Lemey, Philippe, Lott, Martin, Martin, Darren P, Moulton, Vincent
Abstract Background Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains a challenging endeavor. Despite its...
Canducci, Filippo, Marinozzi, Maria, Sampaolo, Michela, Berrè, Stefano, Bagnarelli, Patrizia, Degano, Massimo, ...
Abstract The characteristics of intra-host human immunodeficiency virus type 1 (HIV-1) env evolution were evaluated in untreated HIV-1-infected subjects with different patterns of disease...
Genetic Variation in Mother-Child Acute Seroconverter Pairs from Zambia (2008)
Hoffmann, Federico G., He, Xiang, West, John T., Lemey, Philippe, Kankasa, Chipepo, Wood, Charles
Objective: To characterize the envelope (env) glycoprotein of HIV-1 in mother-infant pairs (MIP) that underwent near simultaneous or acute-phase seroconversion, we examined the env sequence of the...
Camacho, Ricardo, Shapiro, Beth, Rambaut, Andrew, ...
The human immunodeficiency virus (HIV) has a genome that is rich in adenine, and its rapid evolution shows an observed bias of guanine (G) to adenine (A) mutations. Two mechanisms have been proposed...
Ancient papillomavirus-host co-speciation in Felidae (2007)
Rector, Annabel, Lemey, Philippe, Tachezy, Ruth, Mostmans, Sara, Ghim, Shin-Je, Van Doorslaer, Koenraad, ...
Abstract Background Estimating evolutionary rates for slowly evolving viruses such as papillomaviruses (PVs) is not possible using fossil calibrations directly or sequences sampled over a time-scale...
Philippe Lemey, Alexei J. Drummond, Oliver G. Pybus, Beth Shapiro, Helena Barroso, ...
Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood...
Philippe Lemey, Alexei J. Drummond, Oliver G. Pybus, Beth Shapiro, Helena Barroso, ...
Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood...
Role of viral evolutionary rate in HIV-1 disease progression in a linked cohort (2005)
Mikhail, Meriet, Wang, Bin, Lemey, Philippe, Beckthold, Brenda, Vandamme, Anne-Mieke, Gill, M John, ...
Abstract Background The actual relationship between viral variability and HIV disease progression and/or non-progression can only be extrapolated through epidemiologically-linked HIV-infected...
Evolutionary Dynamics of Human Retroviruses Investigated Through Full Genome Scanning (2005)
Lemey, Philippe, Van Dooren, Sonia, Vandamme, Anne-Mieke
To test hypotheses on the differences in retroviral genetic diversity, we compared the evolutionary dynamics of the Human Immunodeficiency Virus type 1 (HIV-1) group M and the Primate T-cell...
Evolutionary Dynamics of Human Retroviruses Investigated Through Full-Genome Scanning (2005)
Lemey, Philippe, Van Dooren, Sonia, Vandamme, Anne-Mieke
To test hypotheses on the differences in retroviral genetic diversity, we compared the evolutionary dynamics of the human immunodeficiency virus type 1 (HIV-1) group M and the primate T-cell...
Evolutionary Dynamics of Human Retroviruses Investigated Through Full Genome Scanning (2005)
Lemey, Philippe, Van Dooren, Sonia, Vandamme, Anne-Mieke
To test hypotheses on the differences in retroviral genetic diversity, we compared the evolutionary dynamics of the Human Immunodeficiency Virus type 1 (HIV-1) group M and the Primate T-cell...
Keyaerts, Els; U0035321, Ghijsels, Erik, Lemey, Philippe; U0036765, Maes, Piet; U0040919, Zachee, Pierre; U0011133, Daelemans, Ronald, ...
A 37-year-old Belgian patient presented with acute nephropathia epidemica (NE) shortly after a camping holiday in southern France. Unusual symptoms were initial noncardiogenic lung involvement,...
Tracing the origin and history of the HIV-2 epidemic
Lemey, Philippe, Pybus, Oliver G., Wang, Bin, Saksena, Nitin K., Salemi, Marco, Vandamme, Anne-Mieke
In this study we date the introduction of HIV-2 into the human population and estimate the epidemic history of HIV-2 subtype A in Guinea-Bissau, the putative geographic origin of HIV-2. The...
Thoelen, Inge, Moës, Elien, Lemey, Philippe, Mostmans, Sara, Wollants, Elke, Lindberg, A. Michael, ...
The sequence identity of the enterovirus VP1 gene has been shown to correlate with the serotype concept. Enterovirus molecular typing methods are therefore often based on sequencing of the VP1...
Zlateva, Kalina T., Lemey, Philippe, Vandamme, Anne-Mieke, Van Ranst, Marc
Human respiratory syncytial virus (HRSV) is the most common etiological agent of acute lower respiratory tract disease in infants and can cause repeated infections throughout life. In this study, we...
