E C Holmes

Summary

Affiliation: Pennsylvania State University
Country: USA

Publications

  1. doi request reprint Rates of evolutionary change in viruses: patterns and determinants
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 9:267-76. 2008
  2. pmc Cross-species virus transmission and the emergence of new epidemic diseases
    Colin R Parrish
    Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    Microbiol Mol Biol Rev 72:457-70. 2008
  3. pmc Endogenous lentiviruses in the ferret genome
    Jie Cui
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
    J Virol 86:3383-5. 2012
  4. pmc Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1
    Charles T T Edwards
    Nuffield Department of Clinical Medicine, University of Oxford, The Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
    BMC Evol Biol 6:28. 2006
  5. pmc Ancient lentiviruses leave their mark
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 104:6095-6. 2007
  6. pmc Viral evolution in the genomic age
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
    PLoS Biol 5:e278. 2007
  7. pmc RNA virus genomics: a world of possibilities
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, Mueller Laboratory, University Park, Pennsylvania 16802, USA
    J Clin Invest 119:2488-95. 2009
  8. pmc Evolution in health and medicine Sackler colloquium: The comparative genomics of viral emergence
    Edward C Holmes
    Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 107:1742-6. 2010
  9. ncbi request reprint The evolutionary genetics of viral emergence
    E C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    Curr Top Microbiol Immunol 315:51-66. 2007
  10. doi request reprint Importation and co-circulation of multiple serotypes of dengue virus in Sarawak, Malaysia
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Virus Res 143:1-5. 2009

Detail Information

Publications95

  1. doi request reprint Rates of evolutionary change in viruses: patterns and determinants
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 9:267-76. 2008
    ....
  2. pmc Cross-species virus transmission and the emergence of new epidemic diseases
    Colin R Parrish
    Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    Microbiol Mol Biol Rev 72:457-70. 2008
    ....
  3. pmc Endogenous lentiviruses in the ferret genome
    Jie Cui
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
    J Virol 86:3383-5. 2012
    ..These data support the notion that lentiviruses have evolved on timescales of millions of years...
  4. pmc Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1
    Charles T T Edwards
    Nuffield Department of Clinical Medicine, University of Oxford, The Peter Medawar Building for Pathogen Research, Oxford, OX1 3SY, UK
    BMC Evol Biol 6:28. 2006
    ..Despite this, the magnitude of this population bottleneck is unclear...
  5. pmc Ancient lentiviruses leave their mark
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 104:6095-6. 2007
  6. pmc Viral evolution in the genomic age
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
    PLoS Biol 5:e278. 2007
  7. pmc RNA virus genomics: a world of possibilities
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, Mueller Laboratory, University Park, Pennsylvania 16802, USA
    J Clin Invest 119:2488-95. 2009
    ..However, genomic data have so far made fewer inroads into areas of more direct importance for disease, prevention, and control; thus, harnessing their full potential remains an important goal...
  8. pmc Evolution in health and medicine Sackler colloquium: The comparative genomics of viral emergence
    Edward C Holmes
    Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 107:1742-6. 2010
    ....
  9. ncbi request reprint The evolutionary genetics of viral emergence
    E C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    Curr Top Microbiol Immunol 315:51-66. 2007
    ....
  10. doi request reprint Importation and co-circulation of multiple serotypes of dengue virus in Sarawak, Malaysia
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Virus Res 143:1-5. 2009
    ..In sum, our analysis reveals a frequent traffic of DENV in South-East Asia, with Sarawak representing a local sink population...
  11. pmc The evolution of viral emergence
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 103:4803-4. 2006
  12. pmc What does virus evolution tell us about virus origins?
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, Pennsylvania 16802, USA
    J Virol 85:5247-51. 2011
    ..I also highlight the advances that are needed to come to a better understanding of virus origins, most notably the ability to accurately infer deep evolutionary history from the phylogenetic analysis of conserved protein structures...
  13. pmc Extensive geographical mixing of 2009 human H1N1 influenza A virus in a single university community
    Edward C Holmes
    Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    J Virol 85:6923-9. 2011
    ..H1N1/09 influenza A virus is therefore characterized by a remarkable spatial fluidity, which is likely to impede community-based methods for its control, including class cancellations, quarantine, and chemoprophylaxis...
