A comparative study of the RNA-2 nucleotide sequences of two sweet clover necrotic mosaic virus strains

The nucleotide sequences of the RNA-2s of two strains of sweet clover necrotic mosaic virus (SCNMV-38 and -59) have been determined. The RNA-2s of SCNMV-38 and -59 consist of 1446 and 1449 nucleotides, respectively, and both contain one major open reading frame (ORF) which potentially can encode polypeptides of 326 amino acid residues (about 36.5K), designated SC38P2 and SC59P2, respectively. The nucleotide sequences of SCNMV-38 and -59 RNA-2s show 93.2% similarity, and the amino acid sequences of SC38P2 and SC59P2 are 91.7% identical, although the identical nucleotides and amino acids are not distributed uniformly in RNA-2 and the encoded proteins. Two highly conserved regions (from positions 23 to 221 and 297 to 326) and a relatively divergent region (from positions 222 to 296) are found in the P2 proteins of these strains. A similar pattern is apparent on comparison of the nucleotide and deduced amino acid sequences of RNA-2 of these SCNMV strains with those of the Australian and Czechoslovakian isolates of red clover necrotic mosaic virus.