Development of a heterologous, multigenotype vaccine against hepatitis C virus infection

BACKGROUND: Unquestionably viral diversity and genetic heterogeneity in hepatitis C virus (HCV) infection and other viral diseases play an essential role in viral immune escape and the development of chronicity. Despite this knowledge most vaccine approaches against HCV have excluded this important issue. Moreover the feasibility of developing an effective HCV vaccine has been questioned, mainly because prophylactic immunity against HCV cannot be achieved in chimpanzees by either vaccination or previous HCV infection, and reinfection in men has been reported, most likely due to genetic shift and immune escape. To analyse and characterize a new technique of a 'multigenotype'- and/or 'library'-vaccine, we established an envelope 1 (E1) plasmid vaccine against HCV and characterized humoral and cellular immune responses after vaccination in a mouse model. MATERIAL AND METHODS: Normally genetic information of one or two target proteins is cloned into a DNA-vaccine. In our approach we cloned a defined number of different genotypes and subtypes (defined vaccine, DV) or the genetic information from 20 patients (undefined) into a plasmid (library vaccine, LV). RESULTS: As expected, immunized animals showed both stronger humoral (ELISA) and cellular (T-cell proliferation, ELISPOT) immune responses against genotype 1, since the stimulating antigen was genotype 1 derived. However, not all genotype 1 immunized animals recognized this viral antigen leading to the assumption that some epitopes lost their immunogenicity through a change in the amino acid sequence. Interestingly, some of the genotype 4 and 5 immunized mice sera were able to react against E1 protein. CONCLUSION: Most of the assays showed immune reactivity against the DV or LV vaccine demonstrating the cross-reactive potential of such a vaccination approach. This cloning and immunization strategy based on the viral heterogeneity of the virus has in our view major implications for HCV, a virus with a broad viral genetic diversity, and may become in the future in the context of DNA- or viral-based vaccination strategies a possibility to overcome viral immune escape both in the prophylactic or therapeutic setting.     

Hepatitis viruses: genetic variants and clinical significance

Variants of hepatitis B, C, and delta virus have been identified in patients both with acute and chronic infections. In the hepatitis B virus genome, naturally occurring mutations have been found in all viral genes, most notably in the genes coding for the structural envelope and nucleocapsid proteins. In the hepatitis C virus genome, the regions coding for the structural envelope proteins El and E2, as well as the 3′-contiguous non-structural regionNS1, were found to be hypervariable. Viral variants may be associated with a specific clinical course of the infection, e.g., acute, fulminant or chronic hepatitis. Specific mutations may reduce viral clearance by immune mechanisms (‘vaccine escape’ and ‘immune escape’), response to antiviral therapy (‘therapy escape’), as well as detection (‘diagnosis escape’). The exact contribution, however, of specific mutations to the pathogenesis and natural course of hepatitis B, C, or delta virus infection, including hepatocellular carcinoma development, and the response to antiviral treatment remains to be established.     

Naturally selected hepatitis C virus polymorphisms confer broad neutralizing antibody resistance

For hepatitis C virus (HCV) and other highly variable viruses, broadly neutralizing mAbs are an important guide for vaccine development. The development of resistance to anti-HCV mAbs is poorly understood, in part due to a lack of neutralization testing against diverse, representative panels of HCV variants. Here, we developed a neutralization panel expressing diverse, naturally occurring HCV envelopes (E1E2s) and used this panel to characterize neutralizing breadth and resistance mechanisms of 18 previously described broadly neutralizing anti-HCV human mAbs. The observed mAb resistance could not be attributed to polymorphisms in E1E2 at known mAb-binding residues. Additionally, hierarchical clustering analysis of neutralization resistance patterns revealed relationships between mAbs that were not predicted by prior epitope mapping, identifying 3 distinct neutralization clusters. Using this clustering analysis and envelope sequence data, we identified polymorphisms in E2 that confer resistance to multiple broadly neutralizing mAbs. These polymorphisms, which are not at mAb contact residues, also conferred resistance to neutralization by plasma from HCV-infected subjects. Together, our method of neutralization clustering with sequence analysis reveals that polymorphisms at noncontact residues may be a major immune evasion mechanism for HCV, facilitating viral persistence and presenting a challenge for HCV vaccine development.     

