Network Analysis of the Chronic Hepatitis C Virome Defines Hypervariable Region 1 Evolutionary Phenotypes in the Context of Humoral Immune Responses

Abstract

Hypervariable region 1 (HVR1) of hepatitis C virus (HCV) comprises the first 27 N-terminal amino acid residues of E2. It is classically seen as the most heterogeneous region of the HCV genome. In this study, we assessed HVR1 evolution by using ultradeep pyrosequencing for a cohort of treatment-naive, chronically infected patients over a short, 16-week period. Organization of the sequence set into connected components that represented single nucleotide substitution events revealed a network dominated by highly connected, centrally positioned master sequences. HVR1 phenotypes were observed to be under strong purifying (stationary) and strong positive (antigenic drift) selection pressures, which were coincident with advancing patient age and cirrhosis of the liver. It followed that stationary viromes were dominated by a single HVR1 variant surrounded by minor variants comprised from conservative single amino acid substitution events. We present evidence to suggest that neutralization antibody efficacy was diminished for stationary-virome HVR1 variants. Our results identify the HVR1 network structure during chronic infection as the preferential dominance of a single variant within a narrow sequence space. IMPORTANCEHCV infection is often asymptomatic, and chronic infection is generally well established in advance of initial diagnosis and subsequent treatment. HVR1 can undergo rapid sequence evolution during acute infection, and the variant pool is typically seen to diverge away from ancestral sequences as infection progresses from the acute to the chronic phase. In this report, we describe HVR1 viromes in chronically infected patients that are defined by a dominant epitope located centrally within a narrow variant pool. Our findings suggest that weakened humoral immune activity, as a consequence of persistent chronic infection, allows for the acquisition and maintenance of host-specific adaptive mutations at HVR1 that reflect virus fitness. Hepatitis C virus (HCV) infection is a global health issue and is recognized as a major etiological agent of liver-related diseases (1). It has been estimated that the current prevalence of HCV represents approximately 2% of the global adult (15 years of age and older) population (2). Following transmission, HCV infection may remain asymptomatic for decades, resulting in the majority of infections initially passing undetected (3). It is estimated that up to 4 million Americans are living with the virus, the majority of whom became infected prior to the isolation and identification of the virus (4, 5). Consequently, the U.S. Centers for Disease Control and Prevention now recommend that Americans born from 1945 to 1965 be screened for the presence of the virus notwithstanding the presence of clinical symptoms (3, 5).HCV is a single-stranded positive-sense RNA virus of considerable genomic heterogeneity. A recent reclassification defined the HCV global distribution into 7 genotypes and 67 subtypes, with genotypes 1 and 3 accounting for the majority of infections worldwide (6...

Hypervariable Region 1 in Envelope Protein 2 of Hepatitis C Virus: A Linchpin in Neutralizing Antibody Evasion and Viral Entry

“…This is supported by the correlation between persistence and higher non-synonymous to synonymous substitution rates in HVR1 ( 142 ), thus indicating that HVR1-directed immune responses can help the virus persist. The observed positive selection of HVR1 ( 101 – 103 ), combined with studies of HVR1 variants in immune-complexed HCV further supports this hypothesis ( 143 , 144 ). In addition, the appearance of HVR1-specific antibodies in patient sera was associated with emergence of immune-complexes of particles carrying that specific HVR1 sequence, leading to a large reduction of that viral population within the patient ( 144 ).…”

“…One study, finding no evidence of positive selection and no correlation between evolutionary rate and HVR1-specific antibody responses in patients, suggested that random drift might be the cause for HVR1 variation ( 100 ). However, many studies did observe strong positive selection of HCV, particularly in HVR1 ( 101 – 103 ) and a large body of data now supports that HVR1 variation is due to antibody-driven immune selection. Firstly, antibodies against HVR1 are commonly detectable in chronically infected patients ( 37 , 104 – 110 ) and the early induction of such antibodies is associated with acute self-limited infection ( 111 ).…”

Internal Disequilibria and Phenotypic Diversification during Replication of Hepatitis C Virus in a Noncoevolving Cellular Environment

“…The distribution of mutations along the HCV genome differed from the distribution observed when comparing clinical isolates (69)(70)(71)(72). In particular, it is noteworthy that hypervariable regions 1 and 2 (HVR1 and HVR2) in HCV p200 include only 1 amino acid replacement relative to HCV p0 (1.78% of the total versus 66% of the total within NS5A turbed environment constitutes an ideal scenario to test the molecular-clock hypothesis with an RNA virus.…”

Reverse epitope mapping of the E2 glycoprotein in antibody associated hepatitis C virus

“…We have observed that the host humoral immune system targets viral variants which are often clonotypic in nature [21–23]. Data from previous research has shown that total IgGs obtained from sera lacking detectable AAV were unable to target viral variants from the pool of quasispecies.…”