Evidence for multiple recombination events within foot‐and‐mouth disease viruses circulating in West Eurasia

Abstract

Phylogenetic studies on foot‐and‐mouth disease viruses (FMDVs) circulating in the West Eurasian region have largely focused on the genomic sequences encoding the structural proteins that determine the serotype. The present study has compared near‐complete genome sequences of FMDVs representative of the viruses that circulate in this region. The near‐complete genome sequences (ca. 7,600 nt) were generated from multiple overlapping RT‐PCR products. These amplicons were from FMDVs belonging to serotypes O, A and Asia‐1, including members of the O‐PanAsia‐II and the A‐Iran05 lineages, and of Group‐II and Group‐VII (Sindh‐08) within serotype Asia‐1, which are currently predominant and widespread in West Eurasia. These new sequences were analysed together with other sequences obtained from GenBank. Comparison of different regions of the FMDVs genomes revealed evidence for multiple, inter‐serotypic, recombination events between FMDVs belonging to the serotypes O, A and Asia‐1. It is concluded from the present study that dramatic changes in virus sequences can occur in the field through recombination between different FMDV genomes. These analyses provide information about the ancestry of the serotype O, A and Asia‐1 FMDVs that are currently circulating within the West Eurasian region.

Early origin and global colonisation of foot-and-mouth disease virus

“…Again, we found that, although not absolute, Euro-Asiatic FMDVs tended to cluster together separately from the SAT stains (> 97% bootstrap support). However, in stark contrast to what we observed in the P1 tree, serotypes A, O, C and Asia1 appeared to intermix with one another in all of these trees, consistent with previous results 33 . Furthermore, a similar pattern was also found for the SAT1-3 serotypes.…”

“…As previously noted, only a few recombination events were detected in the P1 region, which codes for capsid protein subunits [15][16][17][18][19] . A previous study of serotype O, A, and Asia-1 FMDVs circulating in West Eurasia also showed that, while the VP1-3 phylogenies were the same, a phylogeny estimated from the VP4 coding region was different from the rest 33 . This finding was consistent and further supported that the VP4 region is a recombination hotspot, and that the VP1-3 regions share the same evolutionary history.…”

“…Given how common it is, recombination likely plays an important role in survival and adaption of viruses in the face of new environments. In FMD endemic areas, especially those with high incidence rates of FMDV persistent infection, co-infection of FMDVs can indeed occur 42 , and intra-host recombination could play a significant role in increasing the genetic diversity of the virus, generating new virus variants 18,19 , and potentially altering the virus biology 33 . Although not directly shown in this study, it has been noted that recombination in the capsid protein coding region could occur, and this could potentially reduce the success of FMD vaccination programs 33 .…”

In silico Evolutionary Divergence Analysis Suggests the Potentiality of Capsid Protein VP2 in Serotype-Independent Foot-and-Mouth Disease Virus Detection

“…Similarly, inter-lineage divergence in the VP2 region of African (5.4%) and Asian (3.9%) topotypes was the highest and the lowest lineage level divergence for serotype A. This difference in divergence among lineages within the same serotype may possibly be due to the recombination events in FMDVs within the conserved region of VP2 as described by Jamal et al (40,41). Importantly, at each hierarchical level, the divergence values for VP2 were lower than those for VP1, except the sub-lineage-level divergence of A/IRN-05 lineage where the values were equal.…”

Sequence Analysis of Egyptian Foot-And-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus

“…This is challenging not only because there are seven immunologically distinct serotypes of FMDV: O, A, C, Asia 1 and Southern African Territories (SAT) 1, SAT 2, SAT 3. Like many RNA viruses, FMDV has high genetic variability, caused by error-prone RNA replication and extensive intra-and inter-serotype recombination [1,5]. Within each serotype, the many subtypes and lineages are evolving rapidly and are spread within and between known epidemiological clusters (so-called virus pools) by trade in live animals and animal products [1].…”