YS01Protective Effect of HLA‐B57 on HCV Genotype 2 Infection in a West African Population

Background Recovery from Hepatitis C virus (HCV) infection is considered infrequent (<20%) in western populations but reaches 50% in West Africa where genotype 2 infection is predominant (Candotti J Virol 2003; 77: 7914). Aim To investigate cellular immune responses as alternative diagnostic of HCV infection and the possible involvement of viral or host genetic factors in recovery. Methods Samples from 104 Ghanaian blood donors screened with anti‐HCV rapid tests and enzyme immunoassay were collected between 2000 and 2005. HCV antibody screening was confirmed using genotype 2 recombinant core, E2 and NS3 proteins by Western blot. HCV viral load and genotype were determined. Cellular response to recombinant HCV genotype 2 proteins was tested by IFN gamma ELISpot on frozen cells. HLA genotype was determined by sequence specific oligonucleotide probes. Results A total of 104 donors were stratified in 37 chronic, 35 recovered infections and 32 false positive. 81% of subjects with chronic infections with RNA detected carried genotype 2 HCV RNA. Cellular immune response was investigated in 35 frozen peripheral blood mononuclear cell (PBMC) samples suitable for interferon‐gamma ELISpot assay. 12 confirmed recovered, one chronically infected and no false positive controls reacted to at least one recombinant protein. The magnitude of response was considerably higher in recovered cases. HLA‐B*57 was significantly more frequent in the group which had recovered from HCV infection compared with chronically infected subjects (P < 0.01, OR = 8.02). This allele is significantly more frequent in West Africa than in Europe or North America. Discussion and conclusions Cases classified as recovered by serological means were confirmed by the presence of T‐cells stimulated by viral proteins. Genotype 2 HCV tends to have lower viral load and better response to anti‐viral treatment suggesting that the local genotype might be more susceptible to immune control. However, genetic factors of the host might also influence the clinical outcome. It could be hypothesised that HLA‐B*5703 is the HLA molecule most efficient at presenting peptides from genotype 2 HCV in this population.     

Characterization of the cellular immune response in hepatitis C virus infection

Hepatitis C virus (HCV), a hepatotropic RNA virus, is a major causative agent of chronic hepatitis, liver cirrhosis, and hepatocellular carcinomas. The host immune responses, especially cellular immune responses, play an important role in viral clearance, liver injury, and persistent HCV infection. A thorough characterization of the HCV cellular immune responses is important for understanding the interplays between host immune system and viral components, as well as for developing effective therapeutic and prophylactic HCV vaccines. Recent advances that provide better understanding the cell immune responses in HCV infection are summarized in this article. © 2009 Wiley Periodicals, Inc. Med Res Rev, 29, No. 6, 843–866, 2009     

Impact of antigenic evolution and original antigenic sin on SARS-CoV-2 immunity

Infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and vaccinations targeting the spike protein (S) offer protective immunity against coronavirus disease 2019 (COVID-19). This immunity may further be shaped by cross-reactivity with common cold coronaviruses. Mutations arising in S that are associated with altered intrinsic virus properties and immune escape result in the continued circulation of SARS-CoV-2 variants. Potentially, vaccine updates will be required to protect against future variants of concern, as for influenza. To offer potent protection against future variants, these second-generation vaccines may need to redirect immunity to epitopes associated with immune escape and not merely boost immunity toward conserved domains in preimmune individuals. For influenza, efficacy of repeated vaccination is hampered by original antigenic sin, an attribute of immune memory that leads to greater induction of antibodies specific to the first-encountered variant of an immunogen compared with subsequent variants. In this Review, recent findings on original antigenic sin are discussed in the context of SARS-CoV-2 evolution. Unanswered questions and future directions are highlighted, with an emphasis on the impact on disease outcome and vaccine design.     

