Phylogenetic analyses of the polyprotein coding sequences of serotype O foot-and-mouth disease viruses in East Africa: evidence for interserotypic recombination

Abstract

Background: Foot-and-mouth disease (FMD) is endemic in East Africa with the majority of the reported outbreaks attributed to serotype O virus. In this study, phylogenetic analyses of the polyprotein coding region of serotype O FMD viruses from Kenya and Uganda has been undertaken to infer evolutionary relationships and processes responsible for the generation and maintenance of diversity within this serotype. FMD virus RNA was obtained from six samples following virus isolation in cell culture and in one case by direct extraction from an oropharyngeal sample. Following RT-PCR, the single long open reading frame, encoding the polyprotein, was sequenced.

Results: Phylogenetic comparisons of the VP1 coding region showed that the recent East African viruses belong to one lineage within the EA-2 topotype while an older Kenyan strain, K/52/1992 is a representative of the topotype EA-1. Evolutionary relationships between the coding regions for the leader protease (L), the capsid region and almost the entire coding region are monophyletic except for the K/52/1992 which is distinct. Furthermore, phylogenetic relationships for the P2 and P3 regions suggest that the K/52/1992 is a probable recombinant between serotypes A and O. A bootscan analysis of K/52/1992 with East African FMD serotype A viruses (A21/KEN/1964 and A23/KEN/1965) and serotype O viral isolate (K/117/1999) revealed that the P2 region is probably derived from a serotype A strain while the P3 region appears to be a mosaic derived from both serotypes A and O.

Conclusions: Sequences of the VP1 coding region from recent serotype O FMDVs from Kenya and Uganda are all representatives of a specific East African lineage (topotype EA-2), a probable indication that hardly any FMD introductions of this serotype have occurred from outside the region in the recent past. Furthermore, evidence for interserotypic recombination, within the non-structural protein coding regions, between FMDVs of serotypes A and O has been obtained. In addition to characterization using the VP1 coding region, analyses involving the non-structural protein coding regions should be performed in order to identify evolutionary processes shaping FMD viral populations.

Figure 1

Genomic structure of FMDV. Genome organization of FMD viruses modified from [1]. The 5'untranslated region (ca. 1300 nt.), polyprotein region (ca. 7000 nt.) and the 3'untranslated region (ca 90 nt.) are shown. P1-2A, P2 and P3 indicate the precursors or intermediates for the capsid region proteins, 2BC proteins and the 3ABCD proteins, respectively.

Figure 2

Phylogenetic relationships of the VP1 coding region of type O East African viruses in comparison to other FMD virus serotypes. Evolutionary relationships of the VP1 coding region of FMD type O viruses from East Africa are shown in comparison to other FMD virus serotypes. The tree was estimated using Bayesian inference analysis (MrBAYES) and percentage node values represent posterior probabilties (values that concentrate on a single tree when data is informative given a specified model of evolution for a particular sequence data set).

Figure 3

Phylogenetic relationships derived for the polyprotein coding region. Evolutionary relationships of the type O East African strains based on the polyprotein coding region (6719 nt) in comparison with selected sequences of type O from Asia, Europe and South America. Sequences of serotypes A, C, SAT 1, 2 and 3 are also included. Trees were estimated as for Figure 2.

Figure 4

Phylogenetic relationships derived for P2 coding regions. Evolutionary relationships of the type O East African strains based on the P2 coding region with selected sequences of type O from Asia, Europe and South America. Trees were estimated as in Figure 2.

Figure 5

Phylogenetic relationships derived for P3 coding regions. Evolutionary relationships of the type O East African strains based on the P3 coding region with selected sequences of type O from Asia, Europe and South America. Trees were estimated as in Figure 2.

Figure 6

Detection of recombination between serotypes O and A using Simplot analyses. Recombination analyses using SimPlot 2.5 software (Ray, 1999). K/52/1992 was queried against AY593766/A/KEN/1965 (blue), AY593761/A/KEN/1964 (red) and K/117/1999 (green). Similarity plot with the Y-axis showing proportion of nucleotide identity and the X-axis showing the nucleotide positions along the alignment.

Figure 7

Detection of recombination between serotypes O and A using bootscan analyses. Analyses were performed as in Figure 6. Bootscan plot with the Y-axis showing percentage permutated trees while the X-axis shows nucleotide positions along the alignment