Drexler, J., Drosten, C., Holmes, E., et al (2019). Shared Common Ancestry of Rodent Alphacoronaviruses Sampled Globally. Viruses, 11(2), 1-14. [More Information]
• Koh, C., Audsley, M., Di Giallonardo, F., Kerton, E., Young, P., Holmes, E., McGraw, E. (2019). Sustained Wolbachia-mediated blocking of dengue virus isolates following serial passage in Aedes aegypti cell culture. Virus Evolution, 5(1), 1-9. [More Information]
• Mahar, J., Hall, R., Shi, M., Mourant, R., Huang, N., Strive, T., Holmes, E. (2019). The discovery of three new hare lagoviruses reveals unexplored viral diversity in this genus. Virus Evolution, 5(1), 1-11. [More Information]
• Holmes, E. (2019). The future of biosecurity in Australia. Journal and Proceedings of the Royal Society of New South Wales, 152(1), 121-128. [More Information]
• Grubaugh, N., Ladner, J., Lemey, P., Pybus, O., Rambaut, A., Holmes, E., Andersen, K. (2019). Tracking virus outbreaks in the twenty-first century. Nature Microbiology, 4(1), 10-19. [More Information]
• Wille, M., Shi, M., Klaassen, M., Hurt, A., Holmes, E. (2019). Virome heterogeneity and connectivity in waterfowl and shorebird communities. The ISME Journal, 13(10), 2603-2616. [More Information]

2018

• Cobbin, J., Britton, P., Burrell, R., Thosar, D., Selvakumar, K., Eden, J., Jones, C., Holmes, E. (2018). A complex mosaic of enteroviruses shapes community-acquired hand, foot and mouth disease transmission and evolution within a single hospital. Virus Evolution, 4(2), 1-11. [More Information]
• Wille, M., Netter, H., Littlejohn, M., Yuen, L., Shi, M., Eden, J., Klaassen, M., Holmes, E., Hurt, A. (2018). A Divergent Hepatitis D-Like Agent in Birds. Viruses, 10(12), 1-9. [More Information]
• Aghazadeh, M., Shi, M., Barrs, V., McLuckie, A., Lindsay, S., Jameson, B., Hampson, B., Holmes, E., Beatty, J. (2018). A Novel Hepadnavirus Identified in an Immunocompromised Domestic Cat in Australia. Viruses, 10(5), 1-6. [More Information]
• Schlub, T., Buchmann, J., Holmes, E. (2018). A simple method to detect candidate overlapping genes in viruses using single genome sequences. Molecular Biology and Evolution, 35(10), 2572-2581. [More Information]
• Fukuto, H., Vadyvaloo, V., McPhee, J., Poinar, H., Holmes, E., Bliska, J. (2018). A Single Amino Acid Change in the Response Regulator PhoP, Acquired during Yersinia pestis Evolution, Affects PhoP Target Gene Transcription and Polymyxin B Susceptibility. Journal of Bacteriology, 200(9), 1-14. [More Information]
• Roediger, B., Lee, Q., Tikoo, S., Cobbin, J., Henderson, J., Jormakka, M., O'Rourke, M., Padula, M., Pinello, N., Henry, M., Wynne, M., Lisowski, L., Tay, S., Harris, D., Bertolino, P., Wong, J., Gorrell, M., Holmes, E., Jolly, C., Weninger, W., et al (2018). An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis. Cell, 175(2), 530-540. [More Information]
• Di Giallonardo, F., Audsley, M., Shi, M., Young, P., McGraw, E., Holmes, E. (2018). Complete genome of Aedes aegypti anphevirus in the Aag2 mosquito cell line. Journal of General Virology, 99(6), 832-836. [More Information]
• Geoghegan, J., Saavedra, A., Duchene, S., Sullivan, S., Barr, I., Holmes, E. (2018). Continental synchronicity of human influenza virus epidemics despite climactic variation. PLoS Pathogens, 14(1), 1-16. [More Information]
• Mahar, J., Read, A., Gu, X., Urakova, N., Mourant, R., Piper, M., Haboury, S., Holmes, E., Strive, T., Hall, R. (2018). Detection and Circulation of a Novel Rabbit Hemorrhagic Disease Virus in Australia. Emerging Infectious Diseases, 24(1), 22-31. [More Information]
• Edwards, R., Tuipulotu, D., Amos, T., O'Meally, D., Richardson, M., Russell, T., Vallinoto, M., Carneiro, M., Ferrand, N., Wilkins, M., Holmes, E., Shine, R., et al (2018). Draft genome assembly of the invasive cane toad, Rhinella marina. GigaScience, 7(9), 1-13. [More Information]
• Qi, W., Jia, W., Liu, D., Li, J., Bi, Y., Xie, S., Li, B., Hu, T., Du, Y., Eden, J., Holmes, E., et al (2018). Emergence and Adaptation of a Novel Highly Pathogenic H7N9 Influenza Virus in Birds and Humans from a 2013 Human-Infecting Low-Pathogenic Ancestor. Journal of Virology, 92(2), 1-12. [More Information]
• Duchene, S., Holmes, E. (2018). Estimating evolutionary rates in giant viruses using ancient genomes. Virus Evolution, 4(1), 1-4. [More Information]
• Di Giallonardo, F., Kok, J., Fernandez, M., Carter, I., Geoghegan, J., Dwyer, D., Holmes, E., Eden, J. (2018). Evolution of human respiratory syncytial virus (RSV) over multiple seasons in New South Wales, Australia. Viruses, 10(9), 1-13. [More Information]
• Geoghegan, J., Holmes, E. (2018). Evolutionary Virology at 40. Genetics, 210, 1151-1162. [More Information]
• Nie, F., Lin, X., Hao, Z., Chen, X., Wang, Z., Wang, M., Wu, J., Wang, H., Zhao, G., Ma, R., Holmes, E., et al (2018). Extensive diversity and evolution of hepadnaviruses in bats in China. Virology, 514, 88-97. [More Information]
• Geoghegan, J., Di Giallonardo, F., Cousins, K., Shi, M., Williamson, J., Holmes, E. (2018). Hidden diversity and evolution of viruses in market fish. Virus Evolution, 4(2), 1-11. [More Information]
• Leopardi, S., Holmes, E., Gastaldelli, M., Tassoni, L., Priori, P., Scaravelli, D., Zamperin, G., de Benedictis, P. (2018). Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses. Infection, Genetics and Evolution, 58, 279-289. [More Information]
• Panzarin, V., Holmes, E., Abbadi, M., Zamperin, G., Quartesan, R., Milani, A., Schivo, A., Bille, L., Dalla Pozza, M., Monne, I., et al (2018). Low evolutionary rate of infectious pancreatic necrosis virus (IPNV) in Italy is associated with reduced virulence in trout. Virus Evolution, 4(2), 1-11. [More Information]
• Shi, M., Zhang, Y., Holmes, E. (2018). Meta-transcriptomics and the evolutionary biology of RNA viruses. Virus Research, 243, 83-90. [More Information]
• Voorhees, I., Dalziel, B., Glaser, A., Dubovi, E., Murcia, P., Newbury, S., Toohey-Kurth, K., Su, S., Kriti, D., Van Bakel, H., Holmes, E., et al (2018). Multiple Incursions and Recurrent Epidemic Fade-Out of H3N2 Canine Influenza A Virus in the United States. Journal of Virology, 92(16), 1-15. [More Information]
• Shi, M., White, V., Schlub, T., Eden, J., Hoffman, A., Holmes, E. (2018). No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster. Proceedings of the Royal Society B: Biological Sciences, 285(1883), 1-10. [More Information]
• Holmes, E., Rambaut, A., Andersen, K. (2018). Pandemics: spend on surveillance, not prediction. Nature, 558, 180-182. [More Information]
• Mahar, J., Hall, R., Peacock, D., Kovaliski, J., Piper, M., Mourant, R., Huang, N., Campbell, S., Gu, X., Read, A., Holmes, E., et al (2018). Rabbit Hemorrhagic Disease Virus 2 (RHDV2; GI.2) Is Replacing Endemic Strains of RHDV in the Australian Landscape within 18 Months of Its Arrival. Journal of Virology, 92(2), 1-15. [More Information]
• Liu, J., Xu, J., Liu, L., Wei, X., Song, Y., Fang, B., Yu, X., Li, X., Ye, G., Holmes, E., et al (2018). Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China. Scientific Reports, 8(1), 1-6. [More Information]
• Buchmann, J., Fourment, M., Holmes, E. (2018). The Biological Object Notation (BON): A structured file format for biological data. Scientific Reports, 8(1), 1-8. [More Information]
• Zhang, Y., Wu, W., Shi, M., Holmes, E. (2018). The diversity, evolution and origins of vertebrate RNA viruses. Current Opinion in Virology, 31, 9-16. [More Information]
• Shi, M., Lin, X., Chen, X., Tian, J., Chen, L., Li, K., Wang, W., Eden, J., Shen, J., Liu, L., Holmes, E., et al (2018). The evolutionary history of vertebrate RNA viruses. Nature, 556, 197-202. [More Information]
• Rodriguez-Nevado, C., Lam, T., Holmes, E., Pagan, I. (2018). The impact of host genetic diversity on virus evolution and emergence. Ecology Letters, 21(2), 253-263. [More Information]
• Patterson Ross, Z., Klunk, J., Fornaciari, G., Giuffra, V., Duchene, S., Duggan, A., Poinar, D., Douglas, M., Eden, J., Holmes, E., et al (2018). The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathogens, 14(1), 1-25. [More Information]
• Geoghegan, J., Holmes, E. (2018). The phylogenomics of evolving virus virulence. Nature Reviews Genetics, 19(12), 756-769. [More Information]
• Aghazadeh, M., Shi, M., Pesavento, P., Durham, A., Polley, T., Donahoe, S., Troyer, R., Barrs, V., Holmes, E., Beatty, J. (2018). Transcriptome Analysis and In Situ Hybridization for FcaGHV1 in Feline Lymphoma. Viruses, 10(9), 1-7. [More Information]
• Zhang, Y., Shi, M., Holmes, E. (2018). Using Metagenomics to Characterize an Expanding Virosphere. Cell, 172(6), 1168-1172. [More Information]
• Russo, A., Eden, J., Tuipulotu, D., Shi, M., Selechnik, D., Shine, R., Rollins, L., Holmes, E., White, P. (2018). Viral discovery in the invasive Australian cane toad (Rhinella marina) using metatranscriptomic and genomic approaches. Journal of Virology, 92(17), 1-18. [More Information]
• Geoghegan, J., Pirotta, V., Harvey, E., Smith, A., Buchmann, J., Ostrowski, M., Eden, J., Harcourt, R., Holmes, E. (2018). Virological Sampling of Inaccessible Wildlife with Drones. Viruses, 10(300), 1-7. [More Information]
• Wille, M., Eden, J., Shi, M., Klaassen, M., Hurt, A., Holmes, E. (2018). Virus–virus interactions and host ecology are associated with RNA virome structure in wild birds. Molecular Ecology, 27(24), 5263-5278. [More Information]

