Three strains of European foot-and-mouth disease virus are highly conserved in the 3'-termini and highly variable in the genes of two capsid proteins.

Restriction enzyme-generated subgenomic fragments of cloned cDNA prepared from RNA of the strain O1 Kaufbeuren (O1K) of foot-and-mouth disease virus (FMDV) were compared qualitatively and quantitatively for sequence complementarity with radioactive RNA from strains C Oberbayern (CObb) and A2 Spain (A2S) in hybridization experiments on nitrocellulose membranes. Quantitative comparison of nucleic acid sequences neighbouring (C Obb/O1K) or including (A2S/O1K) the 3' end of the virus genomes demonstrated more than 80% homology. In contrast, sequences coding for the capsid proteins VP1 (10%, CObb/O1K; 16 to 21%, A2S/O1K) and VP3 (12%, A2S/O1K) were remarkably heterologous. Sequences downstream from the gene for VP1, i.e. those coding for non-structural proteins, showed 23 to 51%f homology to both RNAs except for the area coding for protein P56a. Here, the observed homology was 82% to CObb and 39 to 46% to A2S.