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Background & Aims\ud\udHepatitis D virus (HDV) superinfection in patients with hepatitis B virus (HBV) is associated with rapid progression to liver cirrhosis and hepatocellular carcinoma. Treatment options are limited, and no vaccine is available. Although HDV-specific CD8+ T cells are thought to control the virus, little is known about which HDV epitopes are targeted by virus-specific CD8+ T cells or why these cells ultimately fail to control the infection. We aimed to define how HDV escapes the CD8+ T-cell–mediated response.\ud\ud\udMethods\ud\udWe collected plasma and DNA samples from 104 patients with chronic HDV and HBV infection at medical centers in Europe and the Middle East, sequenced HDV, typed human leukocyte antigen (HLA) class I alleles from patients, and searched for polymorphisms in HDV RNA associated with specific HLA class I alleles. We predicted epitopes in HDV that would be recognized by CD8+ T cells and corresponded with the identified virus polymorphisms in patients with resolved (n = 12) or chronic (n = 13) HDV infection.\ud\ud\udResults\ud\udWe identified 21 polymorphisms in HDV that were significantly associated with specific HLA class I alleles (P < .005). Five of these polymorphisms were found to correspond to epitopes in HDV that are recognized by CD8+ T cells; we confirmed that CD8+ T cells in culture targeted these HDV epitopes. HDV variant peptides were only partially cross-recognized by CD8+ T cells isolated from patients, indicating that the virus had escaped detection by these cells. These newly identified HDV epitopes were restricted by relatively infrequent HLA class I alleles, and they bound most frequently to HLA-B. In contrast, frequent HLA class I alleles were not associated with HDV sequence polymorphisms.\ud\ud\udConclusions\ud\udWe analyzed sequences of HDV RNA and HLA class I alleles that present epitope peptides to CD8+ T cells in patients with persistent HDV infection. We identified polymorphisms in the HDV proteome that associate with HLA class I alleles. Some variant peptides in epitopes from HDV were only partially recognized by CD8+ T cells isolated from patients; these could be mutations that allow HDV to escape the immune response, resulting in persistent infection. HDV escape from the immune response was associated with uncommon HLA class I alleles, indicating that HDV evolves, at the population level, to evade recognition by common HLA class I alleles.

Background & Aims Hepatitis C virus (HCV) transmission from a chronic patient to a susceptible individual is a good opportunity to study viral and host factors that may influence the natural course of hepatitis C infection towards either spontaneous recovery or chronicity. To compare a documented case of a bottleneck event in the sexual transmission of HCV from a chronically infected patient to a recipient host that cleared infection. Methods Host genetic components such as Class I and II HLA and IL28B polymorphism (rs12979860 SNPs) were identified by direct sequencing and LightMix analysis, respectively. Deep nucleotide sequence analysis of quasispecies complexity was performed using massive pyrosequencing platform (454 GS-FLX), and the CD4 specific immune response was characterized by ELISPOT. Results and Conclusions Sequencing analysis and CD4 response highlighted several NS3-helicase domains in which an interplay between amino acid variability and CD4 immune response might have contributed either to chronicity in the donor patient or to viral clearance in the receptor (newly infected) patient.

Methods: HepaRG and PHH were either infected with HBV or transfected with either purified viral nucleocapsid or recombinant HBc protein. Moreover engineered HepaRG cell lines, which express HBV proteins, were also used to analyse the role of individual proteins. Ligands of PRRs were used to engage innate receptor and analyse the inhibitory effect of HBV proteins. HBV replication was analysed with standard procedures, whereas the effect of viral proteins on the expression of various interferons (a, b, l. . . ), interferon-induced (ISG) and pro-inflammatory cytokines genes was analysed by RT-qPCR, WB and ELISA. ChIP experiments were also performed to analyse the binding of HBc to target promoters as well as to analyse the recruitment of epigenome-modifying enzymes to target promoters. Results: HBV is capable to inhibit dsRNA-mediated interferon response after only few hours of infection. This inhibition occurs also with Dane-depleted and UV-inactivated virus suggesting that neo-synthesis of HBV protein is not mandatory. Using engineered cell lines we demonstrate that HBc is responsible for this very early inhibition. The transfection of purified nucleocapsid or recombinant HBc leads to the same inhibitory phenotype. HBc needs to be located in the nucleus to inhibit the transcription of targeted genes (i.e. IFNs, ISG), as inhibition of its trafficking, revert the phenotype. ChIP analyses with anti-HBc revealed that HBc is capable to bind to target promoters and to recruit epigenome-modifying enzymes to establish a negative mark on target promoters. Conclusion: Our results demonstrate that HBc is responsible for the very early inhibition of IFN response by HBV. The precocity of this inhibition is instrumental for the establishment of a persistent infection in vitro and is possible because HBc from incoming virions is capable to inhibit gene expression in the nucleus of infected cells by either direct interference with transcriptional machinery or by recruiting epigenome-modifying enzymes leading to repressive marks.