Temporal Variations in the Hepatitis C Virus Intrahost Population during Chronic Infection

Abstract

The intrahost evolution of hepatitis C virus (HCV) holds keys to understanding mechanisms responsible for the establishment of chronic infections and to development of a vaccine and therapeutics. In this study, intrahost variants of two variable HCV genomic regions, HVR1 and NS5A, were sequenced from four treatment-naïve chronically infected patients who were followed up from the acute stage of infection for 9 to 18 years. Median-joining network analysis indicated that the majority of the HCV intrahost variants were observed only at certain time points, but some variants were detectable at more than one time point. In all patients, these variants were found organized into communities or subpopulations. We hypothesize that HCV intrahost evolution is defined by two processes: incremental changes within communities through random mutation and alternations between coexisting communities. The HCV population was observed to incrementally evolve within a single community during approximately the first 3 years of infection, followed by dispersion into several subpopulations. Two patients demonstrated this pattern of dispersion for the rest of the observation period, while HCV variants in the other two patients converged into another single subpopulation after ϳ9 to 12 years of dispersion. The final subpopulation in these two patients was under purifying selection. Intrahost HCV evolution in all four patients was characterized by a consistent increase in negative selection over time, suggesting the increasing HCV adaptation to the host late in infection. The data suggest specific staging of HCV intrahost evolution.Hepatitis C virus (HCV) infection is a major cause of liver disease in the world. It is estimated that ϳ130 million people are infected with HCV globally (2). HCV is a heterogeneous single-stranded (plus-strand) RNA virus belonging to the Flaviviridae. The HCV genome contains one large open reading frame that encodes a polyprotein which can be processed into 10 mature proteins (34). HCV causes chronic infection in 70 to 85% of infected adults. There is no vaccine against HCV, and current antiviral therapy is effective in only 50 to 70% of chronically infected patients (18).HCV intrahost evolution is frequently compared to an "arms race," implying that the HCV genome constantly changes in order to escape from neutralizing adaptive immunoresponses (53). This concept of constant change is seemingly different from the HIV model, according to which intrahost evolution slows down with CD4 ϩ T-cell depletion and quasispecies diversity decreases with the development of AIDS (48). Our limited understanding of the dynamics of HCV intrahost evolution impedes the development of efficient therapeutic and prophylactic interventions.Analysis of HCV longitudinal evolution is significantly hindered by difficulties with identifying and with long-term follow-up of patients, starting from the acquisition of infection. In the present study, we explored HCV evolutionary processes during long-term chronic infection in four treatment-...

Antigenic cooperation among intrahost HCV variants organized into a complex network of cross-immunoreactivity

“…First, the intrahost HIV population diversifies and diverts continuously from acute state to chronic infection until, at the onset of immunodeficiency, it starts losing heterogeneity and eventually stops diverting (8). Surprisingly, a similar temporal pattern of diversity and diversion was observed for intrahost HCV populations (9,10). Furthermore, for HCV, the consistent increase in negative selection during chronic infection was observed (9)(10)(11)(12)(13).…”

“…Surprisingly, a similar temporal pattern of diversity and diversion was observed for intrahost HCV populations (9,10). Furthermore, for HCV, the consistent increase in negative selection during chronic infection was observed (9)(10)(11)(12)(13). The late-stage HCV populations were shown to remain constant and homogeneous under the strong negative selection for years, indicating a high level of intrahost adaptation (9).…”

“…The density of intrahost subpopulations was found to fluctuate significantly in the course of chronic HCV infection, with some subpopulations persisting at low frequency for years until becoming dominant or reemerging at later stages of infection after being undetectable for a long time (9,10,15,16).…”

The long way toward understanding host and viral determinants of therapeutic success in HCV infection

“…In Japan, mutations in the ISDR gene were strongly associated with the sustained virological response to IFN therapy in patients infected with genotype 1b, while the likelihood of this response is less pronounced in Europe suggesting geographical differences in the relationship between ISDR mutations and efficiency of IFN therapy. In a recent study, dynamics of intrahost HCV variants of the NS5A genomic region were sequenced from four treatment-naïve chronically infected patients followed up for 9-18 years from the acute infection stage [18]. The authors established a model of HCV evolution in four stages.…”

“…For example, patients with acute infection (stages one and two) reach a complete virological response to treatment more frequently than patients with chronic infections. Also, variation in quasi-species diversity throughout the course of HCV infection may be related to the reduction in the selection intensity, which is the result of a decline in specific immune responses even if HCV does not cause systemic immunodeficiency [18]. Therefore, it is conceivable that a viral population at a given stage has a specific impact on host immunological properties suggesting that the relationships between HCV variants, immune parameters, and response to IFN-based treatment are highly complex.…”