Holmes, Edward - University of Sydney - School of Biological Sciences

研究领域

Professor Holmes’ interest in the emergence and spread of novel viral infections began in the late 1980s/early 1990s, “as this was a time of the highest rates of HIV-associated deaths and when hepatitis C virus was first identified”. He has spent the past 25 years using molecular genetic techniques to understand the determinants of cross-species pathogen transmission and emergence. His work has helped 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. “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 Professor Holmes. His research has helped to explain the nature of virulence evolution following species jumps and provided insights into many RNA viruses, including dengue virus. His studies on myxomatosis in the European rabbit populations of Australia and Europe revealed multiple genetic routes to high virulence or attenuation. His influenza virus research, including phylogenetic studies showing the emergence of major drug-resistant strains, has implications for disease control and provides key information on how the viruses might evolve in response to future antiviral and vaccination strategies. Currently, he is studying families of viruses and bacterial pathogens to define the patterns/rationale for why some pathogens are more likely to jump between species and spread. The molecular analyses will be used to understand the measurable impact of the novel infections on public and animal health and 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 Professor Holmes. He also is using “ancient DNA” to investigate the causes and patterns of spread of past pandemics such as plague and cholera. Another study will use metagenomics to investigate the cause of disease syndromes of uncertain microbial cause (e.g. Lyme-like syndrome) in Australia.For further information, go to: http://sydney.edu.au/science/biology/viralevolution/index.shtml. Applications from potential Ph.D. students are particularly welcome.

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Sabir, J., Lam, T., Ahmed, M., Li, L., Abo-Aba, S., Qureshi, M., Abu-Zeid, M., Zhang, Y., et al, Holmes, E. (2016). Co-circulation of three camel coronavirus species and recombination of MERS-CoV in Saudi Arabia. Science, 351(6268), 81-84. [More Information] Rambaut, A., Dudas, G., de Carvalho, L., Park, D., Yozwiak, N., Holmes, E., Andersen, K. (2016). Comment on “Mutation rate and genotype variation of Ebola virus from Mali case sequences�? Science, 353(6300), 658-658. [More Information] Feng, K., Sun, M., Iketani, S., Holmes, E., Parrish, C. (2016). Comparing the functions of equine and canine influenza H3N8 virus PA-X proteins: Suppression of reporter gene expression and modulation of global host gene expression. Virology, 496, 138-146. [More Information] Holmes, E. (2016). Complexities of Estimating Evolutionary Rates in Viruses. Journal of Virology, 90(4), 2155-2155. [More Information] Duchene, S., Duchene, D., Di Giallonardo, F., Eden, J., Geoghegan, J., Holt, K., Ho, S., Holmes, E. (2016). Cross-validation to select Bayesian hierarchical models in phylogenetics. BMC Evolutionary Biology, 16(1), 1-8. [More Information] Dill, J., Camus, A., Leary, J., Di Giallonardo, F., Holmes, E., Ng, T. (2016). Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses. Journal of Virology, 90(17), 7920-7933. [More Information] Shi, M., Lin, X., Vasilakis, N., Tian, J., Li, C., Chen, L., Eastwood, G., Diao, X., Chen, M., Chen, X., Holmes, E., et al (2016). Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses. Journal of Virology, 90(2), 659-669. [More Information] Chen, L., Lin, X., Guo, W., Tian, J., Wang, W., Ying, X., Wang, M., Yu, B., Yang, Z., Shi, M., Holmes, E., et al (2016). Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China. Journal of General Virology, 97(4), 844-854. [More Information] Bos, K., Herbig, A., Sahl, J., Waglechner, N., Fourment, M., Forrest, S., Klunk, J., Schuenemann, V., Poinar, D., Kuch, M., Holmes, E., et al (2016). Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus. eLife, 5, 1-11. [More Information] Di Giallonardo, F., Geoghegan, J., Docherty, D., McLean, R., Zody, M., Qu, J., Yang, X., Birren, B., Malboeuf, C., Newman, R., Holmes, E., et al (2016). Fluid spatial dynamics of West Nile virus in the USA: rapid spread in a permissive host environment. Journal of Virology, 90(2), 862-872. [More Information] Lam, T., Zhu, H., Guan, Y., Holmes, E. (2016). Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses. Annual Review of Genomics and Human Genetics, 17, 193-218. [More Information] Li, K., Lin, X., Huang, K., Zhang, B., Shi, M., Guo, W., Wang, M., Wang, W., Xing, J., Li, M., Holmes, E., et al (2016). Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans. Virology, 494, 168-177. [More Information] Tan, Y., Hassan, F., Schuster, J., Simenauer, A., Selvarangan, R., Halpin, R., Lin, X., fedorova, N., Stockwell, T., Lam, T., Holmes, E., et al (2016). Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States. Journal of Virology, 90(4), 1997-2007. [More Information] Abaddi, M., Fusaro, A., Ceolin, C., Quartesan, R., Dalla Pozza, M., Cattoli, G., Toffan, A., Holmes, E., Panzarin, V. (2016). Molecular Evolutionand Phylogeography of Co-circulating IHNV and VHSV in Italy. Frontiers in Microbiology, 7, Article: 1306. [More Information] Geoghegan, J., Senior, A., Holmes, E. (2016). Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence. Proceedings of the Royal Society B, 283(1837), 20160727-9 pages. [More Information] Poon, L., Song, T., Rosenfeld, R., Lin, X., Rogers, M., Zhou, B., Sebra, R., Halpin, R., Guan, Y., Twaddle, A., Holmes, E., et al (2016). Quantifying influenza virus diversity and transmission in humans. Nature Genetics, 48(2), 195-200. [More Information] Bourhy, H., Nakoune, E., Hall, M., Nouvellet, P., Lepelletier, A., Talbi, C., Watier, L., Holmes, E., Cauchemez, S., Lemey, P., et al (2016). Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting. PLoS Pathogens, 12(4), 1-15. [More Information] Valastro, V., Holmes, E., Britton, P., Fusaro, A., Jackwood, M., Cattoli, G., Monne, I. (2016). S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification. Infection, Genetics and Evolution, 39, 349-364. [More Information] Fourment, M., Holmes, E. (2016). Seqotron: A user-friendly sequence editor for Mac OS X. BMC Research Notes, 9(1), 1-4. [More Information] Allison, A., Organtini, L., Zhang, S., Hafenstein, S., Holmes, E., Parrish, C. (2016). Single Mutations in the VP2 300 Loop Region of the Three-Fold Spike of the Carnivore Parvovirus Capsid Can Determine Host Range. Journal of Virology, 90(2), 753-767. [More Information]