Philippe Lemey

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. pmc Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain
    Philippe Lemey
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
    J Virol 79:11981-9. 2005
  2. 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
  3. 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
  4. 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
  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. 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
  7. pmc Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation
    Abby Harrison
    Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
    Viruses 3:83-101. 2011
  8. doi request reprint Phylodynamics of H5N1 avian influenza virus in Indonesia
    Tommy Tsan Yuk Lam
    School of Biological Sciences, The University of Hong Kong, Hong Kong, China
    Mol Ecol 21:3062-77. 2012
  9. pmc Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form
    Ana B Abecasis
    Katholieke Universiteit Leuven, Laboratory for Clinical and Epidemiological Virology, AIDS Reference Laboratory, Rega Institute and University Hospitals, Minderbroedersstraat 10, B 3000 Leuven, Belgium
    J Virol 81:8543-51. 2007
  10. ncbi request reprint Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivo
    Koen Deforche
    Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
    J Comput Biol 14:1105-14. 2007

Collaborators

Detail Information

Publications41

  1. pmc Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain
    Philippe Lemey
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
    J Virol 79:11981-9. 2005
    ....
  2. 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...
  3. 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
    ....
  4. 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...
  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. 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...
  7. pmc Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation
    Abby Harrison
    Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
    Viruses 3:83-101. 2011
    ..This Hepatitis B e antigen rate variation was found to be largely attributable to changes during the course of infection in the preCore and Core genes and their regulatory elements...
  8. doi request reprint Phylodynamics of H5N1 avian influenza virus in Indonesia
    Tommy Tsan Yuk Lam
    School of Biological Sciences, The University of Hong Kong, Hong Kong, China
    Mol Ecol 21:3062-77. 2012
    ..The phylodynamics we uncover share similarities with other recently studied viral invasions, thereby shedding light on the ecological and evolutionary processes that determine disease emergence in a new geographical region...
  9. pmc Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form
    Ana B Abecasis
    Katholieke Universiteit Leuven, Laboratory for Clinical and Epidemiological Virology, AIDS Reference Laboratory, Rega Institute and University Hospitals, Minderbroedersstraat 10, B 3000 Leuven, Belgium
    J Virol 81:8543-51. 2007
    ..We suggest a reanalysis of all pure subtypes and CRFs in order to better understand how high rates of recombination have influenced HIV-1 evolutionary history...
  10. ncbi request reprint Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivo
    Koen Deforche
    Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
    J Comput Biol 14:1105-14. 2007
    ....
  11. doi request reprint Genetic variation in mother-child acute seroconverter pairs from Zambia
    Federico G Hoffmann
    School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588 0666, USA
    AIDS 22:817-24. 2008
    ....
  12. ncbi request reprint Molecular testing of multiple HIV-1 transmissions in a criminal case
    Philippe Lemey
    Rega Institute, KULeuven, B 3000 Leuven, Belgium
    AIDS 19:1649-58. 2005
    ..To test the a priori hypothesis of HIV-1 transmission from one suspect to six recipients in a criminal case...
  13. ncbi request reprint Limitations to contact tracing and phylogenetic analysis in establishing HIV type 1 transmission networks in Cuba
    Sonia Resik
    Tropical Medicine Institute Pedro Kouri, Havana, Cuba
    AIDS Res Hum Retroviruses 23:347-56. 2007
    ..Also, superinfection and incomplete epidemiological information are other factors that will limit the concordance of phylogenetic reconstruction and reported epidemiological linkage...
  14. ncbi request reprint Exploring full-genome sequences for phylogenetic support of HIV-1 transmission events
    Philippe Lemey
