GB virus C (GBV-C) evolutionary patterns revealed by analyses of reference genomes, E2 and NS5B sequences amplified from viral strains circulating in the Lisbon area (Portugal)

► GBV-C ORF, and subgenomic sequence segments were analysed. ► Phylogenetic noise is determined by the sequence size. ► Most regions of the viral genome seem to evolve under the same model assumptions. ► Dispersion of informative sites across the viral coding sequence was non-uniform. ► Recombination affects is frequent and affects phylogenetic congruence.