Philippe Lemey

Summary

Affiliation: Katholieke Universiteit Leuven
Country: Belgium

Publications

  1. 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
  2. ncbi 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
  3. ncbi 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
  4. ncbi 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
  5. 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
  6. pmc Phylogeography takes a relaxed random walk in continuous space and time
    Philippe Lemey
    Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium
    Mol Biol Evol 27:1877-85. 2010
  7. doi Molecular evolutionary analysis and mutational pattern of full-length genomes of hepatitis B virus isolated from Belgian patients with different clinical manifestations
    Mahmoud Reza Pourkarim
    Laboratory of Clinical Virology, Rega Institute for Medical Research, Leuven, Belgium
    J Med Virol 82:379-89. 2010
  8. 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
  9. doi Molecular characterization of hepatitis B virus strains circulating in Belgian patients co-infected with HIV and HBV: overt and occult infection
    Mahmoud Reza Pourkarim
    Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit, Leuven, Belgium
    J Med Virol 83:1876-84. 2011
  10. ncbi 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

Collaborators

Detail Information

Publications62

  1. 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...
  2. ncbi 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...
  3. ncbi 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...
  4. ncbi 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...
  5. 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
    ....
  6. pmc Phylogeography takes a relaxed random walk in continuous space and time
    Philippe Lemey
    Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium
    Mol Biol Evol 27:1877-85. 2010
    ....
  7. doi Molecular evolutionary analysis and mutational pattern of full-length genomes of hepatitis B virus isolated from Belgian patients with different clinical manifestations
    Mahmoud Reza Pourkarim
    Laboratory of Clinical Virology, Rega Institute for Medical Research, Leuven, Belgium
    J Med Virol 82:379-89. 2010
    ..The highest degree of genetic diversity was detected in HBV genotype D. In addition, this study reveals the circulation of exotic HBV genotypes B, C, and E in Belgium. J. Med. Virol. 82:379-389, 2010. (c) 2010 Wiley-Liss, Inc...
  8. 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...
  9. doi Molecular characterization of hepatitis B virus strains circulating in Belgian patients co-infected with HIV and HBV: overt and occult infection
    Mahmoud Reza Pourkarim
    Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit, Leuven, Belgium
    J Med Virol 83:1876-84. 2011
    ....
  10. ncbi 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...
  11. doi Novel hepatitis B virus subgenotype A6 in African-Belgian patients
    Mahmoud Reza Pourkarim
    Laboratory of Clinical Virology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, BE 3000 Leuven, Belgium
    J Clin Virol 47:93-6. 2010
    ..Genome diversity of hepatitis B virus (HBV) is prominent among DNA viruses; which, allowed the virus to be genetically classified into eight genotypes and several subgenotypes...
  12. 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...
  13. ncbi 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
    ....
  14. 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...
  15. doi 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
    ....
  16. doi Are hepatitis B virus "subgenotypes" defined accurately?
    Mahmoud Reza Pourkarim
    Laboratory of Clinical Virology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, B3000 Leuven, Belgium
    J Clin Virol 47:356-60. 2010
    ..Recently, several novel hepatitis B virus (HBV) subgenotypes have been introduced that do not meet proper definition of "subgenotypes". In particular for HBV genotype A, such novel subgenotypes have been reported...
  17. doi Phylogenetic analysis of hepatitis B virus full-length genomes reveals evidence for a large nosocomial outbreak in Belgium
    Mahmoud Reza Pourkarim
    Laboratory of Clinical Virology, Rega Institute for Medical Research, Leuven, Belgium
    J Clin Virol 46:61-8. 2009
    ..Despite increased safety efforts, nosocomial acquired hepatitis B infection remains problematic...
  18. pmc Bayesian phylogeography finds its roots
    Philippe Lemey
    Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium
    PLoS Comput Biol 5:e1000520. 2009
    ..From these analyses, we conclude that our phylogeographic framework will make an important asset in molecular epidemiology that can be easily generalized to infer biogeogeography from genetic data for many organisms...
  19. 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
    ....
  20. ncbi 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...
  21. ncbi 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...
  22. ncbi 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...
  23. pmc Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
    Guy Baele
    Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
    Mol Biol Evol 29:2157-67. 2012
    ..The methods used in this article are now available in BEAST, a powerful user-friendly software package to perform Bayesian evolutionary analyses...
  24. 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
    ....
  25. 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...
  26. pmc Circulation of HRSV in Belgium: from multiple genotype circulation to prolonged circulation of predominant genotypes
    Lieselot Houspie
    Laboratory of Clinical Virology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
    PLoS ONE 8:e60416. 2013
    ..The emergence of the GB13 genotype resulted in a newly established balance between the predominant genotypes...
  27. 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...
  28. 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...
  29. ncbi 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...
  30. pmc A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection
    Philippe Lemey
    Department of Microbiology and Immunology, Rega Institute, KU Leuven, B 3000 Leuven, Belgium
    Bioinformatics 28:3248-56. 2012
    ....
  31. pmc Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape
    Kristof Theys
    Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
    BMC Bioinformatics 11:409. 2010
