Sequence diversity of hepatitis C virus: Implications for immune control and therapy

Figure 1 Published HCV Full Genomes. 169 full length HCV sequences available from the Los Alamos National Laboratory (LANL) HCV Sequence Database are illustrated in a phylogenetic tree. HCV sequences fall into six different clusters (genotype 1-6) and are further classified into subtypes. The sequence from one recombinant virus (genotype 1b/2k) is included.

Figure 2 HLA class I-associated sequence polymorphisms in a CD8 epitope. Viral sequences are aligned to a consensus sequence and sorted into sequences derived from HLA B8-positive and HLA B8-negative subjects. Boxed is the region of a described HLA B8-restricted CD8 epitope. Differences from the consensus sequence are significantly more frequent in HLA-B8 positive subjects (P < 0.001). This association was reported in[68].

Figure 3 Entropy across the HCV polyprotein. 100 HCV genotype 1b sequences were retrieved from the Los Alamos National Laboratory (LANL) HCV Sequence Database. The entropy score was calculated for 300 windows of 20 residues overlapping by 10 residues utilizing the algorithm implemented in the database.