Highlights: Predicting the cross-immunoreactivity of hepatitis C virus hyper-variable region 1 peptides using polynomial neural networks

ABSTRACT The hepatitis C virus (HCV) nonstructural 5A (NS5A) protein has been controversially implicated in the inherent resistance of HCV to interferon (IFN) antiviral therapy in clinical studies. In this study, the relationship between NS5A mutations and selection pressures before and during antiviral therapy and virologic response to therapy were investigated. Full-length NS5A clones were sequenced from 20 HCV genotype 1-infected patients in a prospective, randomized clinical trial of IFN induction (daily) therapy and IFN plus ribavirin combination therapy. Pretreatment NS5A nucleotide and amino acid phylogenies did not correlate with clinical IFN responses and domains involved in NS5A functions in vitro were all well conserved before and during treatment. A consensus IFN sensitivity-determining region (ISDR237–276) sequence associated with IFN resistance was not found, although the presence of Ala245 within the ISDR was associated with nonresponse to treatment in genotype 1a-infected patients (P < 0.01). There were more mutations in the 26 amino acids downstream of the ISDR required for PKR binding in pretreatment isolates from responders versus nonresponders in both HCV-1a- and HCV-1b-infected patients (P < 0.05). In HCV-1a patients, more amino acid changes were observed in isolates from IFN-sensitive patients (P < 0.001), and the mutations appeared to be concentrated in two variable regions in the C terminus of NS5A, that corresponded to the previously described V3 region and a new variable region, 310 to 330. Selection of pretreatment minor V3 quasispecies was observed within the first 2 to 6 weeks of therapy in responders but not nonresponders, whereas the ISDR and PKR binding domains did not change in either patient response group. These data suggest that host-mediated selective pressures act primarily on the C terminus of NS5A and that NS5A can perturb or evade the IFN-induced antiviral response using sequences outside of the putative ISDR. Mechanistic studies are needed to address the role of the C terminus of NS5A in HCV replication and antiviral resistance.

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Characterization of the Cross-Neutralizing Antibody Response Against Hepatitis C Virus in the Liver Transplantation Setting

American Journal of Transplantation ◽

10.1111/j.1600-6143.2011.03440.x ◽

2011 ◽

Vol 11 (4) ◽

pp. 767-774 ◽

Cited By ~ 9

Author(s):

J. Dragun ◽

S. Pérez-del-Pulgar ◽

G. Crespo ◽

S. Ramírez ◽

M. Coto-Llerena ◽

...

Keyword(s):

Liver Transplantation ◽

Hepatitis C Virus ◽

Hepatitis C ◽

Antibody Response ◽

Neutralizing Antibody ◽

The Cross

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3′ Nontranslated RNA Signals Required for Replication of Hepatitis C Virus RNA

Journal of Virology ◽

10.1128/jvi.77.6.3557-3568.2003 ◽

2003 ◽

Vol 77 (6) ◽

pp. 3557-3568 ◽

Cited By ~ 146

Author(s):

MinKyung Yi ◽

Stanley M. Lemon

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Mutational Analysis ◽

Variable Region ◽

Replication Capacity ◽

Deletion Mutants ◽

Stem Loop ◽

Translational Activity ◽

Virus Rna ◽

Native Sequence

ABSTRACT We describe a mutational analysis of the 3′ nontranslated RNA (3′NTR) signals required for replication of subgenomic hepatitis C virus (HCV) RNAs. A series of deletion mutants was constructed within the background of an HCV-N replicon that induces the expression of secreted alkaline phosphatase in order to examine the requirements for each of the three domains comprising the 3′NTR, namely, the highly conserved 3′ terminal 98-nucleotide (nt) segment (3′X), an upstream poly(U)-poly(UC) [poly(U/UC)] tract, and the variable region (VR) located at the 5′ end of the 3′NTR. Each of these domains was found to contribute to efficient replication of the viral RNA in transiently transfected hepatoma cells. Replication was not detected when any of the three putative stem-loop structures within the 3′X region were deleted. Similarly, complete deletion of the poly(U/UC) tract abolished replication. Replacement of a minimum of 50 to 62 nt of poly(U/UC) sequence was required for detectable RNA replication when the native sequence was restored in a stepwise fashion from its 3′ end. Lengthier poly(U/UC) sequences, and possibly pure homopolymeric poly(U) tracts, were associated with more efficient RNA amplification. Finally, while multiple deletion mutations were tolerated within VR, each led to a partial loss of replication capacity. The impaired replication capacity of the deletion mutants could not be explained by reduced translational activity or by decreased stability of the RNA, suggesting that each of these mutations may impair recognition of the RNA by the viral replicase during an early step in negative-strand RNA synthesis. The results indicate that the 3′-most 150 nt of the HCV-N genome [the 3′X region and the 3′ 52 nt of the poly(U/UC) tract] contain RNA signals that are essential for replication, while the remainder of the 3′NTR plays a facilitating role in replication but is not absolutely required.

