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

Conventional methods to define and analyse variance within RNA viruses include RNA 'fingerprinting' (Domingo et al., 1978) and reverse transcriptase-PCR amplification using specifically designed primers (see, for example, Highfield et al., 2009) . Clone libraries and Sanger sequencing were used to identify the DWV type A as being associated with Varroa infestation and colony collapse . Although these techniques are valid for identifying known variants, primer-based methods are prone to missing unidentified variants and are biased towards overrepresented sequences (Gomez et al., 1999) . PCR-based methods are less appropriate to determine the extent of variation in a quasispecies that is not normally distributed that is, where multiple variants exist, each with their own spectrum of mutants (Gomez et al., 1999) . In these instances deep sequencing methods such as Illumina platforms are more suited to discovering new variants as well as to diversity analysis .