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Sequence Variability, Recombination Analysis, and Specific Detection of the W Strain of Plum pox virus

Phytopathology

Authors

Miroslav Glasa1, Tadeusz Malinowski2, Lukáš Predajňa1, Neda Pupola3, Dzintra Dekena4, Lech Michalczuk2 and Thierry Candresse5

1 Institute of Virology, Department of Plant Virology, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovakia
2 Research Institute of Pomology and Floriculture, Pomologiczna 18, 96-100 Skierniewice, Poland
3 Latvia State Institute of Fruit-Growing, Graudu str. 1, Dobele, LV-3701, Latvia
4 Pure Horticultural Research Centre, Abavas iela 2, Pūre, Tukuma novads, LV -3124, Latvia
5 UMR GDPP, INRA, Université Bordeaux 2, Centre INRA de Bordeaux, BP 81, 33883 Villenave d’Ornon Cedex, France

Abstract

Plum pox virus (PPV), a member of the genus Potyvirus, is the causal agent of Sharka, the most detrimental disease of stone-fruit trees worldwide. PPV isolates are grouped into seven distinct strains. The minor PPV-W strain was established recently for the divergent W3174 isolate found in Canada. Here, the partial or complete genomic sequences of four PPV-W isolates from Latvia have been determined. The completely sequenced isolates LV-141pl and LV-145bt share 93.1 and 92.1% nucleotide identity, respectively, with isolate W3174, with two regions of higher (>20%) divergence in the P1/HC-Pro and NIa (VPg) regions. Further analyses demonstrated that these two regions correspond to two independent recombination events in the W3174 genome, one involving PPV-M (approximate genome positions 692 to 1424) and the other PPV-D (nucleotides 5672 to 5789). The LV-141pl and LV-145bt isolates appear to be representatives of the “ancestral” PPV-W strain, not affected by recombination. The PPV-W intrastrain variability is substantially higher than that of all other PPV strains, with potential implications for the serological detection of PPV-W isolates. A PPV-W-specific primer pair has been developed, allowing the specific reverse-transcription polymerase chain reaction detection of all five presently available W isolates. The characterization of these new PPV-W isolates sheds light on PPV-W evolutionary history, further supports the hypothesis of its East-European origin, and opens the way for the biological and epidemiological characterization of this poorly known PPV strain.

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