  14. pmc Why do RNA viruses recombine?
    Etienne Simon-Loriere
    Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, USA
    Nat Rev Microbiol 9:617-26. 2011
    ..Rather, recombination rates seemingly reflect larger-scale patterns of viral genome organization, such that recombination may be a mechanistic by-product of the evolutionary pressures acting on other aspects of virus biology...
  15. doi request reprint The evolution of endogenous viral elements
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Cell Host Microbe 10:368-77. 2011
    ....
  16. doi request reprint Evolutionary history and phylogeography of human viruses
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Annu Rev Microbiol 62:307-28. 2008
    ....
  17. pmc Phylogeography of recently emerged DENV-2 in southern Viet Nam
    Maia A Rabaa
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
    PLoS Negl Trop Dis 4:e766. 2010
    ..However, these data also indicate that more rural areas are also capable of maintaining virus populations and hence fueling DENV evolution over multiple seasons...
  18. pmc Frequent inter-species transmission and geographic subdivision in avian influenza viruses from wild birds
    Rubing Chen
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    Virology 383:156-61. 2009
    ..These results suggest that AIVs can readily infect many of the bird species that share breeding/feeding areas...
  19. pmc Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918
    Martha I Nelson
    Department of Biology, Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
    PLoS Pathog 4:e1000012. 2008
    ..Intra-subtype reassortment therefore appears to be a more important process in the evolution and epidemiology of H1N1 influenza A virus than previously realized...
  20. ncbi request reprint Molecular evolution of dengue 2 virus in Puerto Rico: positive selection in the viral envelope accompanies clade reintroduction
    Shannon N Bennett
    Department of Biology, University of Puerto Rico Rio Piedras, San Juan, PR, USA
    J Gen Virol 87:885-93. 2006
    ....
  21. pmc Multiple introductions of the Old World begomovirus Tomato yellow leaf curl virus into the New World
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    Appl Environ Microbiol 73:7114-7. 2007
    ..This analysis supports a second introduction of this Old World begomovirus into the New World, most likely from Asia...
  22. pmc Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    J Virol 82:957-65. 2008
    ..Our results therefore suggest that the high evolutionary rate of the geminiviruses is not primarily due to frequent recombination and may explain their ability to emerge in novel hosts...
  23. ncbi request reprint A metagenomic survey of microbes in honey bee colony collapse disorder
    Diana L Cox-Foster
    Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
    Science 318:283-7. 2007
    ..One organism, Israeli acute paralysis virus of bees, was strongly correlated with CCD...
  24. pmc Comparative analysis reveals frequent recombination in the parvoviruses
    Laura A Shackelton
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    J Gen Virol 88:3294-301. 2007
    ..Further, the rodent parvoviruses show complex evolutionary histories for separate genomic regions, suggesting recombination at the interspecies level...
  25. pmc The evolutionary and epidemiological dynamics of the paramyxoviridae
    Laura W Pomeroy
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, 501 ASI Building, University Park, PA 16802, USA
    J Mol Evol 66:98-106. 2008
    ....
  26. ncbi request reprint Bayesian estimates of the evolutionary rate and age of hepatitis B virus
    Yang Zhou
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    J Mol Evol 65:197-205. 2007
    ..We conclude that HBV exhibits rapid evolutionary dynamics, typical of other viruses dependent on reverse transcriptase-mediated replication...
  27. ncbi request reprint The evolution of epidemic influenza
    Martha I Nelson
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 8:196-205. 2007
    ....
  28. pmc Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2
    Cadhla Firth
    Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    J Virol 83:12813-21. 2009
    ..This high rate of evolution may allow PCV2 to maintain evolutionary dynamics closer to those of single-stranded RNA viruses than to those of double-stranded DNA viruses, further facilitating the rapid emergence of PCV2 worldwide...
  29. doi request reprint Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence
    Cadhla Ramsden
    Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, USA
    Mol Biol Evol 26:143-53. 2009
    ..Based on the presence of clade-defining amino acids in all genomic segments, we propose that the patterns of amino acid replacement in these viruses are also compatible with a history of host-specific adaptation...
