A traditional evolutionary history of foot-and-mouth disease viruses in Southeast Asia challenged by analyses of non-structural protein coding sequences

Abstract

Recombination of rapidly evolving RNA-viruses provides an important mechanism for diversification, spread, and emergence of new variants with enhanced fitness. Foot-and-mouth disease virus (FMDV) causes an important transboundary disease of livestock that is endemic to most countries in Asia and Africa. Maintenance and spread of FMDV are driven by periods of dominance of specific viral lineages. Current understanding of the molecular epidemiology of FMDV lineages is generally based on the phylogenetic relationship of the capsid-encoding genes, with less attention to the process of recombination and evolution of non-structural proteins. In this study, the putative recombination breakpoints of FMDVs endemic to Southeast Asia were determined using full-open reading frame sequences. Subsequently, the lineages' divergence times of recombination-free genome regions were estimated. These analyses revealed a close relationship between two of the earliest endemic viral lineages that appear unrelated when only considering the phylogeny of their capsid proteins. Contrastingly, one lineage, named O/CATHAY, known for having a particular host predilection (pigs) has evolved independently. Additionally, intra-lineage recombination occurred at different breakpoints compared to the inter-lineage process. These results provide new insights about FMDV recombination patterns and the evolutionary interdependence of FMDV serotypes and lineages.

Figure 1

Similarity plot for unique recombination events (a–e) detected using RDP4 and phylogenetic reconstruction. The query sequence name (recombinant) is indicated at the top of each panel. The x axis indicates the nucleotide position (ORF) of the query sequence at the center of the sliding window (k). The y axis indicates the similarity, s(k), between the corresponding window of the query sequence and each of the reference sequences. A non-recombinant reference sequence from a given lineage was used to represent the relationship between the query (recombinant) sequence and each lineage. The colored bar at the top of each plot indicates the ‘best match’, which is the reference sequence with the highest identity to the query sequence. The specific reference sequence and lineages of the viruses contributing to the recombinant virus are indicated in the legend.

Figure 2

Recombination breakpoints distribution throughout ORF sequences of Southeast Asia endemic Foot-and-mouth disease virus (FMDV) lineages. Based on the recombination points found, nine recombination-free regions (r1–9) were found within the FMDV genomes analyzed. The y-axis represents the number of recombination breakpoints detected within a 300 nt sliding window. The x-axis represents the nt position across the genome (reference for nt position: sequence O/JPN/2000-AB079061).

Figure 3

Maximum clade credibility trees constructed for recombination-free regions r1, r2, r3, r7, r8 and r9. The classification of lineages, topotypes and serotypes are defined by the traditional phylogeny grouping of viruses by their structural proteins coding regions (r2). Color-coding of the tree branches is based on this r2 classification. The topology of the phylogenetic trees based on the non-capsid coding sequence shows a close relationship between the O/Mya-98 and A/Sea-97 lineages, and an independent evolution of the viruses belonging to the O/CATHAY lineage. Recent recombinant viruses are indicated by an asterisk (*).

Figure 4

Within-lineage recombination breakpoints detected by Homoplasy tests (lineages A/Sea-97, O/Mya-98, O/PanAsia, O/CATHAY). P-values < 0.2 are plotted at the center of the window tested. Results are combined for the analyses using window sizes 300 (grey/black), 400 (pink/red) and 600 (light blue/blue). Brighter colors (black, red, blue) show the center of the window for p-value < 0.05. Specific areas with a strong statistical evidence of recombination (clustered p-values < 0.05) are shown in a dashed rectangle.