2017

• Remnant, E., Shi, M., Buchmann, G., Blacquiere, T., Holmes, E., Beekman, M., Ashe, A. (2017). A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations. Journal of Virology, 91(16), e00158-17. [More Information]
• Devault, A., Mortimer, T., Kitchen, A., Kiesewetter, H., Enk, J., Golding, G., Southon, J., Kuch, M., Duggan, A., Aylward, W., Holmes, E., et al (2017). A molecular portrait of maternal sepsis from Byzantine Troy. eLife, 6, 1-31. [More Information]
• Devault, A., Mortimer, T., Kitchen, A., Kiesewetter, H., Enk, J., Golding, G., Southon, J., Kuch, M., Duggan, A., Aylward, W., Holmes, E., et al (2017). A molecular portrait of maternal sepsis from Byzantine troy. eLife, 6. [More Information]
• Simon-Loriere, E., Faye, O., Prot, M., Casademont, I., Fall, G., Fernandez-Garcia, M., Diagne, M., Kipela, J., Fall, I., Holmes, E., et al (2017). Autochthonous Japanese Encephalitis with Yellow Fever Coinfection in Africa. New England Journal of Medicine, 376(15), 1483-1485. [More Information]
• Nicholson, L., Mahar, J., Strive, T., Zheng, T., Holmes, E., Ward, V., Duckworth, J. (2017). Benign Rabbit Calicivirus in New Zealand. Applied and Environmental Microbiology, 83(11), e00090-17. [More Information]
• Holmes, E. (2017). Big Questions in Microbiology: V Is for Virosphere. Cell, 169(5), 770-770. [More Information]
• Pettersson, J., Shi, M., Bohlin, J., Eldholm, V., Brynildsrud, O., Paulsen, K., Andreassen, A., Holmes, E. (2017). Characterizing the virome of Ixodes ricinus ticks from northern Europe. Scientific Reports, 7(1), 1-7. [More Information]
• Porter, A., Duggan, A., Poinar, H., Holmes, E. (2017). Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum. Viruses, 9(10), 1-4. [More Information]
• Geoghegan, J., Duchene, S., Holmes, E. (2017). Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. PLoS Pathogens, 13(2), e1006215. [More Information]
• Di Giallonardo, F., Schlub, T., Shi, M., Holmes, E. (2017). Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species. Journal of Virology, 91(8), 1-15. [More Information]
• Wang, W., Lin, X., Liao, Y., Guan, X., Guo, W., Xing, J., Holmes, E., Zhang, Y. (2017). Discovery of a Highly Divergent Coronavirus in the Asian House Shrew from China Illuminates the Origin of the Alphacoronaviruses. Journal of Virology, 91(17), e00764-17. [More Information]
• Chen, L., Lin, X., Tian, J., Liao, Y., Ying, X., Shao, J., Yu, B., Guo, J., Wang, M., Peng, Y., Shi, M., Holmes, E., et al (2017). Diversity, evolution and population dynamics of avian influenza viruses in the live poultry markets in China. Virology, 505, 33-41. [More Information]
• Faria, N., Quick, J., Claro, I., Theze, J., de Jesus, J., Giovanetti, M., Kraemer, M., Hill, S., Black, A., da Costa, A., Holmes, E., et al (2017). Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature, 546, 406-410. [More Information]
• Hackenbrack, N., Rogers, M., Ashley, R., Keel, M., Kubiski, S., Bryan, J., Ghedin, E., Holmes, E., Hafenstein, S., Allison, A. (2017). Evolution and Cryo-electron Microscopy Capsid Structure of a North American Bat Adenovirus and Its Relationship to Other Mastadenoviruses. Journal of Virology, 91(2), 1-18. [More Information]
• Lin, X., Wang, W., Hao, Z., Wang, Z., Guo, W., Guan, X., Wang, M., Wang, H., Zhou, R., Li, M., Holmes, E., et al (2017). Extensive diversity of coronaviruses in bats from China. Virology, 507, 1-10. [More Information]
• Lu, M., Tian, J., Yu, B., Guo, W., Holmes, E., Zhang, Y. (2017). Extensive diversity of rickettsiales bacteria in ticks from Wuhan, China. Ticks and Tick-borne Diseases, 8(4), 574-580. [More Information]
• Eden, J., Rose, K., Ng, J., Shi, M., Wang, Q., Sintchenko, V., Holmes, E. (2017). Francisella tularensis subsp. holarctica in Ringtail Possums, Australia. Emerging Infectious Diseases, 23(7), 1198-1201. [More Information]
• Kerr, P., Cattadori, I., Rogers, M., Fitch, A., Geber, A., Liu, J., Sim, D., Boag, B., Eden, J., Ghedin, E., Holmes, E., et al (2017). Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia. PLoS Pathogens, 13(3), e1006252. [More Information]
• Shi, M., Neville, P., Nicholson, J., Eden, J., Imrie, A., Holmes, E. (2017). High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia. Journal of Virology, 91(17), e00680-17. [More Information]
• Du, Y., Chen, M., Yang, J., Jia, Y., Han, S., Holmes, E., Cui, J. (2017). Molecular Evolution and Emergence of H5N6 Avian Influenza Virus in Central China. Journal of Virology, 91(12), 1-8. [More Information]
• Cobbin, J., Alfelali, M., Barasheed, O., Taylor, J., Dwyer, D., Kok, J., Booy, R., Holmes, E., Rashid, H. (2017). Multiple Sources of Genetic Diversity of Influenza A Viruses during the Hajj. Journal of Virology, 91(11), 1-18. [More Information]
• Weyrich, L., Duchene, S., Soubrier, J., Arriola, L., Llamas, B., Breen, J., Morris, A., Alt, K., Caramelli, D., Dresely, V., Holmes, E., et al (2017). Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature, 544(7650), 357-361. [More Information]
• Kerr, P., Cattadori, I., Liu, J., Sim, D., Dodds, J., Brooks, J., Kennett, M., Holmes, E., Read, A. (2017). Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype. Proceedings of the National Academy of Sciences of the United States of America, 114(35), 9397-9402. [More Information]
• Dheilly, N., Bolnick, D., Bordenstein, S., Brindley, P., Figueres, C., Holmes, E., Martinez, J., Phillips, A., Poulin, R., Rosario, K. (2017). Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions. msystems, 2(4), 1-4. [More Information]
• Eden, J., Chisholm, R., Bull, R., White, P., Holmes, E., Tanaka, M. (2017). Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants. Virus Evolution, 3(2), vex018. [More Information]
• Chappell, K., Brealey, J., Amarilla, A., Watterson, D., Hulse, L., Palmieri, C., Johnston, S., Holmes, E., Meers, J., Young, P. (2017). Phylogenetic Diversity of Koala Retrovirus within a Wild Koala Population. Journal of Virology, 91(3), e01820-16. [More Information]
• Geoghegan, J., Holmes, E. (2017). Predicting virus emergence amid evolutionary noise. Open Biology, 7(10), 1-9. [More Information]
• Liu, J., Cattadori, I., Sim, D., Eden, J., Holmes, E., Read, A., Kerr, P. (2017). Reverse engineering field isolates of myxoma virus demonstrates that some gene disruptions or losses of function do not explain virulence changes observed in the field. Journal of Virology, 91(20), 1-18. [More Information]
• Voorhees, I., Glaser, A., Toohey-Kurth, K., Newbury, S., Dalziel, B., Dubovi, E., Poulsen, K., Leutenegger, C., Willgert, K., Holmes, E., et al (2017). Spread of Canine Influenza A(H3N2) Virus, United States. Emerging Infectious Diseases, 23(12), 1950-1957. [More Information]
• Tao, Y., Shi, M., Chommanard, C., Queen, K., Markotter, W., Kuzmin, I., Holmes, E., Tong, S. (2017). Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history. Journal of Virology, 91(5), e01953-16. [More Information]
• Fourment, M., Darling, A., Holmes, E. (2017). The impact of migratory flyways on the spread of avian influenza virus in North America. BMC Evolutionary Biology, 17(1). [More Information]
• Dudas, G., Carvalho, L., Bedford, T., Tatem, A., Baele, G., Faria, N., Park, D., Ladner, J., Arias, A., Asogun, D., Holmes, E., et al (2017). Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature, 544(7650), 309-315. [More Information]

2016

• Duggan, A., Perdomo, M., Piombino-Mascali, D., Marciniak, S., Poinar, D., Emery, M., Buchmann, J., Duchene, S., Jankauskas, R., Humphreys, M., Holmes, E., et al (2016). 17th Century Variola Virus Reveals the Recent History of Smallpox. Current Biology, 26(24), 3407-3412. [More Information]
• Huang, C., Liu, W., Xu, W., Jin, T., Zhao, Y., Song, J., Shi, Y., Ji, W., Jia, H., Holmes, E., et al (2016). A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene. PLoS Pathogens, 12(9), 1-25. [More Information]
• Mahar, J., Nicholson, L., Eden, J., Duchene, S., Kerr, P., Duckworth, J., Ward, V., Holmes, E., Strive, T. (2016). Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives. Journal of Virology, 90(20), 9317-9329. [More Information]
• Sabir, J., Lam, T., Ahmed, M., Li, L., Shen, Y., Abo-Aba, S., Qureshi, M., Abu-Zeid, M., Zhang, Y., et al, Holmes, E. (2016). Co-circulation of three camel coronavirus species and recombination of MERS-CoV in Saudi Arabia. Science, 351(6268), 81-84. [More Information]
• Rambaut, A., Dudas, G., de Carvalho, L., Park, D., Yozwiak, N., Holmes, E., Andersen, K. (2016). Comment on "Mutation rate and genotype variation of Ebola virus from Mali case sequences". Science, 353(6300), 658-658. [More Information]
• Feng, K., Sun, M., Iketani, S., Holmes, E., Parrish, C. (2016). Comparing the functions of equine and canine influenza H3N8 virus PA-X proteins: Suppression of reporter gene expression and modulation of global host gene expression. Virology, 496, 138-146. [More Information]
• Holmes, E. (2016). Complexities of Estimating Evolutionary Rates in Viruses. Journal of Virology, 90(4), 2155-2155. [More Information]
• Duchene, S., Duchene, D., Di Giallonardo, F., Eden, J., Geoghegan, J., Holt, K., Ho, S., Holmes, E. (2016). Cross-validation to select Bayesian hierarchical models in phylogenetics. BMC Evolutionary Biology, 16(1), 1-8. [More Information]
• McColl, K., Sunarto, A., Holmes, E. (2016). Cyprinid herpesvirus 3 and its evolutionary future as a biological control agent for carp in Australia. Virology Journal, 13, 1-4. [More Information]
• Dill, J., Camus, A., Leary, J., Di Giallonardo, F., Holmes, E., Ng, T. (2016). Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses. Journal of Virology, 90(17), 7920-7933. [More Information]
• Shi, M., Lin, X., Vasilakis, N., Tian, J., Li, C., Chen, L., Eastwood, G., Diao, X., Chen, M., Chen, X., Holmes, E., et al (2016). Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses. Journal of Virology, 90(2), 659-669. [More Information]
• Chen, L., Lin, X., Guo, W., Tian, J., Wang, W., Ying, X., Wang, M., Yu, B., Yang, Z., Shi, M., Holmes, E., et al (2016). Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China. Journal of General Virology, 97(4), 844-854. [More Information]
• Bos, K., Herbig, A., Sahl, J., Waglechner, N., Fourment, M., Forrest, S., Klunk, J., Schuenemann, V., Poinar, D., Kuch, M., Holmes, E., et al (2016). Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus. eLife, 5, 1-11. [More Information]
• Duchene, S., Geoghegan, J., Holmes, E., Ho, S. (2016). Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods. Bioinformatics, 32(22), 3375-3379. [More Information]
• Guo, W., Tian, J., Lin, X., Ni, X., Chen, X., Liao, Y., Yang, S., Dumler, S., Holmes, E., Zhang, Y. (2016). Extensive genetic diversity of Rickettsiales bacteria in multiple mosquito species. Scientific Reports, 6, 1-11. [More Information]
• Di Giallonardo, F., Geoghegan, J., Docherty, D., McLean, R., Zody, M., Qu, J., Yang, X., Birren, B., Malboeuf, C., Newman, R., Holmes, E., et al (2016). Fluid spatial dynamics of West Nile virus in the USA: rapid spread in a permissive host environment. Journal of Virology, 90(2), 862-872. [More Information]
• Duchene, S., Holt, K., Weill, F., Le Hello, S., Hawkey, J., Edwards, D., Fourment, M., Holmes, E. (2016). Genome-scale rates of evolutionary change in bacteria. Microbial Genomics, 2(11), 1-12. [More Information]
• Lam, T., Zhu, H., Guan, Y., Holmes, E. (2016). Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses. Annual Review of Genomics and Human Genetics, 17, 193-218. [More Information]
• Liu, W., Pickering, P., Duchene, S., Holmes, E., Aaskov, J. (2016). Highly Divergent Dengue Virus Type 2 in Traveler Returning from Borneo to Australia. Emerging Infectious Diseases, 22(12), 2146-2148. [More Information]
• Urbanowicz, R., McClure, C., Sakuntabhai, A., Sall, A., Kobinger, G., Muller, M., Holmes, E., Rey, F., Simon-Loriere, E., Ball, J. (2016). Human Adaptation of Ebola Virus during the West African Outbreak. Cell, 167(4), 1079-1087. [More Information]
• Li, K., Lin, X., Huang, K., Zhang, B., Shi, M., Guo, W., Wang, M., Wang, W., Xing, J., Li, M., Holmes, E., et al (2016). Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans. Virology, 494, 168-177. [More Information]
• Troupin, C., Dacheux, L., Tanguy, M., Sabeta, C., Blanc, H., Bouchier, C., Vignuzzi, M., Duchene, S., Holmes, E., Bourhy, H. (2016). Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts. PLoS Pathogens, 12(12), 1-20. [More Information]
• Tan, Y., Hassan, F., Schuster, J., Simenauer, A., Selvarangan, R., Halpin, R., Lin, X., fedorova, N., Stockwell, T., Lam, T., Holmes, E., et al (2016). Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States. Journal of Virology, 90(4), 1997-2007. [More Information]
• Abaddi, M., Fusaro, A., Ceolin, C., Casarotto, C., Quartesan, R., Dalla Pozza, M., Cattoli, G., Toffan, A., Holmes, E., Panzarin, V. (2016). Molecular Evolutionand Phylogeography of Co-circulating IHNV and VHSV in Italy. Frontiers in Microbiology, 7, 1-13. [More Information]
• Geoghegan, J., Senior, A., Holmes, E. (2016). Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence. Proceedings of the Royal Society B: Biological Sciences, 283(1837), 1-9. [More Information]
• Marciniak, S., Prowse, T., Herring, D., Klunk, J., Kuch, M., Duggan, A., Bondioli, L., Holmes, E., Poinar, H. (2016). Plasmodium falciparum malaria in 1st–2nd century CE southern Italy. Current Biology, 26(23), R1220-R1222. [More Information]
• Poon, L., Song, T., Rosenfeld, R., Lin, X., Rogers, M., Zhou, B., Sebra, R., Halpin, R., Guan, Y., Twaddle, A., Holmes, E., et al (2016). Quantifying influenza virus diversity and transmission in humans. Nature Genetics, 48(2), 195-200. [More Information]
• Shi, M., Lin, X., Tian, J., Chen, L., Chen, X., Li, C., Qin, X., Li, J., Cao, J., Eden, J., Buchmann, J., Holmes, E., et al (2016). Redefining the invertebrate RNA virosphere. Nature, 540(7634), 539-543. [More Information]
• Bourhy, H., Nakoune, E., Hall, M., Nouvellet, P., Lepelletier, A., Talbi, C., Watier, L., Holmes, E., Cauchemez, S., Lemey, P., et al (2016). Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting. PLoS Pathogens, 12(4), 1-15. [More Information]
• Valastro, V., Holmes, E., Britton, P., Fusaro, A., Jackwood, M., Cattoli, G., Monne, I. (2016). S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification. Infection, Genetics and Evolution, 39, 349-364. [More Information]
• Fourment, M., Holmes, E. (2016). Seqotron: A user-friendly sequence editor for Mac OS X. BMC Research Notes, 9(1), 1-4. [More Information]
• Allison, A., Organtini, L., Zhang, S., Hafenstein, S., Holmes, E., Parrish, C. (2016). Single Mutations in the VP2 300 Loop Region of the Three-Fold Spike of the Carnivore Parvovirus Capsid Can Determine Host Range. Journal of Virology, 90(2), 753-767. [More Information]
• Duchene, S., Di Giallonardo, F., Holmes, E. (2016). Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales. Molecular Biology and Evolution, 33(1), 255-267. [More Information]
• Holmes, E., Dudas, G., Rambaut, A., Andersen, K. (2016). The evolution of Ebola virus: Insights from the 2013-2016 epidemic. Nature, 538(7624), 193-200. [More Information]
• Holmes, E. (2016). The Expanding Virosphere. Cell Host and Microbe, 20(3), 279-280. [More Information]
• Geoghegan, J., Senior, A., Di Giallonardo, F., Holmes, E. (2016). Virological factors that increase the transmissibility of emerging human viruses. Proceedings of the National Academy of Sciences of the United States of America, 113(15), 4170-4175. [More Information]