Vijgen, Leen, Keyaerts, Els, Moës, Elien, Thoelen, Inge, Wollants, Elke, Lemey, Philippe, ...
Coronaviruses are enveloped, positive-stranded RNA viruses with a genome of approximately 30 kb. Based on genetic similarities, coronaviruses are classified into three groups. Two group 2...
Genetic Variability of Human Respiratory Coronavirus OC43
Vijgen, Leen, Lemey, Philippe, Keyaerts, Els, Ranst, Marc Van
Role of viral evolutionary rate in HIV-1 disease progression in a linked cohort
Mikhail, Meriet, Wang, Bin, Lemey, Philippe, Beckthold, Brenda, Vandamme, Anne-Mieke, Gill, M John, ...
Molecular Footprint of Drug-Selective Pressure in a Human Immunodeficiency Virus Transmission Chain†
Lemey, Philippe, Derdelinckx, Inge, Rambaut, Andrew, Van Laethem, Kristel, Dumont, Stephanie, Vermeulen, Steve, ...
Known human immunodeficiency virus (HIV) transmission histories are invaluable models for investigating the evolutionary and transmission dynamics of the virus and to assess the accuracy of...
Robbins, Kenneth E., Lemey, Philippe, Pybus, Oliver G., Jaffe, Harold W., Youngpairoj, Ae S., Brown, Teresa M., ...
Human immunodeficiency virus (HIV) type 1 subtype B sequences (whole envelope and the p17 region of gag) were obtained from peripheral blood mononuclear cell samples collected in 1981 from seven...
Zlateva, Kalina T., Lemey, Philippe, Moës, Elien, Vandamme, Anne-Mieke, Van Ranst, Marc
Human respiratory syncytial virus (HRSV) is the most important cause of acute respiratory disease in infants. Two major subgroups (A and B) have been identified based on antigenic differences in the...
Investigating the Origin and Spread of Hepatitis C Virus Genotype 5a†
Verbeeck, Jannick, Maes, Piet, Lemey, Philippe, Pybus, Oliver G., Wollants, Elke, Song, Ernie, ...
Epidemiological and phylogenetic studies of hepatitis C virus (HCV) have identified six major HCV genotypes and have attempted to characterize their origin and spread worldwide. Putative regions of...
The molecular population genetics of HIV-1 group O.
Lemey, Philippe, Pybus, Oliver G, Rambaut, Andrew, Drummond, Alexei J, Robertson, David L, Roques, Pierre, ...
HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics...
Vijgen, Leen, Keyaerts, Els, Lemey, Philippe, Maes, Piet, Van Reeth, Kristien, Nauwynck, Hans, ...
The close genetic and antigenic relatedness among the group 2 coronaviruses human coronavirus OC43 (HCoV-OC43), bovine coronavirus (BCoV), and porcine hemagglutinating encephalomyelitis virus (PHEV)...
Robbins, Kenneth E., Lemey, Philippe, Pybus, Oliver G., Jaffe, Harold W., Youngpairoj, Ae S., Brown, Teresa M., ...
Human immunodeficiency virus (HIV) type 1 subtype B sequences (whole envelope and the p17 region of gag) were obtained from peripheral blood mononuclear cell samples collected in 1981 from seven...
Tracing the origin and history of the HIV-2 epidemic
Lemey, Philippe, Pybus, Oliver G., Wang, Bin, Saksena, Nitin K., Salemi, Marco, Vandamme, Anne-Mieke
In this study we date the introduction of HIV-2 into the human population and estimate the epidemic history of HIV-2 subtype A in Guinea-Bissau, the putative geographic origin of HIV-2. The...
Thoelen, Inge, Moës, Elien, Lemey, Philippe, Mostmans, Sara, Wollants, Elke, Lindberg, A. Michael, ...
The sequence identity of the enterovirus VP1 gene has been shown to correlate with the serotype concept. Enterovirus molecular typing methods are therefore often based on sequencing of the VP1...
Zlateva, Kalina T., Lemey, Philippe, Vandamme, Anne-Mieke, Van Ranst, Marc
Human respiratory syncytial virus (HRSV) is the most common etiological agent of acute lower respiratory tract disease in infants and can cause repeated infections throughout life. In this study, we...
Vijgen, Leen, Keyaerts, Els, Moës, Elien, Thoelen, Inge, Wollants, Elke, Lemey, Philippe, ...
Coronaviruses are enveloped, positive-stranded RNA viruses with a genome of approximately 30 kb. Based on genetic similarities, coronaviruses are classified into three groups. Two group 2...