Activation of the unfolded protein response and autophagy after hepatitis C virus infection suppresses innate antiviral immunity in vitro

Autophagy, a process for catabolizing cytoplasmic components, has been implicated in the modulation of interactions between RNA viruses and their host. However, the mechanism underlying the functional role of autophagy in the viral life cycle still remains unclear. Hepatitis C virus (HCV) is a single-stranded, positive-sense, membrane-enveloped RNA virus that can cause chronic liver disease. Here we report that HCV induces the unfolded protein response (UPR), which in turn activates the autophagic pathway to promote HCV RNA replication in human hepatoma cells. Further analysis revealed that the entire autophagic process through to complete autolysosome maturation was required to promote HCV RNA replication and that it did so by suppressing innate antiviral immunity. Gene silencing or activation of the UPR-autophagy pathway activated or repressed, respectively, IFN-β activation mediated by an HCV-derived pathogen-associated molecular pattern (PAMP). Similar results were achieved with a PAMP derived from Dengue virus (DEV), indicating that HCV and DEV may both exploit the UPR-autophagy pathway to escape the innate immune response. Taken together, these results not only define the physiological significance of HCV-induced autophagy, but also shed light on the knowledge of host cellular responses upon HCV infection as well as on exploration of therapeutic targets for controlling HCV infection.     

Viral escape by selection of cytotoxic T cell-resistant variants in influenza A virus pneumonia

Antigenic variation is a strategy exploited by influenza viruses to promote survival in the face of the host adaptive immune response and constitutes a major obstacle to efficient vaccine development. Thus, variation in the surface glycoproteins hemagglutinin and neuraminidase is reflected by changes in susceptibility to antibody neutralization. This has led to the current view that antibody-mediated selection of influenza A viruses constitutes the basis for annual influenza epidemics and periodic pandemics. However, infection with this virus elicits a vigorous protective CD8(+) cytotoxic T lymphocyte (CTL) response, suggesting that CD8(+) CTLs might exert selection pressure on the virus. Studies with influenza A virus-infected transgenic mice bearing a T cell receptor (TCR) specific for viral nucleoprotein reveal that virus reemergence and persistence occurs weeks after the acute infection has apparently been controlled. The persisting virus is no longer recognized by CTLs, indicating that amino acid changes in the major viral nucleoprotein CTL epitope can be rapidly accumulated in vivo. These mutations lead to a total or partial loss of recognition by polyclonal CTLs by affecting presentation of viral peptide by class I major histocompatibility complex (MHC) molecules, or by interfering with TCR recognition of the mutant peptide-MHC complex. These data illustrate the distinct features of pulmonary immunity in selection of CTL escape variants. The likelihood of emergence and the biological impact of CTL escape variants on the clinical outcome of influenza pneumonia in an immunocompetent host, which is relevant for the design of preventive vaccines against this and other respiratory viral infections, are discussed.     

Immunological significance of cytotoxic T lymphocyte epitope variants in patients chronically infected by the hepatitis C virus.

This study was performed to test the hypothesis that cytotoxic T lymphocyte (CTL) selection of hepatitis C virus (HCV) escape variants plays a role in HCV persistence. The peripheral blood CTL responsiveness of patients with well-established chronic hepatitis C to a panel of 10 prototype HCV peptides (genotype 1a) was compared with the corresponding sequences encoded by the infecting viruses in each patient. Variant viral peptide sequences were threefold more frequent in the presence of a CTL response than in its absence, and CTL responses were detected nearly twice as often in association with variant rather than with prototype viral peptide sequences. Furthermore, over half of the patients were infected with potential CTL escape variants that contained nonimmunogenic and noncross-reactive variant peptides many of which displayed reduced HLA-binding affinity. Surprisingly, follow up analysis over a period of up to 46 mo revealed that, in contrast to the relatively high frequency of escape variants initially observed, the subsequent emergence rate of CTL escape variants was very low. Interestingly, the one escape variant that was detected proved to be a CTL antagonist. Collectively, these observations suggest that CTL selection of epitope variants may have occurred in these patients before their entrance into the study and that it may have played a role in HCV persistence. The low apparent rate of ongoing CTL selection in chronically infected patients, however, suggests that if CTL escape occurs during HCV infection it is probably an early event.     

