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Pablo R Murcia, Gregory J Baillie,
J Conrad Stack,
Carley Jervis,
Debra Elton,
Jennifer A Mumford,
Janet Daly,
Paul Kellam,
Bryan T Grenfell,
Edward C Holmes,
James L N Wood
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ABSTRACT: Influenza A viruses are characterized by their ability to evade host immunity, even in vaccinated individuals. To determine how prior immunity shapes viral diversity in vivo we studied the intra- and inter-host evolution of equine influenza virus in vaccinated horses. Although the level and structure of genetic diversity was similar to that in naïve horses, intra-host bottlenecks may be more stringent in vaccinated animals, and mutations shared among horses often fall close to putative antigenic sites.
Journal of Virology 02/2013; · 5.40 Impact Factor
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ABSTRACT: BACKGROUND: Dynamic changes in Human Immunodeficiency Virus 1 (HIV-1) sequence diversity and divergence are associated with immune control during primary infection and progression to AIDS. Consensus sequencing or single genome amplification sequencing of the HIV-1 envelope (env) gene, in particular the variable (V) regions, are used as a marker for HIV-1 genome diversity, but population diversity is only minimally, or semi-quantitatively sampled using these methods. RESULTS: Here we use second generation deep sequencing to determine inter- and intra-patient sequence heterogeneity and to quantify minor variants in a cohort of individuals either receiving or not receiving antiretroviral treatment following seroconversion; the SPARTAC trial. We show, through a cross-sectional study of sequence diversity of the env V3 in 30 antiretroviral-naive patients during primary infection that considerable population structure diversity exists, with some individuals exhibiting highly constrained plasma virus diversity. Diversity was independent of clinical markers (viral load, time from seroconversion, CD4 cell count) of infection. Serial sampling over 60 weeks of non-treated individuals that define three initially different diversity profiles showed that complex patterns of continuing HIV-1 sequence diversification and divergence could be readily detected. Evidence for minor sequence turnover, emergence of new variants and re-emergence of archived variants could be inferred from this analysis. Analysis of viral divergence over the same time period in patients who received short (12 weeks, ART12) or long course antiretroviral therapy (48 weeks, ART48) and a non-treated control group revealed that ART48 successfully suppressed viral divergence while ART12 did not have a significant effect. CONCLUSIONS: Deep sequencing is a sensitive and reliable method for investigating the diversity of the env V3 as a important component of HIV-1 genome diversity. Detailed insights into the complex early intra-patient dynamics of env V3 diversity and divergence were explored in antiretroviral-naive recent seroconverters. Long course antiretroviral therapy, initiated soon after seroconversion and administered for 48 weeks, restricts HIV-1 divergence significantly. The effect of ART12 and ART48 on clinical markers of HIV infection and progression is currently investigated in the SPARTAC trial.
Retrovirology 01/2013; 10(1):8. · 6.47 Impact Factor
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Joseph Hughes,
Richard C Allen,
Marc Baguelin,
Katie Hampson, Gregory J Baillie,
Debra Elton,
J Richard Newton,
Paul Kellam,
James L N Wood,
Edward C Holmes,
Pablo R Murcia
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ABSTRACT: The ability of influenza A viruses (IAVs) to cross species barriers and evade host immunity is a major public health concern. Studies on the phylodynamics of IAVs across different scales - from the individual to the population - are essential for devising effective measures to predict, prevent or contain influenza emergence. Understanding how IAVs spread and evolve during outbreaks is critical for the management of epidemics. Reconstructing the transmission network during a single outbreak by sampling viral genetic data in time and space can generate insights about these processes. Here, we obtained intra-host viral sequence data from horses infected with equine influenza virus (EIV) to reconstruct the spread of EIV during a large outbreak. To this end, we analyzed within-host viral populations from sequences covering 90% of the infected yards. By combining gene sequence analyses with epidemiological data, we inferred a plausible transmission network, in turn enabling the comparison of transmission patterns during the course of the outbreak and revealing important epidemiological features that were not apparent using either approach alone. The EIV populations displayed high levels of genetic diversity, and in many cases we observed distinct viral populations containing a dominant variant and a number of related minor variants that were transmitted between infectious horses. In addition, we found evidence of frequent mixed infections and loose transmission bottlenecks in these naturally occurring populations. These frequent mixed infections likely influence the size of epidemics.
