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™.