Longitudinal study of foot-and-mouth disease virus in Northern Nigeria: implications for the roles of small ruminants and environmental contamination in endemic settings.

Foot-and-mouth disease (FMD) is a highly contagious disease affecting cloven-hoofed ungulates. This study aimed to enhance our understanding of the role of small ruminants and environmental contamination in the epidemiology and endemicity of FMD. A longitudinal study was conducted between March 2021 and October 2021 in northern Nigeria, where monthly samples were collected from five households, one livestock market and one transhumance location in two local government areas (LGA) identified as being at high risk of FMD. Serum samples (n = 783), oral swabs (n = 424) and environmental swabs (n = 458) were collected and tested for the presence of foot-and-mouth disease virus (FMDV) RNA by rRT-PCR. Serum samples (n = 780) were also tested for the presence of antibodies against FMDV non-structural proteins. The proportion of FMDV RNA positive samples increased in all sample types collected in one LGA during the period when an FMD outbreak was reported in the same LGA. In contrast, sero-positive samples did not differ by month but differed between LGAs and amongst species. The force of infection estimated from age-seroprevalence data for each household was significantly lower in goats compared with both cattle or sheep. Five O/EA-3 topotype sequences were obtained from selected FMDV RNA positive samples; findings which support the use of environmental swabs to detect circulating FMDV strains in endemic settings. These results show oral and environmental swabs are suitable sampling methods for early detection at animal and herd level, respectively and provide insights on the role of small ruminants on FMD epidemiology.