PLoS Pathogens 12/2012; 8(12):e1003081. · 9.13 Impact Factor
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Pablo R Murcia,
Joseph Hughes,
Patrizia Battista,
Lucy Lloyd, Gregory J Baillie,
Ricardo H Ramirez-Gonzalez,
Doug Ormond,
Karen Oliver,
Debra Elton,
Jennifer A Mumford,
Mario Caccamo,
Paul Kellam,
Bryan T Grenfell,
Edward C Holmes,
James L N Wood
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ABSTRACT: Influenza viruses are characterized by an ability to cross species boundaries and evade host immunity, sometimes with devastating consequences. The 2009 pandemic of H1N1 influenza A virus highlights the importance of pigs in influenza emergence, particularly as intermediate hosts by which avian viruses adapt to mammals before emerging in humans. Although segment reassortment has commonly been associated with influenza emergence, an expanded host-range is also likely to be associated with the accumulation of specific beneficial point mutations. To better understand the mechanisms that shape the genetic diversity of avian-like viruses in pigs, we studied the evolutionary dynamics of an Eurasian Avian-like swine influenza virus (EA-SIV) in naïve and vaccinated pigs linked by natural transmission. We analyzed multiple clones of the hemagglutinin 1 (HA1) gene derived from consecutive daily viral populations. Strikingly, we observed both transient and fixed changes in the consensus sequence along the transmission chain. Hence, the mutational spectrum of intra-host EA-SIV populations is highly dynamic and allele fixation can occur with extreme rapidity. In addition, mutations that could potentially alter host-range and antigenicity were transmitted between animals and mixed infections were commonplace, even in vaccinated pigs. Finally, we repeatedly detected distinct stop codons in virus samples from co-housed pigs, suggesting that they persisted within hosts and were transmitted among them. This implies that mutations that reduce viral fitness in one host, but which could lead to fitness benefits in a novel host, can circulate at low frequencies.
PLoS Pathogens 05/2012; 8(5):e1002730. · 9.13 Impact Factor
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Gregory J Baillie,
Monica Galiano,
Paul-Michael Agapow,
Richard Myers,
Rachael Chiam,
Astrid Gall,
Anne L Palser,
Simon J Watson,
Jessica Hedge,
Anthony Underwood,
Steven Platt,
Estelle McLean,
Richard G Pebody,
Andrew Rambaut,
Jonathan Green,
Rod Daniels,
Oliver G Pybus,
Paul Kellam,
Maria Zambon
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ABSTRACT: Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza virus during the course of an epidemic. Here we sequenced 153 pandemic influenza H1N1/09 virus genomes from United Kingdom isolates from the first (127 isolates) and second (26 isolates) waves of the 2009 pandemic and used their sequences, dates of isolation, and geographical locations to infer the genetic epidemiology of the epidemic in the United Kingdom. We demonstrate that the epidemic in the United Kingdom was composed of many cocirculating lineages, among which at least 13 were exclusively or predominantly United Kingdom clusters. The estimated divergence times of two of the clusters predate the detection of pandemic H1N1/09 virus in the United Kingdom, suggesting that the pandemic H1N1/09 virus was already circulating in the United Kingdom before the first clinical case. Crucially, three clusters contain isolates from the second wave of infections in the United Kingdom, two of which represent chains of transmission that appear to have persisted within the United Kingdom between the first and second waves. This demonstrates that whole-genome analysis can track in fine detail the behavior of individual influenza virus lineages during the course of a single epidemic or pandemic.
