Ramsden, Cadhla, Holmes, Edward C., Charleston, Michael A.
Hantaviruses are considered one of the best examples of a long-term association between RNA viruses and their hosts. Based on the appearance of strong host specificity, it has been suggested that...
Immune and artificial selection in the haemagglutinin (H) glycoprotein of measles virus (2008)
Christopher H. Woelk, Li Jin, Edward C. Holmes
We present a maximum likelihood (ML) analysis of the selection pressures that have shaped the evolution of the large (L) protein and the haemagglutinin (H) glycoprotein of measles virus (MV). A...
Global distribution of novel rhinovirus genotype (2008)
Briese, Thomas, Renwick, Neil, Venter, Marietjie, Jarman, Richard G., Ghosh, Dhrubaa, Kondgen, Sophie, ...
Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America....
Global distribution of novel rhinovirus genotype (2008)
Briese, Thomas, Renwick, Neil, Venter, Marietjie, Jarman, Richard G., Ghosh, Dhrubaa, Kondgen, Sophie, ...
Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America....
Boosting Virology in Brazil (2008)
Leda Fátima Jamal, Edison Luiz Durigon, Eduardo Massad, José Fernando Perez, ...
High Rates of Molecular Evolution in Hantaviruses (2008)
Ramsden, Cadhla, Melo, Fernando L., Figueiredo, Luiz. M., Holmes, Edward C., Zanotto, Paolo M.A.
Hantaviruses are rodent-borne Bunyaviruses that infect the Arvicolinae, Murinae, and Sigmodontinae subfamilies of Muridae. The rate of molecular evolution in the hantaviruses has been previously...
Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient (2007)
Aaskov, John G., Buzacott, Katie, Field, Emma J., Lowry, Kym S., Berlioz-Arthaud, Alain, Holmes, Edward C.
Between 2000 and 2004, dengue virus type 1 (DENV-1) genotypes I and II from Asia were introduced into the Pacific region and co-circulated in some localities. Envelope protein gene sequences of...
Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient (2007)
Aaskov, John G., Buzacott, Katie, Field, Emma J., Lowry, Kym S., Berlioz-Arthaud, Alain, Holmes, Edward C.
Between 2000 and 2004, dengue virus type 1 (DENV-1) genotypes I and II from Asia were introduced into the Pacific region and co-circulated in some localities. Envelope protein gene sequences of...
Brault, Aaron C., Huang, Claire Y-H, Langevin, Stanley A., Kinney, Richard M., Bowen, Richard A., Ramey, Wanichaya N., ...
West Nile virus ( WNV), first recognized in North America in 1999, has been responsible for the largest arboviral epiornitic and epidemic of human encephalitis in recorded history. Despite the well-...
Phylogenetic Analysis Reveals the Global Migration of Seasonal Influenza A Viruses (2007)
Martha I. Nelson, Lone Simonsen, Cecile Viboud, Mark A. Miller, Edward C. Holmes
The winter seasonality of influenza A virus in temperate climates is one of the most widely recognized, yet least understood, epidemiological patterns in infectious disease. Central to understanding...
Simonsen, Lone, Viboud, Cécile, Grenfell, Bryan T., Dushoff, Jonathan, Jennings, Lance, Smit, Marita, ...
A dramatic rise in the frequency of resistance to adamantane drugs by influenza A (H3N2) viruses has occurred in recent years—from ∼2% to ∼90% in multiple countries worldwide—and associated...
Selection for Robustness in Mutagenized RNA Viruses (2007)
Rafael Sanjuán, José M. Cuevas, Victoria Furió, Edward C. Holmes, Andrés Moya
Mutational robustness is defined as the constancy of a phenotype in the face of deleterious mutations. Whether robustness can be directly favored by natural selection remains controversial. Theory...
Juliet E. Bryant, Edward C. Holmes
Yellow fever virus (YFV) remains the cause of severe morbidity and mortality in South America and Africa. To determine the evolutionary history of this important reemerging pathogen, we performed a...
Selection for Robustness in Mutagenized RNA Viruses (2007)
Rafael Sanjuan, Jose M Cuevas, Victoria Furió, Edward C. Holmes, Andres Moya
Mutational robustness is defined as the constancy of a phenotype in the face of deleterious mutations While theory and in silico experiments predict that, at high mutation rates, slow-replicating...
Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient (2007)
Aaskov, John G., Buzacott, Katie, Field, Emma J., Lowry, Kym S., Berlioz-Arthaud, Alain, Holmes, Edward C.
Between 2000 and 2004, dengue virus type 1 (DENV-1) genotypes I and II from Asia were introduced into the Pacific region and co-circulated in some localities. Envelope protein gene sequences of...
Sharp, Emma L., Farrell, Helen E., Borchers, Kerstin, Holmes, Edward C., Davis-Poynter, Nicholas J.
Equid herpesvirus 2 (EHV-2), in common with other members of the subfamily Gammaherpesvirinae, encodes homologues of cellular seven-transmembrane receptors (7TMR), namely open reading frames (ORFs)...
Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient (2007)
Aaskov, John G., Buzacott, Katie, Field, Emma J., Lowry, Kym S., Berlioz-Arthaud, Alain, Holmes, Edward C.