    AIDS 19:1551-2. 2005
  15. pmc Genetic variability and molecular evolution of the human respiratory syncytial virus subgroup B attachment G protein
    Kalina T Zlateva
    Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, B 3000 Leuven, Belgium
    J Virol 79:9157-67. 2005
    ..HRSV-A and -B strains have similar phylodynamic patterns: both subgroups are characterized by global spatiotemporal strain dynamics, where the high infectiousness of HRSV permits the rapid geographic spread of novel strain variants...
  16. pmc Role of viral evolutionary rate in HIV-1 disease progression in a linked cohort
    Meriet Mikhail
    Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Westmead NSW 2145, Sydney, Australia
    Retrovirology 2:41. 2005
    ..By conducting 15 near full-length genome (8.7 kb) analysis from longitudinally derived patient PBMC samples enabled us to investigate the extent of molecular factors, which govern HIV disease progression...
  17. ncbi request reprint A genotypic resistance assay for the detection of drug resistance in the human immunodeficiency virus type 1 envelope gene
    Kristel Van Laethem
    Rega Institute for Medical Research and University Hospitals Leuven, Microbiology and Immunology, Clinical and Epidemiological Virology, AIDS Reference Laboratory, Minderbroedersstraat 10, Leuven 3000, Belgium
    J Virol Methods 123:25-34. 2005
    ..This study demonstrates that the assay is able to genotype genetically diverse HIV-1 strains with a good sensitivity...
  18. 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...
  19. ncbi request reprint Site stripping based on likelihood ratio reduction is a useful tool to evaluate the impact of non-clock-like behavior on viral phylogenetic reconstructions
    Philippe Lemey
    Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B 3000, Leuven, Belgium
    FEMS Immunol Med Microbiol 39:125-32. 2003
    ..Our method was able to rapidly recover clock-like behavior and to indicate the presence and direction of a bias when estimates of divergence times using the unstripped data were flawed...
  20. ncbi request reprint Evolutionary dynamics of human retroviruses investigated through full-genome scanning
    Philippe Lemey
    Rega Institute for Medical Research, KULeuven, Leuven, Belgium
    Mol Biol Evol 22:942-51. 2005
    ..Several evolutionary and statistical assumptions, examined using a Bayesian coalescent method, were shown to have little influence on our inference...
  21. pmc Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event
    Leen Vijgen
    Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, BE 3000 Leuven, Belgium
    J Virol 79:1595-604. 2005
    ....
  22. ncbi request reprint Phylogenetic reconstruction of a known HIV-1 CRF04_cpx transmission network using maximum likelihood and Bayesian methods
    Dimitrios Paraskevis
    National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece
    J Mol Evol 59:709-17. 2004
    ..For patients with known infection dates, the estimated dates of the coalescent events obtained using molecular clock calculations based on a newly developed Bayesian method in gag + env were in agreement with the actual infection dates...
  23. ncbi request reprint Genetic analyses reveal structured HIV-1 populations in serially sampled T lymphocytes of patients receiving HAART
    Simon J Potter
    Retroviral Genetics Laboratory, Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Darcy Road, Westmead, Sydney NSW 2145, Australia
    Virology 348:35-46. 2006
    ....
  24. ncbi request reprint HIV-1 compartmentalization in diverse leukocyte populations during antiretroviral therapy
    Simon J Potter
    Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Darcy Road, Westmead, Sydney NSW 2145, Australia
    J Leukoc Biol 76:562-70. 2004
    ....
  25. pmc Molecular evolution and circulation patterns of human respiratory syncytial virus subgroup a: positively selected sites in the attachment g glycoprotein
    Kalina T Zlateva
    Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
    J Virol 78:4675-83. 2004
    ..The evolutionary rate of HRSV subgroup A isolates was estimated to be 1.83 x 10(-3) nucleotide substitutions/site/year, projecting the most recent common ancestor back to the early 1940s...
  26. 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...
  27. ncbi request reprint Molecular typing and epidemiology of enteroviruses identified from an outbreak of aseptic meningitis in Belgium during the summer of 2000
    Inge Thoelen
    Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Belgium
    J Med Virol 70:420-9. 2003
    ..The RT-nested PCR strategy, carried out directly on clinical samples, is a simple and rapid method for adequate molecular typing of the Group B enteroviruses causing aseptic meningitis...
  28. 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
    ....
  29. 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...
  30. ncbi request reprint Complete genome sequence of Montana Myotis leukoencephalitis virus, phylogenetic analysis and comparative study of the 3' untranslated region of flaviviruses with no known vector
    Nathalie Charlier
    Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Minderbroedersstraat 10, B 3000 Leuven, Belgium
    J Gen Virol 83:1875-85. 2002
    ..The availability of this latter sequence motif allows us to designate a virus as either an NKV or a vector-borne flavivirus...
  31. ncbi request reprint Phylogenetic classification of TT virus groups based on the N22 region is unreliable
    Philippe Lemey
    Rega Institute for Medical Research, KULeuven, Minderbroedersstraat 10, B 3000, Belgium
    Virus Res 85:47-59. 2002
    ..We suggest that care should be taken in future TTV phylogenetic analysis, in particular, larger and more conserved regions should be sequenced to allow between group comparisons...
  32. pmc Analysis of the serotype and genotype correlation of VP1 and the 5' noncoding region in an epidemiological survey of the human enterovirus B species
    Inge Thoelen
    Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
    J Clin Microbiol 42:963-71. 2004
    ..g., primer choice), provided some background knowledge on the local spectrum of enteroviruses already exists...
  33. pmc Ancient papillomavirus-host co-speciation in Felidae
    Annabel Rector
    Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
    Genome Biol 8:R57. 2007
    ....
  34. ncbi request reprint Complete genome sequence, taxonomic assignment, and comparative analysis of the untranslated regions of the Modoc virus, a flavivirus with no known vector
    Pieter Leyssen
    Rega Institute for Medical Research, Katholieke Universiteit Leuven, B 3000 Leuven, Belgium
    Virology 293:125-40. 2002
    ..Also the putative secondary structure of circularized MODV RNA is presented...
  35. pmc Evolutionary history of the closely related group 2 coronaviruses: porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, and human coronavirus OC43
    Leen Vijgen
    Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, B 3000 Leuven, Belgium
    J Virol 80:7270-4. 2006
    ..Using a relaxed molecular clock approach, we reconstructed the evolutionary relationships between PHEV, BCoV, and HCoV-OC43 in real-time units, which indicated relatively recent common ancestors for these species-specific coronaviruses...
  36. 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...
  37. pmc Genetic variability of human respiratory coronavirus OC43
    Leen Vijgen
    J Virol 79:3223-4; author reply 3224-5. 2005
  38. ncbi request reprint Isolation and cloning of the raccoon (Procyon lotor) papillomavirus type 1 by using degenerate papillomavirus-specific primers
    Annabel Rector
    Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, B 3000 Leuven, Belgium
    J Gen Virol 86:2029-33. 2005
    ..Phylogenetic analysis places PlPV-1 together with COPV and FdPV-1 in a monophyletic branch which encompasses the Lambda papillomavirus genus...
  39. ncbi request reprint Full-genome analysis of a highly divergent simian T-cell lymphotropic virus type 1 strain in Macaca arctoides
    Sonia Van Dooren
    Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B 3000 Leuven, Belgium
    J Gen Virol 86:1953-9. 2005
    ..Full-genome molecular-clock analysis supports an archaic introduction of STLV-1 on the Asian continent, at least 269 000-156 000 years ago...
  40. ncbi request reprint Circulation of genetically distinct contemporary human coronavirus OC43 strains
    Leen Vijgen
    Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Belgium
    Virology 337:85-92. 2005
    ..We here describe specific characteristics associated with circulating HCoV-OC43 strains, and we provide substantial evidence for the genetic variability of HCoV-OC43...
  41. doi request reprint Genomic characterization of novel dolphin papillomaviruses provides indications for recombination within the Papillomaviridae
    Annabel Rector
    Laboratory of Clinical Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
    Virology 378:151-61. 2008
    ....