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

Sheila N Balinda1*, Hans R Siegismund2, Vincent B Muwanika1, Abraham K Sangula15, Charles Masembe1, Chrisostom Ayebazibwe4, Preben Normann3 and Graham J Belsham3

Author Affiliations

1 Makerere University, Institute of Environment and Natural Resources P.O. Box 7298, Kampala, Uganda

2 Department of Biology Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark

3 National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark

4 Ministry of Agriculture Animal Industry and Fisheries, P.O. Box 513, Entebbe, Uganda

5 Foot-and-Mouth Disease Laboratory, Embakasi, P. O. Box 18021, 00500, Nairobi, Kenya

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Virology Journal 2010, 7:199  doi:10.1186/1743-422X-7-199

Published: 23 August 2010



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.


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.


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.