Journal of Virology 01/2012; 86(1):11-8. · 5.40 Impact Factor
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Pablo R Murcia, Gregory J Baillie,
Janet Daly,
Debra Elton,
Carley Jervis,
Jennifer A Mumford,
Richard Newton,
Colin R Parrish,
Karin Hoelzer,
Gordon Dougan,
Julian Parkhill,
Nicola Lennard,
Doug Ormond,
Sharon Moule,
Andrew Whitwham,
John W McCauley,
Trevelyan J McKinley,
Edward C Holmes,
Bryan T Grenfell,
James L N Wood
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ABSTRACT: Determining the evolutionary basis of cross-species transmission and immune evasion is key to understanding the mechanisms that control the emergence of either new viruses or novel antigenic variants with pandemic potential. The hemagglutinin glycoprotein of influenza A viruses is a critical host range determinant and a major target of neutralizing antibodies. Equine influenza virus (EIV) is a significant pathogen of the horse that causes periodical outbreaks of disease even in populations with high vaccination coverage. EIV has also jumped the species barrier and emerged as a novel respiratory pathogen in dogs, canine influenza virus. We studied the dynamics of equine influenza virus evolution in horses at the intrahost level and how this evolutionary process is affected by interhost transmission in a natural setting. To this end, we performed clonal sequencing of the hemagglutinin 1 gene derived from individual animals at different times postinfection. Our results show that despite the population consensus sequence remaining invariant, genetically distinct subpopulations persist during the course of infection and are also transmitted, with some variants likely to change antigenicity. We also detected a natural case of mixed infection in an animal infected during an outbreak of equine influenza, raising the possibility of reassortment between different strains of virus. In sum, our data suggest that transmission bottlenecks may not be as narrow as originally perceived and that the genetic diversity required to adapt to new host species may be partially present in the donor host and potentially transmitted to the recipient host.
Journal of Virology 07/2010; 84(14):6943-54. · 5.40 Impact Factor
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ABSTRACT: The patterns and dynamics of evolution in acutely infecting viruses within individual hosts are largely unknown. To this end, we investigated the intrahost variation of canine influenza virus (CIV) during the course of experimental infections in naïve and partially immune dogs and in naturally infected dogs. Tracing sequence diversity in the gene encoding domain 1 of the hemagglutinin (HA1) protein over the time course of infection provided information on the patterns and processes of intrahost viral evolution and revealed some of the effects of partial host immunity. Viral populations sampled on any given day were generally characterized by mean pairwise genetic diversities between 0.1 and 0.2% and by mutational spectra that changed considerably on different days. Some observed mutations may have affected antigenicity or host range, including reversions of CIV host-associated mutations. Patterns of sequence diversity differed between naïve and vaccinated dogs, with some presumably antigenic mutations transiently reaching high frequency in the latter. CIV populations are therefore characterized by the rapid generation and clearance of genetic diversity. Potentially advantageous mutations arise readily during the course of single infections and may give rise to antigenic escape or host range variants.
Journal of Virology 03/2010; 84(10):5329-35. · 5.40 Impact Factor
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ABSTRACT: St. Louis encephalitis virus belongs to the Japanese encephalitis virus serocomplex of the genus Flavivirus, family Flaviviridae. Since the first known epidemic in 1933, the virus has been isolated from a variety of geographical, temporal, and host origins. We have sequenced 10,236 nucleotides of the open reading frame (93.6% of the full-length genome) of 23 of these strains, and have used the sequences to conduct phylogenetic analyses, in order to investigate the forces shaping the evolution of St. Louis encephalitis virus. Contrary to previous reports, we found little evidence for recombination in these isolates. Most of the amino acid sites in the SLEV polyprotein appeared to be under negative selection, with some sites evolving neutrally, and a small number under positive selection. The strongest signal for positive selection was evident in the N-linked glycosylation site of the envelope protein. Intra-strain sequence variability within strains was observed at this site, and analyses suggested that it is under selection in vitro. Furthermore, using heterochronous sequence data, we estimated the most recent expansion of St. Louis encephalitis virus in North America to have happened towards the end of the 19th century.
