Professor Edward Holmes

NHMRC Australia Fellow
Faculty Member, Marie Bashir Institute for Infectious Diseases and Biosecurity
Faculty Member, Charles Perkins Centre, Sydney Medical School
Faculty Member, School of Biological Sciences

Telephone +61 2 9351 5591
Fax +61 2 9351 3890

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Biographical details

Professor Edward Holmes is a NHMRC Australia Fellow at the University of Sydney, Faculty Member at the Marie Bashir Institute for Infectious Diseases and Biosecurity, and Faculty Member of the Charles Perkins Centre at Sydney Medical School. He is a conjoint appointee at Sydney Medical School and theFaculty of Science. Prior to his present appointment, Prof Holmes was the Verne M. Willaman Chair in the Life Sciences at The Pennsylvania State University, USA, where he also was appointed Eberly College of Science Distinguished Senior Scholar (2007-2012)and Professor of Biology (2005-2012). Concurrently, he was an Affiliate Member of the Fogarty International Centre, National Institutes of Health, USA. After completing his PhD at the University of Cambridge, UK in 1990, Prof Holmes undertook postdoctoral research at University of California, Davis, USA, University of Edinburgh, UK, and at Oxford University, UK, where he held various academic posts and from 1999-2004 was Fellow of New College, Oxford. Prof Holmes’ research primarily focuses on the evolution and emergence of infectious diseases, particularly the mechanisms by which pathogens cross species boundaries to emerge in humans. Over the past two decades he has studied the emergence and/or spread of numerous pathogens including avian influenza (bird flu) virus, dengue virus, HIV, hepatitis C virus, measles virus, myxoma virus, RHDV (rabbit haemorrhagic fever virus) and Yersinia pestis (the plague bacterium). Among his many research achievements, of note are his significant contributionsto our understanding of the evolutionary and epidemiological dynamics of influenza, which have assisted in influenza virus strain prediction and vaccine deployment. Based on his track record and significant research output, Professor Holmes has received a number of prestigious fellowships and awards including the highest-ranked competitive biomedical fellowship in Australia (NHMRC Australia Fellow), which he holds currently. In 2010 he won the Faculty Scholars Medal in the Life and Health Sciences at The Pennsylvania State University and in 2003, he was awarded the Scientific Medal for Achievement in Research by a Zoologist Under the Age of 40 by the Zoological Society of London. Professor Holmes’ research contributions are further substantiated by his outstanding publication record – he is the author of 385 peer-reviewed papers and two highly-regarded books, His papers have received > 23,000 citations (29,029 in Google Scholar) with H-index = 80 (93 in Google Scholar).

Professor Holmes collaborates extensively with researchers worldwide (including China, Vietnam, USA and Canada) and holds international appointments in infectious diseases and disease control – he is presently a Member (since 2009) of The Center for Infection and Immunity, Columbia University, New York, USA, and Guest Professor at the Chinese Center for Disease Control and Prevention, Beijing, China.

Research interests

During the late 1980s/early 1990s, Prof Holmes developed an interest in the emergence of novel viral infections and their spread “as this was a time of the highest rates of HIV-associated deaths and also when hepatitis C virus was first identified” he says. He has spent the past two decades using molecular genetic techniques to understand the determinants of cross-species pathogen transmission and emergence. His work has provided key insights into the emergence of novel infections – helping define the barriers faced by viruses as they emerge in new hosts, determine the range of transmission patterns exhibited by emerging viruses, and establish genetic models for host switching. His research has helped to explain the nature of virulence evolution following a species jump. His studies on myxomatosis in the European rabbit populations of Australia and Europe revealed multiple genetic routes to high virulence or attenuation.

“A key question is, how often are new viruses created by jumping to new host species (which is central to the process of viral emergence), compared to their genesis within single hosts?” says Prof Holmes. Using a comparative approach he established that while cross-species transmission is the dominant mechanism, it most often occurs among closely-related host species suggesting that there are major constraints to host jumping, which in turn can inform models of disease emergence. In addition, Prof Holmes’ research has provided fundamental insights into the origin and emergence of specific RNA viruses, including dengue virus, where he was instrumental in describing the global genetic diversity in the human and monkey (reservoir) forms of this virus. His observations of thecontinual introduction and co-circulation of multiple lineages of influenza virus in specific populations have implications for control of this critically important disease, and his phylogenetic studies of influenza virus have revealed the emergence of major drug-resistant strains. His research has enabled accurate assessments of the types of viruses, the reservoir species and the selective pressures involved for emergence in human populations, and how the viruses might evolve in response to future antiviral and vaccination strategies.

Currently, Prof Holmes’ is studying families of viruses and bacterial pathogens to define the patterns/rationale for why some pathogens are more likely than others to cross species boundaries and spread. Importantly, the molecular analyses will be used to inform and understand the measurable impact of the novel infections on public and animal health – to help devise strategies for control and eradication of these infections. “I am interested in the core principles and commonalities regarding pathogens that jump species and spread, and how we can use this information to realistically predict the next pandemic” says Prof Holmes. He also is using “ancient DNA” to investigate the causes and patterns of spread of past pandemics such as plague and cholera. For further information on Prof Holmes’ research, go to: http://sydney.edu.au/science/biology/viralevolution/index.shtml

Associations

• American Society for Microbiology

Awards and honours

• 2011: Australia Fellow, National Health and Medical Research Council (NHMRC), Australia.

