Sequence Recombination and Conservation of Varroa destructor Virus-1 and Deformed Wing Virus in Field Collected Honey Bees (Apis mellifera)

Abstract

We sequenced small (s) RNAs from field collected honeybees (Apis mellifera) and bumblebees ( Bombus pascuorum ) using the Illumina technology. The sRNA reads were assembled and resulting contigs were used to search for virus homologues in GenBank. Matches with Varroa destructor virus-1 (VDV1) and Deformed wing virus (DWV) genomic sequences were obtained for A. mellifera but not B . pascuorum . Further analyses suggested that the prevalent virus population was composed of VDV-1 and a chimera of 5’-DWV-VDV1-DWV-3’. The recombination junctions in the chimera genomes were confirmed by using RT-PCR, cDNA cloning and Sanger sequencing. We then focused on conserved short fragments (CSF, size > 25 nt) in the virus genomes by using GenBank sequences and the deep sequencing data obtained in this study. The majority of CSF sites confirmed conservation at both between-species (GenBank sequences) and within-population (dataset of this study) levels. However, conserved nucleotide positions in the GenBank sequences might be variable at the within-population level. High mutation rates (Pi>10%) were observed at a number of sites using the deep sequencing data, suggesting that sequence conservation might not always be maintained at the population level. Virus-host interactions and strategies for developing RNAi treatments against VDV1/DWV infections are discussed.

Knock‐on community impacts of a novel vector: spillover of emerging DWV‐B from Varroa‐infested honeybees to wild bumblebees

“…We found no evidence of previously reported recombination within the N‐terminal region of the helicase gene (Dalmon et al ). Instead, we found limited evidence of recombination within the rdrp and lp genes, similar to reports from the UK (Moore et al ; Wang et al ). While these data cannot systematically address the question of genome‐wide recombination, our results give little evidence for an important role of recombination in the current spread of DWV.…”

A Virulent Strain of Deformed Wing Virus (DWV) of Honeybees (Apis mellifera) Prevails after Varroa destructor-Mediated, or In Vitro, Transmission

“…In particular, we sought to investigate if high levels of DWV in VH honeybees was associated with the limited accumulation of virus-derived siRNA, implying the virus may express an siRNA suppressor as, for example, demonstrated in Alphavirus infection of mosquitos [66]. Although DWV- and VDV-1 specific siRNAs were recently detected in adult honeybees [67], [68], these studies could not show if RNAi is involved in suppression of the virus, because viral genomic RNA levels were not quantified. Analysis of siRNAs in the honeybees of the frame transfer experiment showed that the predominant DWV- and VDV-1-specific siRNAs were 22 nt in length with genome sense strand-specific siRNAs present at a 3–4 fold excess over antisense.…”

Appearances Can Be Deceptive: Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context

“…Although prohibitive for high throughput diagnostics, the costs of NGS in the context of viral diversity research are often offset by the vast volumes of useful data that can be generated on viral population dynamics, co-infections, mutation frequencies and genetic recombination [22]–[24].…”