Reconstructing the evolutionary history of pandemic foot-and-mouth disease viruses: the impact of recombination within the emerging O/ME-SA/Ind-2001 lineage

Abstract

Foot-and-mouth disease (FMD) is a highly contagious disease of livestock affecting animal production and trade throughout Asia and Africa. Understanding FMD virus (FMDV) global movements and evolution can help to reconstruct the disease spread between endemic regions and predict the risks of incursion into FMD-free countries. Global expansion of a single FMDV lineage is rare but can result in severe economic consequences. Using extensive sequence data we have reconstructed the global space-time transmission history of the O/ME-SA/Ind-2001 lineage (which normally circulates in the Indian sub-continent) providing evidence of at least 15 independent escapes during 2013–2017 that have led to outbreaks in North Africa, the Middle East, Southeast Asia, the Far East and the FMD-free islands of Mauritius. We demonstrated that sequence heterogeneity of this emerging FMDV lineage is accommodated within two co-evolving divergent sublineages and that recombination by exchange of capsid-coding sequences can impact upon the reconstructed evolutionary histories. Thus, we recommend that only sequences encoding the outer capsid proteins should be used for broad-scale phylogeographical reconstruction. These data emphasise the importance of the Indian subcontinent as a source of FMDV that can spread across large distances and illustrates the impact of FMDV genome recombination on FMDV molecular epidemiology.

Emergence of novel lineage of foot‐and‐mouth disease virus serotype Asia1 BD‐18 (G‐IX) in Bangladesh

“…This may be due to a steady transmission of viruses through porous trans-border between these countries. From India, the early landmarks of incursion of G-VIII viruses into Bangladesh might happen (Ullah et al, 2015) and could be an important factor to the emergence of this new lineage, which was not possible to determine in this study due to lack of related se- Bachanek- Bankowska et al, 2018;Zhu et al, 2018). The similar scenario can happen in this case, and high sequence diversity with vaccine strain will ask the burning question in protection of cattle in this region.…”

“…Similarly, there could be immune pressure due to trivalent vaccination programme using genetically divergent vaccine strain (IND63/72) of serotype Asia1 compared to this novel strain, or inappropriately selected local candidate, which might ultimately favour the generation of this new strain of lineage G‐IX (Ullah et al, ). Moreover, Siddique et al () reported a novel sublineage of serotype O from Bangladesh, and then subsequent works by other contemporary groups detected the same strains across 14 countries, even outside Indian subcontinent zone, from where the strains were reported earlier stage of outbreak and spread (Alam et al, ; Bachanek‐Bankowska et al, ; Zhu et al, ). The similar scenario can happen in this case, and high sequence diversity with vaccine strain will ask the burning question in protection of cattle in this region.…”

Comparing Phylogeographies: Incompatible Geographical Histories in Pathogens’ Genomes

“…Whole-genome sequences from a recently analysed FMDV lineage (the O/ME-SA/ Ind-2001) were provided by the World Reference Laboratory for FMD (WRLFMD) at the Pirbright Institute [Bachanek-Bankowska et al, 2018]. Phylogeographic analyses were performed on most loci along the genome, as well as on the WGS.…”

“…This could be due to the effect produced on the WGS topology by recombinant viruses (i.e. the O/BAR/15/2015 and O/BHU/3/2016) [Bachanek-Bankowska et al, 2018], which provide the strongest contribution to incompatibilities (as is evident from the widest branch in Figure 3).…”

“…For influenza B virus we selected 122 and 120 unique genome sequences of, respectively, the Victoria (Vic) and Yamagata (Yam) lineages [Bedford et al, 2015, Langat et al, 2017, characterising five out of the eight gene segments and encoding: the polymerase basic subunits 1 and 2 (PB1 and PB2), the hemagglutinin (HA) and neuraminidase (NA) glycoproteins, and the non-structural protein 1 (NS1) [Bouvier and Palese, 2008]. For FMD we selected 74 whole-genome sequences (WGSs) characterising the O/ME-SA/Ind-2001 lineage [Bachanek-Bankowska et al, 2018], extracting separate alignments for each of the four structural (VP1 to VP4) and six non-structural (2A to 2C, and 3A to 3D) proteins, along with the leader polypeptide (Lpro) and the 5' untranslated region (5'UTR) alignments [Jackson et al, 2003].…”