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Does transmission mode shape PVY quasispecies? Insights from Illumina deep sequencing

Washington Da Silva: Cornell University

<div>Surveys indicate that recombinant strains of <em>Potato virus Y</em> (PVY) have emerged in recent years to predominate in the U.S. potato crop, and that the genetic diversity abounds among and within PVY strains. To investigate how transmission modes (insect and mechanical) are contributing to the evolution and diversification of PVY, we designed an experiment to characterize the virus quasispecies through multiple aphid or mechanical passages of three PVY strains (O, N, and NWi). On average, more single nucleotide variations (SNVs) were detected in PVY<sup>N</sup> populations (250) than in PVY<sup>O</sup> (107) or PVY<sup>NWi</sup> (150). Unique SNVs were detected for each transmission mode for each virus strain and more SNVs were detected in aphid transmitted than mechanical inoculated populations. Many of the SNVs were located in cistrons that encode proteins involved in aphid transmission (HC-Pro and CP) or cell-to-cell movement (P3, CI, and CP). Our data suggest that each transmission mode exerts unique selection pressures on the virus population and allows different mutations to accumulate and become fixed. To date, aphid transmission induces more unique changes in the PVY quasispecies than mechanical inoculation. The next step is to link genotypic changes to phenotypes.</div>