Molecular Phylogenetics and Evolution 06/2008; 47(2):717-28. · 3.61 Impact Factor
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ABSTRACT: Throughout the course of vertebrate evolution, germline retroviral infections have resulted in heritable provirus insertions into host DNA. These endogenous retroviruses (ERVs) contain long terminal repeat (LTR) promoters that can be adopted for use by nearby host genes. It is not known whether the transcription factor (TF) binding sites and tissue-specificities of modern LTR gene promoters have been retained since the time of ERV insertion, or if these features evolved later as the LTR became involved in host gene regulation. To address this issue, we have conducted a case study of the ERV-L LTR promoter of human beta1,3-galactosyltransferase 5 (beta3GAL-T5). We have previously shown that the human beta3GAL-T5 LTR promoter is responsible for the majority of gene transcripts in the colon. The murine beta3gal-t5 gene is also expressed primarily in the colon, despite the absence of an orthologous ERV-L LTR in the mouse genome. We therefore hypothesized that both the ERV-L LTR and the non-retroviral ancestral beta3GAL-T5 promoter were active in the colon at the time of ERV insertion. In support of this hypothesis, we have shown that the orthologous LTRs of four non-human primates are also active in a human colorectal cell line, and that the baboon LTR is active in primary baboon colon tissue. We also present evidence that the functional TF binding sites of the human beta3GAL-T5 LTR promoter were present in the original consensus sequence for this class of LTRs. Upon similar analysis of other ERV sequences, we have concluded that this evolutionary history is shared by certain other LTR gene promoters, and may be a general phenomenon.
Gene 01/2006; 364:2-12. · 2.34 Impact Factor
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ABSTRACT: Betaretroviruses exist in endogenous and exogenous forms in hosts that are widely distributed and evolutionarily distantly related. Here we report the discovery and characterization of several previously unknown betaretrovirus groups in the genomes of Mus musculus and Rattus norvegicus. Each group contains both mouse and rat elements, and several of the groups are more closely related to previously known betaretroviruses from nonmurine hosts. Some of the groups also include members from hosts which were not previously known to harbor betaretroviruses, such as the gray mouse lemur (Microcebus murinus) and Seba's short-tailed bat (Carollia perspicillata). Some of the mouse and rat elements possess intact open reading frames for gag, pro, pol, and/or env genes and display characteristics of having retrotransposed recently. We propose a model whereby betaretroviruses have been evolving within the genomes of murid rodents for at least the last 20 million years and, subsequent to (or concomitant with) the global spread of their murid hosts, have occasionally been transmitted to other species.
Journal of Virology 07/2004; 78(11):5784-98. · 5.40 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: Throughout the course of vertebrate evolution, germline retroviral infections have resulted in heritable provirus insertions into host DNA. These endogenous retroviruses (ERVs) contain long terminal repeat (LTR) promoters that can be adopted for use by nearby host genes. It is not known whether the transcription factor (TF) binding sites and tissue-specificities of modern LTR gene promoters have been retained since the time of ERV insertion, or if these features evolved later as the LTR became involved in host gene regulation. To address this issue, we have conducted a case study of the ERV-L LTR promoter of human β1,3-galactosyltransferase 5 (β3GAL-T5).We have previously shown that the human β3GAL-T5 LTR promoter is responsible for the majority of gene transcripts in the colon. The murine β3gal-t5 gene is also expressed primarily in the colon, despite the absence of an orthologous ERV-L LTR in the mouse genome. We therefore hypothesized that both the ERV-L LTR and the non-retroviral ancestral β3GAL-T5 promoter were active in the colon at the time of ERV insertion. In support of this hypothesis, we have shown that the orthologous LTRs of four non-human primates are also active in a human colorectal cell line, and that the baboon LTR is active in primary baboon colon tissue. We also present evidence that the functional TF binding sites of the human β3GAL-T5 LTR promoter were present in the original consensus sequence for this class of LTRs. Upon similar analysis of other ERV sequences, we have concluded that this evolutionary history is shared by certain other LTR gene promoters, and may be a general phenomenon.
Gene.
