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

To establish the phylogenetic relationship of DWV subtypes and closely related Iflaviruses, we reconstructed the phylogeny of the conserved RdRp amino acid sequences for seven DWV subtypes, spanning all three types that were either sequenced and assembled from the Devon hive or available from genbank (type A: NC_005876.1, NC_004830.2; type B: KC_786222.1, NC_006494.1, JQ_413340), as well as Formica exsecta Virus 1 (NC_023022.1) and Sacbrood Virus (NC_002066.1). We used a Bayesian approach using MrBayes (v. 3.1.2) (Huelsenbeck and Ronquist, 2001) . We assumed a fixed rate model of protein evolution and reconstructed the phylogeny using a model jumping method. This method allows for different models of amino acid substitution to be used in the Markov chain Monte Carlo (MCMC) procedure, with all models contributing to the final result weighted according to their respective posterior probability. We ran two runs of four chains for 4 000 000 MCMC generations, sampling trees every 1000 generations. All trees were drawn using FigTree v.1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/).