Fig. 3

SimPlot analyses of core gene sequences of four Ghanaian HCV isolates. In each of the figure units (a), (b), (c) and (d), upper panel shows sequence similarity plots (SimPlot analysis) and lower panel displays bootscan analyses results. Each analysis was performed by comparing sequence relationships of test viral sequences to representatives of reference genotype 2 and its subtypes 2a, 2b, 2c, 2d, 2e, 2f, 2i, 2 k, 2 m, 2q, 2r, 2 t and 2u retrieved from the International Committee on Taxonomy of Viruses (ICTV) website (https://hcv.lanl.gov/content/sequence/NEWALIGN/align.html/). Similarity plotting and bootscan analyses were performed in SimPlot version 3.5.1 with parameters set at simple consensus sequences; and with window and step sizes of 300 and 20 nucleotides respectively. The Y-axis represents percentage of sequence similarity to the corresponding subtype in the SimPlot analysis. The bootscan panel displays plots of bootstrap values (percentage permuted trees) calculated from multiple genome alignment of test viral sequences with reference subtype sequences. Bootscanning was performed using neighbour-joining method with Kimura-2 parameter modelling for 100 replicates. For all panels the x axis indicates nucleotide positions along the alignment (with gaps removed from the alignment). Reference sequences used are colour-coded and listed on the right of each plot. The analyses show the presence of a unique and complex HCV genotype 2 sequence profile of the Ghanaian isolates (core gene) comprising a 2e fragment (red colour-coded) of about 80 nucleotides from position 455 to 534 of the H77 reference sequence (GenBank accession number AF009606) and other variable fragments belonging to subtypes 2a, 2 k, 2q, 2r, 2u and/or 2