Genetic analysis of foot-and-mouth disease virus serotype A of Indian origin and detection of positive selection and recombination in leader protease- and capsid-coding regions

Abstract

The leader protease (L pro) and capsid-coding sequences (P1) constitute approximately 3 kb of the foot-and-mouth disease virus (FMDV). We studied the phylogenetic relationship of 46 FMDV serotype A isolates of Indian origin collected during the period 1968-2005 and also eight vaccine strains using the neighbour-joining tree and Bayesian tree methods. The viruses were categorized under three major groups -Asian, Euro-South American and European. The Indian isolates formed a distinct genetic group among the Asian isolates. The Indian isolates were further classi?ed into different genetic subgroups (<5% divergence).Post-1995 isolates were divided into two subgroups while a few isolates which originated in the year 2005 from Andhra Pradesh formed a separate group. These isolates were closely related to the isolates of the 1970s. The FMDV isolates seem to undergo reverse mutation or convergent evolution wherein sequences identical to the ancestors are present in the isolates in circulation. The eight vaccine strains included in the study were not related to each other and belonged to different genetic groups. Recombination was detected in the L pro region in one isolate (A IND 20/82) and in the VP1 coding 1D region in another isolate (A RAJ 21/96). Positive selection was identi?ed at aa positions 23 in the L pro (P < 0.05; 0.046*) and at aa 171 in the capsid protein VP1 (P < 0.01; 0.003**).

Molecular Characterization of Foot-and-Mouth Disease Virus: Implications for Disease Control in Bangladesh

“…In the region, other subtypes circulated; in India, not only serotype O (Mason et al., 2003; Saeed et al., 2009) but also serotype C (Nagendrakumar et al., 2005) and serotype A (Nagendrakumar et al., 2009) have been isolated with both O and A isolated frequently and recently. Serotype Asia 1 has also been identified in India (Valarcher et al., 2009).…”

Genetic Characterization of Serotypes A and Asia-1 Foot-and-mouth Disease Viruses in Balochistan, Pakistan, in 2011

“…Based on the VP1 coding nucleotide sequences, FMDV throughout the world has been classified into geographically distinct genotypes that have been termed ‘topotypes’ (Samuel and Knowles, ). Based on ≤15% difference in the VP1 coding region, serotype O, A and Asia‐1 FMDVs within the topotypes are divided into genotypes, which are further classified into lineages and sublineages based on ≤7.5% and ≤5% difference in the VP1 coding region, respectively (Samuel and Knowles, , ; Hemadri et al., ; Mohapatra et al., ; Nagendrakumar et al., ). In case of serotype Asia‐1, the sublineages are referred to as Groups (Valarcher et al., ; Jamal et al., ).…”

Emergence of two novel sublineages Ind2001BD1 and Ind2001BD2 of foot-and-mouth disease virus serotype O in Bangladesh

“…Throughout the world, FMDV has been classified into geographically distinct topotypes (Samuel & Knowles, ) based on the VP1 coding nucleotide sequences. Within serotype O, FMDVs are divided into topotypes and lineages based on 15% and 7.5% differences in the VP1 coding region, respectively (Hemadri, Tosh, Sanyal, & Venkataramanan, ; Mohapatra et al., ; Nagendrakumar, Madhanmohan, Rangarajan, & Srinivasan, ; Samuel & Knowles, ). VP1 protein comprises important antigenic sites on the virion surface, and comparison of VP1 coding sequences from different isolates provides evidence of genetic relatedness among individual FMDV strains, geographical distribution of lineages and genotypes and the source of outbreaks (Knowles & Samuel, ; Samuel & Knowles, ).…”