Viral entry and escape from antibody-mediated neutralization influence hepatitis C virus reinfection in liver transplantation

End-stage liver disease caused by chronic hepatitis C virus (HCV) infection is a leading cause for liver transplantation (LT). Due to viral evasion from host immune responses and the absence of preventive antiviral strategies, reinfection of the graft is universal. The mechanisms by which the virus evades host immunity to reinfect the liver graft are unknown. In a longitudinal analysis of six HCV-infected patients undergoing LT, we demonstrate that HCV variants reinfecting the liver graft were characterized by efficient entry and poor neutralization by antibodies present in pretransplant serum compared with variants not detected after transplantation. Monoclonal antibodies directed against HCV envelope glycoproteins or a cellular entry factor efficiently cross-neutralized infection of human hepatocytes by patient-derived viral isolates that were resistant to autologous host-neutralizing responses. These findings provide significant insights into the molecular mechanisms of viral evasion during HCV reinfection and suggest that viral entry is a viable target for prevention of HCV reinfection of the liver graft.Hepatitis C virus (HCV)–related cirrhosis and hepatocellular carcinoma are leading indications for liver transplantation (LT). A major limitation is the universal HCV reinfection of the graft followed by an accelerated course of virus-induced liver disease (Brown, 2005). A prophylactic strategy for prevention of reinfection is lacking, and interferon-based antiviral therapies have limited efficacy and tolerability in LT recipients (Brown, 2005). Thus, recurrent liver disease with poor outcome has become an increasing problem facing hepatologists and transplant surgeons, underlying the urgent need for novel strategies for prevention of reinfection.The development of preventive antiviral strategies has been hampered by a limited understanding of the mechanisms leading to HCV reinfection. Reinfection occurs within a few hours of graft reperfusion despite the presence of anti-HCV antibodies (Brown, 2005). Evolution of viral quasispecies rapidly changes after transplantation, and only a small fraction of viral variants present before transplantation is selected after LT (Moreno Garcia et al., 2003; Feliu et al., 2004; Brown, 2005; Schvoerer et al., 2007). These observations suggest that HCV has developed efficient strategies to evade host immunity and adapt rapidly to the new host environment. The mechanisms by which viral variants are selected and HCV evades host immunity to establish persistence in transplanted patients are not understood.HCV has a very high replication rate, and the highly error-prone viral polymerase allows for rapid production of minor viral variants that may outpace humoral and cellular immune responses (Bowen and Walker, 2005; Ray et al., 2005; von Hahn et al., 2007; Uebelhoer et al., 2008; Aurora et al., 2009; Dazert et al., 2009). These variants are under constant immune pressure in the infected host, and selection processes lead to domination of the viral quasispecies by the most fit virus that can also evade immune recognition (Uebelhoer et al., 2008).Both viral and host factors are potential determinants for evasion from host responses and adaptation of the virus after transplantation. Viral entry is the very first step of HCV infection (Evans et al., 2007; Zeisel et al., 2007, 2008; von Hahn and Rice, 2008; Ploss et al., 2009) and is thus an important factor for initiation of infection of the naive liver graft. Moreover, viral entry is a major target of neutralizing antibodies, a first-line host defense inhibiting viral spread. Indeed, the rapid induction of cross-neutralizing antibodies in the very early phase of infection has been suggested to contribute to control of HCV infection (Lavillette et al., 2005; Pestka et al., 2007).In this study, we aimed to investigate whether viral entry and escape from neutralizing antibodies are determinants for viral evasion and persistence during the very early phase of graft infection. Infectious retroviral HCV pseudoparticles (HCVpps) have been shown to represent a robust and valid system for the study of HCV entry and antibody-mediated neutralization in clinical cohorts (Lavillette et al., 2005; Dreux et al., 2006; Pestka et al., 2007; Grove et al., 2008; Haberstroh et al., 2008; Zeisel et al., 2008; Witteveldt et al., 2009). Using HCVpps bearing viral envelope glycoproteins derived from patients undergoing LT, we show that efficient viral entry and escape from antibody-mediated neutralization are key determinants for selection of viral variants reinfecting the liver graft. Furthermore, we demonstrate that mAbs directed against viral or host entry factors efficiently cross-neutralized infection of human hepatocytes by patient-derived viral isolates that were resistant to autologous host-neutralizing responses. These results define the molecular mechanisms of viral evasion during HCV reinfection and suggest that viral entry is a viable target for the prevention of HCV reinfection of the liver graft.     

Mutational escape from CD8+ T cell immunity: HCV evolution, from chimpanzees to man

The mechanisms by which the hepatitis C virus (HCV) establishes persistence are not yet fully understood. Previous chimpanzee and now human studies suggest that mutations within MHC class I-restricted HCV epitopes might contribute to viral escape from cytotoxic T lymphocyte (CTL) responses. However, there are several outstanding questions regarding the role of escape mutations in viral persistence and their fate in the absence of immune selection pressure.     