Genetic Variability of Human Respiratory Coronavirus OC43
Vijgen, Leen, Lemey, Philippe, Keyaerts, Els, Ranst, Marc Van
Zlateva, Kalina T., Lemey, Philippe, Moës, Elien, Vandamme, Anne-Mieke, Van Ranst, Marc
Human respiratory syncytial virus (HRSV) is the most important cause of acute respiratory disease in infants. Two major subgroups (A and B) have been identified based on antigenic differences in the...
Role of viral evolutionary rate in HIV-1 disease progression in a linked cohort
Mikhail, Meriet, Wang, Bin, Lemey, Philippe, Beckthold, Brenda, Vandamme, Anne-Mieke, Gill, M John, ...
Molecular Footprint of Drug-Selective Pressure in a Human Immunodeficiency Virus Transmission Chain†
Lemey, Philippe, Derdelinckx, Inge, Rambaut, Andrew, Van Laethem, Kristel, Dumont, Stephanie, Vermeulen, Steve, ...
Known human immunodeficiency virus (HIV) transmission histories are invaluable models for investigating the evolutionary and transmission dynamics of the virus and to assess the accuracy of...
The molecular population genetics of HIV-1 group O.
Lemey, Philippe, Pybus, Oliver G, Rambaut, Andrew, Drummond, Alexei J, Robertson, David L, Roques, Pierre, ...
HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics...
Investigating the Origin and Spread of Hepatitis C Virus Genotype 5a†
Verbeeck, Jannick, Maes, Piet, Lemey, Philippe, Pybus, Oliver G., Wollants, Elke, Song, Ernie, ...
Epidemiological and phylogenetic studies of hepatitis C virus (HCV) have identified six major HCV genotypes and have attempted to characterize their origin and spread worldwide. Putative regions of...
Vijgen, Leen, Keyaerts, Els, Lemey, Philippe, Maes, Piet, Van Reeth, Kristien, Nauwynck, Hans, ...
The close genetic and antigenic relatedness among the group 2 coronaviruses human coronavirus OC43 (HCoV-OC43), bovine coronavirus (BCoV), and porcine hemagglutinating encephalomyelitis virus (PHEV)...
Lemey, Philippe, Kosakovsky Pond, Sergei L, Drummond, Alexei J, Pybus, Oliver G, Shapiro, Beth, Barroso, Helena, ...
Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood...
Ancient papillomavirus-host co-speciation in Felidae
Rector, Annabel, Lemey, Philippe, Tachezy, Ruth, Mostmans, Sara, Ghim, Shin-Je, Van Doorslaer, Koenraad, ...
The evolutionary rate of feline papillomaviruses is inferred from the phylogenetic analysis of their hosts, providing evidence for long-term virus-host co-speciation
Abecasis, Ana B., Lemey, Philippe, Vidal, Nicole, De Oliveira, Túlio, Peeters, Martine, Camacho, Ricardo, ...
Human immunodeficiency virus type 1 (HIV-1) is classified in nine subtypes (A to D, F, G, H, J, and K), a number of subsubtypes, and several circulating recombinant forms (CRFs). Due to the high...
Canducci, Filippo, Marinozzi, Maria Chiara, Sampaolo, Michela, Berrè, Stefano, Bagnarelli, Patrizia, Degano, Massimo, ...
The characteristics of intra-host human immunodeficiency virus type 1 (HIV-1) env evolution were evaluated in untreated HIV-1-infected subjects with different patterns of disease progression,...
Machado, Elizabeth S., Afonso, Adriana O., Nissley, Dwight V., Lemey, Philippe, Cunha, Silvia M., Oliveira, Ricardo H., ...
Genetic History of Hepatitis C Virus in East Asia ▿
Pybus, Oliver G., Barnes, Eleanor, Taggart, Rachel, Lemey, Philippe, Markov, Peter V., Rasachak, Bouachan, ...
The hepatitis C virus (HCV), which currently infects an estimated 3% of people worldwide, has been present in some human populations for several centuries, notably HCV genotypes 1 and 2 in West...
Bayesian Phylogeography Finds Its Roots
Lemey, Philippe, Rambaut, Andrew, Drummond, Alexei J., Suchard, Marc A.
As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic histories. Unfortunately, inference of...
McDonald, Sarah M., Matthijnssens, Jelle, McAllen, John K., Hine, Erin, Overton, Larry, Wang, Shiliang, ...
Group A human rotaviruses (RVs) are a major cause of severe gastroenteritis in infants and young children. Yet, aside from the genes encoding serotype antigens (VP7; G-type and VP4; P-type), little...
Lemey, Philippe, Suchard, Marc, Rambaut, Andrew
Here, we present an analysis of the H1N1pdm genetic data sampled over the initial stages in the epidemic. To infer phylodynamic spread in time and space we employ a recently developed Bayesian...