Risk Factors and Molecular Epidemiology of Foot and Mouth Disease Virus and Other Animal Pathogens Infecting African Buffaloes, Cattle and Goats in Eastern Rwanda.

Abstract

Foot-and-Mouth Disease Virus (FMDV) is a positive-sense RNA virus of the family of the picornaviridæ causing the Foot-and-Mouth Disease (FMD). Although FMD is endemic in Rwanda, there are information gaps with regards to risk factors, seroprevalence and molecular epidemiology of FMDV strains circulating in Eastern Rwanda. The objectives of this study were to identify FMD risk factors, seroprevalence and establish molecular profiles of FMDV in cattle, goats and African buffaloes in Eastern Rwanda. The study was performed in two main parts, first the development of questionnaires to establish risk factors for FMD outbreaks. Descriptive statistics were determined and odds ratios were calculated to determine the effects of risk factors on the occurrence of FMD. Quantum Geographic Information System (QGIS) was used to produce thematic maps on the proportion of putative risk factors for FMD per village. Secondly, surveillance of FMD-susceptible African buffaloes, was also carried out in Akagera National Park. A competitive ELISA kit manufactured by innovative diagnostics (ID.Vet, Grabels, France) was used to detect antibodies against the non-structural protein 3ABC of FMD in sera of animals from 3 districts of the Eastern province in Rwanda. Field and vaccine strains of FMDV were detected using RT-PCR and RT-LAMP assays and thereafter sequenced using the Ion Torrent Next-Generation Sequencing platform (Thermo Fisher Scientific). Epitopes-mapping was done in silico using the VP1-3 proteins of FMDV isolated in East Africa based on a 3D model (PDB ID:5aca) using the PyMol software (Schrödinger, 2021). Questionnaire data revealed that 85.31% (p < 0.01) of the farms experienced more outbreaks during the dry season than the wet season. Univariate analysis revealed that mixed farming (OR = 1.501, p = 0.163), and natural breeding method (OR = 1.626; p = 0.21) were associated with the occurrence of FMD indicating that the two risk factors could be responsible for FMD outbreaks in the farms. The occurrence of FMD in the farms was found to be significantly

associated with a lack of vaccination of calves younger than 12 months in herds (OR = 0.707; p = 0.046). The overall seroprevalence of FMD in the study area was 9.36% for cattle and 2.65% for goats. The phylogenetic analysis revealed the introduction of SAT2, lineage II traditionally known to be in Southern Africa (Zimbabwe). On sequence analysis, FMDV was not detected in buffalo samples. Nevertheless, other pathogens such as orf virus and bacteria were detected suggesting that cattle in the study area may be infected with other pathogens apart from FMDV due to interactions between wildlife and domestic ruminants. In silico analysis revealed that VP1, VP2 and VP3 surface proteins of the East African - FMDV isolates could induce humeral and cell-mediated immunity if administered in cattle. The Wu-Kabat variability index identified variable regions, including the known GH loop, and conserved regions in the VP1, VP2 and VP3 peptides. Epitope mapping revealed 3D-structures having various epitopes located on VP1, VP2 and VP3 model. In conclusion, it appears that some animals were exposed to FMDV with some animals being infected with the disease. Furthermore, the vaccination of all age group would improve the control of FMD. Finally, there appears to be an introduction of SAT 2 strain from Southern Africa into the East African region. Further studies are recommended on molecular epidemiology of FMD virus on buffaloes and livestock in Eastern Rwanda. Although, the generated models appeared to be antigenic, more detailed studies are needed to confirm these predictions. The in silico analysis proposes epitopes and in vitro analysis of vaccines showed the presence of SAT2 serotype in the used vaccine. It appears that African buffaloes in Akagera National Park did not have FMDV. Nevertheless, further studies are required to validate these findings.