Between 2000 and 2004, dengue virus type 1 (DENV-1) genotypes I and II from Asia were introduced into the Pacific region and co-circulated in some localities. Envelope protein gene sequences of...
Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient (2007)
Aaskov, John G., Buzacott, Katie, Field, Emma J., Lowry, Kym S., Berlioz-Arthaud, Alain, Holmes, Edward C.
Between 2000 and 2004, dengue virus type 1 (DENV-1) genotypes I and II from Asia were introduced into the Pacific region and co-circulated in some localities. Envelope protein gene sequences of...
Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient (2007)
Aaskov, John G., Buzacott, Katie, Field, Emma J., Lowry, Kym S., Berlioz-Arthaud, Alain, Holmes, Edward C.
Between 2000 and 2004, dengue virus type 1 (DENV-1) genotypes I and II from Asia were introduced into the Pacific region and co-circulated in some localities. Envelope protein gene sequences of...
Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient (2007)
Aaskov, John G., Buzacott, Katie, Field, Emma J., Lowry, Kym S., Berlioz-Arthaud, Alain, Holmes, Edward C.
Between 2000 and 2004, dengue virus type 1 (DENV-1) genotypes I and II from Asia were introduced into the Pacific region and co-circulated in some localities. Envelope protein gene sequences of...
Pybus, Oliver G., Rambaut, Andrew, Belshaw, Robert, Freckleton, Robert P., Drummond, Alexei J., Holmes, Edward C.
Populations of RNA viruses are often characterized by abundant genetic variation. However, the relative fitness of these mutations is largely unknown, although this information is central to our...
Pybus, Oliver G., Rambaut, Andrew, Belshaw, Robert, Freckleton, Robert P., Drummond, Alexei J., Holmes, Edward C.
Populations of RNA viruses are often characterized by abundant genetic variation. However, the relative fitness of these mutations is largely unknown, although this information is central to our...
Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient (2007)
Aaskov, John G., Buzacott, Katie, Field, Emma J., Lowry, Kym S., Berlioz-Arthaud, Alain, Holmes, Edward C.
Between 2000 and 2004, dengue virus type 1 (DENV-1) genotypes I and II from Asia were introduced into the Pacific region and co-circulated in some localities. Envelope protein gene sequences of...
Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus (2006)
Martha I. Nelson, Lone Simonsen, Cecile Viboud, Mark A. Miller, Jill Taylor, Kirsten St. George, ...
Understanding the evolutionary dynamics of influenza A virus is central to its surveillance and control. While immune-driven antigenic drift is a key determinant of viral evolution across epidemic...
Martha I. Nelson, Lone Simonsen, Cecile Viboud, Mark A. Miller, Jill Taylor, Kirsten St. George, ...
Wolf, Yuri I, Viboud, Cecile, Holmes, Edward C, Koonin, Eugene V, Lipman, David J
Abstract Background The interpandemic evolution of the influenza A virus hemagglutinin (HA) protein is commonly considered a paragon of rapid evolutionary change under positive selection in which...
Edwards, Charles TT, Holmes, Edward C, Wilson, Daniel J, Viscidi, Raphael P, Abrams, Elaine J, Phillips, Rodney E, ...
Abstract Background Genetic diversity of the human immunodeficiency virus type 1 (HIV-1) population within an individual is lost during transmission to a new host. The demography of transmission is...
Avian Influenza Virus Exhibits Rapid Evolutionary Dynamics (2006)
Chen, Rubing, Holmes, Edward C.
Influenza A viruses from wild aquatic birds, their natural reservoir species, are thought to have reached a form of stasis, characterized by low rates of evolutionary change. We tested this...
Shapiro, Beth, Rambaut, Andrew, Pybus, Oliver G., Holmes, Edward C.
RNA virus genomes are compact, often containing multiple overlapping reading frames and functional secondary structure. Consequently, it is thought that evolutionary interactions between nucleotide...
Avian Influenza Virus Exhibits Rapid Evolutionary Dynamics (2006)
Chen, Rubing, Holmes, Edward C.
Influenza A viruses from wild aquatic birds, their natural reservoir species, are thought to have reached a form of stasis, characterized by low rates of evolutionary change. We tested this...
Shapiro, Beth, Rambaut, Andrew, Pybus, Oliver G., Holmes, Edward C.
RNA virus genomes are compact, often containing multiple overlapping reading frames and functional secondary structure. Consequently, it is thought that evolutionary interactions between nucleotide...
Biology Direct BioMed Central (2006)
Yuri I Wolf, Cecile Viboud, Edward C Holmes, Eugene V Koonin, David J Lipman
Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus
Edward C. Holmes, Elodie Ghedin, Naomi Miller, Jill Taylor, Yiming Bao, Kirsten St. George, ...
Evolution of the flu virus is analyzed via genomic phylogeny; humans are found to provide a reservoir of antigenic variability implicit in flu adaptation and virulence.
Edward C. Holmes, Elodie Ghedin, Naomi Miller, Jill Taylor, Yiming Bao, Kirsten St. George, ...
Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2...
Thu, Hlaing Myat, Lowry, Kym S., Jiang, Limin, Hlaing, Thaung, Holmes, Edward C., Aaskov, John G.
Between 1996 and 1998 two clades (B,C; genotype I) of dengue virus type 1 (DENV-1) appeared in Myanmar (Burma) that were new to that location. Between 1998 and 2000 a third clade (A; genotype III) of...