    ..By simulation of evolution over this landscape, the individualized genetic barrier to NFV resistance may be estimated for an isolate...
  32. ncbi 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...
  33. pmc Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning
    Philippe Lemey
    Rega Institute, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
    BMC Bioinformatics 10:126. 2009
    ..We compare the quartet approach with triplet-based methods that employ additional heuristic tests to identify parental and recombinant sequences...
  34. ncbi Covering all bases in HIV research: unveiling a hidden world of viral evolution
    Bram Vrancken
    Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
    AIDS Rev 12:89-102. 2010
    ..We also highlight some of the bioinformatics challenges, as well as advantages and potential limitations of this "deep" sequencing tool, and hint at future research applications...
  35. pmc Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints
    Nuno Rodrigues Faria
    Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
    Philos Trans R Soc Lond B Biol Sci 368:20120196. 2013
    ..Although our evolutionary framework focused on the multi-host reservoir dynamics of bat rabies virus, it is applicable to other pathogens and to other discrete state transition processes...
  36. pmc Accurate model selection of relaxed molecular clocks in bayesian phylogenetics
    Guy Baele
    Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
    Mol Biol Evol 30:239-43. 2013
    ..We also illustrate the importance of using proper priors on a large set of empirical data sets...
  37. doi Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon
    Nuno R Faria
    Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
    Infect Genet Evol 12:453-60. 2012
    ....
  38. 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...
  39. doi Phylodynamic analyses of rotavirus genotypes G9 and G12 underscore their potential for swift global spread
    Jelle Matthijnssens
    Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
    Mol Biol Evol 27:2431-6. 2010
    ..g., a vaccine escape mutant) can spread worldwide in little more than a decade. These results re-emphasize the need for thorough and continued RV surveillance in order to detect such potential spreading events at an early stage...
  40. doi Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency
    Guy Baele
    Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
    Bioinformatics 29:1970-9. 2013
    ..To compare the different models, we use state-of-the-art marginal likelihood estimation techniques, including path sampling and stepping-stone sampling...
  41. pmc Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution
    Guy Baele
    Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
    BMC Bioinformatics 14:85. 2013
    ..Most often, each model's marginal likelihood will be estimated individually, which leads the resulting Bayes factor to suffer from errors associated with each of these independent estimation processes...
  42. ncbi 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...
  43. pmc SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics
    Filip Bielejec
    Rega Institute for Medical Research, Clinical and Epidemiological Virology Section, Katholieke Universiteit Leuven, Leuven, Belgium
    Bioinformatics 27:2910-2. 2011
    ....
  44. ncbi 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...
  45. doi Evolutionary analysis of HBV "S" antigen genetic diversity in Iranian blood donors: a nationwide study
    Mahmoud Reza Pourkarim
    Department of Microbiology and Immunology, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
    J Med Virol 86:144-55. 2014
    ..These findings regarding the significant differences in reactivity of ELISA among different subtypes of HBV and its correlation with the number of mutations at the MHR will be valuable to public health authorities...
  46. pmc Toward a quantitative understanding of viral phylogeography
    Nuno Rodrigues Faria
    Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium
    Curr Opin Virol 1:423-9. 2011
    ..We also outline future areas of research and discuss how these may contribute to a quantitative understanding of the phylodynamics of RNA viruses...
  47. ncbi 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...
  48. ncbi 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...
  49. pmc Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A
    Nuno R Faria
    Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
    J Gen Virol 93:889-99. 2012
    ..We demonstrate that probabilistic models can uncover global patterns of HIV-2A dispersal providing sampling bias is taken into account and we provide a scenario for the international spread of this virus...
  50. pmc High GUD incidence in the early 20 century created a particularly permissive time window for the origin and initial spread of epidemic HIV strains
    João Dinis de Sousa
    Laboratory for Clinical and Evolutionary Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
    PLoS ONE 5:e9936. 2010
    ..Our results suggest that intense GUD in promiscuous urban communities was the main factor driving HIV emergence. Low circumcision rates may have played a role, probably by their indirect effects on GUD...
  51. doi 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...
  52. ncbi Plasma exchange-associated immunoglobulin m-negative hantavirus disease after a camping holiday in southern france
    Els Keyaerts
    Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, BE 3000 Leuven, Belgium
    Clin Infect Dis 38:1350-6. 2004
    ..This is also the first report of proven NE from the Mediterranean part of France...
  53. 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
    ....
  54. 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...
  55. doi 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
    ....
  56. ncbi 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...
  57. ncbi Exploring full-genome sequences for phylogenetic support of HIV-1 transmission events
    Philippe Lemey
    AIDS 19:1551-2. 2005
  58. ncbi 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...
  59. ncbi 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
    ....
  60. pmc Genetic variability of human respiratory coronavirus OC43
    Leen Vijgen
    J Virol 79:3223-4; author reply 3224-5. 2005
  61. ncbi 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
    ....
  62. 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
    ....