Toward Universal Varicella-Zoster Virus (VZV) Genotyping: Diversity of VZV Strains from France and Spain

Abstract

Thirty-one isolates from France and Spain were genotyped using a published method analyzing DNA sequence variation in open reading frame (ORF) 22, together with an evaluation of three well-characterized single nucleotide polymorphisms (SNP) in ORF 38, 54, and 62. Nineteen were allocated to the European (E) genotype, six were mosaic-1 (M1), and two were mosaic-2 (M2). Four strains were assigned to a new genotype, mosaic-4 (M4). All isolates were wild type, with no Oka vaccine-associated markers. No isolates of the mosaic-3 (M3) or Japanese (J) genotype were observed. We also evaluated 13 selected isolates of E, J, M1, and M2 strains (9 of the 31 described above) using an alternative genotyping method based on the assessment of multiple SNP located in ORF 1, 9, 10, 21, 31, 50, 54, 62, and 68. This method assigns wild-type varicella-zoster virus (VZV) strains to seven genotypes: A1, A2, J1, B1, B2, C, and C1. VZV isolates identified as E (ORF22 method) had the genetic signature of genotype C VZV strains, M1 strains were A1, and M2 were A2. No J strains were detected, but parental Oka and vaccine Oka (genotype J) corresponded to genotype J1. M4 isolates (B) share the SNP array observed for M1 and E viruses, and probably represent recombinants between African-Asian (M1) and European (E) viruses. The two genotyping methods, using entirely different genomic targets, produced identical clusters for the strains examined, suggesting robust phylogenetic linkages among VZV strains circulating in Europe.

Identification of Five Major and Two Minor Genotypes of Varicella-Zoster Virus Strains: a Practical Two-Amplicon Approach Used To Genotype Clinical Isolates in Australia and New Zealand

“…Only analysis based on a combination of sequence data from ORF22 and from either ORF21 (SNPs in positions 33725 and 33728), ORF50 (SNP in position 87841), or ORF62 (SNP in position 107165, 108747, or 108951) facilitated the separation of genotypes E1 and E2 from genotype E, thus detecting all five genotypes using only sequence data from two amplicons. It should also be noted that the two-amplicon method reported here also discriminates two additional, previously described genotypes, M3 and M4, both of which were absent from the specimens collected for this study (16,23).…”

“…Recombination between E1 and J strains could also play a role in the appearance of genotype E2 strains. Alternatively, E2 strains might have emerged in Europe (16) in those countries with E1 and M strains in circulation, spreading afterwards to Australia and New Zealand; or recombinant variants of E2 could have been selected by temperate climates to which increasing numbers of people migrated from regions with warmer climates. The migration of persons native to tropical regions has been an ongoing and increasingly common occurrence in Australia and New Zealand for a number of decades.…”

“…Loparev et al (18) performed targeted, multilocus analysis of VZV polymorphisms for a large number of clinical isolates obtained from every populated continent, distinguishing three major genotypes: E (European), J (Japanese), and M (mosaic). The M strains were later subdivided into M1, M2, M3, and M4, which are each considered separate genotypes (16,18,30). Evaluation of the global distribution of VZV strains using sequence variation in a single amplicon from ORF22 sorted VZV isolates from anywhere in the world into four dominant VZV genotypes with a well-defined longitudinal distribution.…”

“…Molecular epidemiology. DNA was purified, and PCR-based diagnostic assays were performed as previously described (16). Australian VZV DNA-positive specimens were placed on Whatman FTA filters and stored at room temperature.…”

Recombination of Globally Circulating Varicella-Zoster Virus

“…The intention was also to introduce criteria so that each existing clade and future novel clades should have at least two whole genomes sequenced to be considered true clades. Although additional clades have been suggested (29,62,63), only clades 1 to 5 have hitherto fulfilled this requirement. One strain sequenced here (Var/Cli/Ves/France/98/ 2013), however, clusters phylogenetically with another strain (Var160; GenBank accession number KC112914.1), separately from strains from clades 1 to 5.…”