Isolation and molecular characterization of Foot and Mouth Disease virus serotype O circulated in Kenya during the period 2013-2018

The endemicity of Foot-and-mouth disease (FMD) in Kenya has been recognized for over a century, with the first recorded cases dating back to 1915. Production of effective vaccines against incursions of infection in endemic areas is achieved by evaluating the genetic and antigenic characteristics of the circulating viruses. The present study aimed to isolate, serotype, and molecularly characterize FMDV from Kenya from 2013-2018. Isolation was done from 58 field samples on BHK-21 cells, and serotyping of the isolated viruses was carried out using antigen ELISA. Isolated viruses were also analyzed using reverse transcription PCR, and the PCR products were subjected to sequencing. Based on the quality of obtained sequence spectra, only 51 isolates were aligned using MEGA v11.0.8, employing the ClustalW algorithm. SeaView version 5.0.4 was used to edit the alignment, and MEGA 11.0.8 was used to construct the phylogenetic tree and align it with the commercially used vaccinal strains (OK77/78 and OK82/98). With a few exceptions, isolates collected over the same period and those from the same regions consistently clustered in the same lineage or closer to each other. A total of 50/51 strains belong to the East African-2 (EA-2) topotype together with the vaccine strain OK82/98. However, only one strain (1/51) isolated from Tana River county belongs to the EA-1 topotype together with the current vaccine strain (OK77/78). None of these isolates was found to belong to the EA-and EA-4 topotypes. This study emphasizes the importance of regular surveillance and characterization of circulating virus strains for developing effective vaccines against FMD. It's proposed that future vaccine candidate strains selection could consider EA-2 topotype strains to control FMDV circulating in Kenya.