2015

• Wang, M., Barasheed, O., Rashid, H., Booy, R., El Bashir, H., Haworth, E., Ridda, I., Holmes, E., Dwyer, D., Nguyen Van Tam, J., et al (2015). A cluster-randomised controlled trial to test the efficacy of facemasks in preventing respiratory viral infection among Hajj pilgrims. Journal of Epidemiology and Global Health, 5, 181-189. [More Information]
• Tan, L., Tuyen, N., Thanh, T., Ngan, T., Van, H., Sabanathan, S., Van, T., Thanh, L., Nguyet, L., Geoghegan, J., Holmes, E., et al (2015). A generic assay for whole-genome amplification and deep sequencingof enterovirus A71. Journal of Virological Methods, 215-216, 30-36. [More Information]
• Lambrechts, L., Ferguson, N., Harris, E., Holmes, E., McGraw, E., O'Neill, S., Ooi, E., Ritchie, S., Ryan, P., Scott, T., et al (2015). Assessing the epidemiological effect of wolbachia for dengue control. The Lancet Infectious Diseases, 15(7), 862-866. [More Information]
• Fourment, M., Holmes, E. (2015). Avian influenza virus exhibits distinct evolutionary dynamics in wild birds and poultry. BMC Evolutionary Biology, 15(1), 1-6. [More Information]
• Buchmann, J., Holmes, E. (2015). Cell Walls and the Convergent Evolution of the Viral Envelope. Microbiology and Molecular Biology Reviews, 79(4), 403-418. [More Information]
• Eden, J., Kovaliski, J., Duckworth, J., Swain, G., Maher, J., Strive, T., Holmes, E. (2015). Comparative phylodynamics of rabbit hemorrhagic disease virus in Australia and New Zealand. Journal of Virology, 89(18), 9548-9558. [More Information]
• Allison, A., Ballard, J., Tesh, R., Brown, J., Rudder, M., Keel, M., Munk, B., Mickley, R., Gibbs, S., Travassos Da Rosa, A., Holmes, E., et al (2015). Cyclic avian mass mortality in the northeastern United States is associated with a novel orthomyxovirus. Journal of Virology, 89(2), 1389-1403. [More Information]
• Duchene, S., Ho, S., Holmes, E. (2015). Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models. BMC Evolutionary Biology, 15(1), 1-10. [More Information]
• Katzelnick, L., Fonville, J., Gromowski, G., Arriaga, J., Green, A., James, S., Lau, L., Montoya, M., Wang, C., VanBlargan, L., Holmes, E., et al (2015). Dengue viruses cluster antigenically but not as discrete serotypes. Science, 349(6254), 1338-1343. [More Information]
• Wang, W., Lin, X., Guo, W., Zhou, R., Wang, M., Wang, C., Ge, S., Mei, S., Li, M., Shi, M., Holmes, E., et al (2015). Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China. Virology, 474, 19-27. [More Information]
• Lam, T., Zhou, B., Wang, J., Chai, Y., Shen, Y., Chen, X., Ma, C., Hong, W., Chen, Y., Zhang, Y., Holmes, E., et al (2015). Dissemination, divergence and establishment of H7N9 influenza viruses in China. Nature, 522(7554), 102-105. [More Information]
• Simon-Loriere, E., Faye, O., Faye, O., Koivogui, L., Magassouba, N., Keita, S., Thiberge, J., Diancourt, L., Bouchier, C., Vandenbogaert, M., Buchmann, J., Holmes, E., et al (2015). Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic. Nature, 524(7563), 102-104. [More Information]
• Escalona, E., Leng, J., Dona, A., Merrifield, C., Holmes, E., Proudman, C., Swann, J. (2015). Dominant components of the Thoroughbred metabolome characterised by H-nuclear magnetic resonance spectroscopy: A metabolite atlas of common biofluids. Equine Veterinary Journal, 47(6), 721-730. [More Information]
• Park, D., Dudas, G., Wohl, S., Goba, A., Whitmer, S., Andersen, K., Sealfon, R., Ladner, J., Kugelman, J., Matranga, C., Holmes, E., et al (2015). Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone. Cell, 161, 1516-1526. [More Information]
• Ernst, T., McCarthy, S., Chidlow, G., Luang-Suarkia, D., Holmes, E., Smith, D., Imrie, A. (2015). Emergence of a new lineage of dengue virus type 2 in travellers entering Western Australia from Indonesia, 2010 - 2012. PLoS Neglected Tropical Diseases, 9(1), 1-15. [More Information]
• Hall, R., Mahar, J., Haboury, S., Stevens, V., Holmes, E., Strive, T. (2015). Emerging Rabbit Hemorrhagic Disease Virus 2 (RHDVb), Australia. Emerging Infectious Diseases, 21(12), 2276-2278. [More Information]
• Feng, K., Gonzalez, G., Deng, L., Yu, H., Tse, V., Huang, L., Huang, K., Wasik, B., Zhou, B., Wentworth, D., Holmes, E., et al (2015). Equine and Canine Influenza H3N8 Viruses Show Minimal Biological Differences Despite Phylogenetic Divergence. Journal of Virology, 89(13), 6860-6873. [More Information]
• Duchene, D., Duchene, S., Holmes, E., Ho, S. (2015). Evaluating the adequacy of molecular clock models using posterior predictive simulations. Molecular Biology and Evolution, 32(11), 2986-2995. [More Information]
• Walker, P., Firth, C., Widen, S., Blasdell, K., Guzman, H., Wood, T., Paradkar, P., Holmes, E., Tesh, R., Vasilakis, N. (2015). Evolution of genome size and complexity in the Rhabdoviridae. PLoS Pathogens, 11(2), 1-25. [More Information]
• Allison, A., Stallknecht, D., Holmes, E. (2015). Evolutionary genetics and vector adaptation of recombinant viruses of the western equine encephalitis antigenic complex provides new insights into alphavirus diversity and host switching. Virology, 474, 154-162. [More Information]
• Di Giallonardo, F., Holmes, E. (2015). Exploring host-pathogen interactions through biological control. PLoS Pathogens, 11(6), 1-5. [More Information]
• Guo, W., Lin, X., Chen, Y., Liu, Q., Wang, W., Wang, C., Li, M., Sun, X., Shi, M., Holmes, E., et al (2015). Fourteen types of co-circulating recombinant enterovirus wereassociated with hand, foot, and mouth disease in children fromWenzhou, China. Journal Of Clinical Virology, 70(1), 29-38. [More Information]
• Lopes, A., Dalton, K., Magalhaes, M., Parra, F., Esteves, P., Holmes, E., Abrantes, J. (2015). Full genomic analysis of new variant Rabbit Hemorrhagic Disease Virus (RHDVb) revealed multiple recombination events. Journal of General Virology, 96, 1309-1319. [More Information]
• Nelson, M., Viboud, C., Vincent, A., Culhane, M., Detmer, S., Wentworth, D., Rambaut, A., Suchard, M., Holmes, E., Lemey, P. (2015). Global migration of influenza A viruses in swine. Nature Communications, 6, 1-11. [More Information]
• Parrish, C., Murcia, P., Holmes, E. (2015). Influenza virus reservoirs and intermediate hosts: Dogs, horses, and new possibilities for influenza virus exposure of humans. Journal of Virology, 89(6), 2990-2994. [More Information]
• Patterson Ross, Z., Komadina, N., Deng, Y., Spirason, N., Kelly, H., Sullivan, S., Barr, I., Holmes, E. (2015). Inter-Seasonal Influenza is Characterized by Extended Virus Transmission and Persistence. PLoS Pathogens, 11(6), 1-16. [More Information]
• Rogers, M., Song, T., Sebra, R., Greenbaum, B., Hamelin, M., Fitch, A., Twaddle, A., Cui, L., Holmes, E., Boivin, G., et al (2015). Intrahost Dynamics of Antiviral Resistance in Influenza A Virus Reflect Complex Patterns of Segment Linkage, Reassortment, and Natural Selection. mBio, 6(2), 1-8. [More Information]
• Li, K., Lin, X., Wang, W., Shi, M., Guo, W., Zhang, X., Xing, J., He, J., Wang, K., Li, M., Holmes, E., et al (2015). Isolation and characterization of a novel arenavirus harbored by rodents and shrews in Zhejiang, China. Virology, 476, 37-42. [More Information]
• Blasdell, K., Guzman, H., Widen, S., Firth, C., Wood, T., Holmes, E., Tesh, R., Vasilakis, N., Walker, P. (2015). Ledantevirus: A Proposed New Genus in the Rhabdoviridae has a Strong Ecological Association with Bats. American Journal of Tropical Medicine and Hygiene, 92(2), 405-410. [More Information]
• Saavedra, A., Cripps, S., Geoghegan, J., Holmes, E., Durrant-Whyte, H. (2015). Modelling the spread of influenza in Western Australia. First International Workshop on Population Informatics for Big Data (ACM-SIGKDD PopInfo'15), Sydney: anu.edu.au.
• Thomas, J., Allison, A., Holmes, E., Phillips, J., Bunting, E., Yabsley, M., Brown, J. (2015). Molecular surveillance for Lymphoproliferative Disease Virus in wild turkeys (Meleagris gallopavo) from the eastern United States. PloS One, 10(4), 1-13. [More Information]
• Kerr, P., Liu, J., Cattadori, I., Ghedin, E., Read, A., Holmes, E. (2015). Myxoma Virus and the Leporipoxviruses: An Evolutionary Paradigm. Viruses, 7, 1020-1061. [More Information]
• Geoghegan, J., Tan, L., Kuhnert, D., Halpin, R., Lin, X., Simenauer, A., Akopov, A., Das, S., Stockwell, T., Shrivastava, S., Holmes, E., et al (2015). Phylodynamics of enterovirus A71-associated hand, foot, and mouth disease in Viet Nam. Journal of Virology, 89(17), 8871-8879. [More Information]
• Pollett, S., Nelson, M., Kasper, M., Tinoco, Y., Simons, M., Romero, C., Silva, M., Lin, X., Halpin, R., Fedorova, N., Holmes, E., et al (2015). Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012. Emerging Infectious Diseases, 21(8), 1330-1338. [More Information]
• Lam, T., Zhu, H., Chong, Y., Holmes, E., Guan, Y. (2015). Puzzling origins of the Ebola outbreak in the Democratic Republic of the Congo, 2014. Journal of Virology, 89(19), 10130-10132. [More Information]
• Wang, W., Yu, B., Lin, X., Kong, D., Wang, J., Tian, J., Li, M., Holmes, E., Zhang, Y. (2015). Reemergence and Autochthonous Transmission of Dengue Virus, Eastern China, 2014. Emerging Infectious Diseases, 21(9), 1670-1673. [More Information]
• Eden, J., Read, A., Duckworth, J., Strive, T., Holmes, E. (2015). Resolving the Origin of Rabbit Hemorrhagic Disease Virus: Insights from an Investigation of the Viral Stocks Released in Australia. Journal of Virology, 89(23), 12217-12220. [More Information]
• Vijaykrishna, D., Holmes, E., Joseph, U., Fourment, M., Su, Y., Halpin, R., Lee, R., Deng, Y., Gunalan, V., Lin, X., Dwyer, D., et al (2015). The contrasting phylodynamics of human infuenza B viruses. eLife, 4, 1-23. [More Information]
• Holmes, E., Zhang, Y. (2015). The evolution and emergence of hantaviruses. Current Opinion in Virology, 10, 27-33. [More Information]
• Duchene, S., Duchene, D., Holmes, E., Ho, S. (2015). The performance of the date-randomization test in phylogenetic analyses of time-structured virus data. Molecular Biology and Evolution, 32(7), 1895-1906. [More Information]
• Sintchenko, V., Holmes, E. (2015). The role of pathogen genomics in assessing disease transmission. BMJ, 350, 1-13. [More Information]
• Simmons, H., Prendeville, H., Dunham, J., Ferrari, M., Earnest, J., Pilson, D., Munkvold, G., Holmes, E., Stephenson, A. (2015). Transgenic virus resistance in crop-wild Cucurbita pepo does not prevent vertical transmission of Zucchini yellow mosaic virus. Plant Disease, 99, 1616-1621. [More Information]
• Li, C., Shi, M., Tian, J., Lin, X., Kang, Y., Chen, L., Qin, X., Xu, J., Holmes, E., Zhang, Y. (2015). Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. eLife, 2015 (4), 1-34. [More Information]
• Di Giallonardo, F., Holmes, E. (2015). Viral biocontrol: grand experiments in disease emergence and evolution. Trends in Microbiology, 23(2), 83-90. [More Information]