  30. pmc The evolutionary dynamics of human influenza B virus
    Rubing Chen
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    J Mol Evol 66:655-63. 2008
    ..Additionally, we suggest that the interaction with influenza A virus may be central in shaping the evolutionary dynamics of influenza B virus, facilitating the shift of dominance between the Vic87 and the Yam88 lineages...
  31. doi request reprint Phylogenetic analysis reveals rapid evolutionary dynamics in the plant RNA virus genus tobamovirus
    Israel Pagán
    Department of Biology, Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
    J Mol Evol 71:298-307. 2010
    ..This is supported by our cophylogeny analysis which revealed significantly discordant evolutionary histories between the tobamoviruses and the plant families they infect...
  32. pmc Long-term evolution of the Luteoviridae: time scale and mode of virus speciation
    Israel Pagán
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    J Virol 84:6177-87. 2010
    ..Finally, our phylogenetic analysis suggested that viral speciation events tended to occur within the same plant host species and country of origin, as expected if speciation is largely sympatric, rather than allopatric, in nature...
  33. pmc Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
    PLoS Biol 3:e300. 2005
    ....
  34. pmc JC virus evolution and its association with human populations
    Laura A Shackelton
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    J Virol 80:9928-33. 2006
    ....
  35. doi request reprint Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses
    Siobain Duffy
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    J Gen Virol 90:1539-47. 2009
    ..We also validated our rate estimates by comparing them with those depicting the emergence of TYLCV in North America. These results further support the notion that geminiviruses evolve as rapidly as many RNA viruses...
  36. ncbi request reprint Comparative analysis reveals no consistent association between the secondary structure of the 3'-untranslated region of dengue viruses and disease syndrome
    Yang Zhou
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    J Gen Virol 87:2595-603. 2006
    ..It was concluded that the 3'-UTR is not the sole determinant of DENV virulence in nature, although variation in secondary structure may greatly influence viral fitness...
  37. pmc Hitchhiking and the population genetic structure of avian influenza virus
    Rubing Chen
    Department of Biology, Center for Infectious Disease Dynamics, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    J Mol Evol 70:98-105. 2010
    ....
  38. pmc Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States
    Martha I Nelson
    Department of Biology, Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
    PLoS Pathog 4:e1000133. 2008
    ....
  39. pmc Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses
    Cadhla Firth
    Department of Biology, The Pennsylvania State University, USA
    Mol Biol Evol 27:2038-51. 2010
    ....
  40. pmc Stochastic processes are key determinants of short-term evolution in influenza a virus
    Martha I Nelson
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
    PLoS Pathog 2:e125. 2006
    ..Thus, predicting future patterns of influenza virus evolution for vaccine strain selection is inherently complex and requires intensive surveillance, whole-genome sequencing, and phenotypic analysis...
  41. pmc Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity
    Gue Su Chang
    Department of Biology, Pennsylvania State University, State College, PA 16802, USA
    Proc Natl Acad Sci U S A 105:13474-9. 2008
    ....
  42. ncbi request reprint Inferring the timescale of dengue virus evolution under realistic models of DNA substitution
    Eleca J Dunham
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    J Mol Evol 64:656-61. 2007
    ....
  43. doi request reprint High rates of molecular evolution in hantaviruses
    Cadhla Ramsden
    Department of Biology, Center for Infectious Disease Dynamics, The Pennsylvania State University, PA, USA
    Mol Biol Evol 25:1488-92. 2008
    ..The disparity between this substitution rate and that estimated assuming rodent-hantavirus codivergence suggests that the codivergence hypothesis may need to be reevaluated...
  44. ncbi request reprint Selection-driven evolution of emergent dengue virus
    Shannon N Bennett
    Department of Biology, University of Puerto Rico Rio Piedras, San Juan, Puerto Rico, USA
    Mol Biol Evol 20:1650-8. 2003
    ..Our study therefore demonstrates viral genetic turnover within a focal population and the potential importance of adaptive evolution in viral epidemic expansion...
