title: Novel approach for genotyping varicella-zoster virus strains from Germany.
abstract: In this study, we present a novel genotyping scheme to classify German wild-type varicella-zoster virus (VZV) strains and to differentiate them from the Oka vaccine strain (genotype B). This approach is based on analysis of four loci in open reading frames (ORFs) 51 to 58, encompassing a total length of 1,990 bp. The new genotyping scheme produced identical clusters in phylogenetic analyses compared to full-genome sequences from well-characterized VZV strains. Based on genotype A, D, B, and C reference strains, a dichotomous identification key (DIK) was developed and applied for VZV strains obtained from vesicle fluid and liquor samples originating from 42 patients suffering from varicella or zoster between 2003 and 2006. Sequencing of regions in ORFs 51, 52, 53, 56, 57, and 58 identified 18 single-nucleotide polymorphisms (SNPs), including two novel ones, SNP 89727 and SNP 92792 in ORF51 and ORF52, respectively. The DIK as well as phylogenetic analysis by Bayesian inference showed that 14 VZV strains belonged to genotype A, and 28 VZV strains were classified as genotype D. Neither Japanese (vaccine)-like B strains nor recombinant-like C strains were found within the samples from Germany. The novel genotyping scheme and the DIK were demonstrated to be practical and simple and allow the highly efficient replication of phylogenetic patterns in VZV initially derived from full-genome DNA sequence analyses. Therefore, this approach may allow us to draw a more comprehensive picture of wild-type VZV strains circulating in Germany and Central Europe by high-throughput procedures in the future.
authors.affiliation: Institute of Medical Virology, Hospital of the Johann Wolfgang Goethe University, Paul Ehrlich Strasse 40, D-60596, Frankfurt am Main, Germany. jonassi@gmx.de
authors.forename: Jonas
authors.initials: J
authors.lastname: Schmidt-Chanasit
authors.forename: Martin
authors.initials: M
authors.lastname: Stürmer
authors.forename: Anke
authors.initials: A
authors.lastname: Hahn
authors.forename: Susanne G
authors.initials: SG
authors.lastname: Schäd
authors.forename: Gerd
authors.initials: G
authors.lastname: Gross
authors.forename: Rainer G
authors.initials: RG
authors.lastname: Ulrich
authors.forename: Gerald
authors.initials: G
authors.lastname: Heckel
authors.forename: Hans Wilhelm
authors.initials: HW
authors.lastname: Doerr
mesh_terms: D005838:Genotype; D014645:Herpesvirus 3, Human / Q000145:classification* / Q000235:genetics; D006801:Humans; D016366:Open Reading Frames; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA