Comparison of the Nucleotide Sequence at the 5′ End of RNAs from Nine Aphthoviruses, Including Representatives of the Seven Serotypes

Abstract

The sequence of about 70 nucleotides at the 5'' end of the RNA of 9 different aphthoviruses (foot-and-mouth disease viruses), including representatives of the 7 serotypes of the virus, was determined by partial enzyme digestion of 32P-end-labeled S fragment, i.e., that part of the RNA lying to the 5'' side of the poly(C) tract and including the 5'' end of the molecule. The S fragments were prepared from polyadenylated virus-specific RNA extracted from infected cells by digestion with RNase H in the presence of oligo(dG)12-18. The first 27 nucleotides from the 5'' end were highly conserved in all the RNA. This region was followed by a more variable region of about 15 nucleotides, showing some length and sequence heterogeneity and including potential but probably non-utilized initiation codons. In agreement with previous homology studies, the sequencing results showed that the European serotypes A, O and C form a group distinct from the SAT serotypes and that the Asia 1 serotype is closely related to the European group. The lengths of the S fragments of 2 different RNA were confirmed as containing 360-400 nucleotides by gel electrophoresis with reference to nucleotide markers of known size.