Evolutionary genetics of Foot-and-Mouth disease virus in Kenya

Abstract

Foot-and-mouth disease (FMD) is endemic in Kenya and the East African region in general. The epidemiology of the disease in the region is complex with six of the seven foot-and-mouth disease virus (FMDV) serotypes reported to cause outbreaks and a further complication from the presence of large populations of African buffalo that are known to play an important role in the epidemiology of the southern Africa Territories (SAT) serotypes. A sustained campaign since the 1950s in Kenya to control FMD mainly by vaccination, combined with quarantine and zoosanitary measures has been undertaken but with limited success partly due to inadequate knowledge on circulating viruses which diminishes chances of efficient vaccine choices and diagnosis. In order to get insights about processes shaping evolution of the five FMDV serotypes (O, A, C, SAT 1 and SAT 2) recorded to cause outbreaks in Kenya; complete VP1 coding sequences obtained from isolates preserved at the Embakasi FMD laboratory spanning a period of 50 years were analyzed. A total of 129 (O = 46, A = 32, C = 8, SAT 1 = 11 and SAT 2 = 32) sequences were generated in the study while 130 (O = 27, A = 19, C = 9, SAT 1 = 42 and SAT 2 = 33) others were sourced from published reports. Several relatively up-to-date sequence analysis algorithms such as genealogy-based coalescent methods were used to analyse the data. Patterns of evolution among serotype O foot-and-mouth disease viruses in East Africa, revealed the emergence and expansion of the topotype previously designated EA-2 within Kenya and Uganda with cross-border disease transmission within the region and incursions of topotypes EA-3 and EA-4 into Kenya and Uganda probably from neighboring Ethiopia and Sudan. The patterns of genetic variation and distribution of FMD serotype A virus in Kenya, identified two currently circulating virus lineages with a countrywide distribution. Very low nucleotide diversity and remarkably little change were observed amongst serotype C isolates collected over a period of nearly 40 years. This result was interpreted as being suggestive of re-introductions of the vaccine strain into the field. Analysis of serotype SAT 1 isolates showed that two virus groups; one group exclusive to Uganda while the other is present within Kenya and Tanzania are in circulation. Our results also revealed remarkably low evolutionary rates for the SAT 1 viruses. Serotype SAT 2 analysis results presented evidence for co-circulation of two extremely divergent lineages in Kenya. In general, our observations highlight the importance of characterization of fairly representative virus isolates both on a temporal and spatial scale to be able to discern disease dynamics in a region. It is evident that FMD viruses circulate and are shared within and beyond the East African region necessitating a regional approach to the control of transboundary animal diseases.