Genotype analysis of varicella-zoster virus isolates from suburban Shanghai Municipal Province, China.

To determine the predominant genotype of the varicella-zoster virus (VZV) in suburban Shanghai Municipal Province, specimens were collected from the lesions of 95 outpatients clinically diagnosed with varicella or herpes zoster. Of these, 69 patients (72.6%) were positive for VZV DNA. The 69 isolates were all genotyped as the genotype J1/clade 2. Based on sequencing of the 447 bp sequence in ORF22, 66 isolates were identified as genotype J/clade 2 strains and three were identified as type M2/clade 4 strains. To confirm the classification of these three strains, we determined the presence of 27 single-nucleotide polymorphisms (SNPs) and found that isolates 1270/1450 shared seven SNPs that differed from those of clade 2, in which three SNPs were unique to clade 3 and another three were unique to clade 4. Isolate 1456 had two markers of clade 4 that differed from clade 2. The phylogenetic tree showed that our isolates clustered primarily with clade 2 and that the three M2/J1 strains clustered between clades 2 and 4. It is likely that isolates 1270/1450/1446 may represent a new subclade of either clade 2 or 4, or some recombinant events. In addition, our isolates were WT strains. We also observed significant inter-strain variations.