Dynamics of widespread foot‐and‐mouth disease virus serotypes A,O and Asia‐1 in southern Asia: A Bayesian phylogenetic perspective

Foot‐and‐mouth disease (FMD ) is, arguably, the animal disease with the most devastating global economic impact owing in part, to the severe trade restrictions imposed upon affected countries and regions. South Asia is one of the regions where widespread lineages of the FMDV virus (FMDV ) have emerged. Here, we performed an integrative phylogenetic analysis of all FMDV serotypes (A, O and Asia‐1) circulating in southern Asia, including viral sequences collected until 2013. Our results describe the occurrence of FMD caused by different serotypes and lineages, focusing in the cycles where a specific lineage predominates within a region for a protracted period and then are rapidly or progressively replaced by an emergent or re‐emergent strain that is introduced from an adjacent region. Transmission between the two main regions in southern Asia (the Indian subcontinent and the region comprised by Afghanistan, Iran and Pakistan) has been limited. Results of time divergence estimation of lineages that currently circulate in this region indicate that the most recent common ancestor of endemic lineages are: 1992 1989–1995] for lineage O/PanAsia; 1997 1995–1999] for PanAsia2; 2001 1998–2004] for O/Ind2001; 2001 2000–2002] for A/Iran‐05; 1990 1988–1991] for A/G‐18 (G‐VII ); 2003 2000–2006] for Asia‐1 Sindh08 and 2002 1999–2004] for Asia‐1 G‐VIII . We estimated the mean of the overall substitution rate of the VP 1 coding region (substitution/site/year) for serotype O (5.95 × 10⁻³), serotype A (1.19 × 10⁻²) and serotype Asia‐1 (3.08 × 10⁻³). The potential factors driving the lineage turnover are discussed. Our results provide insights into the ecological and evolutionary factors driving the emergence of FMDV .