Phylogeographic and cross-species transmission dynamics of SAT1 and SAT2 foot-and-mouth disease virus in Eastern Africa

Authors: OMONDI, GEORGE - University Of Minnesota; ALKHAMIS, MOHAMMED - University Of Minnesota; OBANDA, VINCENT - Kenya Wildlife Service; GAKUYA, FRANCIS - Kenya Wildlife Service; SANGULA, ABRAHAM - Kenya Agricultural Research Institute; Pauszek, Steven; PEREZ, ANDRES - University Of Minnesota; NGULU, S - Kenya Wildlife Service; VAN AARDT, R - Kenya Wildlife Service; Arzt, Jonathan; VANDERWAAL, KIMBERLY - University Of Minnesota

Submitted to: Molecular Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/30/2019
Publication Date: 5/9/2019
Citation: Omondi, G., Alkhamis, M., Obanda, V., Gakuya, F., Sangula, A., Pauszek, S.J., Perez, A., Ngulu, S., Van Aardt, R., Arzt, J., Vanderwaal, K. 2019. Phylogeographic and cross-species transmission dynamics of SAT1 and SAT2 foot-and-mouth disease virus in Eastern Africa. Molecular Ecology. https://doi.org/10.1111/mec.15125.
DOI: https://doi.org/10.1111/mec.15125

Interpretive Summary: Foot-and-mouth disease (FMD) is the most important infectious disease limiting global trade in animal products. FMD has not occurred in the USA since 1929, but it remains a serious threat to USA agriculture. To better understand how FMD virus (FMDV) evolves under natural conditions, we undertook a study of the biology of how the virus changes and moves over time in naturally infected cattle and buffalo in Eastern Africa with emphasis of Kenya. To achieve this goal, new information about current field viruses was compared with historical data compiled from previous studies. One of the important conclusions was that some FMDV strains (referred to as SAT1) had originated in Zimbabwe; whereas, other FMDV strains (referred to as SAT2) originated in Kenya and moved between Tanzania, Kenya, and Uganda. Also, we found that viruses in livestock did not circulate within wild animals. This information would be highly relevant if an outbreak ever occurred in the USA because of similarities in viruses and the host populations.

Technical Abstract: Understanding the dynamics of diseases, such as the endemic and economically constraining foot-and-mouth disease virus (FMDV), is critical in designing control programs in Africa. This study investigates the evolutionary epidemiology of SAT1 and SAT2 FMDV in Eastern Africa, as well as between cattle and wild African buffalo. Implementing phylodynamic models in a Bayesian statistical framework, we analyzed 437 SAT1 and 746 SAT2 VP1 gene segments collected between 1975 and 2016 from 15 and 34 countries, respectively. The root state posterior probabilities inferred from our analyses suggest Zimbabwe as the ancestral location for SAT1 currently circulating in Eastern Africa (P=0.67). For the SAT2 clade, Kenya is inferred to be the ancestral location for introduction of the virus into other countries in Eastern Africa (P=0.72). Salient (Bayes Factor >10) viral dispersal routes were inferred from Tanzania to Kenya, and from Kenya to Uganda for SAT1 and SAT2, respectively. Results suggest that cattle are the source of the SAT1 and SAT2 clades currently circulating in Eastern Africa. In addition, our results suggest that the majority of SAT1 and SAT2 in livestock come from other livestock rather than wildlife; with limited evidence that buffalo serve as reservoirs for the cattle. Insights from the present study highlight the role of cattle movements and anthropogenic activities in shaping the evolutionary history of SAT1 and SAT2 in Eastern Africa, and specifically, for the first time we elucidate the dynamics between host species in this region, which is key to guiding surveillance, disease prevention and control.