Characterization of a Novel RNA Virus Discovered in the Autumnal Moth Epirrita autumnata in Sweden

de Miranda, Joachim R.; Hedman, Harald; Onorati, Piero; Stephan, Jörg; Karlberg, Olof; Bylund, Helena; Terenius, Olle

Virus genomes often mimic the compositional biases of their hosts' genomes [18] , such that they can be clearly separated by compositional bias according to their host type [19] . Compositional bias analyses can therefore assist in virus host identification. The codon usage and dinucleotide frequencies for the different codon regions of the virus nucleotide sequences (Supplementary Materials Table S2 ) were obtained at www.bioinformatics.org using the Sequence Manipulation Suite [20] . The dinucleotide frequency bias for each of the 16 dinucleotides was calculated as the ratio of the observed and expected dinucleotide frequencies, the latter being the product of the corresponding mononucleotide frequencies [19] . These multivariate data were used in correspondence analyses [19, 21] to identify clusters of sequences with similar compositional bias in a multidimensional space. The analyses were conducted in R (www.R-project.org) using the ade4 package [22] . The translation initiation contexts between the −3 and +6 positions around the AUG start codons [23] of the different ORFs of the different viruses were tabulated by hand, converted to frequencies, and represented as stacked letters.