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


OBJECTIVE
To genotype VZV strains in Australia using high-resolution melt (HRM) analysis of SNPs in five gene targets.


METHODS
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 (33725 C>T), 37 (66288 G>A), 60 (101464 C>A) and 62 (106262 T>C) using a double-stranded (ds) DNA saturating dye, LC Green Plus.


RESULTS
For each genotype, melt curve temperature (Tm) shifts differentiated the nucleotide present at that locus (P<0.0001) with melting curve shifts between alleles ranging from 0.56 degrees C (ORF 37) to 3.34 degrees 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.
Toi
Cheryl S
CS
Clinical Virology, Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia. cheryl.toi@swahs.health.nsw.gov.au
Dwyer
Dominic E
DE
D000704:Analysis of Variance; D019433:Chickenpox Vaccine / Q000235:genetics* / Q000302:isolation & purification; D004279:DNA, Viral / Q000235:genetics* / Q000302:isolation & purification; D005814:Genes, Viral; D005838:Genotype; D014645:Herpesvirus 3, Human / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D009691:Nucleic Acid Denaturation; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide
D019433:Chickenpox Vaccine; D004279:DNA, Viral