• 2010: Fogarty International Center Director’s Merit Award to the Multinational Influenza Seasonal Mortality Study Team (MISMS). National Institutes of Health, USA.

• 2010: Faculty Scholars Medal in the Life and Health Sciences. The Pennsylvania State University, USA.

• 2008: Kavli Fellow, National Academy of Sciences, USA.

• 2003: Scientific Medal for achievement in research by a zoologist under the age of 40. Zoological Society of London, UK.

In the media

International links

China

(Chinese Center for Disease Control and Prevention) 2014-Present: Guest Professor

United States

(The Center for Infection and Immunity, Columbia University, New York) 2009-Present: Member

Selected grants

2014

  • Towards real time data sharing to support patient-centred care, quality health delivery, improvement programmes, performance management and research; Morris J, Roberts C, Simpson S, Kay J, Venkatesh S, Fazekas B, Arthur J, Feng D, Holmes E, James D, Yang J, Engel A; NSW Ministry of Health, Office for Health and Medical Research/Bioinformatics Collaborative Grants Program.
  • Defining the evolution of pathogen virulence to enhance rabbit biocontrol; Kerr P, Holmes E, Strive T; Australian Research Council (ARC)/Discovery Projects (DP).
  • Black Death genomics and the evolution of pathogen virulence; Holmes E, Poinar H, Iredell J; National Health and Medical Research Council (NHMRC)/Project Grants.

2013

  • Genomic Sequencing Centers for Infectious Diseases; Wentworth D, Holmes E; National Institutes of Health (USA)/Research Support.
  • Genetic variability of non-segmented negative-sense RNA virus populations and host adaptation; Holmes E, Bourhy H; Agence Nationale de la Recherche/Research Grant.
  • Cluster-randomised controlled trial to test the effectiveness of facemasks in preventing influenza, corona and other respiratory viruses among Hajj pilgrims; Holmes E, Rashid H; The Qatar Foundation/Research Grant.

2012

  • The Evolutionary and Biological Bases of Host Switching in Viruses; Holmes E, Parrish C, Holmes E; National Institutes of Health (USA)/Research Support.
  • Genomic analysis of the canonical case of virulence evolution: myxomatosis in Australia; Holmes E, Read A, Kerr P; National Institutes of Health (USA)/Research Support.
  • Australia Fellowship; Holmes E; National Health and Medical Research Council (NHMRC)/Career Awards: Australian Fellowship.

Selected publications

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Books

  • Holmes, E. (2009). The Evolution and Emergence of RNA Viruses. Oxford: Oxford University Press.

Book Chapters

  • 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. (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 Elsevier.

Journals

  • 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 (PNAS) of the United States of America, 118(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 of London. 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.
  • 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. The Journal of General Virology, 95(Pt4), 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.
  • 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]
  • 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), 1525-5514. [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]
  • 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]
  • 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.
  • 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]
  • 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. The 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]
  • 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., Holmes, E., et al (2014). Yersinia pestis and the Plague of Justinian 541-543 AD: a genomic analysis. Lancet Infectious Diseases, 14(4), 319-326. [More Information]
  • 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 (PNAS) 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. Biological Sciences, 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 (PNAS) 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 of London. B Biological Sciences, 280(1750), 20122173. [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. Biological Sciences, 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). 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]
  • 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), 1-12. [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), 1-9. [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), 1-13. [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), 1-15. [More Information]
  • 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. P L o S Pathogens, 7(6), 1-10. [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: an international journal of applied plant pathology, 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 (PNAS) 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. P L o S 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 (PNAS) 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]
  • 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), 1-11. [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), 1-11. [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), 1-10. [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), 1-11. [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), 1-16. [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 (PNAS) 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]
  • 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), 1-5. [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), 1-6. [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.
  • 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.
  • 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), 1-11. [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), 1-10. [More Information]
  • Rambaut, A., Holmes, E. (2009). The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic. PLoS Currents, , 1-4. [More Information]
  • 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]
  • 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]
  • 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), 1-6. [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 (PNAS) 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, 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]

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 (PNAS) of the United States of America, 118(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 of London. 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.
  • 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. The Journal of General Virology, 95(Pt4), 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.
  • 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]
  • 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), 1525-5514. [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]
  • 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]
  • 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.
  • 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]
  • 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. The 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]
  • 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., Holmes, E., et al (2014). Yersinia pestis and the Plague of Justinian 541-543 AD: a genomic analysis. Lancet Infectious Diseases, 14(4), 319-326. [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 (PNAS) 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. Biological Sciences, 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 (PNAS) 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 of London. B Biological Sciences, 280(1750), 20122173. [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. Biological Sciences, 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), 1-12. [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), 1-9. [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), 1-13. [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), 1-15. [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. P L o S Pathogens, 7(6), 1-10. [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: an international journal of applied plant pathology, 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 (PNAS) 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. P L o S 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 (PNAS) 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), 1-11. [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), 1-11. [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), 1-10. [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), 1-11. [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), 1-16. [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 (PNAS) 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), 1-5. [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), 1-6. [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.
  • 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.
  • 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), 1-11. [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), 1-10. [More Information]
  • Rambaut, A., Holmes, E. (2009). The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic. PLoS Currents, , 1-4. [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 Elsevier.
  • 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), 1-6. [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 (PNAS) 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, 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]

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