Thu, Hlaing Myat, Lowry, Kym S., Jiang, Limin, Hlaing, Thaung, Holmes, Edward C., Aaskov, John G.
Between 1996 and 1998 two clades (B,C; genotype I) of dengue virus type 1 (DENV-1) appeared in Myanmar (Burma) that were new to that location. Between 1998 and 2000 a third clade (A; genotype III) of...
Shelley Cook, Mawlouth Diallo, Amadou A. Sall, Alan Cooper, Edward C. Holmes
Correct classification of the insect vector is central to the study of arboviral disease. A simple molecular method for identification of the main vectors of the mosquito-borne viruses, dengue,...
Thu, Hlaing Myat, Lowry, Kym S., Jiang, Limin, Hlaing, Thaung, Holmes, Edward C., Aaskov, John G.
Between 1996 and 1998 two clades (B,C; genotype I) of dengue virus type 1 (DENV-1) appeared in Myanmar (Burma) that were new to that location. Between 1998 and 2000 a third clade (A; genotype III) of...
Holmes, Edward C., Ghedin, Elodie, Miller, Naomi, Taylor, Jill, Bao, Yiming, St. George, Kirsten, ...
Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2...
Holmes, Edward C., Ghedin, Elodie, Miller, Naomi, Taylor, Jill, Bao, Yiming, St. George, Kirsten, ...
Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2...
Thu, Hlaing Myat, Lowry, Kym S., Jiang, Limin, Hlaing, Thaung, Holmes, Edward C., Aaskov, John G.
Between 1996 and 1998 two clades (B,C; genotype I) of dengue virus type 1 (DENV-1) appeared in Myanmar (Burma) that were new to that location. Between 1998 and 2000 a third clade (A; genotype III) of...
Thu, Hlaing Myat, Lowry, Kym S., Jiang, Limin, Hlaing, Thaung, Holmes, Edward C., Aaskov, John G.
Between 1996 and 1998 two clades (B,C; genotype I) of dengue virus type 1 (DENV-1) appeared in Myanmar (Burma) that were new to that location. Between 1998 and 2000 a third clade (A; genotype III) of...
Thu, Hlaing Myat, Lowry, Kym S., Jiang, Limin, Hlaing, Thaung, Holmes, Edward C., Aaskov, John G.
Between 1996 and 1998 two clades (B,C; genotype I) of dengue virus type 1 (DENV-1) appeared in Myanmar (Burma) that were new to that location. Between 1998 and 2000 a third clade (A; genotype III) of...
Edward C. Holmes, Elodie Ghedin, Naomi Miller, Jill Taylor, Yiming Bao, Kirsten St. George, ...
Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2...
Thu, Hlaing Myat, Lowry, Kym S., Jiang, Limin, Hlaing, Thaung, Holmes, Edward C., Aaskov, John G.
Between 1996 and 1998 two clades (B,C; genotype I) of dengue virus type 1 (DENV-1) appeared in Myanmar (Burma) that were new to that location. Between 1998 and 2000 a third clade (A; genotype III) of...
Thu, Hlaing Myat, Lowry, Kym S., Jiang, Limin, Hlaing, Thaung, Holmes, Edward C., Aaskov, John G.
Between 1996 and 1998 two clades (B,C; genotype I) of dengue virus type 1 (DENV-1) appeared in Myanmar (Burma) that were new to that location. Between 1998 and 2000 a third clade (A; genotype III) of...
Craig, Scott B., Thu, Hlaing Myat, Lowry, Kym S., Wang, Xiao-fang, Holmes, Edward C., Aaskov, John G.
Envelope (E) protein genes sampled from populations of dengue 2 (DEN-2) virus in individual Aedes aegypti mosquitoes and in serum from dengue patients were copied to cDNA, cloned, and sequenced. The...
Craig, Scott B., Thu, Hlaing Myat, Lowry, Kym S., Wang, Xiao-fang, Holmes, Edward C., Aaskov, John G.
Envelope (E) protein genes sampled from populations of dengue 2 (DEN-2) virus in individual Aedes aegypti mosquitoes and in serum from dengue patients were copied to cDNA, cloned, and sequenced. The...
Craig, Scott B., Thu, Hlaing Myat, Lowry, Kym S., Wang, Xiao-fang, Holmes, Edward C., Aaskov, John G.
Envelope (E) protein genes sampled from populations of dengue 2 (DEN-2) virus in individual Aedes aegypti mosquitoes and in serum from dengue patients were copied to cDNA, cloned, and sequenced. The...
Craig, Scott B., Thu, Hlaing Myat, Lowry, Kym S., Wang, Xiao-fang, Holmes, Edward C., Aaskov, John G.
Envelope (E) protein genes sampled from populations of dengue 2 (DEN-2) virus in individual Aedes aegypti mosquitoes and in serum from dengue patients were copied to cDNA, cloned, and sequenced. The...
Craig, Scott B., Thu, Hlaing Myat, Lowry, Kym S., Wang, Xiao-fang, Holmes, Edward C., Aaskov, John G.
Envelope (E) protein genes sampled from populations of dengue 2 (DEN-2) virus in individual Aedes aegypti mosquitoes and in serum from dengue patients were copied to cDNA, cloned, and sequenced. The...
