Diversity in a honey bee pathogen: first report of a third master variant of the Deformed Wing Virus quasispecies

Mordecai, Gideon J; Wilfert, Lena; Martin, Stephen J; Jones, Ian M; Schroeder, Declan C

Illumina Hi-seq (2 × 100) pair-end sequencing of asymptomatic honey bees from Devon was carried out on colonies that either survived (GD2) or collapsed (GD1) because of OCL (Highfield et al., 2009) . To assess DWV diversity within the samples the raw reads were searched against a custom DWV family database (including KV and VDV-1 genomes) and reads matching to any of the DWV genomes were extracted. The coverage for the number of reads that matched to a custom DWV BLAST database was estimated using the Lander/Waterman equation (that is, the depth of sequencing). Genome coverage depth ranged from 457 to 165 927 × (average coverage was 86 838 × ) (Supplementary Table S1 ).