학술논문

Molecular characterization of varicella zoster virus isolated from clinical samples in India.
Document Type
Article
Source
Indian Journal of Medical Research. Oct2021, Vol. 154 Issue 4, p592-597. 6p.
Subject
*WHOLE genome sequencing
*VARICELLA-zoster virus
*SINGLE nucleotide polymorphisms
*NUCLEOTIDE sequencing
*GENOMES
Language
ISSN
0971-5916
Abstract
Background & objectives: Varicella zoster virus (VZV) strains are classified into six different clades based on the sequencing of its genome. Clades 4 and 5 are reported from India based on the single-nucleotide polymorphism (SNP). Till now, multiple clade circulations using partial sequences have been reported from India due to the lack of availability of the full VZV genome sequence. This study conducted a genome sequencing of VZV in India to identify circulating clade. Methods: Four clinical samples obtained from symptomatic patients tested positive for VZV by real-time PCR were used. These four samples were preferred to retrieve the genomic VZV sequence using the nextgeneration sequencing method. A reference-based assembly method was used to retrieve the genome of VZV, which was further analyzed. Results: At the least, 98 per cent of the whole-genome sequences were recovered from the four samples. The VZV sequences obtained in this study formed a separate monophyletic branch with clade 5, indicating it to be evolved from a distinct ancestor. The nucleotide-based analysis revealed 13 different SNP mutations and one multiple nucleotide variation in the VZV sequences when compared to one of the clade 5 genomes having accession number: DQ457052.1. Interpretation & conclusions: The present study described approximately 98 per cent of the genome sequence of VZV from India. The availability of these genomic sequences will lead to enrichment in the clinical genomic data set from India. The available data would help in the development of diagnostic methods along with evolutionary analysis. We hypothesize the existence of a new sub-clade that belongs to clade 5 and propose further experiments to confirm these results. [ABSTRACT FROM AUTHOR]