Although recombination is known to occur in FMDV, it is considered only a minor determinant of virus sequence diversity. This is because recombination appears to be highly suppressed at phylogenetic scales; inter-serotypic recombination events are rare; and in those a mosaic structure is present whereby recombination only occurs almost exclusively in non-structural proteins. Here we show that co-inoculation of closely related strains in buffaloes results over time in extensive within-host recombination in the genomic region coding for structural proteins. This enables us to directly estimate recombination rates for the first time. 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. Thanks to the features of our experimental setup, we are also able to build a high-resolution map of effective within-host recombination in the capsid-coding region. We find that the linkage disequilibrium pattern inside VP1 points to 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 those intra-host results are not immediately transportable to a phylogenetic setting, they force us to reconsider the relevance of recombination and epistasis, suggesting that they must play a major and so far underappreciated role in the molecular evolution of the virus at all time scales.
Author summaryRecombination in the capsid-coding region of the Foot-and-Mouth Disease virus genome is highly suppressed at phylogenetic scales. However, the role of recombination in the intra-host dynamics of the virus is not known. In our experiment, a co-infection of African buffaloes with closely related FMDV strains results in a population structure of the intra-host viral swarm, allowing us to detect recombination events. For structural protein-coding sequences, the swarm dynamics is driven by extensive within-host recombination. During the acute infection phase, we infer intra-host recombination rates of 0.1 per base per year, comparable to the typical mutation rate of the virus. The recombination map reveals two linkage blocks within the VP1 protein-coding sequence. Epistatic interactions between co-evolved mutations in VP1 are caused by intra-host selection at the RNA and protein level and are present both within and between blocks. Our findings support a major role for recombination and epistasis in the intra-host evolution of FMDV.
