Identification of a ninth Foot-and-Mouth disease virus type O topotype and evidence for a recombination event in its evolution

Introduction: Eight geographically distinct genotypes (topotypes) were previously identified for footand-mouth disease virus (FMDV) type O using partial VP1 sequences. These findings were confirmed using a smaller dataset of complete VP1 sequences. During routine molecular epidemiological surveillance we have identified a ninth topotype present in East Africa. Materials and Methods: Complete VP1 or P1 sequences were determined following RT-PCR amplification of vRNA and phylogenetic trees constructed using the Neighbor-joining algorithm. Scanning analysis was performed using SimPlot. Results: The complete VP1 sequences for 30 FMDV-O isolates from East Africa were determined and compared to representatives of the existing eight topotypes. These comparisons demonstrated the presence of a ninth FMDV-O topotype in Tanzania (1996, 1998), Malawi (1998), Kenya (2002), Uganda (2002, 2004), Burundi (2003) and Rwanda (2004). Further comparisons of the complete P1 capsid-coding region of two representatives of the new topotype, named East Africa 2 (EA-2), with representatives of each of the other eight topotypes confirmed these relationships. Scanning analysis of the P1 region showed that all the topotypes were distinct from each, apart from EA-2 and ME-SA which were more closely related at the 3’ end of VP1. Discussion: The presence of a previously unrecognised FMDV-O topotype in East Africa had been missed during the original work on topotype classification since, when the partial 3’ end sequences of these viruses was compared to other type O viruses, they appeared to be part of the ME-SA topotype. We conclude that at some time in its history a member of the EA-2 topotype underwent genetic recombination with a ME-SA virus with a cross-over point somewhere near the end of the VP1 gene. Introduction: Phylogenetic analysis using partial or complete nucleotide sequence data of the VP1 gene is now an internationally accepted method of studying the epidemiology of foot-and-mouth disease (OIE, 2004). Foot-and-mouth disease type O viruses have previously been divided into eight topotypes (geographically distinct genotypes) (Samuel and Knowles, 2001). In general, nucleotide differences between members of each FMDV O topotype exceeded 15%. The topotypes were named by the geographic region in which they occurred: viz. Europe-South America (Euro-SA), Cathay, Middle EastSouth Asia (ME-SA), southeast Asia (SEA), East Africa (EA), West Africa (WA), Indonesia-1 (ISA-1) and Indonesia-2 (ISA-2). There have been very few studies on the European FMDV serotypes in Africa (Knowles et al., 1998; Samuel et al., 1999; Samuel and Knowles, 2001; Sangare et al., 2001; Sahle et al., 2004; Bronsvoort et al., 2004). However, these studies have shown that there are distinct genetic lineages of both FMDV-O and FMDV-A circulating in East and West Africa and that viruses occurring in North Africa may be introduced from a variety of sources (Europe, South America, Middle East and West Africa). Outbreaks of FMD types O and A in southern Africa are very infrequent and are usually introduced from outside the continent (Knowles et al., 1998; Knowles et al., 2001; Sangare et al., 2001). In this study we have examined 40 FMDV type O isolates from Africa and classified them by phylogenetic comparison with previously characterized viruses. Since submission of the title and abstract of this paper, nucleotide sequence data published by Sahle et al. (2004) has been released and some of our conclusions have therefore been modified. Materials and Methods: Viruses All the virus isolates were obtained from the FAO World Reference Laboratory for Foot-and-Mouth Dusease (WRLFMD) strain collection either as 10% epithelial suspensions or as cell culture passaged material (Table 1).