Genome Sequence Analysis of New Isolates of the Winona Strain of Plum pox virus and the First Definitive Evidence of Intrastrain Recombination Events

Plum pox virus (PPV) is genetically diverse with nine different strains identified. Mutations, indel events, and interstrain recombination events are known to contribute to the genetic diversity of PPV. This is the first report of intrastrain recombination events that contribute to PPV's genetic diversity. Fourteen isolates of the PPV strain Winona (W) were analyzed including nine new strain W isolates sequenced completely in this study. Isolates of other strains of PPV with more than one isolate with the complete genome sequence available in GenBank were included also in this study for comparison and analysis. Five intrastrain recombination events were detected among the PPV W isolates, one among PPV C strain isolates, and one among PPV M strain isolates. Four (29%) of the PPV W isolates analyzed are recombinants; one of which (P2-1) is a mosaic, with three recombination events identified. A new interstrain recombinant event was identified between a strain M isolate and a strain Rec isolate, a known recombinant. In silico recombination studies and pairwise distance analyses of PPV strain D isolates indicate that a threshold of genetic diversity exists for the detectability of recombination events, in the range of approximately 0.78×10(-2) to 1.33×10(-2) mean pairwise distance. RDP4 analyses indicate that in the case of PPV Rec isolates there may be a recombinant breakpoint distinct from the obvious transition point of strain sequences. Evidence was obtained that indicates that the frequency of PPV recombination is underestimated, which may be true for other RNA viruses where low genetic diversity exists.

Molecular, ultrastructural, and biological characterization of Pennsylvania isolates of Plum pox virus

Plum pox virus (PPV) was identified in Pennsylvania in 1999. The outbreak was limited to a four-county region in southern Pennsylvania. Initial serological and molecular characterization indicated that the isolates in Pennsylvania belong to the D strain of PPV. The Pennsylvania isolates were characterized by sequence analysis, electron microscopy, host range, and vector transmission to determine how these isolates related to their previously studied European counterparts. Genetically, Pennsylvania (PPV-Penn) isolates were more closely related to each other than to any other PPV-D strains, and isolates from the United States, Canada, and Chile were more closely related to each other than to European isolates. The PPV-Penn isolates exist as two clades, suggesting the possibility of multiple introductions. Electron microscopy analysis of PPV-Penn isolates, including cytopathological studies, indicated that the virions were similar to other Potyvirus spp. PPV-Penn isolates had a herbaceous host range similar to that of European D isolates. There were distinct differences in the transmission efficiencies of the two PPV-Penn isolates using Myzus persicae and Aphis spiraecola as vectors; however, both PPV-Penn isolates were transmitted by M. persicae more efficiently than a European D isolate but less efficiently than a European M isolate.

Correlation between the composition of multivalent antibody conjugates with colloidal gold nanoparticles and their affinity

Interactions between multivalent preparations of antibodies (conjugated with colloidal gold nanoparticles (GNP) as a carrier system) and a multivalent ligand were investigated. The aim of the present study was to reveal the relationship between the affinity of the conjugate and its composition (i.e., the valency). Surface plasmon resonance was applied to study the affinity and the kinetics of the interaction of multivalent conjugates and multivalent virus (on the example of the plum pox virus (PPV)). Three monoclonal antibodies against PPV were prepared. Five GNP preparations with an average particle size in the range from 5 to 60nm (according to electron microscopy measurements) were obtained. The series of preparations allowed us to synthesize GNP-antibody conjugates with different surface areas for immobilization of antibodies, and, consequently, conjugates with different valencies. It was shown that the affinity of the conjugates changes with size of colloidal carriers (i.e. with the valency of the conjugates). The affinity of the virus-antibody interaction (antibodies with affinities of 1.46.10(-8)M and 1.73.10(-8)M) is one to three orders of magnitude lower (depending on the valency of the conjugate) compared to that of the interactions of the virus with GNP conjugates (conjugates with the affinity varying from 1.69.10(-9) to 7.02.10(-12)M and from 2.39.10(-9) to 2.62.10(-11)M, respectively). An increase in the conjugate size leads to an increase in its affinity. The similar trends were observed for the potato virus X.

The complete genome sequence of an El Amar isolate of plum pox virus (PPV) and its phylogenetic relationship to other PPV strains

The genomic sequence of an El Amar isolate of plum pox virus (PPV) from Egypt was determined by sequencing overlapping cDNA fragments. This is the first complete sequence of a member of the El Amar (EA) strain of PPV. The genome consists of 9791 nt, excluding a poly(A) tail at the 3' terminus. The complete nt sequence of PPV EA is 79-80%, 80%, 77%, and 77% homologous with isolates of strains D/M, Rec (BOR3), C, and W, respectively. The polyprotein identity ranged from 87-91%. Phylogenetic analysis using the complete genome sequence of PPV EA confirmed its strain status. No significant recombination signals were identified using PhylPro and SimPlot scans of the PPV EA sequence, however an interesting recombination signal was identified in the P1/HC-Pro region of PPV W3174.