Molecular characterization of foot-and-mouth disease virus causing an FMD outbreak in cattle in Ulanga District, Tanzania

Abstract

Foot-and-mouth disease (FMD) is a highly contagious transboundary viral disease that affects cloven-hoofed animals and causes substantial economic losses through reduced livestock productivity and trade restrictions. In Tanzania, the disease remains endemic, yet molecular epidemiological information from many regions is limited. This study aimed to molecularly characterize Foot-and-Mouth Disease Virus (FMDV) associated with an outbreak in cattle in the Ulanga District, Morogoro Region, Tanzania. During the outbreak investigation conducted in 2019, epithelial tissue samples were collected from 11 clinically affected cattle on a single farm and analyzed using one-step reverse transcription polymerase chain reaction (RT-PCR) targeting the VP1 gene. Positive amplicons were sequenced, and phylogenetic analysis was performed using partial VP1 nucleotide sequences to determine the genetic relationships between the detected viruses and representative East African FMDV isolates. Four of the 11 samples (36.4%) tested positive for FMDV. Sequence analysis identified all positive samples as belonging to the Southern African Territories 1 (SAT1) serotype. The Ulanga SAT1 isolates shared 99% nucleotide sequence similarity among themselves and >90% similarity with previously reported SAT1 isolates from Uganda, indicating close genetic relatedness with East African strains. Phylogenetic analysis further demonstrated clustering of the Ulanga isolates with other regional SAT1 viruses. Although this study was limited to a single outbreak involving a small number of samples, it confirms the occurrence of the SAT1 serotype in Ulanga District and contributes baseline molecular epidemiological information for southeastern Tanzania. The findings support the importance of continued molecular surveillance across different geographical areas to improve understanding of FMDV diversity and to inform evidence-based disease surveillance, vaccine selection, and control strategies in Tanzania.