Maximum likelihood tree reconstructed with consensus NS5b, 5'UTR and consensus HVR1 gene sequences generated in this study.

<p>HCV-1 isolates are shown in black unfilled circles while HCV-2 are shown in black filled circles.</p

Maximum likelihood tree reconstructed with NS5b gene sequences from West and Central Africa.

<p>Sequences from Ghana generated in this study are shown as red filled circles, those reported from West Africa as black filled triangles and those from Central Africa as black unfilled squares. Ghanaian sequences obtained from the GenBank are shown in blue filled circles.</p

Bayesian skyline plot, showing the epidemic history of HCV genotype 2.

<p>The thick black line in the middle represents the estimated mean effective number of infections through time in years. The two grey lines represent the 95% highest posterior density of this estimate.</p

Maximum likelihood tree reconstructed with intra-host variants of HVR1 gene sequences of HCV genotype 1.

<p>Only unique haplotypes are shown. Individual samples are labeled with distinct identifiers beginning with letter ‘k’ and displayed with different colors.</p

PFnet of all sequences present in two patients at different time points.

<p>Each time point is shown with a different color. Sequences found on the first time point are shown in red and the second time point in blue. Each node represents a single sequence variant. The size of the node reflects frequency of the corresponding variant in the population. This network includes all of the links in any minimum spanning tree. The time interval between each time point is ~2 months.</p