Detection and localization of single-base sequence differences in foot-and-mouth disease virus genomes by the RNase mismatch cleavage method.

The RNase mismatch cleavage method was examined for its efficiency of indicating single-base sequence differences in the capsid protein-coding regions of different foot-and-mouth disease virus subtype O1 strains. The method was found suitable for indicating such differences. RNase A as well as RNase T1 contributed to substrate conversion. Examples for the cleavage of eleven different single-base mismatches in RNA double-strands are now known. All virus genomes found to differ from each other exhibited three or more non-neighboured single-base sequence differences. Other genomes found to be indistinguishable by this method were those of a recent field isolate adapted to cell culture, and those of a vaccine production strain; its progeny was transmitted to pig and cow and then analyzed. The results suggest that host change does not necessarily select for antigenic variant virus, and that virus submitted to some kind of selection pressure is changed at more than one position.