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Comparative Analysis of Within-Host Mutation Patterns and Diversity of Hepatitis C Virus Subtypes 1a, 1b, and 3a

Viruses ◽

10.3390/v13030511 ◽

2021 ◽

Vol 13 (3) ◽

pp. 511

Author(s):

Kaho H. Tisthammer ◽

Weiyan Dong ◽

Jeffrey B. Joy ◽

Pleuni S. Pennings

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Mutation Frequency ◽

Evolutionary Dynamics ◽

Rna Virus ◽

Human Subjects ◽

Variable Region ◽

Purifying Selection ◽

Treatment Naïve ◽

Host Evolution

Understanding within-host evolution is critical for predicting viral evolutionary outcomes, yet such studies are currently lacking due to difficulty involving human subjects. Hepatitis C virus (HCV) is an RNA virus with high mutation rates. Its complex evolutionary dynamics and extensive genetic diversity are demonstrated in over 67 known subtypes. In this study, we analyzed within-host mutation frequency patterns of three HCV subtypes, using a large number of samples obtained from treatment-naïve participants by next-generation sequencing. We report that overall mutation frequency patterns are similar among subtypes, yet subtype 3a consistently had lower mutation frequencies and nucleotide diversity, while subtype 1a had the highest. We found that about 50% of genomic sites are highly conserved across subtypes, which are likely under strong purifying selection. We also compared within-host and between-host selective pressures, which revealed that Hyper Variable Region 1 within hosts was under positive selection, but was under slightly negative selection between hosts, which indicates that many mutations created within hosts are removed during the transmission bottleneck. Examining the natural prevalence of known resistance-associated variants showed their consistent existence in the treatment-naïve participants. These results provide insights into the differences and similarities among HCV subtypes that may be used to develop and improve HCV therapies.

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Hepatitis C Virus Infection Induces Inflammatory Cytokines and Chemokines Mediated by the Cross Talk between Hepatocytes and Stellate Cells

Journal of Virology ◽

10.1128/jvi.00974-13 ◽

2013 ◽

Vol 87 (14) ◽

pp. 8169-8178 ◽

Cited By ~ 46

Author(s):

H. Nishitsuji ◽

K. Funami ◽

Y. Shimizu ◽

S. Ujino ◽

K. Sugiyama ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Virus Infection ◽

Inflammatory Cytokines ◽

Cross Talk ◽

Stellate Cells ◽

Hepatitis C Virus Infection ◽

Cytokines And Chemokines ◽

The Cross

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Proof of concept for rational design of hepatitis C virus E2 core nanoparticle vaccines

Science Advances ◽

10.1126/sciadv.aaz6225 ◽

2020 ◽

Vol 6 (16) ◽

pp. eaaz6225 ◽

Cited By ~ 8

Author(s):

