<<

REVIEW ARTICLE Molecular Biology of C Kenneth E. Drazan

Hepatitis C infection (HCV) is an emerging epidemic. not be ascribed to any of the hepatic known at specialists are managing this disease with limited that time (, , and hepatitis delta scientific information about the underlying pathogenesis viruses). The discovery and characterization of a novel and treatment. The current review offers a molecular dissection of infection, a snapshot of the HCV life cycle, RNA with characteristics typical of the family and emerging strategies for antiviral therapy. (Liver Flaviviridae4 provided the tools to study the epidemio- Transpl 2000;6:396-406.) logical importance of this agent in these cases of Non A Non B hepatitis (NANBH). The virus, known as ersistent infection with virus (HCV) is HCV, was shown to be the cause of most cases of the predominant cause of chronic in NANBH. More than 50% of the patients become P 5 the United States, and the World Health Organization chronic carriers. The persistent infection commonly recently estimated that 3% of the world’s population results in chronic active hepatitis, which may lead to 6,7 has been infected with this pathogen.1 This statistic liver and . Ran- suggests those 170 million chronic carriers of HCV are dom screening of blood donor populations has indi- at risk for developing cirrhosis and/or liver cancer. cated as many as 500 million chronic carriers of the Together with alcoholic liver disease, hepatitis C is the virus worldwide, highlighting HCV as a major human 8 most common cause of cirrhosis and the major indica- pathogen. tion for liver transplantation in the United States. After liver transplantation, recurrence of HCV infection is Biological Process of Infection common, but in many cases, the hepatitis is mild and the long-term survival rate averages 65% after 5 years.2 To discuss the relevance of antiviral therapy and its At the current rate of infection, the pool of patients future, it is necessary to first review current knowledge with chronic hepatitis C would increase by 4% in the of the virus. Unfortunately, approaches to the develop- next decade. At the current attack rate of infection, the ment of in vitro replication systems for propagation of number of deaths caused by HCV in the United States this virus have been particularly difficult, and reliable is estimated at 8,800/yr, but by the year 2008, this may systems for efficient long-term virus replication are reach 35,000.3 irreproducible. Nevertheless, reports of virus replica- 9 Despite increasing experience in the medical and tion have been made using systems from hepatic tissue 10 surgical management of HCV-related disease, this and peripheral-blood mononuclear cells. In vitro pathogen, its biological characteristics, and the tempo infection systems have been reported from human T- 11,12 13 of recurrence using a varying immunosuppressive and B-cell lines, human fetal liver cells, and 14 cocktail are not completely understood. These notions chimpanzee . compel liver transplantation physicians to rapidly One of the most promising in vitro infection familiarize themselves with HCV.Toward this end, this systems reported to date uses human hepatoma cells in review integrates current knowledge of the molecular which a subgenomic portion of the virus persisted for 104 mechanisms of HCV pathogenesis. up to a year postinfection. Additional evidence was 15 Toward the end of the 1980s, a significant number reported by Sun and Feitelson that HepG2 cells are of cases of parenterally transmitted could tropic and supportive of a consensus HCV RNA . Data reported by Mizutani et al16 and Sugiyama et al17 using the human T-lymphotrophic From the Liver Transplant Program, Stanford University, Palo Alto, virus type 1–infected T-cell (HTLV-1) line, MT-2, also CA. supported viral expression. In these studies, there was Address reprint requests to Kenneth E. Drazan, MD, 750 Welch Rd, apparent selection from the of a Suite 319, Palo Alto, CA 94304. Telephone: 650-498-5688; FAX: single genomic sequence, presumably representing a 650-498-5690; E-mail: [email protected] virus naturally adapted for growth in this cell line. Copyright ௠ 2000 by the American Association for the Study of Liver Diseases Whether the viruses in these studies, which are appar- 1527-6465/00/0604-0001$3.00/0 ently adapted for tissue culture growth, can replicate in doi:10.1053/jlts.2000.6449 other cell lines remains to be established.