Secretion of Hepatitis C Virus Envelope Glycoproteins Depends on Assembly of Apolipoprotein B Positive Lipoproteins

The density of circulating hepatitis C virus (HCV) particles in the blood of chronically infected patients is very heterogeneous. The very low density of some particles has been attributed to an association of the virus with apolipoprotein B (apoB) positive and triglyceride rich lipoproteins (TRL) likely resulting in hybrid lipoproteins known as lipo-viro-particles (LVP) containing the viral envelope glycoproteins E1 and E2, capsid and viral RNA. The specific infectivity of these particles has been shown to be higher than the infectivity of particles of higher density. The nature of the association of HCV particles with lipoproteins remains elusive and the role of apolipoproteins in the synthesis and assembly of the viral particles is unknown. The human intestinal Caco-2 cell line differentiates in vitro into polarized and apoB secreting cells during asymmetric culture on porous filters. By using this cell culture system, cells stably expressing E1 and E2 secreted the glycoproteins into the basal culture medium after one week of differentiation concomitantly with TRL secretion. Secreted glycoproteins were only detected in apoB containing density fractions. The E1–E2 and apoB containing particles were unique complexes bearing the envelope glycoproteins at their surface since apoB could be co-immunoprecipitated with E2-specific antibodies. Envelope protein secretion was reduced by inhibiting the lipidation of apoB with an inhibitor of the microsomal triglyceride transfer protein. HCV glycoproteins were similarly secreted in association with TRL from the human liver cell line HepG2 but not by Huh-7 and Huh-7.5 hepatoma cells that proved deficient for lipoprotein assembly. These data indicate that HCV envelope glycoproteins have the intrinsic capacity to utilize apoB synthesis and lipoprotein assembly machinery even in the absence of the other HCV proteins. A model for LVP assembly is proposed.     

Immunizations with chimeric hepatitis B virus-like particles to induce potential anti-hepatitis C virus neutralizing antibodies

BACKGROUND: Virus-like particles (VLPs) are highly immunogenic and proven to induce protective immunity. The small surface antigen (HBsAg-S) of hepatitis B virus (HBV) self-assembles into VLPs and its use as a vaccine results in protective antiviral immunity against HBV infections. Chimeric HBsAg-S proteins carrying foreign epitopes allow particle formation and have the ability to induce anti-foreign humoral and cellular immune responses. METHODS/RESULTS: The insertion of the hypervariable region 1 (HVR1) sequence derived from the envelope protein 2 (E2) of hepatitis C virus (HCV) into the major antigenic site of HBsAg-S ('a'-determinant) resulted in the formation of highly immunogenic VLPs that retained the antigenicity of the inserted HVR1 sequence. BALB/c mice were immunized with chimeric VLPs, which resulted in antisera with anti-HCV activity. The antisera were able to immunoprecipitate native HCV envelope complexes (E1E2) containing homologous or heterologous HVR1 sequences. HCV E1E2 pseudotyped HIV-1 particles (HCVpp) were used to measure entry into HuH-7 target cells in the presence or absence of antisera that were raised against chimeric VLPs. Anti-HVR1 VLP sera interfered with entry of entry-competent HCVpps containing either homologous or heterologous HVR1 sequences. Also, immunizations with chimeric VLPs induced antisurface antigen (HBsAg) antibodies, indicating that HBV-specific antigenicity and immunogenicity of the 'a'-determinant region is retained. CONCLUSIONS: A multivalent vaccine against different pathogens based on the HBsAg delivery platform should be possible. We hypothesize that custom design of VLPs with an appropriate set of HCV-neutralizing epitopes will induce antibodies that would serve to decrease the viral load at the initial infecting inoculum.     

DNA vaccines.

Chronic infections with hepatitis B (HBV) and hepatitis C (HCV) virus are worldwide problems often leading to the development of chronic liver disease and hepatocellular carcinoma. Genetic immunizations with DNA encoding for structural and nonstructural proteins of HCV and HBV in experimental mice generate a broad base CD4+ and CD8+ cellular immune response which may be required for viral clearance from the host. DNA based immunization is a promising antiviral approach for the development of therapeutic and prophylactic vaccine against HBV and HCV.     

