Comparison of the nuclear inclusion b protein and coat protein genes of five papaya ringspot virus strains distinct in geographic origin and pathogenicity

A complementary DNA library was constructed to the genomic RNA of an isolate of papaya ringspot virus (PRSV), PRSV YK (YK),that represents the most prevalent mosaic strain of Taiwan. A 2.96-kb clone. pYKB9, corresponding to the 3'-region of YK RNA was selected by immunoscreening with the antiserum to the coat protein (CP). The clone had 2,960 nucleotide residues and represented part of the nuclear inclusion a (NIa) gene, the complete nuclear inclusion b (NIb) gene. the entire CP gene. and the 3'-noncoding region of YK RNA. The nucleotide sequence was compared to those of the 3' regions of the published Hawaii severe strain, HA (HA), the Hawaii mild strain HA 5-1 (HA 5-1), the nonpapaya-infecting Florida strain. PRSV W(fl) (W(fl)), and the nonpapaya-infecting Australia strain PRSV W(aust) (W(aust)). The NIb region had 83.1% nucleotide identity and 95.7% amino acid identity compared to that of HA, with a total of 262 nucleotide differences resulting in only 22 amino acid changes. A similar trend also was found when the NIb region of YK was compared to the partially elucidated NIb regions of HA 5-1 and PRSV W(fl), with 84.7 and 85.2% nucleotide identities (l47 and 151 nucleotide differences), respectively: both resulting in 97.6% amino acid identity (only eight amino acid changes). Most of the nucleotide differences between the Asian and American strains occurred in wobble bases and, thus, conserved the amino acid residues, suggesting a common selection pressure to keep the same protein conformation. The CP region showed 89.6-90.3% nucleotide identities and 93.2-94.8% amino acid identities with the compared strains and the 3' noncoding region showed 91.4 and 96.4% identities. Analysis of the N terminus of YK CP supported the cleavage site as previously predicted, VYHE/SRGT; however, a possible alternative site at VFHQ/SKNE, 20 amino acids downstream, also was present. The different amino acid residues among the CP of PRSV strains were located mostly at the N-terminal regions of the CP. Alignment of the CP of five sequenced PRSV strains indicated that the variation followed the differences in geographic origins rather than host specificity.