Craig, Scott B., Thu, Hlaing Myat, Lowry, Kym S., Wang, Xiao-fang, Holmes, Edward C., Aaskov, John G.
Envelope (E) protein genes sampled from populations of dengue 2 (DEN-2) virus in individual Aedes aegypti mosquitoes and in serum from dengue patients were copied to cDNA, cloned, and sequenced. The...
Craig, Scott B., Thu, Hlaing Myat, Lowry, Kym S., Wang, Xiao-fang, Holmes, Edward C., Aaskov, John G.
Envelope (E) protein genes sampled from populations of dengue 2 (DEN-2) virus in individual Aedes aegypti mosquitoes and in serum from dengue patients were copied to cDNA, cloned, and sequenced. The...
Selection-Driven Evolution of Emergent Dengue Virus (2003)
Bennett, Shannon N., Holmes, Edward C., Chirivella, Maritza, Rodriguez, Dania M., Beltran, Manuela, Vorndam, Vance, ...
In the last four decades the incidence of dengue fever has increased 30-fold worldwide and over half the world's population is now threatened with infection from one or more of four co-circulating...
Inferring the Rate and Time-Scale of Dengue Virus Evolution (2003)
Twiddy, S. Susanna, Holmes, Edward C., Rambaut, Andrew
Dengue is often referred to as an emerging disease because of the rapid increases in incidence and prevalence that have been observed in recent decades. To understand the rate at which genetic...
Selection-Driven Evolution of Emergent Dengue Virus (2003)
Bennett, Shannon N., Holmes, Edward C., Chirivella, Maritza, Rodriguez, Dania M., Beltran, Manuela, Vorndam, Vance, ...
In the last four decades the incidence of dengue fever has increased 30-fold worldwide, and over half the world's population is now threatened with infection from one or more of four co-circulating...
Selection-Driven Evolution of Emergent Dengue Virus (2003)
Bennett, Shannon N., Holmes, Edward C., Chirivella, Maritza, Rodriguez, Dania M., Beltran, Manuela, Vorndam, Vance, ...
In the last four decades the incidence of dengue fever has increased 30-fold worldwide and over half the world's population is now threatened with infection from one or more of four co-circulating...
Craig, Scott B., Thu, Hlaing Myat, Lowry, Kym S., Wang, Xiao-fang, Holmes, Edward C., Aaskov, John G.
Envelope (E) protein genes sampled from populations of dengue 2 (DEN-2) virus in individual Aedes aegypti mosquitoes and in serum from dengue patients were copied to cDNA, cloned, and sequenced. The...
Urwin, Rachel, Holmes, Edward C., Fox, Andrew J., Derrick, Jeremy P., Maiden, Martin C. J.
Previous estimates of rates of synonymous (dS) and nonsynonymous (dN) substitution among Neisseria meningitidis gene sequences suggested that the surface loops of the variable outer membrane protein...
Evidence for the Non-quasispecies Evolution of RNA Viruses (2001)
Jenkins, Gareth M., Worobey, Michael, Woelk, Christopher H., Holmes, Edward C.
The quasispecies model of RNA virus evolution differs from those formulated in conventional population genetics in that neutral mutations do not lead to genetic drift of the population, and natural...
Homologous Recombination in GB Virus C/Hepatitis G Virus (2001)
Worobey, Michael, Holmes, Edward C.
Analysis of 33 GB virus C/hepatitis G virus (GBV-C/HGV) full or nearly full genome sequences revealed several putative inter- and intrasubtype recombinants. The breakpoints of the recombinant regions...
Population Structure and Evolution of the Bacillus cereus Group (1998)
Priest, Fergus G., Barker, Margaret, Baillie, Les W., Holmes, Edward C., Maiden, Martin C.
Representative strains of the Bacillus cereus group of bacteria, including Bacillus anthracis (11 isolates), B. cereus (38 isolates), Bacillus mycoides (1 isolate), Bacillus thuringiensis (53...
Molecular epidemiology and evolution of emerging infectious diseases (1998)
Molecular epidemiology is an emerging science. The development of new and rapid protocols to isolate and identify pathogens, coupled with the sophisticated phylogenetic analysis of their gene...
Feil, Edward J., Holmes, Edward C., Bessen, Debra E., Chan, Man-Suen, Day, Nicholas P. J., Enright, Mark C., ...
The identification of clones within bacterial populations is often taken as evidence for a low rate of recombination, but the validity of this inference is rarely examined. We have used statistical...
Widespread intra-serotype recombination in natural populations of dengue virus
Worobey, Michael, Rambaut, Andrew, Holmes, Edward C.
Diversity analysis of 71 published dengue virus gene sequences revealed several strains that appeared to be mosaics comprising gene regions with conflicting evolutionary histories. Subsequent maximum...
Genetic Diversity of Borrelia burgdorferi Sensu Lato in Ticks from Mainland Portugal
De Michelis, Simona, Sewell, Henna-Sisko, Collares-Pereira, Margarida, Santos-Reis, Margarida, Schouls, Leo M., Benes, Vladimir, ...
To date Borrelia lusitaniae is the only genospecies of Borrelia burgdorferi sensu lato isolated from Ixodes ricinus ticks collected in Portugal and Tunisia. This suggests that the genospecies...
Brault, Aaron C., Powers, Ann M., Holmes, Edward C., Woelk, C. H., Weaver, Scott C.