2014

• Qin, X., Shi, M., Tian, J., Lin, X., Gao, D., He, J., Wang, J., Li, C., Kang, Y., Yu, B., Holmes, E., et al (2014). A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proceedings of the National Academy of Sciences of the United States of America, 111(18), 6744-6749. [More Information]
• Cui, J., Schlub, T., Holmes, E. (2014). An allometric relationship between the genome length and virion volume of viruses. Journal of Virology, 88(11), 6403-6410. [More Information]
• Duchene, S., Holmes, E., Ho, S. (2014). Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proceedings of the Royal Society B: Biological Sciences, 281(1786), 1-7. [More Information]
• Dunham, J., Simmons, H., Holmes, E., Stephenson, A. (2014). Analysis of viral (zucchini yellow mosaic virus) genetic diversity during systemic movement through a Cucurbita pepo vine. Virus Research, 191(1), 172-179. [More Information]
• Vasilakis, N., Castro-Llanos, F., Widen, S., Aguilar, P., Guzman, H., Guevara, C., Fernandez, R., Auguste, A., Wood, T., Popov, V., Holmes, E., et al (2014). Arboretum and Puerto Almendras viruses: two novel rhabdoviruses isolated from mosquitoes in Peru. Journal of General Virology, 95(Part 4), 787-792. [More Information]
• Allison, A., Kevin, K., Philips, J., Cartoceti, A., Munk, B., Nemeth, N., Welsh, T., Thomas, J., Crum, J., Lichtenwalner, A., Holmes, E., et al (2014). Avian oncogenesis induced by lymphoproliferative disease virus: A neglected or emerging retroviral pathogen? Virology, 450-451, 2-12. [More Information]
• Lin, X., Zhou, R., Fan, F., Ying, X., Sun, X., Wang, W., Holmes, E., Zhang, Y. (2014). Biodiversity and evolution of Imjin virus and Thottapalayam virus in Crocidurinae shrews in Zhejiang Province, China. Virus Research, 189, 114-120. [More Information]
• Wang, C., Gao, J., Li, M., Guo, W., Lu, M., Wang, W., Hu, M., Li, M., Yang, J., Liang, H., Holmes, E., et al (2014). Co-circulation of Hantaan, Kenkeme, and Khabarovsk Hantaviruses in Bolshoy Ussuriysky Island, China. Virus Research, 191(1), 51-58. [More Information]
• Chen, Z., Qin, X., Song, R., Shen, Y., Chen, X., Wang, W., Zhao, Y., Zhang, J., He, J., Holmes, E., et al (2014). Co-Circulation of Multiple Hemorrhagic Fever Diseases with Distinct Clinical Characteristics in Dandong, China. PloS One, 9(2), 187-11. [More Information]
• Zhang, G., Li, C., Li, Q., Bo, L., Larkin, D., Lee, C., Storz, J., Antunes, A., Greenwold, M., Cui, J., et al (2014). Comparative genomics reveal insights into avian genome evolution and adaptation. Science, 346(6215), 1311-1319. [More Information]
• Dalziel, B., Huang, K., Geoghegan, J., Arinaminpathy, N., Dubovi, E., Grenfell, B., Ellner, S., Holmes, E., Parrish, C. (2014). Contact Heterogeneity, Rather Than Transmission Efficiency, Limits the Emergence and Spread of Canine Influenza Virus. PLoS Pathogens, 10(10), 1-13. [More Information]
• Monne, I., Fusaro, A., Nelson, M., Bonfanti, L., Mulatti, P., Hughes, J., Murcia, P., Schivo, A., Valastro, V., Moreno, A., Holmes, E., et al (2014). Emergence of a Highly Pathogenic Avian Influenza Virus from a Low Pathogenic Progenitor. Journal of Virology, 88(8), 4375-4388. [More Information]
• Trinidad, L., Blasdell, K., Albert, J., Davis, S., Melville, L., Kirkland, P., Coulibaly, F., Holmes, E., Walker, P. (2014). Evolution of Bovine Ephemeral Fever Virus in the Australian Episystem. Journal of Virology, 88(3), 1525-1535. [More Information]
• Kang, Y., Diao, X., Zhao, G., Chen, M., Xiong, Y., Mang, S., Fu, W., Guo, Y., Pan, B., Chen, X., Holmes, E., et al (2014). Extensive diversity of Rickettsiales bacteria in two species of ticks from China and the evolution of the Rickettsiales. BMC Evolutionary Biology, 14(1), 1-12. [More Information]
• Holmes, E. (2014). Freezing viruses in time. Proceedings of the National Academy of Sciences of the United States of America, 111(47), 16643-16644. [More Information]
• Allison, A., Mead, D., Palacios, G., Tesh, R., Holmes, E. (2014). Gene duplication and phylogeography of North American members of the Hart Park serogroup of avian rhabdoviruses. Virology, 448, 284-292. [More Information]
• Allison, A., Kohler, D., Ortega, A., Hoover, E., Groves, D., Holmes, E., Parrish, C. (2014). Host-Specific Parvovirus Evolution in Nature Is Recapitulated by In Vitro Adaptation to Different Carnivore Species. PLoS Pathogens, 10(11), 1-18. [More Information]
• Elsworth, P., Cooke, B., Kovaliski, J., Sinclair, R., Holmes, E., Strive, T. (2014). Increased virulence of rabbit haemorrhagic disease virus associated with genetic resistance in wild Australian rabbits (Oryctolagus cuniculus). Virology, 464-465, 415-423. [More Information]
• Nelson, M., Wentworth, D., Culhane, M., Vincent, A., Viboud, C., LaPointe, M., Lin, X., Holmes, E., Detmer, S. (2014). Introductions and evolution of human-origin seasonal influenza A viruses in multinational swine populations. Journal of Virology, 88(17), 10110-10119. [More Information]
• Blasdell, K., Widen, S., Diviney, S., Firth, C., Wood, T., Guzman, H., Holmes, E., Tesh, R., Vasilakis, N., Walker, P. (2014). Koolpinyah and Yata viruses: two newly recognised ephemeroviruses from tropical regions of Australia and Africa. Veterinary Microbiology, 174, 547-553. [More Information]
• Cui, J., Zhao, W., Huang, Z., Jarvis, E., Gilbert, M., Walker, P., Holmes, E., Zhang, G. (2014). Low frequency of paleoviral infiltration across the avian phylogeny. Genome Biology, 15(12), 1-13. [More Information]
• Kovaliski, J., Sinclair, R., Mutze, G., Peacock, D., Strive, T., Abrantes, J., Esteves, P., Holmes, E. (2014). Molecular epidemiology of Rabbit Haemorrhagic Disease Virus in Australia: When one became many. Molecular Ecology, 23(2), 408-420. [More Information]
• Lopes, A., Capucci, L., Gavier-Widén, D., Le Gall-Reculé, G., Brocchi, E., Barbieri, I., Quéméner, A., Le Pendu, J., Geoghegan, J., Holmes, E., et al (2014). Molecular evolution and antigenic variation of European brown hare syndrome virus (EBHSV). Virology, 468-470, 104-112. [More Information]
• Nelson, M., Njouom, R., Viboud, C., Niang, M., Kadjo, H., Ampofo, W., Tarnagda, Z., Adebayo, A., Miller, M., Holmes, E., et al (2014). Multiyear Persistence of 2 Pandemic A/H1N1 Influenza Virus Lineages in West Africa. The Journal of Infectious Diseases, 210(1), 121-125. [More Information]
• Fourment, M., Holmes, E. (2014). Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evolutionary Biology, 14, 1-12. [More Information]
• Holmes, E. (2014). Pandemics-Keep Calm and Carry On. PLoS Biology, 12(2), 1-2. [More Information]
• Geoghegan, J., Walker, P., Duchemin, J., Jeanne, I., Holmes, E. (2014). Seasonal Drivers of the Epidemiology of Arthropod-Borne Viruses in Australia. PLoS Neglected Tropical Diseases, 8(11), 1-10. [More Information]
• Devault, A., Golding, G., Waglechner, N., Enk, J., Kuch, M., Tien, J., Shi, M., Fisman, D., Dhody, A., Forrest, S., Holmes, E., et al (2014). Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849. New England Journal of Medicine, 370(4), 334-340. [More Information]
• Eden, J., Hewitt, J., Lim, K., Boni, M., Merif, J., Greening, G., Ratcliff, R., Holmes, E., Tanaka, M., Rawlinson, W., et al (2014). The emergence and evolution of the novel epidemic norovirus GII.4 variant Sydney 2012. Virology, 450-451, 106-113. [More Information]
• Barasheed, O., Rashid, H., Alfelali, M., Tashani, M., Azeem, M., Bokhary, H., Kalantan, N., Samkari, J., Heron, L., Kok, J., Holmes, E., Dwyer, D., Booy, R., et al (2014). Viral respiratory infections among Hajj pilgrims in 2013. Virologica Sinica, 29(6), 364-371. [More Information]
• Zhang, Y., Holmes, E. (2014). What is the time-scale of hantavirus evolution? Infection, Genetics and Evolution, 25, 144-145. [More Information]
• Wagner, D., Klunk, J., Harbeck, M., Devault, A., Waglechner, N., Sahl, J., Enk, J., Birdsell, D., Kuch, M., Lumibao, C., Fourment, M., Holmes, E., et al (2014). Yersinia pestis and the Plague of Justinian 541-543 AD: a genomic analysis. The Lancet Infectious Diseases, 14(4), 319-326. [More Information]
• Wagner, D., Keim, P., Scholz, H., Holmes, E., Poinar, H. (2014). Yersinia pestis and the three plague pandemics: Authors' reply. The Lancet Infectious Diseases, 14(10), 919-919. [More Information]

