Systematic Evaluation and Application of Single-Nucleotide Polymorphism-Based Genotyping Methods in Varicella-Zoster Virus Molecular Epidemiology Surveillance - China, 2017-2026.

INTRODUCTION

In China, no standardized single-nucleotide polymorphism (SNP) scheme exists for varicella-zoster virus (VZV) genotyping. The 5-SNP scheme with two amplicon gene fragments lacks systematic validation. This study aimed to evaluate the accuracy and applicability of this genotyping method.

METHODS

A total of 280 complete genomes were genotyped using 5 SNPs extracted from ORF22 (four SNPs) and ORF38 (one SNP) fragments. The results were compared with those of the phylogenetic clustering method as a reference. Concordance with reference was used to estimate the accuracy of the SNP scheme. The evaluated SNP scheme was applied to a national VZV surveillance screen containing 549 clinical samples from 17 Chinese provincial-level administrative divisions (2017-2026).

RESULTS

A 97.9% concordance was observed between the 5-SNP scheme and phylogenetic clustering methods. The 2.1% discordance was mostly attributed to putative recombination and early circulation of strains from patients with herpes zoster. During the national VZV surveillance screening, 434 samples were amplified, sequenced, and genotyped using a 5-SNP scheme. Of the genotyped samples, 90.3% and 8.8% were identified as clades 2 and 5, respectively, using four ORF22 SNPs, and the remaining 0.9% as clade 4, using ORF38 SNP. All samples showed 100% intragenotypic SNP profile consistency.

CONCLUSION

The unified 5-SNP scheme is accurate and practical for VZV surveillance in China; however, periodic evaluation is required.