O G Pybus

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. doi request reprint The ecology and age structure of a highly pathogenic avian influenza virus outbreak in wild mute swans
    O G Pybus
    Department of Zoology, University of Oxford, Oxford, OX1 3PS
    Parasitology 139:1914-23. 2012
  2. pmc Unifying the spatial epidemiology and molecular evolution of emerging epidemics
    Oliver G Pybus
    Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 109:15066-71. 2012
  3. pmc Disease-associated XMRV sequences are consistent with laboratory contamination
    Stephane Hue
    MRC Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, 46 Cleveland St, London W1T 4JF, UK
    Retrovirology 7:111. 2010
  4. pmc Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach
    Dimitrios Paraskevis
    Katholieke Universiteit Leuven, Rega Institute for Medical Research, Minderbroederstraat 10, B 3000 Leuven, Belgium
    Retrovirology 6:49. 2009
  5. pmc The mode and tempo of hepatitis C virus evolution within and among hosts
    Rebecca R Gray
    Department of Zoology, Oxford University, South Parks Road, UK
    BMC Evol Biol 11:131. 2011
  6. 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
  7. ncbi request reprint Investigating the endemic transmission of the hepatitis C virus
    Oliver G Pybus
    Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, UK
    Int J Parasitol 37:839-49. 2007
  8. doi request reprint Evolutionary analysis of the dynamics of viral infectious disease
    Oliver G Pybus
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Nat Rev Genet 10:540-50. 2009
  9. ncbi request reprint The mid-depth method and HIV-1: a practical approach for testing hypotheses of viral epidemic history
    O G Pybus
    Department of Zoology, University of Oxford, United Kingdom
    Mol Biol Evol 16:953-9. 1999
  10. ncbi request reprint The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach
    O G Pybus
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 20:381-7. 2003

Collaborators

Detail Information

Publications74

  1. doi request reprint The ecology and age structure of a highly pathogenic avian influenza virus outbreak in wild mute swans
    O G Pybus
    Department of Zoology, University of Oxford, Oxford, OX1 3PS
    Parasitology 139:1914-23. 2012
    ..Our study population may represent a valuable resource for investigating the natural ecology and epidemiology of avian influenza...
  2. pmc Unifying the spatial epidemiology and molecular evolution of emerging epidemics
    Oliver G Pybus
    Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 109:15066-71. 2012
    ..More generally, our approach demonstrates that easily obtainable genetic data can be used to measure the spatial dynamics of natural populations that are otherwise difficult or costly to quantify...
  3. pmc Disease-associated XMRV sequences are consistent with laboratory contamination
    Stephane Hue
    MRC Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, 46 Cleveland St, London W1T 4JF, UK
    Retrovirology 7:111. 2010
    ..Controversy has arisen from the failure of some studies to detect XMRV in PC or CFS patients and from inconsistent detection of XMRV in healthy controls...
  4. pmc Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach
    Dimitrios Paraskevis
    Katholieke Universiteit Leuven, Rega Institute for Medical Research, Minderbroederstraat 10, B 3000 Leuven, Belgium
    Retrovirology 6:49. 2009
    ..However the spatial diffusion of the epidemic from the perspective of the virus has not previously been traced...
  5. pmc The mode and tempo of hepatitis C virus evolution within and among hosts
    Rebecca R Gray
    Department of Zoology, Oxford University, South Parks Road, UK
    BMC Evol Biol 11:131. 2011
    ..We use a powerful Bayesian inference framework that incorporates both among-lineage rate heterogeneity and phylogenetic uncertainty into estimates of evolutionary parameters...
  6. 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...
  7. ncbi request reprint Investigating the endemic transmission of the hepatitis C virus
    Oliver G Pybus
    Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, UK
    Int J Parasitol 37:839-49. 2007
    ..Our analyses indicate that the mechanical transmission of HCV is plausible and that much further research into endemic HCV is needed...
  8. doi request reprint Evolutionary analysis of the dynamics of viral infectious disease
    Oliver G Pybus
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Nat Rev Genet 10:540-50. 2009
    ..In this Review, we outline the questions that can be answered using viral evolutionary analysis across a wide range of biological scales...
  9. ncbi request reprint The mid-depth method and HIV-1: a practical approach for testing hypotheses of viral epidemic history
    O G Pybus
    Department of Zoology, University of Oxford, United Kingdom
    Mol Biol Evol 16:953-9. 1999
    ..We posit that this difference in growth rate reflects the different transmission routes and epidemiological histories of the two subtypes...
