The nucleotide sequence of potato virus A genomic RNA and its sequence similarities with other potyviruses

The complete nucleotide sequence of potato virus A (PVA) was obtained from six independent cDNA clones. The RNA genome of PVA is 9565 nucleotides long and contains one open reading frame (ORF) of 9177 bases encoding a large polyprotein of 3059 amino acids with a calculated M(r) of 340K. Seven potential proteinase NIa, one HC-pro and one P1 proteinase recognition sites were found in PVA polyprotein by searching for cleavage site consensus sequences amongst the potyvirus group. The non-coding region preceding the ORF is 161 nucleotides long. The termination codon is followed by a 227-nucleotide sequence. Overall nucleotide sequence identity compared with several completely sequenced potyvirus genomes is between 53 and 58%, with overall amino acid sequence identity between 65 and 71%. When the putative amino acid sequences of individual proteins of PVA were compared with the corresponding proteins of other potyviruses, P1 and P3 appeared the least conserved (34 to 53%) whereas the other proteins were in most cases from 63 to 80% identical to each other.