Pervasive within-host recombination and epistasis as major determinants of the molecular evolution of the foot-and-mouth disease virus capsid

Abstract

Although recombination is known to occur in foot-and-mouth disease virus (FMDV), it is considered only a minor determinant of virus sequence diversity. Analysis at phylogenetic scales shows inter-serotypic recombination events are rare, whereby recombination occurs almost exclusively in non-structural proteins. In this study we have estimated recombination rates within a natural host in an experimental setting. African buffaloes were inoculated with a SAT-1 FMDV strain containing two major viral sub-populations differing in their capsid sequence. This population structure enabled the detection of extensive within-host recombination in the genomic region coding for structural proteins and allowed recombination rates between the two sub-populations to be estimated. Quite surprisingly, the effective recombination rate in VP1 during the acute infection phase turns out to be about 0.1 per base per year, i.e. comparable to the mutation/substitution rate. Using a high-resolution map of effective within-host recombination in the capsid-coding region, we identified a linkage disequilibrium pattern in VP1 that is consistent with a mosaic structure with two main genetic blocks. Positive epistatic interactions between co-evolved variants appear to be present both within and between blocks. These interactions are due to intra-host selection both at the RNA and protein level. Overall our findings show that during FMDV co-infections by closely related strains, capsid-coding genes recombine within the host at a much higher rate than expected, despite the presence of strong constraints dictated by the capsid structure. Although these intra-host results are not immediately translatable to a phylogenetic setting, recombination and epistasis must play a major and so far underappreciated role in the molecular evolution of the virus at all scales.

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

“…These hotspots separated the ORF into three distinct regions, corresponding well to the established functional areas 6 . This suggested that recombination in FMDV is constrained by biological functions, and further supported the idea of mosaic structure of FMDV genome 17 – 19 . The genome of other viruses has also been observed to have a mosaic and modular nature, such as foamy virus 31 , and enteroviruses 32 , for example.…”

“…The third region mapped to the P2 and P3 regions (nt 3,034–6,840; P2–3 alignment), excluding the 2A coding region. As previously noted, only a few recombination events were detected in the P1 region, which codes for capsid protein subunits 15 – 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. This finding suggested that the interaction between protein subunits required to form a functional capsid protein shall, especially the VP1-3 proteins, is highly constrained, such that recombinants involving exchanging genomic materials in this region are strongly unfavoured by natural selection 19 . Potential recombination was then checked again within these three alignments.…”

“…Recent studies, however, showed that recombination is a common feature of FMDV, and different parts of its genome can have different evolutionary histories 15 – 19 . Most importantly, one of the major recombination regions could be mapped to the P1 region, containing the VP1 protein coding region.…”

Persistent Infection of African Buffalo (Syncerus caffer) with Foot-and-Mouth Disease Virus: Limited Viral Evolution and No Evidence of Antibody Neutralization Escape

“…Recombination occurred at a high rate during the acute phase of infection postinoculation and at a lower rate during the persistent phase, as discussed in detail in a companion publication by Ferretti and colleagues (28).…”