Detection and genomic characterisation of foot-and-mouth disease virus serotypes circulating in Cameroon using environmental sampling

Foot-and-mouth disease virus (FMDV) is a highly contagious, economically important disease of livestock and wildlife species. Active monitoring and understanding the epidemiology of FMDV underpin the foundations of control programmes. In many endemic areas, however, veterinary resources are limited, resulting in a requirement for simple sampling techniques to increase and supplement surveillance efforts. In this study, environmental sampling was used for the first time at livestock markets and abattoirs across Cameroon to assess the opportunities for broad scale, non-invasive disease surveillance at such sites. Environmental samples (n = 1994) were collected from six locations across Cameroon between May and July 2019. Concurrent with environmental sampling, a questionnaire was used to gather descriptive information on the use and practices of market and abattoir sites. Samples were screened for the presence of FMDV RNA using a pan-serotype FMDV specific real-time RT-PCR assay. Positive samples were characterised at the genomic level using next generation sequencing in combination with a novel probe-based enrichment strategy. A total of 173/1994 (8.68%) environmental samples were found to be positive for FMDV RNA. Genome length sequences were obtained from environmental samples, with phylogenetically relevant capsid sequences obtained from 14 samples, with representatives of serotypes O (n = 6), A (n = 7) and SAT 2 (n = 3). The questionnaire results revealed that animals in Cameroon can be transported long distances to markets and abattoirs, with varying levels of control and biosecurity practices in place. The approaches used in this study have highlighted that environmental sampling is an effective and non-invasive approach to assessing FMDV presence. Furthermore, the study has demonstrated that livestock markets, abattoirs and trucks could be targeted for the introduction of biosecurity interventions as well as providing opportunities for carrying out disease surveillance. Information resulting from such surveillance could provide valuable knowledge of circulating viruses within a region of interest, aiding strategic approaches for surveillance and control of FMDV.