2013

• Cui, J., Eden, J., Holmes, E., Wang, L. (2013). Adaptive evolution of bat dipeptidyl peptidase 4 (dpp4): Implications for the origin and emergence of Middle East Respiratory Syndrome Coronavirus. Virology Journal, 10, 1-5. [More Information]
• Wang, L., Yin, Q., He, G., Rossiter, S., Holmes, E., Cui, J. (2013). Ancient invasion of an extinct gammaretrovirus in cetaceans. Virology, 441(1), 66-69. [More Information]
• Quan, P., Firth, C., Conte, J., Williams, S., Zambrana-Torrelio, C., Anthony, S., Ellison, J., Gilbert, A., Kuzmin, I., Niezgoda, M., Holmes, E., et al (2013). Bats are a major natural reservoir for hepaciviruses and pegiviruses. Proceedings of the National Academy of Sciences of the United States of America, 110(20), 8194-8199. [More Information]
• Kerr, P., Rogers, M., Fitch, A., DePasse, J., Cattadori, I., Hudson, P., Tscharke, D., Holmes, E., Ghedin, E. (2013). Comparative analysis of the complete genome sequence of the Californian MSW strain of myxoma virus reveals potential host adaptations. Journal of Virology, 87(22), 12080-12089. [More Information]
• Viboud, C., Nelson, M., Tan, Y., Holmes, E. (2013). Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission. Philosophical Transactions of the Royal Society B, 368(1614), 1-9. [More Information]
• Levitt, A., Singh, R., Cox-Foster, D., Rajotte, E., Hoover, K., Ostiguy, N., Holmes, E. (2013). Cross-species transmission of honey bee viruses in associated arthropods. Virus Research, 176(1-2), 232-240. [More Information]
• Rabaa, M., Simmons, C., Fox, A., Le, M., Nguyen, T., Le, H., Gibbons, R., Nguyen, X., Holmes, E., Aaskov, J. (2013). Dengue Virus in Sub-tropical Northern and Central Viet Nam: Population Immunity and Climate Shape Patterns of Viral Invasion and Maintenance. PLoS Neglected Tropical Diseases, 7(12), 1-12. [More Information]
• Tan, Y., Guan, W., Lam, T., Pan, S., Wu, S., Zhan, Y., Viboud, C., Holmes, E., Yang, Z. (2013). Differing epidemiological dynamics of influenza B lineages in Guangzhou, southern China, 2009-2010. Journal of Virology, 87(22), 12447-12456. [More Information]
• Tao, Y., Shi, M., Conrardy, C., Kuzmin, I., Recuenco, S., Agwanda, B., Alvarez, D., Ellison, J., Gilbert, A., Moran, D., Holmes, E., et al (2013). Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae. Journal of General Virology, 94(Part 4), 738-748. [More Information]
• Chen, X., Tan, Y., He, M., Lam, T., Lu, X., Viboud, C., He, J., Zhang, S., Lu, J., Wu, C., Holmes, E., et al (2013). Epidemiological Dynamics and Phylogeography of Influenza Virus in Southern China. The Journal of Infectious Diseases, 207(1), 106-114. [More Information]
• Murcia, P., Baillie, G., Stack, J., Jervis, C., Elton, D., Mumford, J., Daly, J., Kellam, P., Grenfell, B., Holmes, E., et al (2013). Evolution of equine influenza virus in vaccinated horses. Journal of Virology, 87(8), 4768-4771. [More Information]
• Allison, A., Kohler, D., Fox, K., Brown, J., Gerhold, R., Shearn-Bochsler, V., Dubovi, E., Parrish, C., Holmes, E. (2013). Frequent Cross-Species Transmission of Parvoviruses among Diverse Carnivore Hosts. Journal of Virology, 87(4), 2342-2347. [More Information]
• Rabaa, M., Klungthong, C., Yoon, I., Holmes, E., Chinnawirotpisan, P., Thaisomboonsuk, B., Srikiatkhachorn, A., Rothman, A., Tannitisupawong, D., Aldstadt, J., et al (2013). Frequent In-Migration and Highly Focal Transmission of Dengue Viruses among Children in Kamphaeng Phet, Thailand. PLoS Neglected Tropical Diseases, 7(1), 1-14. [More Information]
• Simon-Loriere, E., Holmes, E. (2013). Gene duplication is infrequent in the recent evolutionary history of RNA viruses. Molecular Biology and Evolution, 30(6), 1263-1269. [More Information]
• Kerr, P., Rogers, M., Fitch, A., DePasse, J., Cattadori, I., Twaddle, A., Hudson, P., Tscharke, D., Read, A., Holmes, E., et al (2013). Genome scale evolution of myxoma virus (MYXV) reveals host-pathogen adaptation and rapid geographic spread. Journal of Virology, 87(23), 12900-12915. [More Information]
• Nguyen, N., Kien, D., Tuan, T., Quyen, N., Tran, C., Thi, L., Thi, D., Nguyen, H., Farrar, J., Holmes, E., et al (2013). Host and viral features of human dengue cases shape the population of infected and infectious Aedes aegypti mosquitoes. Proceedings of the National Academy of Sciences of the United States of America, 110(22), 9072-9077. [More Information]
• Hayward, J., Tachedjian, M., Cui, J., Field, H., Holmes, E., Wang, L., Tachedjian, G. (2013). Identification of diverse full-length endogenous betaretroviruses in megabats and microbats. Retrovirology, 10, 1-29. [More Information]
• Stack, J., Murcia, P., Grenfell, B., Wood, J., Holmes, E. (2013). Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic variation. Proceedings of the Royal Society B: Biological Sciences, 280(1750), 1-9. [More Information]
• Ghedin, E., Rogers, M., Widen, S., Guzman, H., Travassos Da Rosa, A., Wood, T., Fitch, A., Popov, V., Holmes, E., Walker, P., et al (2013). Kolenté virus, a rhabdovirus species isolated from ticks and bats in the Republic of Guinea. Journal of General Virology, 94(PART 12), 2609-2615. [More Information]
• Vasilakis, N., Widen, S., Travassos Da Rosa, A., Wood, T., Walker, P., Holmes, E., Tesh, R. (2013). Malpais spring virus is a new species in the genus vesiculovirus. Virology Journal, 10, 1-5. [More Information]
• Tong, S., Zhu, X., Li, Y., Shi, M., Zhang, J., Bourgeois, M., Yang, H., Chen, X., Recuenco, S., Gomez, J., Holmes, E., et al (2013). New World Bats Harbor Diverse Influenza A Viruses. PLoS Pathogens, 9(10), 1-12. [More Information]
• Vasilakis, N., Widen, S., Mayer, S., Seymour, R., Wood, T., Popov, V., Guzman, H., Travassos Da Rosa, A., Ghedin, E., Holmes, E., et al (2013). Niakha virus: A novel member of the family Rhabdoviridae isolated from phlebotomine sandflies in Senegal. Virology, 444(1-2), 80-89. [More Information]
• Wang, W., Wang, R., Lin, X., Guo, W., Li, M., Mei, S., Li, Z., Cong, M., Jiang, R., Zhou, R., Holmes, E., et al (2013). Ongoing Spillover of Hantaan and Gou Hantaviruses from Rodents Is Associated with Hemorrhagic Fever with Renal Syndrome (HFRS) in China. PLoS Neglected Tropical Diseases, 7(10), 1-8. [More Information]
• Ke, R., Aaskov, J., Holmes, E., Lloyd-Smith, J. (2013). Phylodynamic Analysis of the Emergence and Epidemiological Impact of Transmissible Defective Dengue Viruses. PLoS Pathogens, 9(2), 1-11. [More Information]
• Guo, W., Lin, X., Wang, W., Tian, J., Cong, M., Zhang, H., Wang, R., Zhou, R., Wang, J., Li, M., Holmes, E., et al (2013). Phylogeny and Origins of Hantaviruses Harbored by Bats, Insectivores, and Rodents. PLoS Pathogens, 9(2), 1-13. [More Information]
• Nougairede, A., de Fabritus, L., Aubry, F., Gould, E., Holmes, E., de Lamballerie, X. (2013). Random Codon Re-encoding Induces Stable Reduction of Replicative Fitness of Chikungunya Virus in Primate and Mosquito Cells. PLoS Pathogens, 9(2), 1-18. [More Information]
• Shi, M., Holmes, E., Brar, M., Leung, F. (2013). Recombination Is Associated with an Outbreak of Novel Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Viruses in China. Journal of Virology, 87(19), 10904-10907. [More Information]
• Saira, K., Lin, X., DePasse, J., Halpin, R., Twaddle, A., Stockwell, T., Angus, B., Cozzi-Lepri, A., Delfino, M., Dugan, V., Dwyer, D., Holmes, E., et al (2013). Sequence Analysis of In Vivo Defective Interfering-Like RNA of Influenza A H1N1 Pandemic Virus. Journal of Virology, 87(14), 8064-8074. [More Information]
• Lam, T., Chong, Y., Shi, M., Hon, C., Li, J., Martin, D., Tang, J., Mok, C., Shih, S., Yip, C., Holmes, E., et al (2013). Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments. Infection, Genetics and Evolution, 18, 367-378. [More Information]
• Simon-Loriere, E., Holmes, E., Pagan, I. (2013). The Effect of Gene Overlapping on the Rate of RNA Virus Evolution. Molecular Biology and Evolution, 30(8), 1916-1928. [More Information]
• Bhatt, S., Lam, T., Lycett, S., Brown, A., Bowden, T., Holmes, E., Guan, Y., Wood, J., Brown, I., Kellam, P., et al (2013). The evolutionary dynamics of influenza A virus adaptation to mammalian hosts. Philosophical Transactions of the Royal Society B, 368(1614), 1-8. [More Information]
• Fusaro, A., Monne, I., Salomoni, A., Angot, A., Trolese, M., Ferre, N., Mutinelli, F., Holmes, E., Capua, I., Lemey, P., et al (2013). The introduction of fox rabies into Italy (2008-2011) was due to two viral genetic groups with distinct phylogeographic patterns. Infection, Genetics and Evolution, 17, 202-209. [More Information]
• Pepperell, C., Casto, A., Kitchen, A., Granka, J., Cornejo, O., Holmes, E., Birren, B., Galagan, J., Feldman, M. (2013). The role of selection in shaping diversity of natural M.tuberculosis populations. PLoS Pathogens, 9(8), 1-14. [More Information]
• Shi, M., Lemey, P., Brar, M., Suchard, M., Murtaugh, M., Carman, S., D'Allaire, S., Delisle, B., Lambert, M., Gagnon, C., Qu, Y., Holmes, E., et al (2013). The spread of Type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in North America: A phylogeographic approach. Virology, 447(1-2), 146-154. [More Information]
• Holmes, E. (2013). Virus Evolution. In David M Knipe, and Peter M Howley (Eds.), Fields Virology, (pp. 286-313). Philadelphia: Lippincott Williams and Wilkins, Inc (Wolters Kluwer Health).
• Holmes, E. (2013). What can we predict about viral evolution and emergence? Current Opinion in Virology, 3(2), 180-184. [More Information]
• Simmons, H., Dunham, J., Zinn, K., Munkvold, G., Holmes, E., Stephenson, A. (2013). Zucchini yellow mosaic virus (ZYMV, Potyvirus): Vertical transmission, seed infection and cryptic infections. Virus Research, 176(1-2), 259-264. [More Information]

