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

Scientific Reports
Marco TelfordGabriel Santpere

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 lea...Continue Reading

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Citations

Jul 10, 2019·Scientific Reports·Louise ZanellaPriscilla Brebi
Aug 11, 2020·PLoS Genetics·Xiaoxi LiuYoichiro Kamatani
Jun 20, 2020·Virus Evolution·Diego ForniManuela Sironi
Jul 30, 2020·Molecular Biology and Evolution·Amr AswadBenedikt B Kaufer
Nov 12, 2020·Biomolecules·Gabriel SantpereIsidre Ferrer
Apr 27, 2021·PLoS Genetics·Shohei KojimaNicholas F Parrish
Apr 13, 2021·The FEBS Journal·Avindra Nath, Tory P Johnson

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Datasets Mentioned

BETA
KC465951.1
KP257584.1
KT895199.1
KT355575.1
AB021506.1
PRJNA412600
MG894368-76

Methods Mentioned

BETA
PCR
PCA
genotyping

Software Mentioned

SAMtools
Stats R package
MAFFT
Stats
Annovar
MEGA7
RepeatMasker
Repeat Masker Repeat Finder
Robustbase R package
vcftools

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