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

Miroslav Glasa, Tadeusz Malinowski, Lukáš Predajňa, Neda Pupola, Dzintra Dekena, Lech Michalczuk, Thierry Candresse
2011 Phytopathology  
Dzintra Dekena, et al.. Sequence variability, recombination analysis, and specific detection of the W strain of Plum pox virus. ABSTRACT Glasa, M., Malinowski, T., Predajňa, L. Pupola, N., Dekena, D. Michalczuk, L., and Candresse, T. 2011. Sequence variability, recombination analysis, and specific detection of the W strain of Plum pox virus. Phytopathology 101:980-985. Plum pox virus (PPV), a member of the genus Potyvirus, is the causal agent of Sharka, the most detrimental disease of
more » ... t 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-Wspecific primer pair has been developed, allowing the specific reversetranscription 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. The nucleotide sequences reported here have been deposited in the GenBank database under accession numbers HQ670745 to HQ670748. * The e-Xtra logo stands for "electronic extra" and indicates that the online version contains one supplemental figure and one supplemental table.
doi:10.1094/phyto-12-10-0334 pmid:21425932 fatcat:5yifxg5r75fzviiu4exktm5acm