2012

• Nielsen, A., Ghyrs, M., Holmes, E., Cui, J. (2012). Co-Circulation and Persistence of Genetically Distinct Saffold Viruses, Denmark. Emerging Infectious Diseases, 18(10), 1694-1696. [More Information]
• Simmons, H., Dunham, J., Stack, J., Dickins, B., Pagan, I., Holmes, E., Stephenson, A. (2012). Deep sequencing reveals persistence of intra- and inter-host genetic diversity in natural and greenhouse populations of zucchini yellow mosaic virus. Journal of General Virology, 93(8), 1831-1840. [More Information]
• Cui, J., Holmes, E. (2012). Endogenous Hepadnaviruses in the Genome of the Budgerigar (Melopsittacus undulatus) and the Evolution of Avian Hepadnaviruses. Journal of Virology, 86(14), 7688-7691. [More Information]
• Cui, J., Holmes, E. (2012). Endogenous Lentiviruses in the Ferret Genome. Journal of Virology, 86(6), 3383-3385. [More Information]
• Cui, J., Holmes, E. (2012). Endogenous RNA viruses of plants in insect genomes. Virology, 427(2), 77-79. [More Information]
• Cui, J., Holmes, E. (2012). Evidence for an endogenous papillomavirus-like element in the platypus genome. Journal of General Virology, 93(6), 1362-1366. [More Information]
• Murcia, P., Hughes, J., Battista, P., Lloyd, L., Baillie, G., Ramirez-Gonzalez, R., Ormond, D., Oliver, K., Elton, D., Mumford, J., et al (2012). Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs. PLoS Pathogens, 8(5), e1002730. [More Information]
• Nelson, M., Vincent, A., Kitikoon, P., Holmes, E., Gramer, M. (2012). Evolution of novel reassortant A/H3N2 influenza viruses in North American swine and humans, 2009-2011. Journal of Virology, 86(16), 8872-8878. [More Information]
• Shi, M., Jagger, B., Wise, H., Digard, P., Holmes, E., Taubenberger, J. (2012). Evolutionary conservation of the PA-X open reading frame in segment 3 of influenza a virus. Journal of Virology, 86(22), 12411-12413. [More Information]
• Kerr, P., Ghedin, E., DePasse, J., Fitch, A., Cattadori, I., Hudson, P., Tscharke, D., Read, A., Holmes, E. (2012). Evolutionary History and Attenuation of Myxoma Virus on Two Continents. PLoS Pathogens, 8(10), e1002950. [More Information]
• Nelson, M., Detmer, S., Wentworth, D., Tan, Y., Schwartzbard, A., Halpin, R., Stockwell, T., Lin, X., Vincent, A., Gramer, M., et al (2012). Genomic reassortment of influenza A virus in North American swine, 1998-2011. Journal of General Virology, 93(12), 2584-2589. [More Information]
• Nelson, M., Gramer, M., Vincent, A., Holmes, E. (2012). Global transmission of influenza viruses from humans to swine. Journal of General Virology, 93(10), 2195-2203. [More Information]
• Thai, K., Henn, M., Zody, M., Tricou, V., Nguyet, N., Charlebois, P., Lennon, N., Green, L., De Vries, P., Hien, T., et al (2012). High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections. Journal of Virology, 86(2), 835-843. [More Information]
• Cui, J., Tachedjian, G., Tachedjian, M., Holmes, E., Zhang, S., Wang, L. (2012). Identification of diverse groups of endogenous gammaretroviruses in mega- and microbats. Journal of General Virology, 93(Pt 9), 2037-2045. [More Information]
• Pagan, I., Holmes, E., Simon-Lorière, E. (2012). Level of gene expression is a major determinant of protein evolution in the viral order Mononegavirales. Journal of Virology, 86(9), 5253-5263. [More Information]
• Lam, T., Ip, H., Ghedin, E., Wentworth, D., Halpin, R., Stockwell, T., Spiro, D., Dusek, R., Bortner, J., Hoskins, J., et al (2012). Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds. Ecology Letters, 15(1), 24-33. [More Information]
• Panzarin, V., Fusaro, A., Monne, I., Cappellozza, E., Patarnello, P., Bovo, G., Capua, I., Holmes, E., Cattoli, G. (2012). Molecular epidemiology and evolutionary dynamics of betanodavirus in southern Europe. Infection, Genetics and Evolution, 12(1), 63-70. [More Information]
• Cook, S., Moureau, G., Kitchen, A., Gould, E., de Lamballerie, X., Holmes, E., Harbach, R. (2012). Molecular evolution of the insect-specific flaviviruses. Journal of General Virology, 93(2), 223-234. [More Information]
• Boni, M., Smith, G., Holmes, E., Vijaykrishna, D. (2012). No evidence for intra-segment recombination of 2009 H1N1 influenza virus in swine. Gene, 494(2), 242-245. [More Information]
• Lam, T., Hon, C., Lemey, P., Pybus, O., Shi, M., Tun, H., Li, J., Jiang, J., Holmes, E., Leung, F. (2012). Phylodynamics of H5N1 avian influenza virus in Indonesia. Molecular Ecology, 21(12), 3062-3077. [More Information]
• Bhardwaj, G., Ko, K., Hong, Y., Zhang, Z., Ho, N., Chintapalli, S., Kline, L., Gotlin, M., Hartranft, D., Patterson, M., et al (2012). Phyrn: A robust method for phylogenetic analysis of highly divergent sequences. PloS One, 7(4), e34261. [More Information]
• Ghedin, E., Holmes, E., DePasse, J., Pinilla, L., Fitch, A., Hamelin, M., Papenburg, J., Boivin, G. (2012). Presence of oseltamivir-resistant pandemic A/H1N1 minor variants before drug therapy with subsequent selection and transmission. The Journal of Infectious Diseases, 206(10), 1504-1511. [More Information]
• Allison, A., Harbison, C., Pagan, I., Stucker, K., Kaelber, J., Brown, J., Ruder, M., Keel, M., Dubovi, E., Holmes, E., et al (2012). Role of multiple hosts in the cross-species transmission and emergence of a pandemic parvovirus. Journal of Virology, 86(2), 865-872. [More Information]
• Allison, A., Holmes, E., Potgieter, A., Wright, I., Sailleau, C., Breard, E., Ruder, M., Stallknecht, D. (2012). Segmental configuration and putative origin of the reassortant orbivirus, epizootic hemorrhagic disease virus serotype 6, strain Indiana. Virology, 424(1), 67-75. [More Information]
• Holt, K., Baker, S., Weill, F., Holmes, E., Kitchen, A., Yu, J., Sangal, V., Brown, D., Coia, J., Kim, D., et al (2012). Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nature Genetics, 44(9), 1056-1059. [More Information]
• Lam, T., Zhu, H., Smith, D., Guan, Y., Holmes, E., Pybus, O. (2012). The recombinant origin of emerging human norovirus GII.4/2008: intra-genotypic exchange of the capsid P2 domain. Journal of General Virology, 93(4), 817-822. [More Information]
• Stucker, K., Pagan, I., Cifuente, J., Kaelber, J., Lillie, T., Hafenstein, S., Holmes, E., Parrish, C. (2012). The role of evolutionary intermediates in the host adaptation of canine parvovirus. Journal of Virology, 86(3), 1514-1521. [More Information]
• Hughes, J., Allen, R., Baguelin, M., Hampson, K., Baillie, G., Elton, D., Newton, J., Kellam, P., Wood, J., Holmes, E., et al (2012). Transmission of Equine Influenza Virus during an Outbreak Is Characterized by Frequent Mixed Infections and Loose Transmission Bottlenecks. PLoS Pathogens, 8(12), e1003081. [More Information]

2011

• Ghedin, E., Laplante, J., DePasse, J., Wentworth, D., Santos, R., Lepow, M., Porter, J., Stellrecht, K., Lin, X., Operario, D., et al (2011). Deep Sequencing Reveals Mixed Infection with 2009 Pandemic Influenza (H1N1) Virus Strains and the Emergence of Oseltamivir Resistance. The Journal of Infectious Diseases, 203(2), 168-174. [More Information]
• Raghwani, J., Rambaut, A., Holmes, E., Hang, V., Hien, T., Farrar, J., Wills, B., Lennon, N., Birren, B., Henn, M., et al (2011). Endemic Dengue Associated with the Co-Circulation of Multiple Viral Lineages and Localized Density-Dependent Transmission. PLoS Pathogens, 7(6), e1002064. [More Information]
• Cattoli, G., Fusaro, A., Monne, I., Coven, F., Joannis, T., El-Hamid, H., Hussein, A., Cornelius, C., Amarin, N., Mancin, M., et al (2011). Evidence for differing evolutionary dynamics of A/H5N1 viruses among countries applying or not applying avian influenza vaccination in poultry. Vaccine, 29(50), 9368-9375. [More Information]
• Simmons, H., Holmes, E., Gildow, F., Bothe-Goralczyk, M., Stephenson, A. (2011). Experimental Verification of Seed Transmission of Zucchini yellow mosaic virus. Plant Disease, 95(6), 751-754. [More Information]
• Holmes, E., Ghedin, E., Halpin, R., Stockwell, T., Zhang, X., Fleming, R., Davey, R., Benson, C., Mehta, S., Taplitz, R., et al (2011). Extensive geographical mixing of 2009 human H1N1 influenza a virus in a single university community. Journal of Virology, 85(14), 6923-6929. [More Information]
• Kitchen, A., Shackelton, L., Holmes, E. (2011). Family level phylogenies reveal modes of macroevolution in RNA viruses. Proceedings of the National Academy of Sciences of the United States of America, 108(1), 238-243. [More Information]
• Vasilakis, N., Cardosa, J., Hanley, K., Holmes, E., Weaver, S. (2011). Fever from the forest: prospects for the continued emergence of sylvatic dengue virus and its impact on public health. Nature Reviews Microbiology, 9(7), 532-541. [More Information]
• Murcia, P., Wood, J., Holmes, E. (2011). Genome-Scale Evolution and Phylodynamics of Equine H3N8 Influenza A Virus. Journal of Virology, 85(11), 5312-5322. [More Information]
• Holmes, E. (2011). Genomics: Plague's progress. Nature, 478(7370), 465-466. [More Information]
• Morens, D., Holmes, E., Davis, A., Taubenberger, J. (2011). Global Rinderpest Eradication: Lessons Learned and Why Humans Should Celebrate Too. The Journal of Infectious Diseases, 204(4), 502-505. [More Information]
• Liu, W., Rourke, M., Holmes, E., Aaskov, J. (2011). Persistence of Multiple Genetic Lineages within Intrahost Populations of Ross River Virus. Journal of Virology, 85(11), 5674-5678. [More Information]
• Fusaro, A., Monne, I., Salviato, A., Valastro, V., Schivo, A., Amarin, N., Gonzalez, C., Ismail, M., Al-Ankari, A., Al-Blowi, M., et al (2011). Phylogeography and evolutionary history of reassortant H9N2 viruses with potential human health implications. Journal of Virology, 85(16), 8413-8421. [More Information]
• Nelson, M., Tan, Y., Ghedin, E., Wentworth, D., St. George, K., Edelman, L., Beck, E., Fan, J., Lam, T., Kumar, S., et al (2011). Phylogeography of the Spring and Fall Waves of the H1N1/09 Pandemic Influenza Virus in the United States. Journal of Virology, 85(2), 828-834. [More Information]
• Simmons, H., Holmes, E., Stephenson, A. (2011). Rapid turnover of intra-host genetic diversity in Zucchini yellow mosaic virus. Virus Research, 155(2), 389-396. [More Information]
• Lam, T., Zhu, H., Wang, J., Smith, D., Holmes, E., Webster, R., Webby, R., Peiris, J., Guan, Y. (2011). Reassortment Events among Swine Influenza A Viruses in China: Implications for the Origin of the 2009 Influenza Pandemic. Journal of Virology, 85(19), 10279-10285. [More Information]
• Torres-Pérez, F., Palma, R., Hjelle, B., Holmes, E., Cook, J. (2011). Spatial but not temporal co-divergence of a virus and its mammalian host. Molecular Ecology, 20(19), 4109-4122. [More Information]
• Nelson, M., Lemey, P., Tan, Y., Vincent, A., Lam, T., Detmer, S., Viboud, C., Suchard, M., Rambaut, A., Holmes, E., et al (2011). Spatial Dynamics of Human-Origin H1 Influenza A Virus in North American Swine. PLoS Pathogens, 7(6), 1-11. [More Information]
• Bahl, J., Nelson, M., Chan, K., Chen, R., Vijaykrishna, D., Halpin, R., Stockwell, T., Lin, X., Wentworth, D., Ghedin, E., et al (2011). Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans. Proceedings of the National Academy of Sciences of the United States of America, 108(48), 19359-19364. [More Information]
• My, P., Rabaa, M., Vinh, H., Holmes, E., Hoang, N., Vinh, N., Phuong, L., Tham, N., Bay, P., Campbell, J., et al (2011). The Emergence of Rotavirus G12 and the Prevalence of Enteric Viruses in Hospitalized Pediatric Diarrheal Patients in Southern Vietnam. American Journal of Tropical Medicine and Hygiene, 85(4), 768-775. [More Information]
• Holmes, E. (2011). The Evolution of Endogenous Viral Elements. Cell Host and Microbe, 10(4), 368-377. [More Information]
• Bhatt, S., Holmes, E., Pybus, O. (2011). The genomic rate of molecular adaptation of the human influenza A virus. Molecular Biology and Evolution, 28(9), 2443-2451. [More Information]
• Holmes, E. (2011). What Does Virus Evolution Tell Us about Virus Origins? Journal of Virology, 85(11), 5247-5251. [More Information]
• Simon-Loriere, E., Holmes, E. (2011). Why do RNA viruses recombine? Nature Reviews Microbiology, 9(8), 617-626. [More Information]

