Whole genome diversity of inherited chromosomally integrated HHV-6 derived from healthy individuals of diverse geographic origin

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  • dc.contributor.author Telford, Marco, 1984-ca
  • dc.contributor.author Navarro i Cuartiellas, Arcadi, 1969-ca
  • dc.contributor.author Santpere Baró, Gabriel, 1981-ca
  • dc.date.accessioned 2018-05-04T07:42:57Z
  • dc.date.available 2018-05-04T07:42:57Z
  • dc.date.issued 2018
  • dc.description.abstract Human herpesviruses 6-A and -B (HHV-6A, HHV-6B) are ubiquitous in human populations worldwide. These viruses have been associated with several diseases such as multiple sclerosis, Hodgkin's lymphoma or encephalitis. Despite of the need to understand the genetic diversity and geographic stratification of these viruses, the availability of complete viral sequences from different populations is still limited. Here, we present nine new inherited chromosomally integrated HHV-6 sequences from diverse geographical origin which were generated through target DNA enrichment on lymphoblastoid cell lines derived from healthy individuals. Integration with available HHV-6 sequences allowed the assessment of HHV-6A and -6B phylogeny, patterns of recombination and signatures of natural selection. Analysis of the intra-species variability showed differences between A and B diversity levels and revealed that the HHV-6B reference (Z29) is an uncommon sequence, suggesting the need for an alternative reference sequence. Signs of geographical variation are present and more defined in HHV-6A, while they appear partly masked by recombination in HHV-6B. Finally, we conducted a scan for signatures of selection in protein coding genes that yielded at least 6 genes (4 and 2 respectively for the A and B species) showing significant evidence for accelerated evolution, and 1 gene showing evidence of positive selection in HHV-6A.
  • dc.description.sponsorship This work was supported by Ministerio de Ciencia e Innovación, Spain (BFU2012-38236 and BFU2015-68649-P to A.N.), by Direcció General de Recerca, Generalitat de Catalunya (2014SGR1311 and 2014SGR866), by the Spanish National Institute of Bioinformatics (PT13/0001/0026) and the REEM (RD12/0032/0011, RD16/0015/0017) of the Instituto de Salud Carlos III and by FEDER (Fondo Europeo de Desarrollo Regional)/FSE (Fondo Social Europeo).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Telford M, Navarro A, Santpere G. Whole genome diversity of inherited chromosomally integrated HHV-6 derived from healthy individuals of diverse geographic origin. Sci Rep. 2018 Dec;8(1):3472. DOI: 10.1038/s41598-018-21645-x
  • dc.identifier.doi http://dx.doi.org/10.1038/s41598-018-21645-x
  • dc.identifier.issn 2045-2322
  • dc.identifier.uri http://hdl.handle.net/10230/34554
  • dc.language.iso eng
  • dc.publisher Nature Publishing Groupca
  • dc.relation.ispartof Scientific Reports. 2018 Dec;8(1):3472
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2012-38236
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-68649-P
  • dc.rights © The Author(s) 2018. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Genome informatics
  • dc.subject.keyword Phylogenetics
  • dc.subject.keyword Population genetics
  • dc.subject.keyword HHV-6
  • dc.title Whole genome diversity of inherited chromosomally integrated HHV-6 derived from healthy individuals of diverse geographic originca
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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