Evidence for positive selection and recombination hotspots in Deformed wing virus (DWV)

A Dalmon,J Vallon,B Moury,M Coulon,Y Le Conte,M Thomasson,C Desbiez,C Alaux

doi:10.1038/srep41045

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.

Highlights

Varroa spread has contributed to a large increase in viral pathologies[8,9]
The two sequences were aligned with the 12 Deformed wing virus (DWV)/Varroa destructor virus-1 (VDV-1) complete genomes, which were available in GenBank (Table 1)
If we apply this rule to DWV and VDV-1, we can consider the first peak of identity from 95.8% to 99.2% to be characteristic of the variants (Table 1), whereas identity levels from 84.1% to 84.9% are characteristic of the DWV and VDV-1 “strains”

Summary

Introduction

Among the twenty distinct virus species from the different genera that have been characterized in honey bees[10], at least eight viral diseases have been associated with the presence of Varroa destructor[11] Of these diseases, deformed wing virus (DWV, genus Iflavirus, family Iflaviridae, order Picornavirales) is often considered one of the most damaging viruses in honey bee colonies[12,13,14,15,16]. We combined these sequences with additional sequences that were available in databanks; we searched for recombination breakpoints and analyzed their distributions across the virus genome We compared both highly conserved and more variable genome regions among the partial virus sequences (42 isolates) that were obtained from colonies exposed to conventional Varroa management strategies and colonies tolerant to Varroa[33]. We searched for positively selected codons under the assumption that proteins that are critically involved in virus replication, transmission and adaptation to the host immune system could be evolving, at least in part, under positive selective pressure[34,35,36]

Methods

Results

Conclusion