396 Liver Transplantation, Vol 6, No 4 (July), 2000: pp 396-406 Molecular Biology of HCV 397

Animal models of HCV infection have been as virally infected liver by lethal irradiation, followed by challenging to devise as the dissection of the virus itself. severe combined immunodeficiency mouse bone mar- The chimpanzee was recognized early as a useful study row reconstitution. The durability of this system to subject in the pathogenesis of HCV. Early in the field show HCV in the serum extended to greater than 30 of HCV research, the chimpanzee model proved days.105 The system is currently being used for the critical to the determination of the physicochemical evaluation of antiviral compounds and neutralizing analysis of the virus. For instance, treatment of infec- antibody preparations. tious human sera with lipid solvents led to viral Examination of the viral particle itself has shed light inactivation, thus identifying its harbored lipid enve- on a potential mechanism for into human lope.18 The model was also used for evaluating a tissue. The size of the viral particle (virion) was number of procedures for inactivating the virus in previously estimated at 80 nm by ultracentrifugation,22 biological products, such as formalin, chloroform, whereas filtration studies suggested 30 Ϯ 60 nm.23 heat, and ultraviolet radiation. Several studies have shown that the buoyant density of The greatest benefit from the chimpanzee model HCV in infectious serum is less than that in noninfec- was making genetic characterization of the virus pos- tious serum,24 and the density (1 Ϯ 06 g/mL) sug- sible. In this model, the nonhuman primate was used gested an association with the low-density lipoprotein as an in vivo propagation system to achieve sufficient (LDL) fraction,25 which was subsequently verified by quantities of virus to perform sequencing and muta- Prince et al.26 Typically, HCV-infected serum also tional analysis. contains a higher density fraction in which the virus Despite its cost and obvious limitations, informa- isadherent to immunoglobulins.24 As expected, virus in tion from nonhuman primates has led to a plethora of the lipoprotein fraction appears to be relatively more critical molecular observations. A brief list of these infectious than the antibody-coated fraction. Using achievements follows: (1) genetic drift occurs in the very low-density lipoprotein (VLDL)–associated virus, hypervariable region (HVR) of the envelope proteins, highly purified particles have been observed that (2) antibodies directed against these epitopes may be appear to have prominent spikes on their surface,27 protective in naive subjects, (3) regions of the viral probably representing portions of the genome critical to in vitro infection are also essential in viral lipid coat. The observation of an association live subjects, and (4) the nature and tempo of the early between HCV and lipoproteins may be critical for the cellular immune response dictates viral eradication virus replication cycle because LDL and VLDL are versus chronic infection. A recent presentation by taken up by hepatocytes through the LDL receptor Barryetal19 from Stanford University on the use of (LDLR, discussed next). complementary DNA microarray (gene chip) technol- ogy showed a pattern of genetic responses within the of chimpanzees inoculated with HCV. In this Identifying the HCV Receptor provocative report, the evaluation of hepatic messenger Insight into the mechanism by which HCV gains entry RNA after HCV infection (24 hours) showed a classic into host cells is critical to understanding primary inflammatory response, angiogenesis, and attenuation infection and reinfection posttransplantation. Current of extracellular matrix degradation. Later time points research has focused on 2 molecular ligands as loci for (3 days) confirmed a T-lymphocyte presence but an viral attachment and entry into human tissue (Fig. 1). attenuated CD4 response. As previously mentioned, an early observation in the Two other novel systems are worth mentioning, study of HCV is its association with the lipoprotein although their contributions remain to be seen. Xie et fraction of human sera. The observation that HCV is al reported on the successful infectivity of primary associated with LDL,26 VLDL,26,28 and immunoglobu- hepatocytes obtained from the tree shrew, Tupaia lins24,25,29 has led to the assumption that these com- belangeri, a small primate, using HCV-positive serum. plexes favor binding of the virus to target cells. LDL is The study only examined short-term parameters, but internalized by LDLR-mediated endocytosis.30 The the prospect of a small-animal model for such studies is LDLR is the main representative of a family of hopeful.20 A unique murine system, referred to as the cell-surface receptors (LDLR gene family) that share Trimera Mouse System, has been devised at the characteristic sequences; for example, a ligand-binding Weizmann Institute of Science for the in vivo analysis domain.31 Members of the LDLR gene family function of human viruses.21 In this experimental model, nor- as receptors for minor-group virus32 and mal mice are prepared for implantation of normal or subgroup A Rous sarcoma virus.33 This suggests the 398 Kenneth E. Drazan

Figure 1.

Figure 2.

