Global identification of three major genotypes of varicella-zoster virus: longitudinal clustering and strategies for genotyping

Abstract

By analysis of a single, variable, and short DNA sequence of 447 bp located within open reading frame 22 (ORF22), we discriminated three major varicella-zoster virus (VZV) genotypes. VZV isolates from all six inhabited continents that showed nearly complete homology to ORF22 of the European reference strain Dumas were assigned to the European (E) genotype. All Japanese isolates, defined as the Japanese (J) genotype, were identical in the respective genomic region and proved the most divergent from the E strains, carrying four distinct variations. The remaining isolates carried a combination of E- and J-specific variations in the target sequence and thus were collectively termed the mosaic (M) genotype. Three hundred twenty-six isolates collected in 27 countries were genotyped. A distinctive longitudinal distribution of VZV genotypes supports this approach. Among 111 isolates collected from European patients, 96.4% were genotype E. Consistent with this observation, approximately 80% of the VZV strains from the United States were also genotype E. Similarly, genotype E viruses were dominant in the Asian part of Russia and in eastern Australia. M genotype viruses were strongly dominant in tropical regions of Africa, Indochina, and Central America, and they were common in western Australia. However, genotype M viruses were also identified as a minority in several countries worldwide. Two major intertypic variations of genotype M strains were identified, suggesting that the M genotype can be further differentiated into subgenotypes. These data highlight the direction for future VZV genotyping efforts. This approach provides the first simple genotyping method for VZV strains in clinical samples.

FIG. 1.

Analysis of genotypic variation using data from multiple VZV ORFs. The alignment of SNP in ORF1, -22, -31, -37, -54, -67, and -62 was performed for clinical isolates of VZV from around the world. RFLP of Pst⁺ Bgl⁻, Pst⁺ Bgl⁺, and Pst⁻ Bgl⁻ isolates was also performed. Numbers in the top rows indicate ORF and position of the SNPs in the genome, with the European VZV strain Dumas as a reference for the base pair numbers. The ORF54 SNP is the site that has been used in some protocols to discriminate the Oka vaccine strain from most wild-type strains. Green indicates mutations common to the E genotype reference strain; yellow indicates mutations in common with the J genotype Oka parental strain; red indicates strain-specific individual mutations; white indicates bases common to both the J and E reference strains.

FIG. 2.

Analysis of genotypic variation using the 447-bp ORF22 site. Nucleotide diversity found in the 447-bp fragment of ORF22 was used to type all 326 VZV isolates displayed in Table 1. Dumas and Oka parental strains are included as the reference standard for E and J genotypes, respectively. All E and J strains displayed the same SNP patterns. Some variability was apparent among M genotype strains. The examples displayed represent all of the VZV variations that were observed; the figure has been condensed to make it more readable. The color scheme for the boxes is as for Fig. 1.

FIG. 3.

Genetic relatedness of global VZV strains. Phylogenetic analysis of ORF31 and -22 of VZV strains was performed by the neighbor-joining method (Clustal). All different structural variants detected in this study are included (16).

FIG. 4.

Global distribution of the three major genotypes. Marked areas indicate the major circulating genotype (>70%) for the region. The 326 strains used in previous analysis (Table 1) are all represented; additionally, a number of other more recently acquired strains were analyzed only by ORF22 genotyping: Brazil, 10 isolates (8 M, 2 E); Argentina, 6 E isolates; Cote D'Ivoire, 5 M isolates; Ethiopia, 5 M isolates; Zimbabwe, 3 M isolates; South Africa, 3 E isolates; Thailand, 1 M isolate; Vietnam, 2 M isolates; north China, 3 E isolates; Great Britain, 5 E isolates; Tajikistan, 2 E isolates; Kazakhstan, 2 E isolates; Uzbekistan, 2 E isolates; Kyrgyzstan 2 E isolates; Turkmenistan, 2 E isolates; Azerbaijan, 2 E isolates. (Modified with permission, Corel Corp., copyright [copy] 2004.)