Epidemic-epizootic Venezuelan equine encephalitis (VEE) viruses (VEEV) have emerged repeatedly via convergent evolution from enzootic predecessors. However, previous sequence analyses have failed to...
Craig, Scott, Thu, Hlaing Myat, Lowry, Kym, Wang, Xiao-fang, Holmes, Edward C., Aaskov, John
Envelope (E) protein genes sampled from populations of dengue 2 (DEN-2) virus in individual Aedes aegypti mosquitoes and in serum from dengue patients were copied to cDNA, cloned, and sequenced. The...
Considerable uncertainty surrounds the evolutionary rates of and selection pressures acting on arthropod-borne RNA viruses (arboviruses). In particular, it is unclear why arboviruses such as dengue...
Sheridan, Isabelle, Pybus, Oliver G., Holmes, Edward C., Klenerman, Paul
Hepatitis C virus (HCV) persists in the majority of those infected despite host immune responses. Evidence has accrued that selectively fixed mutations in the envelope genes (E1 and E2) are...
Urwin, Rachel, Russell, Joanne E., Thompson, Emily A. L., Holmes, Edward C., Feavers, Ian M., Maiden, Martin C. J.
The bacterium Neisseria meningitidis is a major cause of meningitis and septicemia worldwide. Outer membrane proteins (OMPs) are candidates in the search for comprehensive meningococcal vaccines;...
Population Structure and Evolution of the Bacillus cereus Group†
Priest, Fergus G., Barker, Margaret, Baillie, Les W. J., Holmes, Edward C., Maiden, Martin C. J.
Representative strains of the Bacillus cereus group of bacteria, including Bacillus anthracis (11 isolates), B. cereus (38 isolates), Bacillus mycoides (1 isolate), Bacillus thuringiensis (53...
High rate of viral evolution associated with the emergence of carnivore parvovirus
Shackelton, Laura A., Parrish, Colin R., Truyen, Uwe, Holmes, Edward C.
Canine parvovirus (CPV) is an emerging DNA virus that was first observed to cause disease in canines in 1978 and has since become a ubiquitous pathogen worldwide. CPV emerged from feline...
Holmes, Edward C, Ghedin, Elodie, Miller, Naomi, Taylor, Jill, Bao, Yiming, St George, Kirsten, ...
Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2...
Phylogeography, Population Dynamics, and Molecular Evolution of European Bat Lyssaviruses
Davis, Patricia L., Holmes, Edward C., Larrous, Florence, Tjørnehøj, Kirsten, Alonso, Wladimir J., ...
European bat lyssaviruses types 1 and 2 (EBLV-1 and EBLV-2) are widespread in Europe, although little is known of their evolutionary history. We undertook a comprehensive sequence analysis to infer...
Pillay, Thillagavathie, Zhang, Hua-Tang, Drijfhout, Jan W., Robinson, Nicola, Brown, Helen, Khan, Munira, ...
The role of cytotoxic T-lymphocyte (CTL) escape in rapidly progressive infant human immunodeficiency virus type 1 (HIV-1) infection is undefined. The data presented here demonstrate that infant...
Milicic, Anita, Edwards, Charles T. T., Hué, Stéphane, Fox, Julie, Brown, Helen, Pillay, Tilly, ...
Antigenic variation inherent in human immunodeficiency virus type 1 (HIV-1) virions that successfully instigate new infections transferred by sex has not been well defined. Yet this is the viral...
Invasion and Maintenance of Dengue Virus Type 2 and Type 4 in the Americas†
Carrington, Christine V. F., Foster, Jerome E., Pybus, Oliver G., Bennett, Shannon N., Holmes, Edward C.
Dengue virus type 4 (DENV-4) was first reported in the Americas in 1981, where it caused epidemics of dengue fever throughout the region. In the same year, the region's first epidemic of dengue...
Zhang, Chunlin, Mammen, Mammen P., Chinnawirotpisan, Piyawan, Klungthong, Chonticha, Rodpradit, Prinyada, Monkongdee, Patama, ...
The evolution of dengue virus (DENV) is characterized by phylogenetic trees that have a strong temporal structure punctuated by dramatic changes in clade frequency. To determine the cause of these...
Edwards, Charles T. T., Pfafferott, Katja J., Goulder, Philip J. R., Phillips, Rodney E., Holmes, Edward C.
The hypothesis that the intrapatient emergence of cytotoxic T-lymphocyte escape variants contributes to the evolution of human immunodeficiency virus type 1 at the population (interpatient) level was...
Edwards, Charles TT, Holmes, Edward C, Wilson, Daniel J, Viscidi, Raphael P, Abrams, Elaine J, Phillips, Rodney E, ...
Phylogenetic Evidence for the Rapid Evolution of Human B19 Erythrovirus
Shackelton, Laura A., Holmes, Edward C.
Human B19 erythrovirus is a ubiquitous viral pathogen, commonly infecting individuals before adulthood. As with all autonomous parvoviruses, its small single-stranded DNA genome is replicated with...
Feil, Edward J., Holmes, Edward C., Bessen, Debra E., Chan, Man-Suen, Day, Nicholas P. J., Enright, Mark C., ...
The identification of clones within bacterial populations is often taken as evidence for a low rate of recombination, but the validity of this inference is rarely examined. We have used statistical...
Widespread intra-serotype recombination in natural populations of dengue virus
Worobey, Michael, Rambaut, Andrew, Holmes, Edward C.
Diversity analysis of 71 published dengue virus gene sequences revealed several strains that appeared to be mosaics comprising gene regions with conflicting evolutionary histories. Subsequent maximum...
Genetic Diversity of Borrelia burgdorferi Sensu Lato in Ticks from Mainland Portugal
De Michelis, Simona, Sewell, Henna-Sisko, Collares-Pereira, Margarida, Santos-Reis, Margarida, Schouls, Leo M., Benes, Vladimir, ...
To date Borrelia lusitaniae is the only genospecies of Borrelia burgdorferi sensu lato isolated from Ixodes ricinus ticks collected in Portugal and Tunisia. This suggests that the genospecies...
Brault, Aaron C., Powers, Ann M., Holmes, Edward C., Woelk, C. H., Weaver, Scott C.
Epidemic-epizootic Venezuelan equine encephalitis (VEE) viruses (VEEV) have emerged repeatedly via convergent evolution from enzootic predecessors. However, previous sequence analyses have failed to...
Craig, Scott, Thu, Hlaing Myat, Lowry, Kym, Wang, Xiao-fang, Holmes, Edward C., Aaskov, John
Envelope (E) protein genes sampled from populations of dengue 2 (DEN-2) virus in individual Aedes aegypti mosquitoes and in serum from dengue patients were copied to cDNA, cloned, and sequenced. The...
Considerable uncertainty surrounds the evolutionary rates of and selection pressures acting on arthropod-borne RNA viruses (arboviruses). In particular, it is unclear why arboviruses such as dengue...
Sheridan, Isabelle, Pybus, Oliver G., Holmes, Edward C., Klenerman, Paul
Hepatitis C virus (HCV) persists in the majority of those infected despite host immune responses. Evidence has accrued that selectively fixed mutations in the envelope genes (E1 and E2) are...
Urwin, Rachel, Russell, Joanne E., Thompson, Emily A. L., Holmes, Edward C., Feavers, Ian M., Maiden, Martin C. J.
The bacterium Neisseria meningitidis is a major cause of meningitis and septicemia worldwide. Outer membrane proteins (OMPs) are candidates in the search for comprehensive meningococcal vaccines;...
Population Structure and Evolution of the Bacillus cereus Group†
Priest, Fergus G., Barker, Margaret, Baillie, Les W. J., Holmes, Edward C., Maiden, Martin C. J.
Representative strains of the Bacillus cereus group of bacteria, including Bacillus anthracis (11 isolates), B. cereus (38 isolates), Bacillus mycoides (1 isolate), Bacillus thuringiensis (53...
High rate of viral evolution associated with the emergence of carnivore parvovirus
Shackelton, Laura A., Parrish, Colin R., Truyen, Uwe, Holmes, Edward C.
Canine parvovirus (CPV) is an emerging DNA virus that was first observed to cause disease in canines in 1978 and has since become a ubiquitous pathogen worldwide. CPV emerged from feline...
Edwards, Charles T. T., Pfafferott, Katja J., Goulder, Philip J. R., Phillips, Rodney E., Holmes, Edward C.
The hypothesis that the intrapatient emergence of cytotoxic T-lymphocyte escape variants contributes to the evolution of human immunodeficiency virus type 1 at the population (interpatient) level was...
Holmes, Edward C, Ghedin, Elodie, Miller, Naomi, Taylor, Jill, Bao, Yiming, St George, Kirsten, ...
Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2...
Phylogeography, Population Dynamics, and Molecular Evolution of European Bat Lyssaviruses
Davis, Patricia L., Holmes, Edward C., Larrous, Florence, Tjørnehøj, Kirsten, Alonso, Wladimir J., ...
European bat lyssaviruses types 1 and 2 (EBLV-1 and EBLV-2) are widespread in Europe, although little is known of their evolutionary history. We undertook a comprehensive sequence analysis to infer...
Pillay, Thillagavathie, Zhang, Hua-Tang, Drijfhout, Jan W., Robinson, Nicola, Brown, Helen, Khan, Munira, ...
The role of cytotoxic T-lymphocyte (CTL) escape in rapidly progressive infant human immunodeficiency virus type 1 (HIV-1) infection is undefined. The data presented here demonstrate that infant...
Milicic, Anita, Edwards, Charles T. T., Hué, Stéphane, Fox, Julie, Brown, Helen, Pillay, Tilly, ...
Antigenic variation inherent in human immunodeficiency virus type 1 (HIV-1) virions that successfully instigate new infections transferred by sex has not been well defined. Yet this is the viral...
Invasion and Maintenance of Dengue Virus Type 2 and Type 4 in the Americas†
Carrington, Christine V. F., Foster, Jerome E., Pybus, Oliver G., Bennett, Shannon N., Holmes, Edward C.
Dengue virus type 4 (DENV-4) was first reported in the Americas in 1981, where it caused epidemics of dengue fever throughout the region. In the same year, the region's first epidemic of dengue...
Zhang, Chunlin, Mammen, Mammen P., Chinnawirotpisan, Piyawan, Klungthong, Chonticha, Rodpradit, Prinyada, Monkongdee, Patama, ...