Figure 3. Molecular Biology of HCV 399 possibility that the LDLR (or members of the gene Does this prove that CD81 is the cellular receptor for family) might also function as a receptor for HCV. HCV? Certainly not, but the findings of CD81 Although these studies provide firm evidence for HCV localizing with HCV has interesting implications for virion binding to the LDLR, internalization through the coexistent syndromes manifest in patients with this ligand was not shown. chronic active hepatitis C. HCV infection is associated More convincing evidence was presented in a recent with B-cell lymphoproliferative disorders, such as study in which cells and mice null for LDLR that were mixed-type II cryoglobulinemia38 and non-Hodgkin’s resistant to viral entry were rendered susceptible to .39 On B cells, it has been observed that infection by genetic engineering with the human CD81 is a member of a signaling complex which LDLR.34 At present, it must be considered that other regulates the threshold for B-cell activation and prolif- receptors for HCV belonging to the LDLR gene family eration. Could a population of individuals exist with or others exist that may also mediate the binding and CD81 polypmorphisms such that they may be resistant uptake of HCV. to HCV tropism? Unfortunately, no clinical studies to A second suspect responsible for HCV tropism is date have identified such individuals. Although murine CD81.35 The HCV envelope protein, E2, binds hu- models of CD81 knockouts have been developed man CD81,36 a ubiquitously expressed transmembrane without lethality,40 testing HCV infection in this molecule belonging to the family of tetraspanins. experimental model is untenable because of lack of CD81 expression on B lymphocytes has been shown to species tropism. be critical for HCV envelope protein E2 binding.37 Molecular Analysis of the HCV Genome ; Figure 1. HCV particles are associated with LDL and The genomic organization of HCV is shown schemati- VLDL molecules in the circulation of infected humans. In cally in Figure 2. Genomic organization of HCV RNA addition, the LDL receptor has been identified as capable indicated the virus is closely related to the pestivirus of transporting HCV particles across the cell membrane. genera within the family, , but has now CD81 is a ubiquitously expressed tetraspan molecule that been classified in its own subgenera, Hepacicvirus. The also associates with HCV. The protein, E2, binds 1 of the extracellular domains of CD81; however, viral genome is a single-stranded RNA molecule the consequence of this discrete interaction is less well approximately 9.5 kb in length that is positive sense understood. After viral binding to its cellular receptor, and possesses a unique open-reading frame, coding for HCV sheds its lipid envelope to deliver its genetic load a single polyprotein. The viral genome is flanked by (RNA) and structural proteins into the cytosol. untranslated regions (UTRs) at its 5Ј and 3Ј ends. The Figure 2. The organization of the hepatitis C genome is length of the polyprotein-encoding region varies accord- similar to other RNA viruses, such as and pestivirus. ing to the isolate and of the virus from 3,008 The genome is 9.5 kb in length and has a single internal to 3,037 amino acids.41 Apart from differences in coding and 2 flanking noncoding regions. The coding length, HCV (subfamilies) show diversities region contains the genetic information for 9 viral of approximately 30% in the sequences of proteins, 3 structural (core, envelope 1, envelope 2), and 6 nonstructural (NS2 to 5). The nonstructural proteins are their whole, showing at least 6 genotypes and more members of the replicase complex. Both structural and than 30 subtypes throughout the world.42 The impor- nonstructural proteins have been implicated in modulat- tance of the genomic heterogeneity is that some ing the host immune response and carcinogenesis. The Ј Ј genotypes appear to be associated with more severe flanking noncoding regions (5 UTR and 3 UTR) are pathological states and are more refractory to treat- unique RNA molecules that usurp and orchestrate the 42 host cell machinery to convert the viral RNA genome into ment. Genotyping is becoming a common clinical viral proteins. assay in the management of newly diagnosed HCV, but not during clinical flare or after liver transplantation. Figure 3. The HCV genome, delivered to the cytoplasm after viral infection, harnesses the cell’s to 5ЈUTR translate viral RNA into viral proteins. This critical step is initiated by the 5ЈUTR by virtue of its unique and highly An obvious characteristic of HCV is the presence of a conserved secondary structure, termed the internal ribo- long UTR at the 5Ј end of the genome, and detailed some entry site (IRES). This strategy is rarely used by molecular analysis indicates polyprotein synthesis is human genes except under stress. Complete of 43 the viral genome, proceeding from 5Ј to 3Ј, results in the initiated at the internal end of this region. This production of a single viral polyprotein that must be region of the genome was predicted by its primary reduced to subunits to effect viral replication. sequence to form extensive secondary structures,44 400 Kenneth E. Drazan which were biochemically