Serological and Molecular Investigation of Foot and Mouth Disease Virus and other animal pathogens at the Interface of Akagera National Park and Surrounding Cattle Farms between 2017 and 2020

Background Foot-and-Mouth Disease Virus (FMDV) is a positive-sense RNA virus of the family of the picornaviridæ and responsible for the disease with the highest economic impact, the Foot-and-Mouth Disease (FMD). FMD is endemic in Rwanda but there are gaps in knowing the seroprevalence and molecular epidemiology. This study reports the FMD seroprevalence and molecular characterization of FMDV in Eastern Rwanda. Surveillance in FMDV wild reservoirs, the African buffaloes, was also carried out revealing the presence of other pathogens and commensals. Results The overall seroprevalence of FMD in the study area is at 9.36% in cattle and 2.65% in goats. We detected FMDV using molecular diagnostic tools such as RT-PCR and RT-LAMP and the phylogenetic analysis of the obtained sequences revealed the presence of serotype SAT 2, lineage II. Sequencing of oropharyngeal fluids collected from African buffaloes revealed the presence of several pathogens and commensals but no FMDV was detected in buffaloes. The plethora of pathogens identified from the buffalo gut gives an idea of the health challenges faced by cattle keepers in Eastern Rwanda due to possible cross infectivity on wildlife-domestic animals interface regions. Conclusions We recommend further studies to focus on sampling more African buffaloes since the number sampled was statistically insignificant to conclusively exclude the presence or absence of FMDV in Eastern Rwanda buffaloes. The use of RT-PCR alongside RT-LAMP demonstrates that the latter can be adopted in endemic areas such as Rwanda to fill in the gaps in terms of molecular diagnostics. The identification of lineage II of SAT 2 in Rwanda for the first time shows that the pools as previously established are not static over time.