Selection Pressure From Neutralizing Antibodies Drives Sequence Evolution During Acute Infection With Hepatitis C Virus

Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.
Gastroenterology (Impact Factor: 16.72). 04/2009; 136(7):2377-86. DOI: 10.1053/j.gastro.2009.02.080
Source: PubMed


Despite recent characterization of hepatitis C virus-specific neutralizing antibodies, it is not clear to what extent immune pressure from neutralizing antibodies drives viral sequence evolution in vivo. This lack of understanding is particularly evident in acute infection, the phase when elimination or persistence of viral replication is determined and during which the importance of the humoral immune response has been largely discounted.
We analyzed envelope glycoprotein sequence evolution and neutralization of sequential autologous hepatitis C virus pseudoparticles in 8 individuals throughout acute infection.
Amino acid substitutions occurred throughout the envelope genes, primarily within the hypervariable region 1 of E2. When individualized pseudoparticles expressing sequential envelope sequences were used to measure neutralization by autologous sera, antibodies neutralizing earlier sequence variants were detected at earlier time points than antibodies neutralizing later variants, indicating clearance and evolution of viral variants in response to pressure from neutralizing antibodies. To demonstrate the effects of amino acid substitution on neutralization, site-directed mutagenesis of a pseudoparticle envelope sequence revealed amino acid substitutions in hypervariable region 1 that were responsible for a dramatic decrease in neutralization sensitivity over time. In addition, high-titer neutralizing antibodies peaked at the time of viral clearance in all spontaneous resolvers, whereas chronically evolving subjects displayed low-titer or absent neutralizing antibodies throughout early acute infection.
These findings indicate that, during acute hepatitis C virus infection in vivo, virus-specific neutralizing antibodies drive sequence evolution and, in some individuals, play a role in determining the outcome of infection.

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Available from: Stuart C Ray, Dec 22, 2014
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    • "Finally, as an application of this developed approach, we investigate the selective and demographic history of human cytomegalovirus (HCMV), a common β-herpes virus with seroprevalence of 30–90% in the USA (Dowd et al., 2009). This population was chosen for study as the demographic history associated with infection has been investigated extensively and described to include drastic population size changes (see Renzette et al., 2011, 2013, 2014); strong evidence of extensive positive selection associated with colonization has also been described – impacting ∼20% of open reading frames across the genome (Renzette et al., 2013). "
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    ABSTRACT: The ability to infer the parameters of positive selection from genomic data has many important implications, from identifying drug-resistance mutations in viruses to increasing crop yield by genetically integrating favorable alleles. Although it has been well-described that selection and demography may result in similar patterns of diversity, the ability to jointly estimate these two processes has remained elusive. Here, we use simulation to explore the utility of the joint site frequency spectrum to estimate selection and demography simultaneously, including developing an extension of the previously proposed Jaatha program (Mathew et al., 2013). We evaluate both complete and incomplete selective sweeps under an isolation-with-migration model with and without population size change (both population growth and bottlenecks). Results suggest that while it may not be possible to precisely estimate the strength of selection, it is possible to infer the presence of selection while estimating accurate demographic parameters. We further demonstrate that the common assumption of selective neutrality when estimating demographic models may lead to severe biases. Finally, we apply the approach we have developed to better characterize the within-host demographic and selective history of human cytomegalovirus (HCMV) infection using published next generation sequencing data.
    Frontiers in Genetics 09/2015; 6:268. DOI:10.3389/fgene.2015.00268
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    • "For proof of principle that antibodies induced by AS03-M are broadly neutralizing within one HCV genotype, we tested the neutralization of 19 additional HCVpps from genotypes 1a and 1b [5]. When the cutoff for neutralization was set to 50% the AS03-M serum was able to neutralized 4 of 19 (21%) HCVpp (Figure 4D). "
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    ABSTRACT: Hepatitis C virus (HCV) infection is still a serious global health burden. Despite improved therapeutic options, a preventative vaccine would be desirable especially in undeveloped countries. Traditionally, highly conserved epitopes are targets for antibody-based prophylactic vaccines. In HCV-infected patients, however, neutralizing antibodies are primarily directed against hypervariable region I (HVRI) in the envelope protein E2. HVRI is the most variable region of HCV, and this heterogeneity contributes to viral persistence and has thus far prevented the development of an effective HVRI-based vaccine. The primary goal of an antibody-based HCV vaccine should therefore be the induction of cross-reactive HVRI antibodies. In this study we approached this problem by presenting selected cross-reactive HVRI variants in a highly symmetric repeated array on capsid-like particles (CLPs). SplitCore CLPs, a novel particulate antigen presentation system derived from the HBV core protein, were used to deliberately manipulate the orientation of HVRI and therefore enable the presentation of conserved parts of HVRI. These HVRI-CLPs induced high titers of cross-reactive antibodies, including neutralizing antibodies. The combination of only four HVRI CLPs was sufficient to induce antibodies cross-reactive with 81 of 326 (24.8%) naturally occurring HVRI peptides. Most importantly, HVRI CLPs with AS03 as an adjuvant induced antibodies with a 10-fold increase in neutralizing capability. These antibodies were able to neutralize infectious HCVcc isolates and 4 of 19 (21%) patient-derived HCVpp isolates. Taken together, these results demonstrate that the induction of at least partially cross-neutralizing antibodies is possible. This approach might be useful for the development of a prophylactic HCV vaccine and should also be adaptable to other highly variable viruses.
    PLoS ONE 07/2014; 9(7):e102235. DOI:10.1371/journal.pone.0102235 · 3.23 Impact Factor
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    • "Strong evidence now exists that NAbs play a major role in clearance of HCV infections. Longitudinal analysis of HCV infection cohorts reveals that broadly specific NAb (brNAb) elicited early in infection correlates with viral clearance (Lavillette et al., 2005; Pestka et al., 2007; Dowd et al., 2009). By contrast, people who failed to make NAbs progressed to chronic infection. "
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    ABSTRACT: Despite 20 years of research, a vaccine to prevent hepatitis C virus (HCV) infection has not been developed. A vaccine to prevent HCV will need to induce broadly reactive immunity able to prevent infection by the 7 genetically and antigenically distinct genotypes circulating world-wide. HCV encodes two surface exposed glycoproteins, E1 and E2 that function as a heterodimer to mediate viral entry. Neutralizing antibodies (NAbs) to both E1 and E2 have been described with the major NAb target being E2. The function of E2 is to attach virions to host cells via cell surface receptors that include, but is not limited to, the tetraspanin CD81 and scavenger receptor class B type 1. However, E2 has developed a number of immune evasion strategies to limit the effectiveness of the NAb response and possibly limit the ability of the immune system to generate potent NAbs in natural infection. Hypervariable regions that shield the underlying core domain, subdominant neutralization epitopes and glycan shielding combine to make E2 a difficult target for the immune system. This review summarizes recent information on the role of NAbs to prevent HCV infection, the targets of the NAb response and structural information on glycoprotein E2 in complex with neutralizing antibodies. This new information should provide a framework for the rational design of new vaccine candidates that elicit highly potent broadly reactive NAbs to prevent HCV infection.
    Frontiers in Microbiology 07/2014; 5:329. DOI:10.3389/fmicb.2014.00329 · 3.99 Impact Factor
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