Molecular characterization of Mumps virus genotype C detected from Dibrugarh district of Assam, India

Abstract

Background & objectives Mumps, a contagious disease caused by the mumps virus (MuV) involves parotid gland inflammation, with potential complications affecting organs other than the parotid glands and central nervous system. Despite successful vaccination, a resurgence of mumps occurred, raising concerns about vaccine effectiveness. This study aimed to examine the entire genome of a representative MuV genotype C from Dibrugarh, Assam, and compare it with references to detect genetic variations in the circulating strain. Methods Representative MuV genotype C from our published study was subjected to whole genome sequencing. MuV genome was analyzed against the reference genome and vaccine strains before being subjected to mutational profiling, N-glycosylation site determination, and phylogenetic analysis. The Immune Epitope Database was used for epitope screening, and selected epitopes were mapped against Assam MuV for conservancy studies. Results Mutational analysis of Assam MuV with WHO (World health Organization) reference, vaccine strains Jeryl Lynn (Genotype A), and L Zagreb (Genotype N) showed variations in seven genes. Phylogenetic analysis established Assam MuV as genotype C. Epitope conservancy analysis highlighted subtle variations in experimentally determined T-cell epitopes for HN and F proteins, emphasizing overall epitope stability. Interpretation & conclusions Genome sequencing has evolved into a standard and potent method for investigating and recording circulating MuV as it provides information on surveillance, mutation analysis, and transmission dynamics. Despite mumps' global effect, genomic studies are limited, particularly in north-east. Our study provides first comprehensive whole-genome report on circulating MuV genotype C in Assam. This research contributes vital genomic data, filling gaps in MuV genetic epidemiology, supporting global research, and assessing vaccine effectiveness.

Keywords: Epitopes; genotype C; mumps virus; parotitis; phylogenetic tree; whole genome sequencing.

Fig. 1.

The phylogenetic tree for the whole genome of mumps virus (MuV) representing the 12 genotypes of MuV. The Assam MuV genotype C is represented with red dot. The WHO (world health organization) reference strains are labeled with blue dot, the vaccine strains are labelled with yellow dot and the strains representing both the WHO reference strain and the vaccine strain are labeled in purple diamond. The sequences are named as follows: Accession number followed by isolate/strain name as in GenBank. The tree was generated using MEGA XI software.

Fig. 2.

Conservancy analysis of Assam MuV T-cell epitopes that were mapped with experimentally determined T-cell epitopes of MuV reported in IEDB (A) HN protein and (B) F protein and further compared against both the vaccine strains. IEDB, immune epitope database.