  45. pmc Declining growth rate of West Nile virus in North America
    Katherine W Snapinn
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    J Virol 81:2531-4. 2007
    ..However, there has also been a marked decrease in the recent growth rate of WN02, suggesting that WNV has reached its peak prevalence in North America...
  46. ncbi request reprint Avian influenza virus exhibits rapid evolutionary dynamics
    Rubing Chen
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, PA, USA
    Mol Biol Evol 23:2336-41. 2006
    ....
  47. ncbi request reprint Comment on "Large-scale sequence analysis of avian influenza isolates"
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
    Science 313:1573; author reply 1573. 2006
    ..However, we show that this observation is likely to be an artifact related to the location of PB1-F2 in the +1 reading frame of the PB1 gene...
  48. ncbi request reprint The evolutionary biology of dengue virus
    Edward C Holmes
    Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Novartis Found Symp 277:177-87; discussion 187-92, 251-3. 2006
    ..Finally, I note that a fuller understanding of DENV evolution will require more extensive study of the sylvatic cycle, particularly in Africa, which has been largely ignored to date...
  49. doi request reprint Rapid evolutionary dynamics of zucchini yellow mosaic virus
    Heather E Simmons
    Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    J Gen Virol 89:1081-5. 2008
    ..Finally, an analysis of phylogeographical structure provides strong evidence for the in situ evolution of ZYMV within individual countries...
  50. pmc When HIV spread afar
    Edward C Holmes
    Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 104:18351-2. 2007
  51. doi request reprint The role of alternative genetic codes in viral evolution and emergence
    Laura A Shackelton
    Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    J Theor Biol 254:128-34. 2008
    ..As such, in the face of new emerging viruses, hosts with codon reassignments would have a significant selective advantage compared to hosts utilizing the universal code...
  52. pmc Phylogenetic analysis reveals the global migration of seasonal influenza A viruses
    Martha I Nelson
    Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, USA
    PLoS Pathog 3:1220-8. 2007
    ....
  53. pmc Yellow fever virus exhibits slower evolutionary dynamics than dengue virus
    Amadou A Sall
    Institut Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal
    J Virol 84:765-72. 2010
    ....
  54. ncbi request reprint Detection of TT virus among chimpanzees in the wild using a noninvasive technique
    Oliver E Barnett
    Department of Biological Sciences, The Open University, Walton Hall, Milton Keynes, Buckinghamshire MK7 6AA, UK
    J Wildl Dis 40:230-7. 2004
    ..Our findings are discussed with respect to potential zoonotic events that may result from increased levels of human encroachlment into wild habitats...
  55. ncbi request reprint The phylogeography of human viruses
    Edward C Holmes
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS UK
    Mol Ecol 13:745-56. 2004
    ..Key research questions for the future will also be established...
  56. pmc High-resolution phylogenetic analysis of hepatitis C virus adaptation and its relationship to disease progression
    Isabelle Sheridan
    Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, United Kingdom
    J Virol 78:3447-54. 2004
    ..Such analyses could play a similarly informative role in studies of other persistent virus infections, such as human immunodeficiency virus...
  57. ncbi request reprint The population genetics and evolutionary epidemiology of RNA viruses
    Andres Moya
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Apartado Postal 22085, 46071 Valencia, Spain
    Nat Rev Microbiol 2:279-88. 2004
  58. pmc Phylogenetic analysis reveals the emergence, evolution and dispersal of carnivore parvoviruses
    Karin Hoelzer
    Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    J Gen Virol 89:2280-9. 2008
    ..Such limited viral migration contrasts with the global spread of the virus observed during the early phase of the CPV pandemic, but corresponds to the more endemic nature of current CPV infections...
  59. ncbi request reprint Distinct patterns of natural selection in the reverse transcriptase gene of HIV-1 in the presence and absence of antiretroviral therapy
    Elcio de S Leal
    Laboratory of Molecular Evolution and Bioinformatics LEMB, Department of Microbiology, University of Sao Paulo, Sao Paulo, CEP 05508 900, Brazil
    Virology 325:181-91. 2004
    ..Finally, we show that compensatory changes are likely to be important in the development of HIV drug resistance by counter-acting the deleterious effects normally associated with drug resistance mutations...
  60. pmc Viral evolution and the emergence of SARS coronavirus
    Edward C Holmes
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Philos Trans R Soc Lond B Biol Sci 359:1059-65. 2004
    ....
  61. ncbi request reprint Genetic constraints and the adaptive evolution of rabies virus in nature
    Edward C Holmes
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
    Virology 292:247-57. 2002
    ..Assuming that the average rate of synonymous change does not vary among species, we estimated that the current genetic diversity in lyssavirus genotype 1 may have arisen only during the last 500 years...
  62. ncbi request reprint Unifying the epidemiological and evolutionary dynamics of pathogens
    Bryan T Grenfell
    Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
    Science 303:327-32. 2004
    ..A central pillar of this model is the Evolutionary Infectivity Profile, which captures the relationship between immune selection and pathogen transmission...
  63. ncbi request reprint Origins, evolution, and vector/host coadaptations within the genus Flavivirus
    Ernest A Gould
    Institute of Virology and Environmental Microbiology, Oxford University, Oxford, OX1 3SR, United Kingdom
    Adv Virus Res 59:277-314. 2003
    ..This review also considers some of the likely implications of persistent/chronic infections in relation to virus dispersal and recombination between related flaviviruses on phylogenetic analysis and vaccine development strategies...
  64. ncbi request reprint Evolution of major histocompatibility complex class I genes in Cetartiodactyls
    Edward C Holmes
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Immunogenetics 55:193-202. 2003
    ....
  65. ncbi request reprint The extent of codon usage bias in human RNA viruses and its evolutionary origin
    Gareth M Jenkins
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Virus Res 92:1-7. 2003
    ..This suggests that translational selection may also have some influence in shaping codon usage bias...
  66. ncbi request reprint The extent of homologous recombination in members of the genus Flavivirus
    S Susanna Twiddy
    Department of Zoology, University of Oxford, South Parks Road, UK
    J Gen Virol 84:429-40. 2003
    ....
  67. ncbi request reprint Phylogenetic evidence for frequent positive selection and recombination in the meningococcal surface antigen PorB
    Rachel Urwin
    The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, UK
    Mol Biol Evol 19:1686-94. 2002
    ..These data show that phylogenetic inference can be used to complement immunological and biochemical data in the choice of vaccine candidates...
  68. ncbi request reprint Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses
    Elizabeth R Chare
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    J Gen Virol 84:2691-703. 2003
    ..Consequently, recombination rate is unlikely to be a trait that is set by natural selection to create advantageous or purge deleterious mutations...
  69. ncbi request reprint Error thresholds and the constraints to RNA virus evolution
    Edward C Holmes
    Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, UK
    Trends Microbiol 11:543-6. 2003
    ..Documenting the constraints to RNA virus evolution has important implications for predicting the emergence of new viruses and for improving therapeutic procedures...
  70. ncbi request reprint A revised evolutionary history of hepatitis B virus (HBV)
    Mario Ali Fares
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Department de Genètica, Universitat de Valencia, Valencia, Spain
    J Mol Evol 54:807-14. 2002
    ..Finally, we provide a new estimate of the mean substitution rate in HBV, 4.2 x 10(-5), which suggests that divergence of HBV in humans and apes has occurred only in the last 6000 years...
  71. ncbi request reprint The causes and consequences of HIV evolution
    Andrew Rambaut
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Nat Rev Genet 5:52-61. 2004
  72. pmc Diverse dengue type 2 virus populations contain recombinant and both parental viruses in a single mosquito host
    Scott Craig
    School of Life Sciences, Queensland University of Technology, Brisbane, Australia
    J Virol 77:4463-7. 2003
    ..Finally, one clone was identified as a recombinant genome composed of portions of these two "parental" genotypes. This is the first report of recombinant and parental dengue viruses in a single host...
  73. ncbi request reprint The evolution of large DNA viruses: combining genomic information of viruses and their hosts
    Laura A Shackelton
    Department of Zoology, Tinbergen Building, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Trends Microbiol 12:458-65. 2004
  74. pmc The evolutionary genetics and emergence of avian influenza viruses in wild birds
    Vivien G Dugan
    Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Pathog 4:e1000076. 2008
    ....