  10. ncbi request reprint The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach
    O G Pybus
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 20:381-7. 2003
    ..Because our results are consistent with a demographic scenario specified a priori, they also provide an objective test of inference methods based on the coalescent process...
  11. 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...
  12. ncbi request reprint GENIE: estimating demographic history from molecular phylogenies
    O G Pybus
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Bioinformatics 18:1404-5. 2002
    ..The methods are based on population genetic models known collectively as coalescent theory...
  13. pmc Model selection and the molecular clock
    Oliver G Pybus
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS Biol 4:e151. 2006
  14. ncbi request reprint The epidemic behavior of the hepatitis C virus
    O G Pybus
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Science 292:2323-5. 2001
    ..Our model builds a bridge between the disciplines of population genetics and mathematical epidemiology by using pathogen gene sequences to infer the population dynamic history of an infectious disease...
  15. pmc Testing macro-evolutionary models using incomplete molecular phylogenies
    O G Pybus
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Proc Biol Sci 267:2267-72. 2000
    ..When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time...
  16. pmc An integrated framework for the inference of viral population history from reconstructed genealogies
    O G Pybus
    Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
    Genetics 155:1429-37. 2000
    ..We also provide the first (albeit tentative) genetic evidence for a recent decrease in the growth rate of subtype B...
  17. pmc Genetic history of hepatitis C virus in East Asia
    Oliver G Pybus
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    J Virol 83:1071-82. 2009
    ..Our analysis explains the generation and maintenance of HCV diversity in Asia and could provide a template for further investigations of HCV spread in other regions...
  18. ncbi request reprint Bayesian coalescent inference of past population dynamics from molecular sequences
    A J Drummond
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 22:1185-92. 2005
    ....
  19. pmc Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection
    C T T Edwards
    Nuffield Department of Clinical Medicine, University of Oxford, UK, and Department of Pediatrics, The Johns Hopkins Hospital, Baltimore, MD 21287, USA
    Genetics 174:1441-53. 2006
    ..This suggests the presence of deleterious mutations. We therefore conclude that intrahost HIV-1 evolution in envelope is dominated by purifying selection against low-frequency deleterious mutations that do not reach fixation...
  20. ncbi request reprint New inferences from tree shape: numbers of missing taxa and population growth rates
    O G Pybus
    Department of Zoology, University of Oxford, South Parks Road, UK
    Syst Biol 51:881-8. 2002
    ..Results of an analysis of the phylogeny of the mosquito-borne flaviviruses suggest that there could be several thousand currently unidentified viruses in this clade...
  21. pmc Discovery and analysis of the first endogenous lentivirus
    Aris Katzourakis
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Proc Natl Acad Sci U S A 104:6261-5. 2007
    ..Although the virus we describe is defective, reconstruction of an infectious progenitor could provide novel insights into lentivirus biology and host interactions...
  22. ncbi request reprint Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth
    Polly R Walker
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Infect Genet Evol 5:199-208. 2005
    ....
  23. ncbi request reprint Exploring the demographic history of DNA sequences using the generalized skyline plot
    K Strimmer
    Department of Zoology, University of Oxford
    Mol Biol Evol 18:2298-305. 2001
    ..We investigate the performance of our approach using simulation and subsequently apply it to HIV-1 sequences from central Africa and mtDNA sequences from red pandas...
  24. 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...
  25. doi request reprint Phylogeography and molecular epidemiology of hepatitis C virus genotype 2 in Africa
    Peter V Markov
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    J Gen Virol 90:2086-96. 2009
    ..We discuss this contrast in the context of possible parenteral HCV exposure during public-health campaigns undertaken during the colonial era...
  26. ncbi request reprint HIV evolutionary dynamics within and among hosts
    Philippe Lemey
    Department of Zoology, University of Oxford, Oxford, UK
    AIDS Rev 8:125-40. 2006
    ..Characterizing the impact of HIV transmission on viral genetic diversity will be a key factor in reconciling the different population genetic processes within and among hosts...
  27. ncbi request reprint Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak
    Tulio de Oliveira
    Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
    Nature 444:836-7. 2006
    ....
  28. doi request reprint Pacing a small cage: mutation and RNA viruses
    Robert Belshaw
    Department of Zoology, University of Oxford, Oxford, UK
    Trends Ecol Evol 23:188-93. 2008
    ..We explain the many terms used in investigating RNA viral evolution and highlight the specific experimental and comparative work that needs to be done...
  29. doi request reprint Macroevolution of complex retroviruses
    Aris Katzourakis
    Zoology Department, University of Oxford, Oxford OX1 3PS, UK
    Science 325:1512. 2009
    ....
  30. pmc Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics
    Philippe Lemey
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 3:e29. 2007
    ....
  31. pmc The evolution of genome compression and genomic novelty in RNA viruses
    Robert Belshaw
    Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
    Genome Res 17:1496-504. 2007
    ..We suggest that RNA viruses are a good model system for the investigation of general evolutionary relationship between genome attributes such as mutational robustness, mutation rate, and size...
  32. ncbi request reprint Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty
    Joe Parker
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
    Infect Genet Evol 8:239-46. 2008
    ..Finally, we re-analyse two existing published data sets as case studies. Our framework aims to provide an improvement over existing methods for this problem...
  33. doi request reprint Detecting natural selection in RNA virus populations using sequence summary statistics
    Samir Bhatt
    Department of Zoology, University of Oxford, United Kingdom
    Infect Genet Evol 10:421-30. 2010
    ..Our results suggest that variants of the McDonald-Kreitman test could prove useful in the analysis of very large sets of highly diverse viral genetic data...
  34. 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...
  35. ncbi request reprint Rise and fall of the Beringian steppe bison
    Beth Shapiro
    Henry Wellcome Ancient Biomolecules Centre, Oxford University, South Parks Road, Oxford OX13PS, UK
    Science 306:1561-5. 2004
    ....
  36. 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...
  37. ncbi request reprint Comparative population dynamics of mosquito-borne flaviviruses
    S Susanna Twiddy
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Infect Genet Evol 3:87-95. 2003
    ..We therefore demonstrate that the use of these coalescent methods may be extremely valuable in monitoring responses to interventions such as vaccination or vector control...
  38. pmc The evolutionary dynamics of influenza A virus adaptation to mammalian hosts
    S Bhatt
    Department of Zoology, University of Oxford, Oxford, UK
    Philos Trans R Soc Lond B Biol Sci 368:20120382. 2013
    ..This dynamics is replicated independently in the polymerase genes of the TR lineage, which established in swine following separate transmission from non-swine hosts...
  39. ncbi request reprint Inference of viral evolutionary rates from molecular sequences
    Alexei Drummond
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Adv Parasitol 54:331-58. 2003
    ....
  40. pmc Full-length characterization of hepatitis C virus subtype 3a reveals novel hypervariable regions under positive selection during acute infection
    Isla Humphreys
    Oxford NIHR Biomedical Research Centre and Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
    J Virol 83:11456-66. 2009
    ..Further defining the functional significance of these regions may have important implications for genotype 3a E2 virus-receptor interactions and for vaccine studies that aim to induce cross-reactive anti-E2 antibodies...
  41. ncbi request reprint Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus
    Michael Worobey
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Science 296:211 discussion 211. 2002
  42. pmc HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering
    Philippa C Matthews
    Department of Paediatrics, Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
    J Virol 83:4605-15. 2009
    ..In conclusion, these data highlight the fact that HLA can be a strong selection force for both intra- and interclade HIV evolution at a population level...
  43. ncbi request reprint Epidemiology: Sexual transmission of HIV in Africa
    Polly R Walker
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Nature 422:679. 2003
  44. ncbi request reprint Do antiviral CD8+ T cells select hepatitis C virus escape mutants? Analysis in diverse epitopes targeted by human intrahepatic CD8+ T lymphocytes
    H Komatsu
    Nuffield Department of Medicine, University of Oxford, Oxford, UK
    J Viral Hepat 13:121-30. 2006
    ..Furthermore, longitudinal studies to identify the differences between 'selecting' and 'nonselecting' intrahepatic CD8+ T-cell responses are needed in HCV infection...
  45. ncbi request reprint The evolutionary dynamics of endogenous retroviruses
    Aris Katzourakis
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Trends Microbiol 13:463-8. 2005
    ..We hope the model will provide a useful framework for understanding ERV evolution, enabling the testing of evolutionary hypotheses and the estimation of parameters governing ERV proliferation...
  46. ncbi request reprint Increased positive selection pressure in persistent (SSPE) versus acute measles virus infections
    Christopher H Woelk
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    J Gen Virol 83:1419-30. 2002
    ..Finally, using H gene data, we estimated the rate of molecular evolution for SSPE strains as 3.4 x 10(-4) substitutions/site/year, which is similar to previous estimates obtained for acute strains...
  47. pmc The generation of influenza outbreaks by a network of host immune responses against a limited set of antigenic types
    Mario Recker
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 104:7711-6. 2007
    ....
