Research Topics
| Philippe LemeySummaryAffiliation: University of Oxford Country: UK Publications
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Detail Information
Publications
Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chainPhilippe Lemey
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
J Virol 79:11981-9. 2005....
HIV evolutionary dynamics within and among hostsPhilippe 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...- Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamicsPhilippe Lemey
Department of Zoology, University of Oxford, Oxford, United Kingdom
PLoS Comput Biol 3:e29. 2007.... - Unifying the spatial epidemiology and molecular evolution of emerging epidemicsOliver 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... - The mode and tempo of hepatitis C virus evolution within and among hostsRebecca 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... - Genetic history of hepatitis C virus in East AsiaOliver 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... - Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variationAbby 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... 
Phylodynamics of H5N1 avian influenza virus in IndonesiaTommy 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...- Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant formAna 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... - Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivoKoen Deforche
Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
J Comput Biol 14:1105-14. 2007.... - Genetic variation in mother-child acute seroconverter pairs from ZambiaFederico G Hoffmann
School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588 0666, USA
AIDS 22:817-24. 2008.... - Molecular testing of multiple HIV-1 transmissions in a criminal casePhilippe 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... - Limitations to contact tracing and phylogenetic analysis in establishing HIV type 1 transmission networks in CubaSonia 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... - Exploring full-genome sequences for phylogenetic support of HIV-1 transmission eventsPhilippe Lemey
AIDS 19:1551-2. 2005 - Genetic variability and molecular evolution of the human respiratory syncytial virus subgroup B attachment G proteinKalina 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... - Role of viral evolutionary rate in HIV-1 disease progression in a linked cohortMeriet 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... - A genotypic resistance assay for the detection of drug resistance in the human immunodeficiency virus type 1 envelope geneKristel 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... - U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strainsKenneth 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... - Site stripping based on likelihood ratio reduction is a useful tool to evaluate the impact of non-clock-like behavior on viral phylogenetic reconstructionsPhilippe 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... - Evolutionary dynamics of human retroviruses investigated through full-genome scanningPhilippe 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... - Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission eventLeen 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.... - Phylogenetic reconstruction of a known HIV-1 CRF04_cpx transmission network using maximum likelihood and Bayesian methodsDimitrios 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... - Genetic analyses reveal structured HIV-1 populations in serially sampled T lymphocytes of patients receiving HAARTSimon 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.... - HIV-1 compartmentalization in diverse leukocyte populations during antiretroviral therapySimon 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.... - Molecular evolution and circulation patterns of human respiratory syncytial virus subgroup a: positively selected sites in the attachment g glycoproteinKalina 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... - The molecular population genetics of HIV-1 group OPhilippe 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... - Molecular typing and epidemiology of enteroviruses identified from an outbreak of aseptic meningitis in Belgium during the summer of 2000Inge 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... - Tracing the origin and history of the HIV-2 epidemicPhilippe Lemey
Rega Institute for Medical Research, Katholieke Universiteit Leuven, Belgium
Proc Natl Acad Sci U S A 100:6588-92. 2003.... - A Bayesian statistical analysis of human T-cell lymphotropic virus evolutionary ratesPhilippe 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... - Complete genome sequence of Montana Myotis leukoencephalitis virus, phylogenetic analysis and comparative study of the 3' untranslated region of flaviviruses with no known vectorNathalie 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... - Phylogenetic classification of TT virus groups based on the N22 region is unreliablePhilippe 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... - Analysis of the serotype and genotype correlation of VP1 and the 5' noncoding region in an epidemiological survey of the human enterovirus B speciesInge 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... - Ancient papillomavirus-host co-speciation in FelidaeAnnabel Rector
Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
Genome Biol 8:R57. 2007.... - Complete genome sequence, taxonomic assignment, and comparative analysis of the untranslated regions of the Modoc virus, a flavivirus with no known vectorPieter 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... - Evolutionary history of the closely related group 2 coronaviruses: porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, and human coronavirus OC43Leen 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... - Investigating the origin and spread of hepatitis C virus genotype 5aJannick 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... - Genetic variability of human respiratory coronavirus OC43Leen Vijgen
J Virol 79:3223-4; author reply 3224-5. 2005 - Isolation and cloning of the raccoon (Procyon lotor) papillomavirus type 1 by using degenerate papillomavirus-specific primersAnnabel 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... - Full-genome analysis of a highly divergent simian T-cell lymphotropic virus type 1 strain in Macaca arctoidesSonia 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... - Circulation of genetically distinct contemporary human coronavirus OC43 strainsLeen 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... - Genomic characterization of novel dolphin papillomaviruses provides indications for recombination within the PapillomaviridaeAnnabel 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....