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In India, widespread foot-and-mouth disease (FMD) outbreaks occurred in 2021. The objective of this study was to identify genetic lineages and evaluate the antigenic relationships of FMD virus (FMDV) isolates gathered from outbreaks reported between 2019 and 2022. Our study shows that the lineages O/ME–SA/Ind2001e and the O/ME–SA/Cluster-2018 were both responsible for the FMD outbreaks on an epidemic scale during 2021. This observation is in contrast to earlier findings that suggested epidemic-scale FMD outbreaks in India are often connected to a single genetic lineage. Additionally, we report here the identification of the O/ME–SA/PanAsia-2/ANT10 sub-lineage in India for the first time, which was connected to two intermittent outbreaks in Jammu and Kashmir. The current study demonstrates that the O/ME–SA/ind2001e lineage has a strong presence outside of the Indian subcontinent. Furthermore, the O/ME–SA/Cluster-2018 was observed to have a wider geographic distribution than previously, and like the O/ME–SA/Ind2001d and O/ME–SA/Ind2001e lineages in the past, it may eventually spread outside of its geographic niche. For O/ME–SA/Ind2001e and O/ME–SA/Cluster-2018, the predicted substitution rate for the VP1 region was 6.737 × 10−3 and 8.257 × 10−3 nt substitutions per site per year, respectively. The time of the most recent common ancestor of the O/ME–SA/Ind2001e and O/ME–SA/Cluster-2018 strains suggests that the viruses possibly emerged during 2003–2011 and 2009–2017, respectively. Recent sightings of the O/ME–SA/PanAsia2/ANT10 virus in India and the O/ME–SA/Ind2001e virus in Pakistan point to possible cross-border transit of the viruses. The results of a two-dimensional viral neutralization test revealed that all of the field isolates were antigenically matched to the currently used Indian vaccine strain O INDR2/1975. These results suggest that the serotype O vaccine strain can protect against outbreaks brought on by all three circulating lineages. [ABSTRACT FROM AUTHOR]

Foot‐and‐mouth disease (FMD) is endemic in India with a preponderance of outbreaks caused by FMD virus (FMDV) serotype O. Out of the 11 global topotypes of serotype O, only ME‐SA topotype has been reported in the country so far. Lineage O/ME‐SA/Ind2001 and O/ME‐SA/PanAsia are documented as the most dominant ones in terms of the number of outbreaks caused by them. To understand the distribution of topotype/lineages in India and their antigenic behaviour during the year 2014–2018, a total of 286 FMDV serotype O viral isolates were sequence determined at the VP1 region, and 109 isolates were characterized antigenically. All the isolates grouped in the ME‐SA topotype, being distributed in lineage O/ME‐SA/Ind2001 (within sub‐lineages O/ME‐SA/Ind2001d and O/ME‐SA/Ind2001e), and a new group designated here as O/ME‐SA/2018 cluster. The sub‐lineage O/ME‐SA/Ind2001e reported for the first time in India during the year 2015, replaced sub‐lineage O/ME‐SA/Ind2001d gradually, which was dominating since 2008. During the years 2014–2018, the sub‐lineage O/ME‐SA/Ind2001e was found to be the most predominant one whose mean evolutionary rate was observed to be faster than that of the sub‐lineage O/ME‐SA/Ind2001d. The codon sites 45 and 85 of VP1 were found to be under diversifying selection in a large proportion of trees. The common ancestor predicted for sub‐lineages O/ME‐SA/Ind2001e and O/ME‐SA/2018 dates back to 2012 and 2016, respectively. The sustenance and spread of the new O/ME‐SA/2018 cluster need to be assessed by continued surveillance. The Indian vaccine strain O/INDR2/1975 was found to provide adequate antigenic coverage to the emerging and prevalent serotype O lineages. The trait association tests showed frequent virus exchange among different states, which could be an important confounder in the region‐specific assessment of effectiveness of FMD control programme. [ABSTRACT FROM AUTHOR]

Foot-and-mouth disease Virus (FMDV) serotype Asia1 is prevalent in the Indian subcontinent, with only G-III and G-VIII reported in India until 2020. However, in 2019, a novel genetic group within serotype Asia1, designated as G-IX, emerged in Bangladesh, followed by its detection in India in 2020. This report presents analyses of the complete coding region sequences of the G-IX lineage isolates. The length of the open reading frame (ORF) of the two G-IX isolates was 6990 nucleotides without any deletion or insertion. The G-IX isolates showed the highest sequence similarity with an isolate of G-III at the ORF, L, P2, and P3 regions, and with an isolate of G-VIII at the P1 region. Phylogenetic analysis based on the capsid region (P1) supports the hypothesis that G-VIII and G-IX originated from a common ancestor, as speculated earlier. Further, VP1 region-based phylogenetic analyses revealed the re-emergence of G-VIII after a gap of 3 years. One isolate of G-VIII collected during 2023 revealed a codon insertion in the G-H loop of VP1. The vaccine matching studies support the suitability of the currently used Indian vaccine strain IND63/1972 to contain outbreaks due to viruses belonging to G-IX.