The optimisation and application of a novel BaseScope™ RNA-ISH assay for the detection of foot-and-mouth disease virus in carrier African buffalo (Syncerus caffer) from South Africa

The detection of foot-and-mouth disease is limited to BSL-3 laboratories and its detection in carrier animals require increased test sensitivity. In-situ-hybridisation utilises the propensity of a labelled single-stranded sequence of DNA or RNA to anneal to a complementary target. It can be performed on formalin-fixed tissues and with some of the most recent advances, show an increased test sensitivity. BaseScope™ incorporates an additional signal amplification step, which makes it possible to detect RNA splicing variants, point mutations, small insertions or deletions, and short RNA targets (50-300 nucleotides). This study aimed to adjust and optimise the BaseScope™ assay to detect foot-and-mouth disease virus in a novel, carrier wildlife species, i.e., buffalo. Specific steps were adjusted to attempt to address some of the rigidity involved in the workflow. However, none of the in-house reagents or equipment attempted as an alternative to the original and prescribed workflow was successful. This demonstrates the fastidious nature of this diagnostic modality and the synergistic characteristics of a commercial assay. However, keeping tissues in formalin for up to 7 days and storing cut sections for up to 3 months did not have a negative impact on the results. This further demonstrated the reliability of BaseScope™.