Sequence recombination and conservation of Varroa destructor virus-1 and deformed wing virus in field collected honey bees (Apis mellifera)

• Published in: PloS one Vol. 8; no. 9; p. e74508
• Main Authors: Wang, Hui, Xie, Jiazheng, Shreeve, Tim G, Ma, Jinmin, Pallett, Denise W, King, Linda A, Possee, Robert D
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 18.09.2013; Public Library of Science (PLoS)
• Subjects: Analysis; Animals; Apis mellifera; Base Sequence; Bees; Bees - virology; Bioinformatics; Bombus; Bombus pascuorum; Bumblebees; Chimera; Chimeras; Cloning; Computer viruses; Conservation; Conserved sequence; Conserved Sequence - genetics; Councils; Deformation; Deoxyribonucleic acid; DNA; DNA sequencing; Ecology; European honeybee; Gene sequencing; Genome, Viral - genetics; Genomes; Genomics; Health aspects; Homology; Hydrology; Infections; Insect viruses; Insect Viruses - genetics; Mutation; Mutation rates; Polymerase chain reaction; Population studies; Proteins; Recombination; Recombination, Genetic - genetics; Reproducibility of Results; RNA, Small Interfering - metabolism; RNA-mediated interference; Sequence Analysis, DNA; Trends; Varroa destructor; Varroidae - virology; Viruses; Wildlife conservation; Wings, Animal - virology; United Kingdom > UK; Beijing China; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0074508

We sequenced small (s) RNAs from field collected honeybees (Apis mellifera) and bumblebees (Bombuspascuorum) using the Illumina technology. The sRNA reads were assembled and resulting contigs were used to search for virus homologues in GenBank. Matches with Varroadestructor 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.