Differentiation between vaccine and wild-type varicella-zoster virus genotypes by high-resolution melt analysis of single nucleotide polymorphisms

Abstract

Background The analysis of single nucleotide polymorphisms (SNPs) of varicella-zoster virus (VZV) has enabled differentiation between wild-type genotypes from the Oka vaccine strain (V-Oka). Objectives To genotype VZV strains in Australia using high-resolution melt (HRM) analysis of SNPs in five gene targets. Study design Extracted DNA from 78 samples obtained from patients with chickenpox and zoster were genotyped by HRM analysis of SNPs in five open reading frames (ORFs): 1 (685 G > A), 21 (33 725 C > T), 37 (66 288 G > A), 60 (101 464 C > A) and 62 (106 262 T > C) using a double-stranded (ds) DNA saturating dye, LC Green Plus. Results For each genotype, melt curve temperature ( T m) shifts differentiated the nucleotide present at that locus ( P < 0.0001) with melting curve shifts between alleles ranging from 0.56 °C (ORF 37) to 3.34 °C (ORF 62). The most common genotypes detected were the European Type C (59%) and B (18%) strains. This was followed by the African/Asian Type A (14%) and Japanese J1 (9%), strains, both prevalent in the Northern Territory and Western Australia. Conclusions HRM analysis of SNPs showed that the European B and C genotypes were most prevalent in Australia, with genotypes A and J strains also present. HRM analysis using a dsDNA dye provides a useful tool in classifying varicella-zoster viruses.