COMPARATIVE SEQUENCE-ANALYSIS OF 4 COMPLETE PRIMARY STRUCTURES OF PLUM POX VIRUS-STRAINS

The complete nucleotide sequence of plum pox virus (PPV) strain SK 68 was determined from a series of overlapping cDNA clones. The exact 5' terminus was determined by direct RNA sequencing. The RNA sequence was 9786 nucleotides in length, excluding a 3' terminal poly(A) sequence. The large open reading frame starts at nucleotide position 147 and is terminated at position 9568. Comparison of cistrons from other plum p ox virus strains with those predicted for the SK 68 strain indicated t he same genomic organizations. Comparison of sequences leads to the fo llowing conclusions: (1) The genetic organization of all four PPV stra ins is identical, containing one large polyprotein gene and two noncod ing regions at the 5' and 3' ends; (2) pairwise comparison of the geno mic sequence of PPV SK 68 with other PPV strains shows 11% alteration. Sequence differences among strains are spread in a uniform manner upo n the genome, except for the P1, HC-pro, and two noncoding regions, wh ich are more conserved (with a 4% and 6.6% change). The stability of t he noncoding regions is probably linked to their role in replication. The sequence variation has little effect on the amino acid sequence of the corresponding polypeptides, as changes occur preferentially in th e third position of the. reading frame triplets, except in the case of the 5' end of the coat protein gene (2.7% average difference in amino acid level, while in the case of coat protein it is 7.7%). The sequen ce analysis of the coat protein region of the four complete and one pa rtial sequence indicates that the Hungarian plum pox virus strain dive rges at the larger extent, similar to the Fl Amar strain, from which o nly less than half of the sequence is available.