About: Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes

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About: Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes
Creator	Breuer, Judith Balloux, Francois Schutten, Martin Brown, Amanda Brown, Julianne Verjans, Georges Einer-Jensen, Katja Depledge, Daniel Van Loenen, Freek Clark, Duncan Griffiths, Paul Milne, Richard Atkinson, Claire Christiansen, Mette Holdstock, Jolyon Lassalle, Florent Reeves, Matthew Tutill, Helena Williams, Rachel
Source	PMC
abstract	Human cytomegalovirus (HCMV) infects most of the population worldwide, persisting throughout the host's life in a latent state with periodic episodes of reactivation. While typically asymptomatic, HCMV can cause fatal disease among congenitally infected infants and immunocompromised patients. These clinical issues are compounded by the emergence of antiviral resistance and the absence of an effective vaccine, the development of which is likely complicated by the numerous immune evasins encoded by HCMV to counter the host's adaptive immune responses, a feature that facilitates frequent super-infections. Understanding the evolutionary dynamics of HCMV is essential for the development of effective new drugs and vaccines. By comparing viral genomes from uncultivated or low-passaged clinical samples of diverse origins, we observe evidence of frequent homologous recombination events, both recent and ancient, and no structure of HCMV genetic diversity at the whole-genome scale. Analysis of individual gene-scale loci reveals a striking dichotomy: while most of the genome is highly conserved, recombines essentially freely and has evolved under purifying selection, 21 genes display extreme diversity, structured into distinct genotypes that do not recombine with each other. Most of these hyper-variable genes encode glycoproteins involved in cell entry or escape of host immunity. Evidence that half of them have diverged through episodes of intense positive selection suggests that rapid evolution of hyper-variable loci is likely driven by interactions with host immunity. It appears that this process is enabled by recombination unlinking hyper-variable loci from strongly constrained neighboring sites. It is conceivable that viral mechanisms facilitating super-infection have evolved to promote recombination between diverged genotypes, allowing the virus to continuously diversify at key loci to escape immune detection, while maintaining a genome optimally adapted to its asymptomatic infectious lifecycle.
has issue date	2016-06-15(xsd:dateTime)
bibo:doi	10.1093/ve/vew017
bibo:pmid	30288299
has license	cc-by
sha1sum (hex)	5ab17b28c65c5fee387a2fa6c33478abd2437c9e
schema:url	https://doi.org/10.1093/ve/vew017
resource representing a document's title	Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes
has PubMed Central identifier	PMC6167919
has PubMed identifier	30288299
schema:publication	Virus Evol
resource representing a document's body	covid:5ab17b28c65c5fee387a2fa6c33478abd2437c9e#body_text
is schema:about of	named entity 'recombines' named entity 'HCMV' named entity 'facilitates' named entity 'Understanding' named entity 'infects' named entity 'population' named entity 'Analysis' named entity 'immune' named entity 'loci' named entity 'vaccine' named entity 'key' named entity 'resistance' named entity 'essentially' named entity 'conserved' named entity 'immune' named entity 'vaccines' named entity 'lifecycle' named entity 'immunity' named entity 'genome' named entity 'genome' named entity 'genetic diversity' named entity 'homologous recombination' named entity 'loci' named entity 'loci' named entity 'highly conserved' named entity 'immunocompromised patients' named entity 'whole-genome' named entity 'evolutionary dynamics' named entity 'vaccine' named entity 'host immunity' named entity 'antiviral' named entity 'genotypes' named entity 'viral genomes' named entity 'fatal disease' named entity 'vaccines' named entity 'immune detection' named entity 'HCMV' named entity 'RNA' named entity 'immune status' named entity 'genomes' named entity 'birth defects' named entity 'Phylogenetic analysis' named entity 'HCMV' named entity 'genome-wide' named entity 'evolutionary trade-off' named entity 'CD8 T-cells' named entity 'HCMV' named entity 'gene' named entity 'gene' named entity 'denaturation' named entity 'SplitsTree4' named entity 'recombination' named entity 'HCMV' named entity 'vertical blue' named entity 'correlation' named entity 'genomes' named entity 'genome-wide' named entity 'primate' named entity 'South Korea' named entity 'genome' named entity 'genome' named entity 'HCMV' named entity 'Positive selection'

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