The evolution of dengue virus (DENV) is characterized by phylogenetic trees that have a strong temporal structure punctuated by dramatic changes in clade frequency. To determine the cause of these...
Phylogenetic Evidence for the Rapid Evolution of Human B19 Erythrovirus
Shackelton, Laura A., Holmes, Edward C.
Human B19 erythrovirus is a ubiquitous viral pathogen, commonly infecting individuals before adulthood. As with all autonomous parvoviruses, its small single-stranded DNA genome is replicated with...
Edwards, Charles TT, Holmes, Edward C, Wilson, Daniel J, Viscidi, Raphael P, Abrams, Elaine J, Phillips, Rodney E, ...
Correction: Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus
Nelson, Martha I, Simonsen, Lone, Viboud, Cecile, Miller, Mark A, Taylor, Jill, St. George, Kirsten, ...
Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus
Nelson, Martha I, Simonsen, Lone, Viboud, Cecile, Miller, Mark A, Taylor, Jill, George, Kirsten St, ...
Understanding the evolutionary dynamics of influenza A virus is central to its surveillance and control. While immune-driven antigenic drift is a key determinant of viral evolution across epidemic...
JC Virus Evolution and Its Association with Human Populations†
Shackelton, Laura A., Rambaut, Andrew, Pybus, Oliver G., Holmes, Edward C.
The ubiquitous human polyomavirus JC (JCV) is a small double-stranded DNA virus that establishes a persistent infection, and it is often transmitted from parents to children. There are at least 14...
Viral evolution and the emergence of SARS coronavirus.
Holmes, Edward C, Rambaut, Andrew
The recent appearance of severe acute respiratory syndrome coronavirus (SARS-CoV) highlights the continual threat to human health posed by emerging viruses. However, the central processes in the...
Extremely Rapid Spread of Human Immunodeficiency Virus Type 1 BF Recombinants in Argentina▿
Aulicino, Paula C., Holmes, Edward C., Rocco, Carlos, Mangano, Andrea, Sen, Luisa
The epidemic of human immunodeficiency virus type 1 (HIV-1) in Argentina is distinctive in that many infections are caused by subtype BF recombinant viruses. To determine their demographic history,...
Out of Africa: A Molecular Perspective on the Introduction of Yellow Fever Virus into the Americas
Bryant, Juliet E, Holmes, Edward C, Barrett, Alan D. T
Yellow fever virus (YFV) remains the cause of severe morbidity and mortality in South America and Africa. To determine the evolutionary history of this important reemerging pathogen, we performed a...
Selection for Robustness in Mutagenized RNA Viruses
Sanjuán, Rafael, Cuevas, José M, Furió, Victoria, Holmes, Edward C, Moya, Andrés
Mutational robustness is defined as the constancy of a phenotype in the face of deleterious mutations. Whether robustness can be directly favored by natural selection remains controversial. Theory...
Declining Growth Rate of West Nile Virus in North America▿
Snapinn, Katherine W., Holmes, Edward C., Young, David S., Bernard, Kristen A., Kramer, Laura D., Ebel, Gregory D.
To determine the demographic history of West Nile virus (WNV) in North America, we employed a coalescent method to envelope coding region data sets for the NY99 and WN02 genotypes. Although the...
Demographic Histories of ERV-K in Humans, Chimpanzees and Rhesus Monkeys
Romano, Camila M., De Melo, Fernando L., Corsini, Marco Aurelio B., Holmes, Edward C., De A. Zanotto, Paolo M.
We detected 19 complete endogenous retroviruses of the K family in the genome of rhesus monkey (Macaca mulatta; RhERV-K) and 12 full length elements in the genome of the common chimpanzee (Pan...
Viral Evolution in the Genomic Age
The remarkable increase in the number of viral genome sequences represents both opportunities and challenges for understanding disease ecology and evolution, and must stimulate researchers to address...
Evolutionary Processes among Sylvatic Dengue Type 2 Viruses▿
Vasilakis, Nikos, Holmes, Edward C., Fokam, Eric B., Faye, Ousmane, Diallo, Mawlouth, Sall, Amadou A., ...
Sylvatic dengue viruses (DENV) are transmitted in an enzootic cycle between nonhuman primates and arboreal Aedes mosquitoes in Southeast Asia and West Africa. Although previous analyses have revealed...
Duffy, Siobain, Holmes, Edward C.
A phylogenetic analysis of three genomic regions revealed that Tomato yellow leaf curl virus (TYLCV) from western North America is distinct from TYLCV isolated in eastern North America and the...
Multiple Reassortment Events in the Evolutionary History of H1N1 Influenza A Virus Since 1918
Nelson, Martha I., Viboud, Cécile, Simonsen, Lone, Bennett, Ryan T., Griesemer, Sara B., St. George, Kirsten, ...
The H1N1 subtype of influenza A virus has caused substantial morbidity and mortality in humans, first documented in the global pandemic of 1918 and continuing to the present day. Despite this disease...
Draenert, Rika, Le Gall, Sylvie, Pfafferott, Katja J., Leslie, Alasdair J., Chetty, Polan, Brander, Christian, ...
Mutations within cytotoxic T lymphocyte (CTL) epitopes impair T cell recognition, but escape mutations arising in flanking regions that alter antigen processing have not been defined in natural human...
