Molecular epidemiology of foot-and-mouth disease viruses collected from Khartoum, Blue Nile, and Northern States of Sudan (2019–2022)

Foot-and-mouth disease (FMD) is a highly contagious transboundary viral disease causing significant economic losses in livestock. This study investigated the serotype distribution and molecular epidemiology of FMD viruses (FMDV) circulating in Sudan between 2019 and 2022. A total of 51 epithelial tissue samples were collected from outbreaks in Khartoum, Blue Nile and Northern States. Samples were analyzed via virus isolation in bovine thyroid cell culture (BTY), antigen detection ELISA, and real-time reverse transcription PCR (rRT-PCR). Antigen detection ELISA successfully typed 13 of 51 (25.5%) epithelial tissue samples, of which 10 were identified as serotype A and 3 as serotype O. In contrast, rRT-PCR detected FMDV RNA in 33 of the 35 samples (94.3%) that were suitable for molecular analysis, showing the superior diagnostic sensitivity of this molecular method. FMDV positive samples were further characterized by sequencing the VP1-coding region. These data demonstrated the presence of two serotypes (A and O), while SAT serotypes were not detected during the study period. Serotype A was detected in outbreaks during 2019, 2021 and 2022, while serotype O predominated in 2020. Phylogenetic analysis of VP1-coding sequences showed that serotype A sequences clustered within the A/AFRICA topotype, lineage G-IV and were closely related to strains from Egypt and Ethiopia. Serotype O sequences were clustered within the EAST AFRICA-3 (EA-3) topotype and showed ≥ 96% identity with the Egyptian isolates. VP1 analysis revealed conserved functional motifs alongside variability within the immunodominant antigenic region, suggestive of ongoing viral evolution with potential implications for vaccine effectiveness. These results suggested the persistent circulation of FMDV serotypes A and O in Sudan with close genetic relationships to viruses recovered from neighboring countries. These findings suggested the transboundary transmission of FMDVs and a role for cross-border livestock movements in virus dissemination. Continuous molecular surveillance and regional cooperation are essential to improve vaccine matching and strengthen FMD control strategies in endemic regions.