Abstract
Ethiopia faces significant economic losses from foot-and-mouth disease (FMD). Laboratory diagnostic tools such as antigen detection ELISA (Ag-ELISA), reverse transcription polymerase chain reaction (RT-PCR), and sequencing provide important information that underpin control initiatives. In this study, 411 samples (275 epithelial tissues, 12 oropharyngeal probang cup scrapings and fluids, 122 swab samples, and two whole blood) collected from cattle with clinical signs of FMD were tested to determine serotype diversity of the FMD viruses (FMDVs) present in Ethiopia during a 5-year period (2019-2023). RT-PCR testing showed that most samples, 81.1% (172/212) were positive for FMDV genome while 48.2% (198/411) of the samples were positive for FMDV antigen using ELISA, identifying serotypes O (10.9%), A (7.3%), Southern African Territories (SAT) 1 (1.7%), and SAT 2 (19.5%). Furthermore, evidence for mixed serotype infection was observed for 36 samples using the Ag-ELISA. Viral protein (VP) 1 sequencing for FMDV was performed on 94 samples, confirming the presence of three FMDV serotypes (O, A, and SAT 2). There was no molecular sequence evidence for outbreaks due to SAT 1 during this period, suggesting that the Ag-ELISA results for this serotype may have been false positives. Together with the Ag-ELISA data, the sequences highlighted a dramatic increase in the dominance of serotype SAT 2 viruses during the period of the study, associated with outbreaks due to the emerging SAT2/XIV topotype after a period of absence of more than 30 years. These data highlight Ethiopia's dynamic FMD landscape, informing national and regional control. These findings are crucial for understanding FMDV in Ethiopia and vaccine selection, although more geographically broad and sequencing-intensive studies may be needed to define a more comprehensive understanding of the national disease epidemiology.