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

Abstract

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 VP1 coding region (substitution/site/year) for serotype O (5.95 × 10 ), serotype A (1.19 × 10 ) and serotype Asia-1 (3.08 × 10 ). The potential factors driving the lineage turnover are discussed. Our results provide insights into the ecological and evolutionary factors driving the emergence of FMDV.

Characterization of naturally occurring, new and persistent subclinical foot‐and‐mouth disease virus infection in vaccinated Asian buffalo in Islamabad Capital Territory, Pakistan

“…Based on estimated VP1 nucleotide substitution rates obtained by Bayesian divergence‐time estimation methods, the number of expected nucleotide changes in VP1 per year has been reported as 3.75 (3.06–4.43; corresponding to 5.92 × 10 −3 substitutions/site/year) for lineage O/PanAsia2, 2.46 (1.76–3.17; 3.88 × 10 −3 substitutions/site/year) for Asia‐1/Sindh08, and 10.95 (8.99–13.10; 1.73 × 10 −2 substitutions/site/year) for A/Iran‐05 (Brito et al., ). Previous studies have reported similar nucleotide substitution rates for O/PanAsia2 and A/Iran‐05 based on linear regression analysis of genetic distances (Jamal, Ferrari, Ahmed, Normann, & Belsham, 2011a; Jamal, Ferrari, Ahmed, Normann, Curry et al., ).…”

“…Sequence analysis of the FMDV VP1‐coding region has suggested that complex mixtures of genotypes may arise during FMDV type O persistent infection in Asian buffalo, providing a potential source of novel viral variants (Barros, Malirat, Rebello, Costa, & Bergmann, ). Likewise, rapid viral evolution has been described during FMDV persistent infection of cattle (Brito et al., ; Gebauer et al., ). However, a different investigation suggested more limited changes within the viral genome during persistent infection in cattle (Parthiban et al., ).…”

Tracing foot-and-mouth disease virus phylogeographical patterns and transmission dynamics.

“…We investigated and compared the historical spreads of FMDV at serotype level, from the ones with local distribution (Asia1 and SATs) to the serotypes with widespread dispersal (O and A) [26,28,34,55,77,78].…”

“…FMDV causes the most influential transboundary animal disease with historical worldwide circulation reported in domestic and wildlife reservoirs [25,26]. FMD is a highly contagious disease caused by a small single-stranded RNA virus of the genus Aphthovirus, member of the family Picornaviridae [27] and classified into seven different serotypes; O, A, C, Asia1 and Southern African Territories (SATs) 1, 2 and 3 [25,[28][29][30] which severely affect the productivity of domesticated livestock, causing great economic losses [31][32][33].…”

“…Individual genes have been widely used to study the phylogenetic relationships among FMD serotypes [43][44][45][46][47][48][49][50], however, little has been done using whole genome sequences (WGS) [26,[51][52][53]. 4 Nevertheless, these studies have been often based on a limited number of sequences (<200), or on phylogenetic methods that do not have the ability to accommodate uncertainty (i.e., Bayesian phylodynamic methods) [54].…”