A Study on the Epidemiological and Molecular Relationships of Circulating Foot and Mouth Disease Viruses in Kenya

Abstract

Foot-and-mouth disease (FMD) is endemic in Kenya causing serious economic losses in the livestock sector. The epidemiology of the disease in small ruminants (SR) in Kenya is not well documented and the field dynamics of FMD epidemiology is scarce. The options for vaccine strain selection for emerging FMD outbreaks in endemic countries are yet to be addressed in East Africa. The general objective of this study was firstly to assess and document the FMD sero-prevalence and risk factors associated with SR nationally and a case study in domestic ruminants in Ukambani region. Secondly it aimed to characterize the foot and mouth disease viruses (FMDV) in circulation in 2013-2018 by molecular techniques. To estimate sero-prevalence and associated risk factors, we carried out a national cross-sectional study. Selection of animals used a multistage cluster sampling approach. Sera totaling 7564 were screened for FMD antibodies of non-structural-proteins using ID Screen® NSP Competition ELISA kit. Identification of risk factors used generalized linear mixed model effects (GLMM) logistic regression analysis with county and villages as random effect variables. The country animal level sero-prevalence in SR was 22.5% (95% CI: 22.3%-24.3%) while herd level sero-prevalence was 77.6% (95% CI: 73.9% - 80.9%). FMD sero-positivity in SR was signifcantly associated with multipurpose production type (OR = 1.307; p = 0.042) and negatively associated were male sex (OR = 0.796; p = 0.007), young age (OR = 0.470; p = 0.010) and sedentary production zone (OR = 0.324; p<0.001). There were no statistically significant intra class correlations among the random effect variables but interactions between age and sex variables were statistically significant (p = 0.019). Herds with animals bought from markets or middlemen, with wildlife interaction, reared in low altitude (<1500m above sea level) all had statistically significant higher sero-positivity. Other risk factors identified included unenclosed animals, shared bull, shared watering, communal

grazing, no vaccination and mixed and migratory grazing systems. Ukambani region had a higher seroprevalence in cattle than small ruminants(40% compared to 19%) and also higher seroprevalence in cattle than the National rate, 40% compared to 37.6 % (unpublished study carried out in the same period). The FMD seroprevalence rate in SR was lower than the National rate at 19%. In the molecular characterization study, the nucleotide sequences encoding the capsid protein VP1 (1D) region of FMDV from virus samples were generated by Reverse transcription polymerase chain reaction and sequencing. Study samples were serotype O and A repository isolates banked at the FMD Laboratory, Embakasi collected during FMD outbreaks from cattle in 2013 to 2018. For serotype O, 60 isolates were characterized(n=60), 58 being field viruses and vaccine strain OK77/78 in duplicate and for serotype A were 21 field isolates and one vaccine strain AK5/80 (n= 22). The consensus sequences and additional files obtained from National Centre for Biotechnology Information (NCBI) were aligned using MEGA v11.0.8, employing the ClustalW algorithm. SeaView v5.0.4 was used to edit the alignment and MEGA v11.0.8 was used to construct phylogenetic trees. To increase the robustness of the sequence analysis 9 and 7 sequences were excluded from O and A sequences respectively due to low quality (error rate > 1%). Phylogenetic analysis showed that with few exceptions samples collected around the same time and those from the same county consistently clustered in the same lineage or closer to each other. Serotype O outbreaks were caused by East African topotype 2 viruses (EA-2) except one outbreak in Taita Taveta County whose isolate belonged to EA-1 topotype together with the current vaccine strain. Another vaccine strain not in use currently K82/98 belongs to EA-2 topotype with these recent isolates. For serotype A study isolates, all belong to Africa G-1 topotype though in 3 lineages. All study isolate sequences tended to cluster closely together in one lineage while few others clustered in another lineage with isolates collected 3-7 years earlier. The vaccine strain

belonged to a third lineage together with isolates collected over 20 years and more closely to isolates of 1990s. This study emphasizes the importance of regular surveillance and characterization of circulating strains for development of effective vaccines to support FMD control strategies. Some animal husbandry practices has significant impact on exposure to foot and mouth disease. It’s proposed that future vaccine candidate strains selection could consider EA-2 topotype strains for serotype O and recent lineage of G1 topotype for serotype A to control FMDV circulating in Kenya.