Evidence of a Naturally Occurring Recombinant Isolate of Plum pox virus from Slovakia.

Abstract

Sharka, caused by the Plum pox virus (PPV), is the most detrimental viral disease of stone fruit trees worldwide. Two main groups of PPV isolates have been identified, PPV-M and PPV-D (1). Natural variability of Slovak PPV isolates in Prunus hosts has been recently evaluated (3). The PPV isolate BOR-3 was isolated in the summer of 1996 from a 5-year-old apricot tree, cv. VS 123/9, in an orchard in western Slovakia. The host apricot tree was propagated from seed; hence infection via aphid transmission from the immediate surroundings is highly probable. In order to retain its original properties, the isolate was transmitted by chip budding from a diseased tree to seedlings of Prunus persica, cv. GF 305. In contrast to other PPV isolates collected from the same location, infection of GF 305 with BOR-3 was either symptomless or produced only weak symptoms. On the other hand, sap-infected young seedlings of P. insititia × P. domestica St. Julien No. 2 presented leaf chlorotic spots and rings similar to those produced by other tested Slovak PPV isolates. Serological typing with group-specific MAbs (1) and restriction fragment length polymorphism of RT-PCR products amplified from the C terminus of the capsid protein (CP) gene demonstrated that BOR-3 is a member of PPV-M group (3). However, nucleotide (nt) sequence analysis of the P3-6K1 genomic region (GenBank accession AF357541) has shown a strong similarity with PPV-D group isolates (reaching 97%). To obtain more information, a 1846-nt long 3 genomic region encompassing the C-terminus of NIb, CP and 3 noncoding region (NCR) was subsequently sequenced (GenBank accession AY028309). The sequence comparison revealed that the BOR-3 isolate was the most identical to the PPV isolate ð6 (GenBank accession S57404) isolated more than 10 years ago in former Yugoslavia, which is about 550 km from the Slovak focus. The ð6 isolate is known to be the only PPV RNA recombinant at present (2). Nucleotide sequence identity in 3'NIb+CP+NCR region between BOR-3 and ð6 isolates reached >98%, contrary to 96% identity with PPV-M isolates (PS, SK68) and 88% identity with PPV-D isolates (Dideron, Rank). Further, the potential recombination site in the BOR-3 genome has been located in the C-terminus of NIb gene near nt position 8450 (numbered according to PPV-PS isolate, AJ243957). This site corresponds to the location of the recombination crossover identified in the PPV-ð6 isolate (2). Despite geographical and temporal distinctiveness of the two PPV isolates, an identical origin of ð6 and BOR-3 cannot be excluded. The hypothesis that these PPV isolates are the product of two independent recombination events at a recombination hot spot in the PPV genome situated near the C terminus of NIb gene also should be considered. Based on these data, the PPV BOR-3 isolate is a product of a natural homologous RNA recombination event between an M and D isolate. Evidence of homologous RNA recombination in this isolate significantly enriches current knowledge on the occurrence of recombination among potyviruses and emphasizes the role of RNA recombination in viral evolution and adaptation. This report indicates that occurrence of recombinants within PPV isolates infecting perennial crops might not be as rare as previously suggested (4).