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

De novo assembly of the Illumina reads yielded a complete genome of a type A variant as well as of a novel DWV variant that we named Type C (Supplementary Table S2 ). Competitive alignment to the now three master variants revealed that out of the~30 million DWV blast positive reads,~27 million were assembled to one of three genomes (Supplementary Table S3 and Supplementary Figure S1 ). Around 3 million assembled to type A,~3.5 thousand to type B and~24 million to Type C. As expected, more reads align to the 3′ region of the genome than the 5′; an artefact of the reverse transcription 3′ bias (Brooks et al., 1995) . Although reads aligned to the whole of the Type C genome, the depth of coverage was lower at the 5′ region (Supplementary Figure S1 ). In addition, coverage of the 5′ region of the type A variant was unusually high, indicating that this disproportionate coverage in the 5′ regions of type A and C could be the evidence of recombination between the two variants. Because of the low read depth and coverage for type B in our samples, a full genome could not be assembled (Supplementary Table S3 and Supplementary Figure S1 ). Nonetheless, closer examination of 3′ region where the RNA-dependent RNA polymerase (RdRp) gene is located (Baker and Schroeder, 2008) revealed that the Devon type B variant shared 100% identity to VDV-1 type B genome in this region (Supplementary Figure S2) . The sequence identity of our newly assembled type A and C variants was compared with other members of the DWV complex (Table 1 and Figure 1 ). Both type B and C differ from the type A nucleotide sequence in similar regions of the genome. However, type B and C share only 79% nucleotide identity in the polyprotein encoding region of the genome and 89% identity in the amino acid sequence.