Pretreatment Sequence Diversity Differences in the Full-Length Hepatitis C Virus Open Reading Frame Correlate with Early Response to Therapy

Abstract

Pegylated alpha interferon and ribavirin therapy for hepatitis C virus (HCV) genotype 1 infection fails for half of Caucasian American patients (CA) and more often for African Americans (AA). The reasons for these low response rates are unknown. HCV is highly genetically variable, but it is unknown how this variability affects response to therapy. To assess effects of viral diversity on response to therapy, the complete pretreatment genotype 1 HCV open reading frame was sequenced using samples from 94 participants in the Virahep-C study. Sequences from patients with >3.5 log declines in viral RNA levels by day 28 (marked responders) were more variable than those from patients with declines of <1.4 log (poor responders) in NS3 and NS5A for genotype 1a and in core and NS3 for genotype 1b. These correlations remained when all T-cell epitopes were excluded, indicating that these differences were not due to differential immune selection. When the sequences were compared by race of the patients, higher diversity in CA patients was found in E2 and NS2 but only for genotype 1b. Core, NS3, and NS5A can block the action of alpha interferon in vitro; hence, these genetic patterns are consistent with multiple amino acid variations independently impairing the function of HCV proteins that counteract interferon responses in humans, resulting in HCV strains with variable sensitivity to therapy. No evidence was found for novel HCV strains in the AA population, implying that AA patients may be infected with a higher proportion of the same resistant strains that are found in CA patients.Chronic infection with hepatitis C virus (HCV) is a major cause of cirrhosis, liver disease, and hepatocellular carcinoma (reviewed in reference 37). About 3.1 million Americans are chronically infected with HCV, causing 8,000 to 10,000 deaths annually (3). Due to the slow progression of hepatitis C virus infections and the increasing prevalence of HCV in the American population, HCV-associated deaths are expected to more than triple over the next two decades, eventually exceeding those from AIDS (45).HCV is a hepatotropic Flavivirus (reviewed in reference 40). The virion contains a lipid envelope with two envelope proteins surrounding a capsid. Within the capsid is a positivepolarity RNA genome about 9,600 nucleotides long that contains an open reading frame (ORF) that encodes a polyprotein of ϳ3,000 amino acids (Fig. 1). The structural proteins include the core protein that forms the capsid and the E1 and E2 surface glycoproteins. The nonstructural proteins include P7 (ion channel), NS2 (protease), NS3 (protease and helicase), NS4A (cofactor for NS3), NS4B (putative organizer of the viral replicase complex), NS5A (implicated in viral replication and pathogenesis), and NS5B (RNA polymerase). An 11th viral protein, the alternate reading frame (ARF) protein, is encoded in the ϩ1 frame within the core region and is of unknown function (7).Six HCV genotypes that are less than 72% identical at the nucleotide level have been identified, and within thes...

Genome-wide hepatitis C virus amino acid covariance networks can predict response to antiviral therapy in humans

“…sequences for the full-length HCV ORF were previously determined from 94 participants in the Virahep-C study (17). The characteristics of these patients are shown in Table 1.…”

“…The spectrum of HCV isolates circulating in the human population appears to range from relatively resistant to relatively sensitive sequences in their responses to IFN-based therapy (17). Therefore, if the covariance networks accurately reflect the HCV population as a whole, essentially every covariance in the All networks - composed of the full set of 47 sequences for each genotype - should be present in at least one of the response-specific networks (i.e., Marked, Poor, SVR, or Non-SVR).…”

“…As part of the Virahep-C study, we analyzed viral genetic patterns associated with response or failure of therapy (17,18). We sequenced the complete pretreatment HCV open reading frame (ORF) from 94 patients and found that HCV genetic variability among sequences from patients in whom therapy efficiently suppressed the virus was significantly higher than among sequences from patients in whom suppression was minimal.…”

Mechanisms of action of interferon and ribavirin in chronic hepatitis C: Summary of a workshop

“…27 Genetic diversity was also noted between the two races, but these were inconsistent and less clear than the differences by response category. These findings are consistent with a more potent immune response imposing greater selective forces on the HCV genome or variations at multiple positions in the HCV genome impairing its ability to resist the antiviral effects of IFN and ribavirin.…”

The hepatitis C virus core gene yields restriction fragments of variable length and polymorphism

“…However, we have found three patterns designated as II, IV, and V which may have arisen from mutation by recombination in the local population 22,23 . Mutations of the core region impact on clinical outcomes [24][25][26] .…”