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

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.

Occurrence of Stone Fruit Viruses in Plum Orchards in Latvia

“…Moreover, in our study one of the most common PPV strains in Western Europe, the strain PPV-D, was detected in all of the PPV positive samples. The most recently discovered strain PPV-W (Winona), and also PPV-D, have been reported in Latvia (Glasa et al, 2011;Malinowski et al, 2012). Our data confirm that actions should be taken and eradication continued to prevent further spread of this detrimental viral disease, which currently is not widely spread in the country.…”

Strain identification and sequence variability of plum pox virus in Turkey

“…Full genomes of PPV-D isolates obtained from many countries including the United States, Canada, and Japan, in addition to European countries, are also available in GenBank. Genomic information has also been produced for PPV-Rec, PPV-W, and PPV-CR (Matic et al, 2006;Thompson et al, 2009;Glasa et al, 2011;Sheveleva et al, 2012;Chirkov et al, 2013;Glasa et al, 2013;Mavrodieva et al, 2013). However, there was a limited genomic record of PPV-T, which was only detected in Turkey and Albania (Ulubaş Serçe et al, 2009;Palmisano et al, 2015), in GenBank.…”

Unfolding the secrets of plum pox virus: from epidemiology to genomics

“…The region spanning the 5΄-terminal end of the CP gene was proven to be useful for recognizing not only divergent strains like EA, W and C but also more similar strains M, D and Rec. Specific primers have been designed discriminating these major strains in a multiplex PCR format (Šubr et al, 2004b) or enabling specific detection of the single strains (PPV-W and PPV-CR; Glasa et al, 2011Glasa et al, , 2012. Another option for strain detection is PCR followed by RFLP analysis (Wetzel et al, 1991a;Glasa et al, 2002).…”