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. 2023 Aug:333:199140.
doi: 10.1016/j.virusres.2023.199140. Epub 2023 Jun 10.

Emergence of a novel genetic lineage 'A/ASIA/G-18/2019' of foot and mouth disease virus serotype A in India: A challenge to reckon with

Jajati Keshari Mohapatra  1 , Shyam Singh Dahiya  2 , Saravanan Subramaniam  2 , Manoranjan Rout  2 , Jitendra Kumar Biswal  2 , Priyabrata Giri  2 , Vinayak Nayak  2 , Rabindra Prasad Singh  2
Affiliations

Emergence of a novel genetic lineage 'A/ASIA/G-18/2019' of foot and mouth disease virus serotype A in India: A challenge to reckon with

Jajati Keshari Mohapatra et al. Virus Res. 2023 Aug.

Abstract

Foot and mouth disease (FMD) has engendered large scale socioeconomic crises on numerous occasions owing to its extreme contagiousness, transboundary nature, complicated epidemiology, negative impact on productivity, trade embargo, and need for intensive surveillance and expensive control measures. Emerging FMD virus variants have been predicted to have originated and spread from endemic Pool 2, native to South Asia, to other parts of the globe. In this study, 26 Indian serotype A isolates sampled between the year 2015 and 2022 were sequenced for the VP1 region. BLAST and maximum likelihood phylogeny suggest emergence of a novel genetic group within genotype 18, named here as 'A/ASIA/G-18/2019' lineage, that is restricted so far only to India and its eastern neighbour, Bangladesh. The lineage subsequent to its first appearance in 2019 seems to have displaced all other prevalent strains, in support of the phenomenon of 'genotype/lineage turnover'. It has diversified into two distinct sub-clusters, reflecting a phase of active evolution. The rate of evolution of the VP1 region for the Indian serotype A dataset was estimated to be 6.747 × 10-3 substitutions/site/year. India is implementing a vaccination centric FMD control programme. The novel lineage showed good antigenic match with the proposed vaccine candidate A IND 27/2011 when tested in virus neutralization test, while the existing vaccine strain A IND 40/2000 showed homology with only 31% of the isolates. Therefore, in order to combat this challenge of antigenic divergence, A IND 27/2011 could be the preferred strain in the Indian vaccine formulations.

Keywords: FMD virus; Novel lineage A/ASIA/G-18/2019; Phylogeny; Serotype A; Vaccine matching.

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Conflict of interest statement

Declaration of Competing Interest The authors declare that they have no known competing financialinterestsor personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig 1
Fig. 1
Maximum likelihood phylogenetic tree reconstructed based on VP1 coding sequence of FMD virus serotype A isolates from India. Sequences generated in this study are identified with red-filled triangles. Bootstrap values >70% are shown next to the nodes.
Fig 2
Fig. 2
Maximum likelihood evolutionary relationship inferred based on VP1 coding sequence of contemporary FMD virus serotype A strains from other countries and from India. Bootstrap values >70% are shown next to the nodes.
Fig 3
Fig. 3
Alignment of deduced VP1 amino acid sequence of strains belonging to subcluster-1 and 2 of the novel A/ASIA/G-18/2019 lineage with that of the vaccine strain A IND 40/2000 and alternate vaccine strain A IND 27/2011. A dot indicates similarity with that of A IND 40/2000 and variations are shown as single letter amino acid codes.
Fig 4
Fig. 4
Maximum clade credibility (MCC) evolutionary relationships of FMD virus serotype A VP1 coding sequences from different states of India. Branches are coloured according to the most probable location state of their descendant nodes. Horizontal branch lengths are drawn to scale, with the bar at the bottom indicating years. The A/ASIA/G-18/2019 lineage is shown within the red box.
Fig 5
Fig. 5
Spatiotemporal dynamics predicted for the A/ASIA/G-18/2019 lineage found in India. The arrows between the locations indicate the migration route of A/ASIA/G-18/2019 lineage. Only the propagation paths with BF> 3 are shown. States are numbered as per predicted chronology of virus dissemination event.
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