4.4 Article

Evolving by deleting: patterns of molecular evolution of Apple stem pitting virus isolates from Poland

Journal

JOURNAL OF GENERAL VIROLOGY
Volume 100, Issue 10, Pages 1442-1456

Publisher

MICROBIOLOGY SOC
DOI: 10.1099/jgv.0.001290

Keywords

ASPV; CP gene; deletions; phylogenetic analysis; population genetics; recombination

Funding

  1. National Science Centre of Poland [2011/03/B/NZ9/01680]
  2. Ministerio de Ciencia, Innovacion y Universidades - FEDER [BFU2015-65037-P]

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In this study, 267 coat protein gene (CP) sequences from 48 Polish isolates of Apple stem pitting virus (ASPV) were determined. The genetic structure of the virus population was analysed and possible mechanisms of molecular evolution explored. We found evidence of recombination within the ASPV population and the presence of 17 ASPV molecular variants that differ in the length, number and arrangement of deletions in the CP. Population genetic analyses showed significant variation among isolates from pear and apple trees, between isolates from the same host species and, more interestingly, within isolates, supporting the existence of significant levels of variability within individual hosts, as expected by a quasispecies population structure. In addition, different tests support that selection might have been an important force driving diversification within isolates: positive selection was found acting upon certain amino acids. Phylogenetic analyses also showed that isolates did not classify according to the host species (pear or apple trees) but according to the pattern of deletions, suggesting a possible role for deletions during clade diversification.

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