2010

• Dacheux, L., Berthet, N., Dissard, G., Holmes, E., Delmas, O., Larrous, F., Guigon, G., Dickinson, P., Faye, O., Sall, A., et al (2010). Application of Broad-Spectrum Resequencing Microarray for Genotyping Rhabdoviruses. Journal of Virology, 84(18), 9557-9574. [More Information]
• Holmes, E. (2010). Does hepatitis C virus really form quasispecies? Infection, Genetics and Evolution, 10(4), 431-432. [More Information]
• Hang, V., Holmes, E., Veasna, D., Quy, N., Hien, T., Quail, M., Churcher, C., Parkhill, J., Cardosa, J., Farrar, J., et al (2010). Emergence of the Asian 1 Genotype of Dengue Virus Serotype 2 in Viet Nam: In Vivo Fitness Advantage and Lineage Replacement in South-East Asia. PLoS Neglected Tropical Diseases, 4(7), e757. [More Information]
• Bennett, S., Drummond, A., Kapan, D., Suchard, M., Muñoz-Jordán, J., Pybus, O., Holmes, E., Gubler, D. (2010). Epidemic Dynamics Revealed in Dengue Evolution. Molecular Biology and Evolution, 27(4), 811-818. [More Information]
• Jahnke, M., Holmes, E., Kerr, P., Wright, J., Strive, T. (2010). Evolution and Phylogeography of the Nonpathogenic Calicivirus RCV-A1 in Wild Rabbits in Australia. Journal of Virology, 84(23), 12397-12404. [More Information]
• Carrillo-Valenzo, E., Danis-Lozano, R., Velasco-Hernández, J., Sánchez-Burgos, G., Alpuche, C., López, I., Rosales, C., Baronti, C., de Lamballerie, X., Holmes, E., et al (2010). Evolution of dengue virus in Mexico is characterized by frequent lineage replacement. Archives of Virology, 155(9), 1401-1412. [More Information]
• Fusaro, A., Nelson, M., Joannis, T., Bertolotti, L., Monne, I., Salviato, A., Olaleye, O., Shittu, I., Sulaiman, L., Lombin, L., et al (2010). Evolutionary Dynamics of Multiple Sublineages of H5N1 Influenza Viruses in Nigeria from 2006 to 2008. Journal of Virology, 84(7), 3239-3247. [More Information]
• Volk, S., Chen, R., Tsetsarkin, K., Adams, A., Garcia, T., Sall, A., Nasar, F., Schuh, A., Holmes, E., Higgs, S., et al (2010). Genome-Scale Phylogenetic Analyses of Chikungunya Virus Reveal Independent Emergences of Recent Epidemics and Various Evolutionary Rates. Journal of Virology, 84(13), 6497-6504. [More Information]
• Grard, G., Moureau, G., Charrel, R., Holmes, E., Gould, E., de Lamballerie, X. (2010). Genomics and evolution of Aedes-borne flaviviruses. Journal of General Virology, 91(1), 87-94. [More Information]
• Boni, M., De Jong, M., van Doorn, H., Holmes, E. (2010). Guidelines for Identifying Homologous Recombination Events in Influenza A Virus. PloS One, 5(5), e10434. [More Information]
• Chen, R., Holmes, E. (2010). Hitchhiking and the Population Genetic Structure of Avian Influenza Virus. Journal of Molecular Evolution, 70(1), 98-105. [More Information]
• Murcia, P., Baillie, G., Daly, J., Elton, D., Jervis, C., Mumford, J., Newton, J., Parrish, C., Hoelzer, K., Dougan, G., et al (2010). Intra- and Interhost Evolutionary Dynamics of Equine Influenza Virus. Journal of Virology, 84(14), 6943-6954. [More Information]
• Hoelzer, K., Murcia, P., Baillie, G., Wood, J., Metzger, S., Osterrieder, N., Dubovi, E., Holmes, E., Parrish, C. (2010). Intrahost Evolutionary Dynamics of Canine Influenza Virus in Naïve and Partially Immune Dogs. Journal of Virology, 84(10), 5329-5335. [More Information]
• Pagan, I., Holmes, E. (2010). Long-Term Evolution of the Luteoviridae: Time Scale and Mode of Virus Speciation. Journal of Virology, 84(12), 6177-6187. [More Information]
• Hayward, J., Dubovi, E., Scarlett, J., Janeczko, S., Holmes, E., Parrish, C. (2010). Microevolution of Canine Influenza Virus in Shelters and Its Molecular Epidemiology in the United States. Journal of Virology, 84(24), 12636-12645. [More Information]
• Jones, A., Lowry, K., Aaskov, J., Holmes, E., Kitchen, A. (2010). Molecular evolutionary dynamics of Ross River virus and implications for vaccine efficacy. Journal of General Virology, 91(1), 182-188. [More Information]
• Talbi, C., Lemey, P., Suchard, M., Abdelatif, E., Elharrak, M., Jalal, N., Faouzi, A., Echevarría, J., Morón, S., Rambaut, A., et al (2010). Phylodynamics and Human-Mediated Dispersal of a Zoonotic Virus. PLoS Pathogens, 6(10), e1001166. [More Information]
• Pagan, I., Firth, C., Holmes, E. (2010). Phylogenetic Analysis Reveals Rapid Evolutionary Dynamics in the Plant RNA Virus Genus Tobamovirus. Journal of Molecular Evolution, 71(4), 298-307. [More Information]
• Rabaa, M., Hang, V., Wills, B., Farrar, J., Simmons, C., Holmes, E. (2010). Phylogeography of Recently Emerged DENV-2 in Southern Viet Nam. PLoS Neglected Tropical Diseases, 4(7), e766. [More Information]
• Singh, R., Levitt, A., Rajotte, E., Holmes, E., Ostiguy, N., vanEngelsdorp, D., Lipkin, W., dePamphilis, C., Toth, A., Cox-Foster, D. (2010). RNA Viruses in Hymenopteran Pollinators: Evidence of Inter-Taxa Virus Transmission via Pollen and Potential Impact on Non-Apis Hymenopteran Species. PloS One, 5(12), e14357. [More Information]
• Romano, C., de Carvalho-Mello, I., Jamal, L., de melo, F., Lamarino, A., Motoki, M., Pinho, J., Holmes, E., Zanotto, P. (2010). Social Networks Shape the Transmission Dynamics of Hepatitis C Virus. PloS One, 5(6), 1-9. [More Information]
• Vasilakis, N., Cardosa, J., Diallo, M., Sall, A., Holmes, E., Hanley, K., Weaver, S. (2010). Sylvatic Dengue Viruses Share the Pathogenic Potential of Urban/Endemic Dengue Viruses. Journal of Virology, 84(7), 3726-3727. [More Information]
• Holmes, E. (2010). The comparative genomics of viral emergence. Proceedings of the National Academy of Sciences of the United States of America, 107(Suppl 1), 1742-1746. [More Information]
• Carpi, G., Holmes, E., Kitchen, A. (2010). The Evolutionary Dynamics of Bluetongue Virus. Journal of Molecular Evolution, 70(6), 583-592. [More Information]
• Holmes, E. (2010). The RNA Virus Quasispecies: Fact or Fiction? Journal of Molecular Biology, 400(3), 271-273. [More Information]
• Balmaseda, A., Standish, K., Mercado, J., Matute, J., Tellez, Y., Saborío, S., Hammond, S., Nuñez, A., Avilés, W., Henn, M., et al (2010). Trends in Patterns of Dengue Transmission over 4 Years in a Pediatric Cohort Study in Nicaragua. The Journal of Infectious Diseases, 201(1), 5-14. [More Information]
• Ghedin, E., Wentworth, D., Halpin, R., Lin, X., Bera, J., DePasse, J., Fitch, A., Griesemer, S., Hine, E., Katzel, D., et al (2010). Unseasonal Transmission of H3N2 Influenza A Virus During the Swine-Origin H1N1 Pandemic. Journal of Virology, 84(11), 5715-5718. [More Information]
• Firth, C., Kitchen, A., Shapiro, B., Suchard, M., Holmes, E., Rambaut, A. (2010). Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses. Molecular Biology and Evolution, 27(9), 2038-2051. [More Information]
• Sall, A., Faye, O., Diallo, M., Firth, C., Kitchen, A., Holmes, E. (2010). Yellow Fever Virus Exhibits Slower Evolutionary Dynamics than Dengue Virus. Journal of Virology, 84(2), 765-772. [More Information]

