title: Evidence for positive selection and recombination hotspots in Deformed wing virus (DWV).
abstract: Deformed wing virus (DWV) is considered one of the most damaging pests in honey bees since the spread of its vector, Varroa destructor. In this study, we sequenced the whole genomes of two virus isolates and studied the evolutionary forces that act on DWV genomes. The isolate from a Varroa-tolerant bee colony was characterized by three recombination breakpoints between DWV and the closely related Varroa destructor virus-1 (VDV-1), whereas the variant from the colony using conventional Varroa management was similar to the originally described DWV. From the complete sequence dataset, nine independent DWV-VDV-1 recombination breakpoints were detected, and recombination hotspots were found in the 5' untranslated region (5' UTR) and the conserved region encoding the helicase. Partial sequencing of the 5' UTR and helicase-encoding region in 41 virus isolates suggested that most of the French isolates were recombinants. By applying different methods based on the ratio between non-synonymous (dN) and synonymous (dS) substitution rates, we identified four positions that showed evidence of positive selection. Three of these positions were in the putative leader protein (Lp), and one was in the polymerase. These findings raise the question of the putative role of the Lp in viral evolution.
authors.affiliation: INRA, Unité Abeilles et Environnement, F-84000 Avignon, France.|UMT PRADE, F-84000 Avignon, France.
authors.forename: A
authors.initials: A
authors.lastname: Dalmon
authors.affiliation: INRA, Unité Pathologie végétale, F-84000 Avignon, France.
authors.forename: C
authors.initials: C
authors.lastname: Desbiez
authors.affiliation: INRA, Unité Abeilles et Environnement, F-84000 Avignon, France.|ANSES, laboratoire de Sophia Antipolis, F-06902 Sophia Antipolis.
authors.forename: M
authors.initials: M
authors.lastname: Coulon
authors.affiliation: INRA, Unité Abeilles et Environnement, F-84000 Avignon, France.
authors.forename: M
authors.initials: M
authors.lastname: Thomasson
authors.affiliation: INRA, Unité Abeilles et Environnement, F-84000 Avignon, France.|UMT PRADE, F-84000 Avignon, France.
authors.forename: Y
authors.initials: Y
authors.lastname: Le Conte
authors.affiliation: INRA, Unité Abeilles et Environnement, F-84000 Avignon, France.|UMT PRADE, F-84000 Avignon, France.
authors.forename: C
authors.initials: C
authors.lastname: Alaux
authors.affiliation: UMT PRADE, F-84000 Avignon, France.
authors.forename: J
authors.initials: J
authors.lastname: Vallon
authors.affiliation: INRA, Unité Pathologie végétale, F-84000 Avignon, France.
authors.forename: B
authors.initials: B
authors.lastname: Moury
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D001516:Bees / Q000821:virology; D019143:Evolution, Molecular; D016679:Genome, Viral; D020125:Mutation, Missense; D017354:Point Mutation; D020365:RNA Helicases / Q000235:genetics; D012328:RNA Viruses / Q000145:classification* / Q000235:genetics*; D011995:Recombination, Genetic; D012641:Selection, Genetic; D014764:Viral Proteins / Q000235:genetics; D000073336:Whole Genome Sequencing
chemical_list: D020121:5' Untranslated Regions; D014764:Viral Proteins; D020365:RNA Helicases