Design of a multi-epitope vaccine against SARS-CoV-2: immunoinformatic and computational methods

A novel infectious agent, SARS-CoV-2, is responsible for causing the severe respiratory disease COVID-19 and death in humans. Spike glycoprotein plays a key role in viral particles entering host cells, mediating receptor recognition and membrane fusion, and are considered useful targets for antiviral vaccine candidates. Therefore, computational techniques can be used to design a safe, antigenic, immunogenic, and stable vaccine against this pathogen. Drawing upon the structure of the S glycoprotein, we are trying to develop a potent multi-epitope subunit vaccine against SARS-CoV-2. The vaccine was designed based on cytotoxic T-lymphocyte and helper T-lymphocyte epitopes with an N-terminal adjuvant via conducting immune filters and an extensive immunoinformatic investigation. The safety and immunogenicity of the designed vaccine were further evaluated via using various physicochemical, allergenic, and antigenic characteristics. Vaccine-target (toll-like receptors: TLR2 and TLR4) interactions, binding affinities, and dynamical stabilities were inspected through molecular docking and molecular dynamic (MD) simulation methods. Moreover, MD simulations for dimeric TLRs/vaccine in the membrane-aqueous environment were performed to understand the differential domain organization of TLRs/vaccine. Further, dynamical behaviors of vaccine/TLR systems were inspected via identifying the key residues (named HUB nodes) that control interaction stability and provide a clear molecular mechanism. The obtained results from molecular docking and MD simulation revealed a strong and stable interaction between vaccine and TLRs. The vaccine''s ability to stimulate the immune response was assessed by using computational immune simulation. This predicted a significant level of cytotoxic T cell and helper T cell activation, as well as IgG, interleukin 2, and interferon-gamma production. This study shows that the designed vaccine is structurally and dynamically stable and can trigger an effective immune response against viral infections.

SARS-CoV-2 infections have spread throughout the world and became a rapidly emerging public health issue. The immunoinformatics approach was applied to design a potent multi-epitope vaccine against this deadly virus.     

Immune responses against human papillomavirus (HPV) infection and evasion of host defense in cervical cancer

Human papillomavirus (HPV) is the most important etiological factor for cervical cancer. A recent study demonstrated that more than 20 HPV types were thought to be oncogenic for uterine cervical cancer. Notably, more than one-half of women show cervical HPV infections soon after their sexual debut, and about 90 % of such infections are cleared within 3 years. Immunity against HPV might be important for elimination of the virus. The innate immune responses involving macrophages, natural killer cells, and natural killer T cells may play a role in the first line of defense against HPV infection. In the second line of defense, adaptive immunity via cytotoxic T lymphocytes (CTLs) targeting HPV16 E2 and E6 proteins appears to eliminate cells infected with HPV16. However, HPV can evade host immune responses. First, HPV does not kill host cells during viral replication and therefore neither presents viral antigen nor induces inflammation. HPV16 E6 and E7 proteins downregulate the expression of type-1 interferons (IFNs) in host cells. The lack of co-stimulatory signals by inflammatory cytokines including IFNs during antigen recognition may induce immune tolerance rather than the appropriate responses. Moreover, HPV16 E5 protein downregulates the expression of HLA-class 1, and it facilitates evasion of CTL attack. These mechanisms of immune evasion may eventually support the establishment of persistent HPV infection, leading to the induction of cervical cancer. Considering such immunological events, prophylactic HPV16 and 18 vaccine appears to be the best way to prevent cervical cancer in women who are immunized in adolescence.     

Hepatitis C infection of B lymphocytes: more tools to address pending questions

Evaluation of: Durand T, Di Liberto G, Colman H et al. Occult infection of peripheral B cells by hepatitis C variants which have low translational efficiency in cultured hepatocytes. Gut 59, 934–942 (2010).