  75. ncbi request reprint Host species barriers to influenza virus infections
    Thijs Kuiken
    Department of Virology, Erasmus Medical Center, 3015 GE Rotterdam, Netherlands
    Science 312:394-7. 2006
    ....
  76. pmc Demographic histories of ERV-K in humans, chimpanzees and rhesus monkeys
    Camila M Romano
    Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute ICBII, University of Sao Paulo, Brazil
    PLoS ONE 2:e1026. 2007
    ..We propose that these differing ERV-K dynamics reflect underlying differences in the evolutionary ecology of the host species, such that host ecology and demography represent important determinants of ERV-K dynamics...
  77. ncbi request reprint A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution
    Beth Shapiro
    Department of Zoology, Oxford University, Oxford, United Kingdom
    Mol Biol Evol 23:1724-30. 2006
    ..Additionally, many comparative analyses that utilize the phylogenetic relationships among gene sequences assume that mutations represent independent, uncorrelated events. Our results show that this assumption may often be invalid...
  78. ncbi request reprint Ngoye virus: a novel evolutionary lineage within the genus Flavivirus
    Gilda Grard
    Unité des Virus Emergents EA3292, IFR48, IRD UR0178, Faculté de médecine La Timone, 27 Boulevard Jean Moulin, 13005 Marseille, France
    J Gen Virol 87:3273-7. 2006
    ..Together with other recent data, these findings suggest that a large number of viruses related distantly to 'classical' arthropod-borne flaviviruses remain to be discovered...
  79. ncbi request reprint Sequence analysis of the equid herpesvirus 2 chemokine receptor homologues E1, ORF74 and E6 demonstrates high sequence divergence between field isolates
    Emma L Sharp
    Department of Infectious Diseases, Animal Health Trust, Kentford, Newmarket CB8 7UU, UK
    J Gen Virol 88:2450-62. 2007
    ..Finally, there was no evidence for genetic linkage between the different gB, E1, ORF74 and E6 genotypes, suggesting frequent intergenic recombination between different EHV-2 strains...
  80. ncbi request reprint The "pressure pan" evolution of human erythrovirus B19 in the Amazon, Brazil
    Ronaldo Barros de Freitas
    Seção de Virologia, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministerio da Saude, Belem, Brazil
    Virology 369:281-7. 2007
    ....
  81. ncbi request reprint Genetic characterization of tick-borne flaviviruses: new insights into evolution, pathogenetic determinants and taxonomy
    Gilda Grard
    Unité des Virus Emergents EA3292, IFR48, IRD UR0178, Faculté de médecine La Timone, 27 Boulevard Jean Moulin, 13005 Marseille, France
    Virology 361:80-92. 2007
    ..Ticks that feed on both categories of vertebrates may constitute the evolutionary bridge between the three distinct identified lineages...
  82. pmc Evolutionary processes among sylvatic dengue type 2 viruses
    Nikos Vasilakis
    Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555 0609, USA
    J Virol 81:9591-5. 2007
    ..Our findings support a recent cross-species transmission event and suggest the possibility of future DENV reemergence from the sylvatic cycle...
  83. ncbi request reprint Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution
    Oliver G Pybus
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 24:845-52. 2007
    ..From this relationship, we propose an empirical threshold for the maximum viable deleterious mutation load in RNA viruses...
  84. pmc A single positively selected West Nile viral mutation confers increased virogenesis in American crows
    Aaron C Brault
    Center for Vector Borne Diseases and Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, California 95616, USA
    Nat Genet 39:1162-6. 2007
    ..These phenotypic and evolutionary results provide compelling evidence for the positive selection of a mutation encoding increased viremia potential and virulence in the AMCR sentinel bird species...
  85. pmc Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient
    John Aaskov
    Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
    J Gen Virol 88:3334-40. 2007
    ..This is the first report of a population of dengue viruses isolated from a patient containing both parental and recombinant viruses...
  86. pmc Global distribution of novel rhinovirus genotype
    Thomas Briese
    Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York 10032, USA
    Emerg Infect Dis 14:944-7. 2008
    ..Molecular dating indicates that these viruses have been circulating for at least 250 years...