Jamal, Leda Fátima, Durigon, Edison Luiz, Massad, Eduardo, Perez, José Fernando, Pinho, João Renato Rebello, ...
The Viral Genetic Diversity Network, established in Brazil to enhance the study of viruses, antiviral drug resistance, and the spread of specific viral genotypes, also increased the net scientific...
Kelleher, Anthony D., Long, Chad, Holmes, Edward C., Allen, Rachel L., Wilson, Jamie, Conlon, Christopher, ...
The immune response to HIV-1 in patients who carry human histocompatibility leukocyte antigen (HLA)-B27 is characterized by an immunodominant response to an epitope in p24 gag (amino acids 263–272,...
Phylogenetic Analysis Reveals the Global Migration of Seasonal Influenza A Viruses
Nelson, Martha I, Simonsen, Lone, Viboud, Cecile, Miller, Mark A, Holmes, Edward C
The winter seasonality of influenza A virus in temperate climates is one of the most widely recognized, yet least understood, epidemiological patterns in infectious disease. Central to understanding...
Genomic Diversity and Evolution of the Lyssaviruses
Delmas, Olivier, Holmes, Edward C., Talbi, Chiraz, Larrous, Florence, Dacheux, Laurent, Bouchier, Christiane, ...
Lyssaviruses are RNA viruses with single-strand, negative-sense genomes responsible for rabies-like diseases in mammals. To date, genomic and evolutionary studies have most often utilized partial...
Duffy, Siobain, Holmes, Edward C.
Geminiviruses are devastating viruses of plants that possess single-stranded DNA (ssDNA) DNA genomes. Despite the importance of this class of phytopathogen, there have been no estimates of the rate...
The Evolutionary Genetics and Emergence of Avian Influenza Viruses in Wild Birds
Dugan, Vivien G., Chen, Rubing, Spiro, David J., Sengamalay, Naomi, Zaborsky, Jennifer, Ghedin, Elodie, ...
We surveyed the genetic diversity among avian influenza virus (AIV) in wild birds, comprising 167 complete viral genomes from 14 bird species sampled in four locations across the United States. These...
Nelson, Martha I., Edelman, Laurel, Spiro, David J., Boyne, Alex R., Bera, Jayati, Halpin, Rebecca, ...
To determine the spatial and temporal dynamics of influenza A virus during a single epidemic, we examined whole-genome sequences of 284 A/H1N1 and 69 A/H3N2 viruses collected across the continental...
Homologous Recombination Is Very Rare or Absent in Human Influenza A Virus ▿
Boni, Maciej F., Zhou, Yang, Taubenberger, Jeffery K., Holmes, Edward C.
To determine the extent of homologous recombination in human influenza A virus, we assembled a data set of 13,852 sequences representing all eight segments and both major circulating subtypes, H3N2...
Jarman, Richard G., Holmes, Edward C., Rodpradit, Prinyada, Klungthong, Chonticha, Gibbons, Robert V., Nisalak, Ananda, ...
To determine the extent and structure of genetic variation in dengue viruses (DENV) on a restricted spatial and temporal scale, we sequenced the E (envelope) genes of DENV-1, -2, and -3 isolates...
Nelson, Martha I., Edelman, Laurel, Spiro, David J., Boyne, Alex R., Bera, Jayati, Halpin, Rebecca, ...
Global Distribution of Novel Rhinovirus Genotype
Briese, Thomas, Renwick, Neil, Venter, Marietjie, Jarman, Richard G., Ghosh, Dhrubaa, Köndgen, Sophie, ...
Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America....
Chang, Gue Su, Hong, Yoojin, Ko, Kyung Dae, Bhardwaj, Gaurav, Holmes, Edward C., Patterson, Randen L., ...
Inferring evolutionary relationships among highly divergent protein sequences is a daunting task. In particular, when pairwise sequence alignments between protein sequences fall
Cardosa, Jane, Ooi, Mong How, Tio, Phaik Hooi, Perera, David, Holmes, Edward C., Bibi, Khatijar, ...
Dengue viruses circulate in both human and sylvatic cycles. Although dengue viruses (DENV) infecting humans can cause major epidemics and severe disease, relatively little is known about the...
Within-Host Genetic Diversity of Endemic and Emerging Parvoviruses of Dogs and Cats ▿
Hoelzer, Karin, Shackelton, Laura A., Holmes, Edward C., Parrish, Colin R.
Viral emergence can result from the adaptation of endemic pathogens to new or altered host environments, a process that is strongly influenced by the underlying sequence diversity. To determine the...
Cross-Species Virus Transmission and the Emergence of New Epidemic Diseases
Parrish, Colin R., Holmes, Edward C., Morens, David M., Park, Eun-Chung, Burke, Donald S., Calisher, Charles H., ...
Summary: Host range is a viral property reflecting natural hosts that are infected either as part of a principal transmission cycle or, less commonly, as “spillover” infections into alternative...
Genomic Epidemiology of a Dengue Virus Epidemic in Urban Singapore▿ †
Schreiber, Mark J., Holmes, Edward C., Ong, Swee Hoe, Soh, Harold S. H., Liu, Wei, Tanner, Lukas, ...
Dengue is one of the most important emerging diseases of humans, with no preventative vaccines or antiviral cures available at present. Although one-third of the world's population live at risk of...