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Complete-genome phylogenetic approach to varicella-zoster virus evolution: genetic divergence and evidence for recombination.

Journal article
Authors Peter Norberg
Jan-Åke Liljeqvist
Tomas Bergström
Scott Sammons
D Scott Schmid
Vladimir N Loparev
Published in Journal of virology
Volume 80
Issue 19
Pages 9569-76
ISSN 0022-538X
Publication year 2006
Published at Institute of Biomedicine, Department of Infectious Medicine
Pages 9569-76
Language en
Links dx.doi.org/10.1128/JVI.00835-06
Keywords Base Sequence, Genome, Viral, genetics, Herpesvirus 3, Human, genetics, Phylogeny, Recombination, Genetic, genetics
Subject categories Medical and Health Sciences

Abstract

Recent studies of varicella-zoster virus (VZV) DNA sequence variation, involving large numbers of globally distributed clinical isolates, suggest that this virus has diverged into at least three distinct genotypes designated European (E), Japanese (J), and mosaic (M). In the present study, we determined and analyzed the complete genomic sequences of two M VZV strains and compared them to the sequences of three E strains and two J strains retrieved from GenBank (including the Oka vaccine preparation, V-Oka). Except for a few polymorphic tandem repeat regions, the whole genome, representing approximately 125,000 nucleotides, is highly conserved, presenting a genetic similarity between the E and J genotypes of approximately 99.85%. These analyses revealed that VZV strains distinctly segregate into at least four genotypes (E, J, M1, and M2) in phylogenetic trees supported by high bootstrap values. Separate analyses of informative sites revealed that the tree topology was dependent on the region of the VZV genome used to determine the phylogeny; collectively, these results indicate the observed strain variation is likely to have resulted, at least in part, from interstrain recombination. Recombination analyses suggest that strains belonging to the M1 and M2 genotypes are mosaic recombinant strains that originated from ancestral isolates belonging to the E and J genotypes through recombination on multiple occasions. Furthermore, evidence of more recent recombination events between M1 and M2 strains is present in six segments of the VZV genome. As such, interstrain recombination in dually infected cells seems to figure prominently in the evolutionary history of VZV, a feature it has in common with other herpesviruses. In addition, we report here six novel genomic targets located in open reading frames 51 to 58 suitable for genotyping of clinical VZV isolates.

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