Genetic and antigenic variation of foot-and-mouth disease virus during persistent infection in naturally infected cattle and Asian buffalo in India

Abstract

The role of foot-and-mouth disease virus (FMDV) persistently infected ruminants in initiating new outbreaks remains controversial, and the perceived threat posed by such animals hinders international trade in FMD-endemic countries. In this study we report longitudinal analyses of genetic and antigenic variations of FMDV serotype O/ME-SA/Ind2001d sublineage during naturally occurring, persistent infection in cattle and buffalo at an organised dairy farm in India. The proportion of animals from which FMDV RNA was recovered was not significantly different between convalescent (post-clinical) and sub-clinically infected animals or between cattle and buffalo across the sampling period. However, infectious virus was isolated from a higher proportion of buffalo samples and for a longer duration compared to cattle. Analysis of the P1 sequences from recovered viruses indicated fixation of mutations at the rate of 1.816 × 10-2substitution/site/year (s/s/y) (95% CI 1.362-2.31 × 10-2s/s/y). However, the majority of point mutations were transitional substitutions. Within individual animals, the mean dN/dS (ω) value for the P1 region varied from 0.076 to 0.357, suggesting the selection pressure acting on viral genomes differed substantially across individual animals. Statistical parsimony analysis indicated that all of the virus isolates from carrier animals originated from the outbreak virus. The antigenic relationship value as determined by 2D-VNT assay revealed fluctuation of antigenic variants within and between carrier animals during the carrier state which suggested that some carrier viruses had diverged substantially from the protection provided by the vaccine strain. This study contributes to understanding the extent of within-host and within-herd evolution that occurs during the carrier state of FMDV.

Impact of mass vaccination on the spatiotemporal dynamics of FMD outbreaks in India, 2008–2016

“…To date, very few studies have been carried out to quantify the spatial distribution of FMD risk in India (Hegde et al., 2014;Sharma et al., 2014), and an evaluation of the success of vaccination programs in reducing outbreaks is key to understanding the role of such programs in controlling FMD and achieving FMD zonal freedom with vaccination. Several studies have recognized the importance of optimizing the vaccination program, controlling animal movements and conducting effective surveillance for FMD control in India (Biswal et al., 2019; Pattnaik et al., 2012). However, rigorous spatial epidemiological methods have yet to be applied to understand how vaccination and other factors relate to the spatiotemporal pattern of outbreaks.…”