Contribution of genome-wide HCV genetic differences to outcome of interferon-based therapy in Caucasian American and African American patients

Abstract

Background: Hepatitis C virus (HCV) has six major genotypes, and patients infected with genotype 1 respond less well to interferon-based therapy than other genotypes. African American patients respond to interferon alpha-based therapy at about half the rate of Caucasian Americans. The effect of HCV's genetic variation on treatment outcome in both racial groups is poorly understood.

Methodology: We determined the near full-length pre-therapy consensus sequences from 94 patients infected with HCV genotype 1a or 1b undergoing treatment with peginterferon alpha-2a and ribavirin through the Virahep-C study. The sequences were stratified by genotype, race and treatment outcome to identify HCV genetic differences associated with treatment efficacy.

Principal findings: HCV sequences from patients who achieved sustained viral response were more diverse than sequences from non-responders. These inter-patient diversity differences were found primarily in the NS5A gene in genotype 1a and in core and NS2 in genotype 1b. These differences could not be explained by host selection pressures. Genotype 1b but not 1a African American patients had viral genetic differences that correlated with treatment outcome.

Conclusions & significance: Higher inter-patient viral genetic diversity correlated with successful treatment, implying that there are HCV genotype 1 strains with intrinsic differences in sensitivity to therapy. Core, NS3 and NS5A have interferon-suppressive activities detectable through in vitro assays, and hence these activities also appear to function in human patients. Both preferential infection with relatively resistant HCV variants and host-specific factors appear to contribute to the unusually poor response to therapy in African American patients.

Figure 1. The HCV genome.

The HCV genome contains a single major open reading frame flanked by untranslated regions. The 10 genes within the open reading frame are indicated.

Figure 2. Phylogenetic tree for the genotype 1 polyprotein sequences.

(A) A maximum-parsimony tree was generated from an alignment of all 47 genotype 1a near full-length polyprotein sequences, with the genotype 1b consensus reference as the out-group. (B) A maximum-parsimony tree was generated from an alignment of all 47 genotype 1b near full-length polyprotein sequences, with the genotype 1a consensus reference as the out-group. Treatment outcome is indicated by SVR (boxed names) and NR (not boxed). AA patient sequences are shown in red; CA patient sequences are in black.

Figure 3. Number of variations per sample by treatment outcome.

The number of variations relative to a population consensus is shown for the polyprotein (PP) and for each gene within the polyprotein. Statistical significance is shown for genes with p≤0.05. (A) Genotype 1a, all variations. (B) Genotype 1b, all variations. (C) Genotype 1a, variations unique to the SVR or NR classes. (D) Genotype 1b, variations unique to the SVR or NR classes.

Figure 4. Number of unique variations in non-epitope regions by treatment outcome.

Variations unique to the SVR or NR sequences that were not in any known or predicted T-cell epitope were compared in the SVR and NR samples. Statistical significance is indicated where p≤0.05. (A) Genotype 1a. (B) Genotype 1b.

Figure 5. Ratio of observed to predicted UU and UA dinucleotide frequencies.

The ratios of observed to predicted frequency of the dinucleotides UU and UA across the polyprotein were compared between SVR and NR patients. Statistical significance is indicated where p≤0.05. (A) Genotype 1a. (B) Genotype 1b.

Figure 6. Number of unique variations per sample by treatment outcome and patient race.

The number of variations unique to either the SVR or NR groups is shown for the polyprotein (PP) and for each HCV gene for CA and AA patients. Statistical significance is shown for genes with p≤0.05. (A) Genotype 1a. (B) Genotype 1b.