Phylogenetic Analysis of Varicella-Zoster Virus: Evidence of Intercontinental Spread of Genotypes and Recombination

Abstract

A heteroduplex mobility assay was used to identify variants of varicella-zoster virus circulating in the United Kingdom and elsewhere. Within the United Kingdom, 58 segregating sites were found out of the 23,266 examined (0.25%), and nucleotide diversity was estimated to be 0.00063. These are an order of magnitude smaller than comparable estimates from herpes simplex virus type 1. Sixteen substitutions were nonsynonymous, the majority of which were clustered within surface-expressed proteins. Extensive genetic correlation between widely spaced sites indicated that recombination has been rare. Phylogenetic analysis of varicellazoster viruses from four continents distinguished at least three major genetic clades. Most geographical regions contained only one of these three strains, apart from the United Kingdom and Brazil, where two or more strains were found. There was minimal genetic differentiation (one or fewer substitutions in 1,895 bases surveyed) between the samples collected from Africa (Guinea Bissau, Zambia) and the Indian subcontinent (Bangladesh, South India), suggesting recent rapid spread and/or low mutation rates. The geographic pattern of strain distribution would favor a major influence of the former. The genetic uniformity of most virus populations makes recombination difficult to detect. However, at least one probable recombinant between two of the major strains was found among the samples originating from Brazil, where mixtures of genotypes co-occur.

Complete-Genome Phylogenetic Approach to Varicella-Zoster Virus Evolution: Genetic Divergence and Evidence for Recombination

“…The VZV genome is so highly conserved that the most distantly related genotypes examined in this study (J and M1) differed by only ϳ0.2%. In a comparison between the European strain Dumas, the Japanese strain P-Oka and the mixed (25,30), the VZV selected strains segregated into at least three genotypes. We performed phylogenetic analyses based on the complete genome (Fig.…”

“…In addition, it was demonstrated that sequence analysis of a 447-nucleotide (nt) region located in open reading frame 22 (ORF22r1) could unerringly recapitulate the genotyping results obtained from analyzing 23 single-nucleotide polymorphisms located in seven open reading frames distributed over the entire genome. These analyses implied that recombination events, which were recently found to be a common feature among wild-type isolates of another alphaherpesvirus, i.e., herpes simplex virus type 1 (5, 31), were of interest for future study as a possible mechanism for VZV strain variation (30). In the studies reported here, we determined the complete genomic sequence of two M VZV strains presented in a previous study (25).…”

“…Genetic diversity among VZV strains was initially defined using either restriction enzyme mapping (1, 22) or variation in the copy number at the tandem repeat regions (6,20,21,39). Phylogenetic analyses of partial VZV genome sequences have recently identified a divergence of VZV into different genotypes and recombinant strains (25,30,44). Loparev et al (25) performed targeted (multiple locus) analysis of VZV polymorphisms for a large number of clinical isolates obtained from all six continents, establishing a divergence into the three genotypes E (European), J (Japanese), and M (mosaic).…”

Natural Recombinant between Equine Herpesviruses 1 and 4 in the ICP4 Gene

“…2. lation as one of dominant virus species. Hitherto intraspecies recombinants have been reported including HSV-1, VZV, and EBV (22)(23)(24)38). On the other hand, interspecies recombinants have been regarded to survive rarely in nature (5).…”

Genotyping of clinical varicella-zoster virus isolates collected from Yunnan in Southwestern China

“…The genome of VZV contained ~25,000 base pairs, including ≥70 open reading frames (ORFs). Genetic variations have been identified in the genome of VZV strains (6)(7)(8)(9)(10)(11)(12)(13). Based on the specific single-nucleotide polymorphisms (SNPs) in ORFs 1, 21, 50 and 54, VZV strains have been divided into the following genotypes: A (Africa/Asia), B and C (Europe and North America), and J (Japanese) (6).…”