Hepatitis C virus (HCV) infection spreads primarily via contact with infected blood and can establish a persistent infection in 80% of infected individuals, progressively causing chronic liver disease that can lead to hepatocellular carcinoma or end-stage liver disease requiring a transplant. There is no vaccine, and current treatment with interferon and ribavirin is costly, poorly tolerated and ineffective for a large proportion of patients. Technical limitations have stifled the study of HCV immunology, and hence the correlates of resolution remain elusive. HCV robustly infects hepatocytes in the liver, yet HCV RNA is often found to be associated with peripheral blood lymphocytes and extrahepatic manifestations of the disease include B-cell abnormalities. The few existing characterized viral clones that can replicate in vitro have consistently failed to infect immune cells; however, some groups have detected low levels of replication in peripheral blood cells, hinting that occult forms of infection may be possible. HCV lymphotropism remains a controversial subject that needs to be elucidated in order to identify viral reservoirs that may provide targets for therapeutic intervention. The precise interactions between HCV and immune cells need to be determined to establish if the virus has developed mechanisms to modulate immune responses. In the study by Durand et al., correlations were sought between cell tropism and mutations in the 5´ noncoding region of the HCV genome, known as the internal ribosome entry site. Key findings are discussed here, highlighting current experimental challenges that surround the topic of HCV lymphotropism.     

Virus-Host Coevolution: Common Patterns of Nucleotide Motif Usage in Flaviviridae and Their Hosts

Virus-host biological interaction is a continuous coevolutionary process involving both host immune system and viral escape mechanisms. Flaviviridae family is composed of fast evolving RNA viruses that infects vertebrate (mammals and birds) and/or invertebrate (ticks and mosquitoes) organisms. These host groups are very distinct life forms separated by a long evolutionary time, so lineage-specific anti-viral mechanisms are likely to have evolved. Flaviviridae viruses which infect a single host lineage would be subjected to specific host-induced pressures and, therefore, selected by them. In this work we compare the genomic evolutionary patterns of Flaviviridae viruses and their hosts in an attempt to uncover coevolutionary processes inducing common features in such disparate groups. Especially, we have analyzed dinucleotide and codon usage patterns in the coding regions of vertebrate and invertebrate organisms as well as in Flaviviridae viruses which specifically infect one or both host types. The two host groups possess very distinctive dinucleotide and codon usage patterns. A pronounced CpG under-representation was found in the vertebrate group, possibly induced by the methylation-deamination process, as well as a prominent TpA decrease. The invertebrate group displayed only a TpA frequency reduction bias. Flaviviridae viruses mimicked host nucleotide motif usage in a host-specific manner. Vertebrate-infecting viruses possessed under-representation of CpG and TpA, and insect-only viruses displayed only a TpA under-representation bias. Single-host Flaviviridae members which persistently infect mammals or insect hosts (Hepacivirus and insect-only Flavivirus, respectively) were found to posses a codon usage profile more similar to that of their hosts than to related Flaviviridae. We demonstrated that vertebrates and mosquitoes genomes are under very distinct lineage-specific constraints, and Flaviviridae viruses which specifically infect these lineages appear to be subject to the same evolutionary pressures that shaped their host coding regions, evidencing the lineage-specific coevolutionary processes between the viral and host groups.     

Simultaneous targeting of HCV replication and viral binding with a single lentiviral vector containing multiple RNA interference expression cassettes.

Chronic hepatitis C virus (HCV) infection has a major medical impact and current treatments are often unsuccessful. RNA interference represents a promising new approach to tackling this problem. The current study details the design and testing of self-inactivating lentiviral vectors (LV) delivering RNA interference to prevent HCV replication and infection. Vectors were constructed with single, double, and triple cassettes expressing short hairpin RNAs (shRNAs) simultaneously targeting two regions of the HCV 1b genome and the host cell receptor, CD81. The shRNAs directed against HCV IRES or NS5b regions were shown to be effective in inhibiting HCV replication in vitro (82 and 98%, respectively). No evidence of shRNA-related interferon production was observed. Vectors containing CD81 shRNA reduced cell surface expression up to 83% and reduced cell binding of HCV surface protein E2 up to 82% while not affecting levels of unrelated surface protein (Ber-EP4) or HCV replication. Double or triple shRNA vectors were independently effective in simultaneously reducing HCV replication, CD81 expression, and E2 binding. This study demonstrates lentiviral delivery of multiple shRNA, inhibiting HCV in a specific, IFN-independent, manner. The targeting of multiple viral and host cell elements simultaneously by RNAi could increase the potency of antiviral gene therapies.