Linling He ◽

Netanel Tzarum ◽

Xiaohe Lin ◽

Benjamin Shapero ◽

Cindy Sou ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

B Cell ◽

Neutralizing Antibodies ◽

Rational Design ◽

Vaccine Development ◽

Variable Region ◽

Improved Stability ◽

Cell Patterns ◽

Neutralizing Epitopes

Hepatitis C virus (HCV) envelope glycoproteins E1 and E2 are responsible for cell entry, with E2 being the major target of neutralizing antibodies (NAbs). Here, we present a comprehensive strategy for B cell–based HCV vaccine development through E2 optimization and nanoparticle display. We redesigned variable region 2 in a truncated form (tVR2) on E2 cores derived from genotypes 1a and 6a, resulting in improved stability and antigenicity. Crystal structures of three optimized E2 cores with human cross-genotype NAbs (AR3s) revealed how the modified tVR2 stabilizes E2 without altering key neutralizing epitopes. We then displayed these E2 cores on 24- and 60-meric nanoparticles and achieved substantial yield and purity, as well as enhanced antigenicity. In mice, these nanoparticles elicited more effective NAb responses than soluble E2 cores. Next-generation sequencing (NGS) defined distinct B cell patterns associated with nanoparticle-induced antibody responses, which target the conserved neutralizing epitopes on E2 and cross-neutralize HCV genotypes.

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In vivoevaluation of the cross-genotype neutralizing activity of polyclonal antibodies against hepatitis C virus

Hepatology ◽

10.1002/hep.24171 ◽

2011 ◽

Vol 53 (3) ◽

pp. 755-762 ◽

Cited By ~ 89

Author(s):

Philip Meuleman ◽

Jens Bukh ◽

Lieven Verhoye ◽

Ali Farhoudi ◽

Thomas Vanwolleghem ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Polyclonal Antibodies ◽

Neutralizing Activity ◽

The Cross

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Monoclonal Antibodies Directed toward the Hepatitis C Virus Glycoprotein E2 Detect Antigenic Differences Modulated by the N-Terminal Hypervariable Region 1 (HVR1), HVR2, and Intergenotypic Variable Region

Journal of Virology ◽

10.1128/jvi.02070-15 ◽

2015 ◽

Vol 89 (24) ◽

pp. 12245-12261 ◽

Cited By ~ 32

Author(s):

Yousef Alhammad ◽

Jun Gu ◽

Irene Boo ◽

David Harrison ◽

Kathleen McCaffrey ◽

...

Keyword(s):

Monoclonal Antibodies ◽

Hepatitis C Virus ◽

Hepatitis C ◽

Hypervariable Region ◽

Variable Region ◽

Antigenic Structure ◽

Variable Regions ◽

Core Domain ◽

Hypervariable Region 1 ◽

Glycoprotein E2

ABSTRACTHepatitis C virus (HCV) envelope glycoproteins E1 and E2 form a heterodimer and mediate receptor interactions and viral fusion. Both E1 and E2 are targets of the neutralizing antibody (NAb) response and are candidates for the production of vaccines that generate humoral immunity. Previous studies demonstrated that N-terminal hypervariable region 1 (HVR1) can modulate the neutralization potential of monoclonal antibodies (MAbs), but no information is available on the influence of HVR2 or the intergenotypic variable region (igVR) on antigenicity. In this study, we examined how the variable regions influence the antigenicity of the receptor binding domain of E2 spanning HCV polyprotein residues 384 to 661 (E2661) using a panel of MAbs raised against E2661and E2661lacking HVR1, HVR2, and the igVR (Δ123) and well-characterized MAbs isolated from infected humans. We show for a subset of both neutralizing and nonneutralizing MAbs that all three variable regions decrease the ability of MAbs to bind E2661and reduce the ability of MAbs to inhibit E2-CD81 interactions. In addition, we describe a new MAb directed toward the region spanning residues 411 to 428 of E2 (MAb24) that demonstrates broad neutralization against all 7 genotypes of HCV. The ability of MAb24 to inhibit E2-CD81 interactions is strongly influenced by the three variable regions. Our data suggest that HVR1, HVR2, and the igVR modulate exposure of epitopes on the core domain of E2 and their ability to prevent E2-CD81 interactions. These studies suggest that the function of HVR2 and the igVR is to modulate antibody recognition of glycoprotein E2 and may contribute to immune evasion.IMPORTANCEThis study reveals conformational and antigenic differences between the Δ123 and intact E2661glycoproteins and provides new structural and functional data about the three variable regions and their role in occluding neutralizing and nonneutralizing epitopes on the E2 core domain. The variable regions may therefore function to reduce the ability of HCV to elicit NAbs directed toward the conserved core domain. Future studies aimed at generating a three-dimensional structure for intact E2 containing HVR1, and the adjoining NAb epitope at residues 412 to 428, together with HVR2, will reveal how the variable regions modulate antigenic structure.

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