Professor Edward Holmes

Australia Fellow

A12 - Macleay Building
The University of Sydney

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

Curriculum vitae Curriculum vitae

Biographical details

I joined the University of Sydney in October 2012. Prior to moving here, I worked at Penn State University (2005-2012), the University of Oxford, where I was also a Fellow of New College (1993-2004), the University of Edinburgh (1991-1993), and the University of California, Davis (1990-1991). My Ph.D. is from the University of Cambridge (1990), and I also have an undergraduate degree from University College London (1986).

I have spent most of my scientific career undertaking research aimed at revealing the principle patterns and processes of viral evolution and emergence. Although I still find work of this type fascinating, and I will continue to explore these themes, I want the molecular evolution and epidemiology I pursue to have a more direct and measurable impact on public and animal health. This will be my primary goal at the University of Sydney.

Research interests

I am an evolutionary biologist who has worked on viruses and other microbes for over 20 years. My main research theme has been to determine the mechanisms by which viruses emerge in new host species, their patterns and dynamics of spread through populations, and their major mechanisms of evolutionary change. My main research tool has been the evolutionary (largely phylogenetic) analysis of gene sequence data. As case studies I have worked on a number of important viruses of humans and other animals, such as HIV, influenza, dengue, rabies and myxoma. I have also published on a number of bacterial diseases. A good summary of my research and ideas can be found in my book on viral evolution.

Please email me if you are interested in joining my exciting research group or wish to discuss specific areas of my research program.

Keywords

Epidemiology; Virology; Bacteriology

Selected grants

2014

  • 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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Journals

  • 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]
  • 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.
  • 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]
  • 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]
  • 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 Vibro cholerae from the Philadelphia cholera outbreak of 1849. The New England Journal of Medicine.
  • 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.
  • 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), 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, 1-9.
  • 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., Lu, X., Viboud, C., He, J., Zhang, S., Lu, J., Wu, C., Fang, S., et al (2013). Epidemiological Dynamics and Phylogeography of Influenza Virus in Southern China. The Journal of Infectious Diseases, 107, 106-114.
  • 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., Holmes, E., Chinnawirotpisan, P., Thaisomboonsuk, B., Srikiatkhachorn, A., Rothman, A., Tannitisupawong, D., Aldstadt, J., Nisalak, A., 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.
  • 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), 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, 1-9.
  • 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.
  • 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, 1-8.
  • 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]

2014

  • 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]
  • 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.
  • 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]
  • 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]
  • 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 Vibro cholerae from the Philadelphia cholera outbreak of 1849. The New England Journal of Medicine.
  • 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.

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), 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, 1-9.
  • 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., Lu, X., Viboud, C., He, J., Zhang, S., Lu, J., Wu, C., Fang, S., et al (2013). Epidemiological Dynamics and Phylogeography of Influenza Virus in Southern China. The Journal of Infectious Diseases, 107, 106-114.
  • 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., Holmes, E., Chinnawirotpisan, P., Thaisomboonsuk, B., Srikiatkhachorn, A., Rothman, A., Tannitisupawong, D., Aldstadt, J., Nisalak, A., 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.
  • 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), 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, 1-9.
  • 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.
  • 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, 1-8.
  • 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]

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