  48. pmc Epistatic interactions between genetic disorders of hemoglobin can explain why the sickle-cell gene is uncommon in the Mediterranean
    Bridget S Penman
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 106:21242-6. 2009
    ..The complex distribution of globin mutants across Africa and the Mediterranean can therefore be explained by their specific intracellular interactions...
  49. doi request reprint Variable epidemic histories of hepatitis C virus genotype 2 infection in West Africa and Cameroon
    Regis Pouillot
    Centre Pasteur du Cameroun, Yaounde, Cameroon
    Infect Genet Evol 8:676-81. 2008
    ..This comparative genetic analysis indicates that Cameroon HCV-2 strains are derived from West African strains and that HCV-2 has undergone radically different epidemiological histories in the two regions...
  50. doi request reprint Complete genome sequencing and phylogenetic analysis of HCV isolates from China reveals a new subtype, designated 6u
    Xueshan Xia
    Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunan, China
    J Med Virol 80:1740-6. 2008
    ..Because its designation does not meet the criteria described in the updated HCV nomenclature proposal, this "6u" isolate should be reclassified...
  51. pmc The molecular population genetics of HIV-1 group O
    Philippe Lemey
    Rega Institute for Medical Research, KULeuven, B 3000 Leuven, Belgium
    Genetics 167:1059-68. 2004
    ..In addition, we show that evolutionary rate estimates for different HIV genes accurately reflect differential selective constraints along the HIV genome...
  52. pmc U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains
    Kenneth E Robbins
    Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
    J Virol 77:6359-66. 2003
    ..Furthermore, the estimated epidemic growth curve shows a period of exponential growth that preceded most of the early documented cases and also indicates a leveling of prevalence rates in the recent past...
  53. ncbi request reprint Phylogenetic analysis of hepatitis C virus isolates indicates a unique pattern of endemic infection in Cameroon
    Jean Ndjomou
    Institute of Medical Microbiology and Immunology, University of Bonn, Sigmund Freud Strasse 25, 53105 Bonn, Germany
    J Gen Virol 84:2333-41. 2003
    ..These results lead to the hypothesis that these HCV genotypes originated and diversified in west Central Africa before spreading to other regions...
  54. ncbi request reprint Viral gene sequences reveal the variable history of hepatitis C virus infection among countries
    Tatsunori Nakano
    Department of Internal Medicine, Ichinomiya Nishi Hospital, Okucho Orikuchinishi 89 1, Ichinomiya, Aichi 491 0201, Japan
    J Infect Dis 190:1098-108. 2004
    ..The analysis of molecular phylogenies estimated from the gene sequences of sampled viruses can provide important insights into epidemiological processes...
  55. 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...
  56. 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
    ....
  57. pmc Investigating the origin and spread of hepatitis C virus genotype 5a
    Jannick Verbeeck
    Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, BE 3000 Leuven, Belgium
    J Virol 80:4220-6. 2006
    ..These findings have major implications for tracing the origin of HCV genotype 5a. Here, we speculate about the possible origins of these clusters...
  58. ncbi request reprint Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages
    Urmas Saarma
    Department of Integrative Zoology, Institute of Zoology and Hydrobiology, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia
    Mol Ecol 16:401-13. 2007
    ..Our approach to estimating the time frame of brown bear evolution demonstrates the importance of using an appropriate mutation rate, and this has implications for other studies of Pleistocene populations...
  59. ncbi request reprint Population genetic history of hepatitis C virus 1b infection in China
    Tatsunori Nakano
    Department of Internal Medicine, Ichinomiya Nishi Hospital, Aichi, Japan
    J Gen Virol 87:73-82. 2006
    ..These results shed light on HCV transmission in China and may help to predict the future burden of HCV-related disease in the country...
  60. ncbi request reprint Complete genomes for hepatitis C virus subtypes 6f, 6i, 6j and 6m: viral genetic diversity among Thai blood donors and infected spouses
    Ling Lu
    Division of Gastroenterology Hepatology, Department of Medicine, University of Kansas Medical Center, 4035 Delp, MS 1023, Kansas City, KS 66160, USA
    J Gen Virol 88:1505-18. 2007
    ..3 to 100%. The similarities of the complete genome sequences from the two couples in the current study are consistent with HCV transmission between spouses...
  61. ncbi request reprint Complete genomes of hepatitis C virus (HCV) subtypes 6c, 6l, 6o, 6p and 6q: completion of a full panel of genomes for HCV genotype 6
    Ling Lu
    Division of Gastroenterology Hepatology, Department of Medicine, University of Kansas Medical Center, 4035 Delp, MS 1023, Kansas City, KS 66160, USA, and The First People s Hospital of Yunnan Province, Kunming, China
    J Gen Virol 88:1519-25. 2007
    ..The utility of this panel of complete sequences for accurate detection and classification of infection, and for estimating the origin of this genotype of HCV, is discussed...
