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J Clin Virol. 2008 Sep;43(1):18-24. doi: 10.1016/j.jcv.2008.03.027. Epub 2008 May 13.

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

Author information

1
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

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 (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.

PMID:
18479962
DOI:
10.1016/j.jcv.2008.03.027
[Indexed for MEDLINE]

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