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

A second novel variant was also assembled by Vicuna. In order to create a consensus sequence of the novel variant, the contigs from three samples were realigned against the DWV genome. Any contigs containing sequence other than the novel variant were removed. If a contig contained the novel variant as well as sequence belonging to the type A DWV genome because of recombination or in silico recombination, the type A DWV regions were trimmed and deleted. A consensus genome of the novel variant was created from these sorted and trimmed contigs. Accordingly, the same steps were carried out on the type A sequence in order to assemble the type A genome consensus from Devon. The DWV scaffolds were then aligned with fulllength genome sequences from the NCBI (National Center for Biotechnology Information) database using the MUSCLE alignment tool (Edgar, 2004) within Geneious and the full-length genome was obtained. Full genome comparisons were visualised in mVISTA (Frazer et al., 2004) .