  62. ncbi request reprint Recent epidemic of acute hepatitis C virus in HIV-positive men who have sex with men linked to high-risk sexual behaviours
    Mark Danta
    UCL Institute of Hepatology, London, UK
    AIDS 21:983-91. 2007
    ..To characterize the mode of hepatitis C virus (HCV) transmission in a recent epidemic of acute HCV in HIV-infected individuals using linked molecular and clinical epidemiological studies...
  63. pmc Temporal and spatial dynamics of human immunodeficiency virus type 1 circulating recombinant forms 08_BC and 07_BC in Asia
    Kok Keng Tee
    Laboratory of Molecular Virology and Epidemiology, AIDS Research Center, National Institute of Infectious Diseases, 1 23 1 Toyama, Shinjuku ku, Tokyo 162 8640, Japan
    J Virol 82:9206-15. 2008
    ..This is the first phylodynamic study depicting the spatiotemporal dynamics of HIV/AIDS in East Asia...
  64. pmc Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups
    Stephane Hue
    Centre for Virology, Division of Infection and Immunity, University College London, 46 Cleveland Street, London W1T 4JF, UK
    Proc Natl Acad Sci U S A 102:4425-9. 2005
    ..Our results provide insights into the complexity of HIV-1 epidemics that must be considered when developing HIV monitoring and prevention initiatives...
  65. pmc Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1
    Robert J Gifford
    Department of Infection, University College London, London, United Kingdom
    J Virol 81:13050-6. 2007
    ..The framework implemented here takes advantage of the vast amount of routinely generated HIV-1 sequence data and can provide epidemiological insights not readily obtainable through standard surveillance methods...
  66. ncbi request reprint A Bayesian statistical analysis of human T-cell lymphotropic virus evolutionary rates
    Philippe Lemey
    Rega Institute for Medical Research, Minderbroedersstraat 10, Katholieke Universiteit Leuven, B 3000 Leuven, Belgium
    Infect Genet Evol 5:291-8. 2005
    ..Statistical uncertainty burdens HTLV rate estimates based on both anthropological calibrations and on pedigree data; the former method rests on an untested assumption, whilst that latter is affected by small sample sizes...
  67. pmc Analysis of the evolutionary forces in an immunodominant CD8 epitope in hepatitis C virus at a population level
    Christoph Neumann-Haefelin
    Department of Medicine II, University of Freiburg, Hugstetter Str 55, 79106 Freiburg, Germany
    J Virol 82:3438-51. 2008
    ....
  68. ncbi request reprint Chronology of the HIV-1 CRF07_BC expansion in East Asia
    Kok Keng Tee
    Laboratory of Molecular Virology and Epidemiology, AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
    AIDS 22:156-8. 2008
    ..The separate introduction of CRF07_BC into Xinjiang occurred in 1992-1995. This study illustrates the temporal dynamics of CRF07_BC spread among IDU across east Asia...
  69. ncbi request reprint Increasing prevalence of HIV-1 subtype A in Greece: estimating epidemic history and origin
    Dimitrios Paraskevis
    Department of Hygiene and Epidemiology, National Retrovirus Reference Center, Athens, Greece
    J Infect Dis 196:1167-76. 2007
    ..In North America and Europe, human immunodeficiency virus (HIV)-1 infection has typically been dominated by subtype B transmission. More recently, however, non-B subtypes have been increasingly reported in Europe...
  70. pmc Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia
    Tommy Tsan Yuk Lam
    School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China
    PLoS Pathog 4:e1000130. 2008
    ..We discuss how the corresponding mutations might drive the adaptation and onward transmission of the newly formed reassortant viruses...
  71. pmc Tracing the origin and history of the HIV-2 epidemic
    Philippe Lemey
    Rega Institute for Medical Research, Katholieke Universiteit Leuven, Belgium
    Proc Natl Acad Sci U S A 100:6588-92. 2003
    ....
  72. ncbi request reprint Host switch leads to emergence of Plasmodium vivax malaria in humans
    Jianbing Mu
    Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
    Mol Biol Evol 22:1686-93. 2005
    ..Taken together, a haplotype network, parasite migration patterns, demographic history, and cophylogeny mapping support an Asian origin via a host switch from macaque monkeys...
  73. 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...