Revisiting the genotyping scheme for varicella-zoster viruses based on whole-genome comparisons
2017
We report
whole-genome sequences(WGSs) for four
varicella-zoster virus(VZV) samples from a
shinglesstudy conducted by Kaiser Permanente of Southern California.
Comparative genomicsand phylogenetic analysis of all published VZV WGSs revealed that strain KY037798 is in
cladeIX, which shall henceforth be designated
clade9. Previously published single nucleotide polymorphisms (SNP)-based genotyping schemes fail to discriminate between
clades6 and VIII and employ positions that are not
clade-specific. We provide an updated list of
clade-specific positions that supersedes the list determined at the 2008 VZV nomenclature meeting. Finally, we propose a new targeted genotyping scheme that will discriminate the circulating VZV
cladeswith at least a twofold redundancy. Genotyping strategies using a
limited setof targeted SNPs will continue to provide an efficient ‘first pass’ method for VZV strain surveillance as vaccination programmes for varicella and zoster influence the dynamics of VZV transmission.
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