  87. ncbi request reprint Sustained transmission of dengue virus type 1 in the Pacific due to repeated introductions of different Asian strains
    Atchareeya A-Nuegoonpipat
    National Institute of Health, Department of Medical Science, Bangkok, Thailand
    Virology 329:505-12. 2004
    ..There was no evidence that the introduction of these viruses into the Pacific was associated with any adaptive changes in the E protein of the viruses...
  88. ncbi request reprint The hepatitis C virus epidemic among injecting drug users
    Oliver G Pybus
    Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
    Infect Genet Evol 5:131-9. 2005
    ..The results provide a baseline for prediction of the future course of the HCV epidemic, and its likely response to transmission control policies...
  89. pmc Genomic diversity and evolution of the lyssaviruses
    Olivier Delmas
    Institut Pasteur, UPRE Lyssavirus Dynamics and Host Adaptation, World Health Organization Collaborating Centre for Reference and Research on Rabies, Paris, France
    PLoS ONE 3:e2057. 2008
    ..In sum, we show that rigorous phylogenetic techniques based on full length genome sequence provide the best discriminatory power for genotype classification within the lyssaviruses...
  90. pmc The genomic and epidemiological dynamics of human influenza A virus
    Andrew Rambaut
    Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK
    Nature 453:615-9. 2008
    ..These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions...
  91. ncbi request reprint Ancient co-speciation of simian foamy viruses and primates
    William M Switzer
    HIV and Retrovirology Branch, Division of HIV AIDS Prevention, National Center for HIV, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, MS G 19, Atlanta, Georgia 30333, USA
    Nature 434:376-80. 2005
    ..These results indicate that SFVs might have co-speciated with Old World primates for at least 30 million years, making them the oldest known vertebrate RNA viruses...
  92. pmc Homologous recombination is very rare or absent in human influenza A virus
    Maciej F Boni
    Resources for the Future, 1616 P St NW, Washington, DC 20036, USA
    J Virol 82:4807-11. 2008
    ..We therefore conclude that, if it occurs at all, homologous recombination plays only a very minor role in the evolution of human influenza A virus...
  93. pmc Invasion and maintenance of dengue virus type 2 and type 4 in the Americas
    Christine V F Carrington
    Department of Pre Clinical Sciences, Faculty of Medical Sciences, University of the West Indies, St Augustine, Trinidad
    J Virol 79:14680-7. 2005
    ..Hence, DENV in the Americas has a clear geographic structure that maintains viral diversity between outbreaks...
  94. pmc Phylogenetic evidence for the rapid evolution of human B19 erythrovirus
    Laura A Shackelton
    Department of Zoology, University of Oxford, United Kingdom
    J Virol 80:3666-9. 2006
    ..This rate is more typical of RNA viruses and suggests that high mutation rates are characteristic of the Parvoviridae...
  95. ncbi request reprint The genesis and spread of reassortment human influenza A/H3N2 viruses conferring adamantane resistance
    Lone Simonsen
    National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 24:1811-20. 2007
    ..More generally, these findings illustrate that drug selection pressure is not the sole factor determining the evolution and maintenance of drug resistance in human pathogens...

Research Grants4

  1. The Evolutionary and Biological Bases of Host Switching in Viruses
    Edward C Holmes; Fiscal Year: 2010
    ..we will also conduct selection studies using cell culture, where we will measure the rate of emergence of antibody escape mutants for both the parvoviruses and influenza viruses, as well as receptor-selected mutants of the parvoviruses ..
  2. The Evolutionary and Biological Bases of Host Switching in Viruses
    Edward Holmes; Fiscal Year: 2007
    ..we will also conduct selection studies using cell culture, where we will measure the rate of emergence of antibody escape mutants for both the parvoviruses and influenza viruses, as well as receptor-selected mutants of the parvoviruses ..
  3. The Evolutionary and Biological Bases of Host Switching in Viruses
    Edward Holmes; Fiscal Year: 2009
    ..we will also conduct selection studies using cell culture, where we will measure the rate of emergence of antibody escape mutants for both the parvoviruses and influenza viruses, as well as receptor-selected mutants of the parvoviruses ..