Molecular Characterization Of Foot-And-Mouth Disease Virus Recently Recovered In Zambezi Region, Namibia

ABSTRACT

Foot-and-mouth disease (FMD) is a severe highly contagious viral disease of clovenhoofed animals that has significant economic impacts. FMD causes significant economic loss in Namibia in which the molecular epidemiology of FMD virus (FMDV) responsible for the outbreaks has not been consistently studied. The general objective of this study was to determine molecular characteristics of FMD viruses of 2019 outbreak in Zambezi region, Namibia. A total of 11 epithelial tissue samples collected from cattle showing FMD clinical signs were used in this study. The RNA extraction and detection of FMDV genome was done by One-step Reverse Transcription Polymerase Chain Reaction (RT-PCR) of 5’ untranslated region (5’UTR) using universal primers. Typing and sequencing was performed using serotype-specific oligonucleotide primers. Phylogenetic analysis was performed using distance matrix neighbour joining method employing the Kimura-2- parameter option. The findings indicated that all 8 sequenced viruses revealed 100% nucleotide identity among themselves. Phylogenetic analysis of 36 sequences including 8 sequences of this study, 7 from publication and other sequences from GenBank revealed that the 2019 isolates clustered together with historic Namibian isolates and those from neighbouring countries. In-depth typing and phylogeny proved that SAT3 viruses of topotype II were responsible for 2019 outbreak. Further analysis revealed that the 2019 isolates closely related to isolates from Botswana, some isolates from Zimbabwe and Kenya but were distantly related to isolates from Zambia and South Africa and no genetic linkage with isolate from Uganda. These findings indicate that topotype II SAT 3 FMD viruses were involved in the 2019 FMD outbreak in Zambezi region, Namibia. Further indepth studies are required to elucidate transmission dynamics and factors associated with 3 the outbreaks so that appropriate FMD control measure (s) in Namibia can be recommended.