2009

• Cardosa, J., Ooi, M., Tio, P., Perera, D., Holmes, E., Bibi, K., Manap, Z. (2009). Dengue Virus Serotype 2 from a Sylvatic Lineage Isolated from a Patient with Dengue Hemorrhagic Fever. PLoS Neglected Tropical Diseases, 3(4), e423. [More Information]
• Dunham, E., Dugan, V., Kaser, E., Perkins, S., Brown, I., Holmes, E., Taubenberger, J. (2009). Different Evolutionary Trajectories of European Avian-Like and Classical Swine H1N1 Influenza A Viruses. Journal of Virology, 83(11), 5485-5494. [More Information]
• Holmes, E., Grenfell, B. (2009). Discovering the Phylodynamics of RNA Viruses. PLoS Computational Biology, 5(10), e1000505. [More Information]
• Dorji, T., Yoon, I., Holmes, E., Wangchuk, S., Tobgay, T., Nisalak, A., Chinnawirotpisan, P., Sangkachantaranon, K., Gibbons, R., Jarman, R. (2009). Diversity and Origin of Dengue Virus Serotypes 1, 2, and 3, Bhutan. Emerging Infectious Diseases, 15(10), 1630-1632. [More Information]
• Talbi, C., Holmes, E., de Benedictis, P., Faye, O., Nakoune, E., Gamatie, D., Diarra, A., Elmamy, B., Sow, A., Adjogoua, E., et al (2009). Evolutionary history and dynamics of dog rabies virus in western and central Africa. Journal of General Virology, 90(4), 783-791. [More Information]
• Chen, R., Holmes, E. (2009). Frequent inter-species transmission and geographic subdivision in avian influenza viruses from wild birds. Virology, 383(1), 156-161. [More Information]
• Bahl, J., Vijaykrishna, D., Holmes, E., Smith, G., Guan, Y. (2009). Gene flow and competitive exclusion of avian influenza A virus in natural reservoir hosts. Virology, 390(2), 289-297. [More Information]
• Schreiber, M., Holmes, E., Ong, S., Soh, H., Liu, W., Tanner, L., Aw, P., Tan, H., Ng, L., Leo, Y., et al (2009). Genomic epidemiology of a dengue virus epidemic in urban Singapore. Journal of Virology, 83(9), 4163-4173. [More Information]
• Ramsden, C., Holmes, E., Charleston, M. (2009). Hantavirus Evolution in Relation to Its Rodent and Insectivore Hosts: No Evidence for Codivergence. Molecular Biology and Evolution, 26(1), 143-153. [More Information]
• Holmes, E., Tio, P., Perera, D., Muhi, J., Cardosa, J. (2009). Importation and co-circulation of multiple serotypes of dengue virus in Sarawak, Malaysia. Virus Research, 143(1), 1-5. [More Information]
• Firth, C., Charleston, M., Duffy, S., Shapiro, B., Holmes, E. (2009). Insights into the Evolutionary History of an Emerging Livestock Pathogen: Porcine Circovirus 2. Journal of Virology, 83(24), 12813-12821. [More Information]
• Cook, S., Moureau, G., Harbach, R., Mukwaya, L., Goodger, K., Ssenfuka, F., Gould, E., Holmes, E., de Lamballerie, X. (2009). Isolation of a novel species of flavivirus and a new strain of Culex flavivirus (Flaviviridae) from a natural mosquito population in Uganda. Journal of General Virology, 90(11), 2669-2678. [More Information]
• Ghedin, E., Fitch, A., Boyne, A., Griesemer, S., DePasse, J., Bera, J., Zhang, X., Halpin, R., Smit, M., Jennings, L., et al (2009). Mixed infection and the genesis of influenza virus diversity. Journal of Virology, 83(17), 8832-8841. [More Information]
• Kerr, P., Kitchen, A., Holmes, E. (2009). Origin and Phylodynamics of Rabbit Hemorrhagic Disease Virus. Journal of Virology, 83(23), 12129-12138. [More Information]
• Botosso, V., Zanotto, P., Ueda, M., Arruda, E., Gilio, A., Vieira, S., Stewien, K., Peret, T., Jamal, L., Pardini, M., et al (2009). Positive Selection Results in Frequent Reversible Amino Acid Replacements in the G Protein Gene of Human Respiratory Syncytial Virus. PLoS Pathogens, 5(1), e1000254. [More Information]
• Holmes, E. (2009). RNA virus genomics: A world of possibilities. Journal of Clinical Investigation, 119(9), 2488-2495. [More Information]
• Nelson, M., Spiro, D., Wentworth, D., Fan, J., Beck, E., St. George, K., Ghedin, E., Halpin, R., Bera, J., Holmes, E., et al (2009). The early diversification of influenza A/H1N1pdm. PLoS Currents, 2009 (NOV), ecurrents.RRN1126. [More Information]
• Rambaut, A., Holmes, E. (2009). The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic. PLoS Currents, , ecurrents.RRN1003. [More Information]
• Holmes, E. (2009). The Evolution and Emergence of RNA Viruses. Oxford: Oxford University Press.
• Holmes, E. (2009). The Evolutionary Genetics of Emerging Viruses. Annual Review of Ecology, Evolution and Systematics, 40, 353-372. [More Information]
• Nelson, M., Simonsen, L., Viboud, C., Miller, M., Holmes, E. (2009). The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Virology, 388(2), 270-278. [More Information]
• Duffy, S., Holmes, E. (2009). Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. Journal of General Virology, 90(6), 1539-1547. [More Information]

2008

• Romano, C., Zanotto, P., Holmes, E. (2008). Bayesian Coalescent Analysis Reveals a High Rate of Molecular Evolution in GB Virus C. Journal of Molecular Evolution, 66(3), 292-297. [More Information]
• Holmes, E. (2008). Comparative Studies of RNA Virus Evolution. In Esteban Domingo, Colin R Parrish, and John J Holland (Eds.), Origin and Evolution of Viruses, (pp. 119-134). London: Academic Press.
• Parrish, C., Holmes, E., Morens, D., Park, E., Burke, D., Calisher, C., Laughlin, C., Saif, L., Daszak, P. (2008). Cross-species virus transmission and the emergence of new epidemic diseases. Microbiology and Molecular Biology Reviews, 72(3), 457-470. [More Information]
• de Graaf, M., Osterhaus, A., Fouchier, R., Holmes, E. (2008). Evolutionary dynamics of human and avian metapneumoviruses. Journal of General Virology, 89(12), 2933-2942. [More Information]
• Holmes, E. (2008). Evolutionary History and Phylogeography of Human Viruses. Annual Review of Microbiology, 62, 307-328. [More Information]
• Palacios, G., Hui, J., Quan, P., Kalkstein, A., Honkavuori, K., Bussetti, A., Conlan, S., Evans, J., Chen, Y., vanEngelsdorp, D., et al (2008). Genetic Analysis of Israel Acute Paralysis Virus: Distinct Clusters Are Circulating in the United States. Journal of Virology, 82(13), 6209-6217. [More Information]
• Delmas, O., Holmes, E., Talbi, C., Larrous, F., Dacheux, L., Bouchier, C., Bourhy, H. (2008). Genomic Diversity and Evolution of the Lyssaviruses. PloS One, 3(4), e2057. [More Information]
• Briese, T., Renwick, N., Venter, M., Jarman, R., Ghosh, D., Köndgen, S., Shrestha, S., Hoegh, A., Casas, I., Holmes, E., et al (2008). Global Distribution of Novel Rhinovirus Genotype. Emerging Infectious Diseases, 14(6), 944-997. [More Information]
• Ramsden, C., Melo, F., Figueiredo, L., Holmes, E., Zanotto, P. (2008). High Rates of Molecular Evolution in Hantaviruses. Molecular Biology and Evolution, 25(7), 1488-1492. [More Information]
• Boni, M., Zhou, Y., Taubenberger, J., Holmes, E. (2008). Homologous Recombination Is Very Rare or Absent in Human Influenza A Virus. Journal of Virology, 82(10), 4807-4811. [More Information]
• Jarman, R., Holmes, E., Rodpradit, P., Klungthong, C., Gibbons, R., Nisalak, A., Rothman, A., Ennis, F., Mammen, M., Endy, T. (2008). Microevolution of Dengue Viruses Circulating among Primary School Children in Kamphaeng Phet, Thailand. Journal of Virology, 82(11), 5494-5500. [More Information]
• Nelson, M., Edelman, L., Spiro, D., Boyne, A., Bera, J., Halpin, R., Ghedin, E., Miller, M., Simonsen, L., Viboud, C., et al (2008). Molecular Epidemiology of A/H3N2 and A/H1N1 Influenza Virus during a Single Epidemic Season in the United States. PLoS Pathogens, 4(8), 1-17. [More Information]
• Nelson, M., Viboud, C., Simonsen, L., Bennett, R., Griesemer, S., St. George, K., Taylor, J., Spiro, D., Sengamalay, N., Ghedin, E., et al (2008). Multiple Reassortment Events in the Evolutionary History of H1N1 Influenza A Virus Since 1918. PLoS Pathogens, 4(2), 1-12. [More Information]
• Hoelzer, K., Shackelton, L., Parrish, C., Holmes, E. (2008). Phylogenetic analysis reveals the emergence, evolution and dispersal of carnivore parvoviruses. Journal of General Virology, 89(9), 2280-2289. [More Information]
• Duffy, S., Holmes, E. (2008). Phylogenetic Evidence for Rapid Rates of Molecular Evolution in the Single-Stranded DNA Begomovirus Tomato Yellow Leaf Curl Virus. Journal of Virology, 82(2), 957-965. [More Information]
• Chang, G., Hong, Y., Ko, K., Bhardwaj, G., Holmes, E., Patterson, R., Van Rossum, D. (2008). Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity. Proceedings of the National Academy of Sciences of the United States of America, 105(36), 13474-13479. [More Information]
• Briese, T., Palacios, G., Lipkin, W., Renwick, N., Venter, M., Jarman, R., Dominguez, S., Holmes, K., Holmes, E. (2008). Prior Evidence of Putative Novel Rhinovirus Species, Australia - In Response. Emerging Infectious Diseases, 14(11), 1823-1825. [More Information]
• Simmons, H., Holmes, E., Stephenson, A. (2008). Rapid evolutionary dynamics of zucchini yellow mosaic virus. Journal of General Virology, 89(4), 1081-1085. [More Information]
• Duffy, S., Shackelton, L., Holmes, E. (2008). Rates of evolutionary change in viruses: patterns and determinants. Nature Reviews Genetics, 9(4), 267-276. [More Information]
• Pomeroy, L., Bjornstad, O., Holmes, E. (2008). The Evolutionary and Epidemiological Dynamics of the Paramyxoviridae. Journal of Molecular Evolution, 66(2), 98-106. [More Information]
• Chen, R., Holmes, E. (2008). The Evolutionary Dynamics of Human Influenza B Virus. Journal of Molecular Evolution, 66(6), 655-663. [More Information]
• Dugan, V., Chen, R., Spiro, D., Sengamalay, N., Zaborsky, J., Ghedin, E., Nolting, J., Swayne, D., Runstadler, J., Happ, G., et al (2008). The Evolutionary Genetics and Emergence of Avian Influenza Viruses in Wild Birds. PLoS Pathogens, 4(5), 1-9. [More Information]
• Rambaut, A., Pybus, O., Nelson, M., Viboud, C., Taubenberger, J., Holmes, E. (2008). The genomic and epidemiological dynamics of human influenza A virus. Nature, 453(7195), 615-619. [More Information]
• Cox-Foster, D., Conlan, S., Holmes, E., Palacios, G., Kalkstein, A., Evans, J., Moran, N., Quan, P., Geiser, D., Briese, T., et al (2008). The Latest Buzz About Colony Collapse Disorder - Response. Science, 319(5864), 724-725. [More Information]
• Bourhy, H., Reynes, J., Dunham, E., Dacheux, L., Larrous, F., Duong, V., Xu, G., Yan, J., Miranda, M., Holmes, E. (2008). The origin and phylogeography of dog rabies virus. Journal of General Virology, 89(11), 2673-2681. [More Information]
• Shackelton, L., Holmes, E. (2008). The role of alternative genetic codes in viral evolution and emergence. Journal of Theoretical Biology, 254(1), 128-134. [More Information]
• Hoelzer, K., Shackelton, L., Holmes, E., Parrish, C. (2008). Within-Host Genetic Diversity of Endemic and Emerging Parvoviruses of Dogs and Cats. Journal of Virology, 82(22), 11096-11105. [More Information]

2007

• Cox-Foster, D., Conlan, S., Holmes, E., Palacios, G., Evans, J., Moran, N., Quan, P., Briese, T., Hornig, M., Geiser, D., et al (2007). A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder. Science, 318(5848), 283-287. [More Information]
• Brault, A., Huang, C., Langevin, S., Kinney, R., Bowen, R., Ramey, W., Panella, N., Holmes, E., Powers, A., Miller, B. (2007). A single positively selected West Nile viral mutation confers increased virogenesis in American crows. Nature Genetics, 39(9), 1162-1166. [More Information]
• Aulicino, P., Holmes, E., Rocco, C., Mangano, A., Sen, L. (2007). Extremely Rapid Spread of Human Immunodeficiency Virus Type 1 BF Recombinants in Argentina. Journal of Virology, 81(1), 427-429. [More Information]
• Aaskov, J., Buzacott, K., Field, E., Lowry, K., Berlioz-Arthaud, A., Holmes, E. (2007). Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient. Journal of General Virology, 88, 3334-3340. [More Information]
• Bryant, J., Holmes, E., Barrett, A. (2007). Out of Africa: A Molecular Perspective on the Introduction of Yellow Fever Virus into the Americas. PLoS Pathogens, 3(5), e75. [More Information]
• Davis, P., Rambaut, A., Bourhy, H., Holmes, E. (2007). The evolutionary dynamics of canid and mongoose rabies virus in southern Africa. Archives of Virology, 152, 1251-1258. [More Information]
• de Freitas, R., Durigon, E., Oliveira, D., Romano, C., Linhares, A., Melo, F., Walshkeller, L., Barbosa, M., Huatuco, E., Holmes, E., et al (2007). The “pressure pan” evolution of human erythrovirus B19 in the Amazon, Brazil. Virology, 369, 281-287. [More Information]