Coevolution of the Hepatitis C Virus Polyprotein Sites in Patients on Combined Pegylated Interferon and Ribavirin Therapy

Abstract

Genotype-specific sensitivity of the hepatitis C virus (HCV) to interferon-ribavirin (IFN-RBV) combination therapy and reduced HCV response to IFN-RBV as infection progresses from acute to chronic infection suggest that HCV genetic factors and intrahost HCV evolution play important roles in therapy outcomes. HCV polyprotein sequences (n ‫؍‬ 40) from 10 patients with unsustainable response (UR) (breakthrough and relapse) and 10 patients with no response (NR) following therapy were identified through the Virahep-C study. Bayesian networks (BNs) were constructed to relate interrelationships among HCV polymorphic sites to UR/NR outcomes. All models showed an extensive interdependence of HCV sites and strong connections (P < 0.003) to therapy response. Although all HCV proteins contributed to the networks, the topological properties of sites differed among proteins. E2 and NS5A together contributed ϳ40% of all sites and ϳ62% of all links to the polyprotein BN. The NS5A BN and E2 BN predicted UR/NR outcomes with 85% and 97.5% accuracy, respectively, in 10-fold cross-validation experiments. The NS5A model constructed using physicochemical properties of only five sites was shown to predict the UR/NR outcomes with 83.3% accuracy for 6 UR and 12 NR cases of the HALT-C study. Thus, HCV adaptation to IFN-RBV is a complex trait encoded in the interrelationships among many sites along the entire HCV polyprotein. E2 and NS5A generate broad epistatic connectivity across the HCV polyprotein and essentially shape intrahost HCV evolution toward the IFN-RBV resistance. Both proteins can be used to accurately predict the outcomes of IFN-RBV therapy.Hepatitis C virus (HCV) is the major etiologic agent of blood-borne non-A, non-B hepatitis (25). Chronic HCV infection is an established risk factor for the development of liver diseases, such as fibrosis, cirrhosis, and hepatocellular carcinoma (33,124,125). Approximately 70% to 80% of HCVinfected patients fail to clear the virus and progress to chronicity (89a). At present, there are no preventive vaccines against HCV. The current, accepted therapeutic approach to treating chronic hepatitis C infection involves a 24-or 48-week course of pegylated alpha interferon (IFN-␣) combined with ribavirin (RBV) (i.e. IFN-RBV therapy) (48, 52). Because only 50% to 70% of chronically infected patients develop a sustained virologic response (SVR) to this treatment (48,52,55,80) and because patient intolerance to such therapy is common (61, 68, 120), the development and application of other therapeutic approaches using antiviral compounds that act against HCV more efficaciously and yet generate lower rates of adverse effects are major clinical management and public health objectives. Therapeutic failure presents in two forms: (i) complete resistance to treatment (no response [NR]) and (ii) unsustainable response (UR), which is characterized by an increase in HCV load observed during therapy after an initial period of decline in viral load (breakthrough) or observed after cessation of therapy (relapse)...

Epistatic connectivity among HCV genomic sites as a genetic marker of interferon resistance

“…As mentioned previously, coordinated evolution among HCV genomic sites reflects many host selection pressures, including innate and adaptive immune responses [47][48][49][50], thus associating host and viral genetic factors. Analysis of individual genomic sites without consideration of their interrelationships is inefficient for the detection of this association.…”

“…However, the extensive epistatic connectivity discovered among HCV genomic sites [47][48][49] suggests that coevolution among sites in any genomic region reflects selection pressures acting on the entire HCV genome in an infected host. Indeed, it was recently reported that each HCV protein [48,49] or small genomic region, such as hypervariable region 1 (HVR1) and a segment of the NS5A gene [50], has a strong association with IFN resistance.…”

“…There is also an equally large body of evidence supporting the crucial role of HCV genetic heterogeneity in overcoming antiviral actions of extraneous IFN [29-31, 36, 37, 39-42]. However, it is only recently that the integrative framework of host-virus interactions in the form of coevolution among HCV genomic sites was considered for the identification of genetic markers of IFN/RBV response [48][49][50].…”

“…Taking into consideration that several HCV proteins are involved in mitigating IFN-mediated antiviral activity [41], it should be expected that coevolution among many sites across the entire HCV genome is linked to selection pressures exerted by IFN. Indeed, recent studies showed that the topology of networks of coordinated substitutions is different for HCV strains that are resistant or sensitive to IFN/RBV treatment [48] and coevolution among sites in each HCV protein is associated with IFN response [49].…”

“…There is no one mutation responsible for IFN resistance. Rather, genome-wide coordination among HCV sites is strongly linked to IFN response and can serve as a complex genetic marker of the resistance [49].…”