A proposal for a common nomenclature for viral clades that form the species varicella-zoster virus: summary of VZV Nomenclature Meeting 2008, Barts and the London School of Medicine and Dentistry, 24-25 July 2008

Abstract

Varicella-zoster virus (VZV), the cause of chickenpox and zoster, was the first human herpesvirus to be sequenced fully and the first for which vaccines have been licensed and widely used. Three groups have published genotyping schemes based on single nucleotide polymorphisms (SNPs) and, between them, have identified five distinct phylogenetic clades, with an additional two putative clades. Sequencing of over 23 whole VZV genomes from around the world further refined the phylogenetic distinctions between SNP genotypes. Widespread surveillance in countries in which the varicella vaccine is now in use and the difficulties posed by three unique genotyping approaches prompted an international meeting, at which a common nomenclature based on phylogenetic clades was agreed upon. In this paper, we review the original genotyping schemes and discuss the basis for a novel common nomenclature for VZV strains. We propose a minimum set of SNPs that we recommend should be used to genotype these viruses. Finally, we suggest criteria by which novel clades can be recognized.

Fig. 1.

Schematic representation of the VZV genome showing the ORFs, numbered from left to right. ▾ represent the positions of single-nucleotide polymorphisms (SNPs) that have been identified as useful for strain genotyping. Black-filled shapes represent ORFs that are transcribed late in the VZV replication cycle. IR, Inverted repeat; TR, terminal repeat; UL, unique long region; US, unique short region.

Fig. 2.

Proposed new VZV nomenclature system, adopted 25 July 2008, Whitechapel, London, UK. Summary: major circulating clusters are designated as clades; there are no geographical implications in the naming system; established clades are designated by Arabic numerals; provisional clades are designated by Roman numerals. Reference strains for each clade are indicated in bold; additional reference strains are required for clades 2, 5, VI and VII.

Fig. 3.

Phylogenetic tree showing five major VZV clades (adapted from Loparev, 2007b). Previous genotyping schemes are shown in the order Breuer/Schmid/Grose.