Evidence of recombination in the capsid-coding region of type A foot-and-mouth disease virus

This study demonstrates recombination in the capsid-coding (P1) region of foot-and-mouth disease virus (FMDV) type A, a finding that challenges previous understanding. Researchers analyzed 14 FMDV type A isolates distributed among three genotypes (IV, VI, and VII) based on VP1 gene sequences. One isolate, IND 170/88, was identified as a hybrid recombinant of genotypes VI and VII through similarity analysis, bootscan analysis, and phylogenetic tree construction. The recombinant contained genotype VI sequences in VP1, VP4, the 5′ region of VP2, and the 3′ region of VP3, while the remaining portions of VP2 and VP3 were characteristic of genotype VII. Two recombination crossover points were identified in conserved regions of the genome, with no insertions or deletions observed. The recombinant virus possessed amino acid residues from both parental viruses at antigenically critical sites, making it an antigenic hybrid. This finding is significant because previous research had not demonstrated recombination in FMDV structural protein-coding regions with heterogenic parents, only in non-structural protein regions. The recombination likely provides selective advantage by allowing viral escape from immune responses directed against either parental virus, which has important implications for disease control in regions where multiple FMDV genotypes co-circulate.

Key findings

• An FMDV type A isolate (IND 170/88) was identified as an intergenotypic recombinant between genotypes VI and VII through molecular and phylogenetic analyses.
• The recombination occurred in the capsid-coding P1 region with two distinct crossover points in conserved genomic regions encoding structural proteins.
• The recombinant virus possessed a mosaic genome structure (genotype VI-VII-VI) and exhibited antigenic characteristics of both parent viruses, potentially enabling immune evasion.
• This represents the first documented evidence of recombination in FMDV structural protein-coding regions involving heterogenic parental strains.
• Recombination in capsid-coding regions contributes to FMDV genetic diversification and may provide selective advantage in regions with co-circulating multiple FMDV genotypes.