Phylogeographical and cross‐species transmission dynamics of SAT1 and SAT2 foot‐and‐mouth disease virus in Eastern Africa

Abstract

Understanding the dynamics of foot-and-mouth disease virus (FMDV), an endemic and economically constraining disease, is critical in designing control programmes 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. Bayesian phylodynamic models were used to analyse SAT1 and SAT2 VP1 gene segments collected between 1975 and 2016, focusing on the SAT1 and SAT2 viruses currently circulating in Eastern Africa. 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 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. While the results may be affected by inherent limitations of imperfect surveillance, our analysis elucidates the dynamics between host species in this region, which is key to guiding disease intervention activities. K E Y W O R D Sancestral reconstruction, FMD, interspecific transmission, molecular epidemiology, phylodynamics, wildlife-livestock interfaces

Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza Outbreaks

“…However, in the presence of a large number of sequences, these strategies are ill timed and require massive computational resources, making them inefficient for targeted and near-realtime surveillance systems. It is worth noting that substitution rate and divergence time inferred by Alkhamis et al (43) using the FMD SAT1 VP1 segment were similar to the evolutionary estimates inferred by Lasecka-Dykes et al (125) using wholegenome sequences, confirming the robustness of phylodynamic methods. Nevertheless, the presence of recombination events can severely impact the robustness of phylodynamic methods leading to inferring biased evolutionary histories (126).…”

“…Retrieving and combining relatives of novel viral isolates in a single dataset will warrant a proper inference of representative phylogenetic relationships of a tree topology based on all available related sequences. As on many occasions, novel sequences might belong to different distinct viral lineages published elsewhere (39,43). The basic local alignment search tool (BLAST; https://blast.ncbi.nlm.nih.gov/Blast.cgi) is the most popular tool for retrieving relatives of novel sequences (Figure 1).…”

The role of African buffalo in the epidemiology of foot‐and‐mouth disease in sympatric cattle and buffalo populations in Kenya

“…From this analysis, we cannot determine whether buffalo were the source of these outbreaks in cattle or whether the buffalo acquire SAT1 and SAT2 virus already circulating in livestock. However, additional analysis by Omondi et al have revealed that currently circulating clades of SAT1 and SAT2 in East Africa likely have a cattle origin, though buffalo may have an ancestral role deeper in the past (Omondi et al., 2019). In addition, further sampling of wildlife populations across Kenya is needed to gain a more representative view of the diversity of FMDV found in buffalo in relation to outbreaks in livestock.…”

“…Speculatively, this could reflect different patterns of host–pathogen co‐evolution in southern versus eastern Africa. Alternatively, given that SAT2 appears better able to cause outbreaks in cattle than SAT1 (Bastos et al., 2001, 2003), the dominance of SAT2 in this East African buffalo population could reflect a higher FMDV burden in cattle populations and subsequent spillover from cattle into buffalo (Omondi et al., 2019).…”

The Carrier Conundrum; A Review of Recent Advances and Persistent Gaps Regarding the Carrier State of Foot-and-Mouth Disease Virus

“…It is believed that FMDV infection in herds of African buffalo is maintained, in part, through transmission from subclinically infected dams to neonates; however, the specific mechanism of transmission and the herd-level persistence of infection have never been determined or tested. Investigations based on phylogenetic analysis of viruses obtained from cattle and buffalo in FMD endemic regions have shown that FMDV populations found in the different host species are generally distinct, although some overlap suggests that inter-species transmission events do occur [129]. However, as FMDV infection in African buffalo is usually subclinical (neoteric), confirmed transmission of FMDV from buffalo to cattle does not necessarily imply the involvement of FMDV carriers.…”