confirmed by Brown et al.45 several host immunoregulatory genes,55 as well as Furthermore, a survey of the sequences within the 5Ј interference in expression of coinfecting of UTR from 39 different isolates and genotypes of HCV hepatitis B56 and human immunodeficiency viruses.57 showed remarkable sequence conservation.46 This re- Perhaps the most interesting recent observations have gion is the most conserved of the genome, a character- been that core can specifically suppress apoptotic cell istic allowing it to be used as a diagnostic locus death in artificial systems58 and also specifically interact (genotype) and marker (HCV RNA) by polymerase with the cytoplasmic tail of the lymphotoxin-␤ recep- chain reaction.47 Within this region, the majority of tor, a member of the family.59 genotypes of HCV possess a translation initiation locus Because lymphotoxin-␤ receptor is known to be closely resembling that of other RNA viruses, such as involved in apoptotic signaling, this strongly suggests polio and influenza.48 This genetic organization is that core may have an immunomodulatory function termed an internal ribosomal entry site (IRES), which and a critical role in the establishment of persistence differentiates the mechanism for viral gene expression and disease pathogenesis. (cap independent) from nearly 98% of human gene Finally, a recent report60 shows an association products (cap dependent).49 The function of the HCV between the core protein and the surface of lipid IRES therefore seems to be to provide a structure able droplets within the cytoplasm. Analysis of the triglycer- to specifically engage the for translation ide populations within the cell indicates that core initiation (protein production; Fig. 3). As in other protein expression stimulates a change in cellular IRES examples (, influenza virus, hepatitis metabolism of triglycerides. Because a characteristic of A), this interaction probably involves complexes with HCV infection is liver steatosis, it is plausible that this cellular proteins.50 is a result of the direct effect of the core protein on lipid metabolism. Virus-Encoded Proteins The nascent viral polyprotein is processed (matured Envelope Proteins E1 and E2 and cleaved) by a combination of host and viral The major viral structural envelope proteins are the proteinases into mature structural proteins and non- , E1 and E2, which are released from the structural (NS) viral enzymes51 (Fig. 3). Proteolytic viral polyprotein by the action of host-cell signal processing of the HCV polyprotein results in at least peptidases. Apart from the interest in understanding 10 distinct viral proteins: core (capsid), E1 (envelope), the biological processes of assembly and morphogen- E2, NS2, NS3, NS4a, NS4b, NS5a, and NS5b. The esis, both E1 and E2 have been extensively studied in structural proteins are located in the amino terminal terms of antigenic variation and mechanisms of persis- (proximal) one third, and the replicative enzymes are tence and are obviously major components of proto- located within the carboxy terminal (distal) two thirds type studies for HCV. E2 presumably repre- of the polyprotein. The initial cleavage of the polypro- sents the most variable region of the HCV genome.61 tein is likely mediated by a host (human) signal This variation is assumed to be caused by random proteinase.52 The viral proteins themselves mediate mutation and selection of mutants capable of escaping further division of the polyprotein.53 from neutralizing antibodies produced in the host. Furthermore, antibodies against E2 correlate with Core protection from HCV challenge in chimpanzees. Di- The protein located at the amino terminus of the rect assays are now available for neutralizing antibodies polyprotein is highly basic in nature and considered in serum62 or in vitro culture.29 likely to be the viral core (capsid) protein. It is released Within the E2 sequence are regions of extreme from the viral polyprotein by nascent proteolytic hypervariability (HVR) that have been the focus of cleavage at amino acid 191 by cellular, not viral, more detailed study; one specific domain is known as .52 The subcellular trafficking of the core HVR-1.63 This region has been suggested to be protein has been an area of interest. In particular, the particularly important in HCV neutralization because nucleolar localization of core may be caused by its of its extreme variability and because this variability ability to bind to ribosomes assembled in the nucleus.54 was not observed in a patient with agammaglobulin- The biological functions of the core protein found emia, even over 2 to 5 years.64 Antibodies to HVR-1 in in the nucleus, if this also occurs in natural virus patient sera have been shown to neutralize binding of replication, are still unclear. Several studies have re- E2,65 whereas peptide antibodies raised to this region ported the suppression by core of transcription of are able to block infection in tissue culture66 and have Molecular Biology of HCV 401 shown efficacy in chimpanzee challenge experiments.67 NS4 Despite this observed protective capacity of antibody, The NS4 region of the polyprotein comprises 2 the extreme heterogeneity in the sequence of this proteins; namely, NS4a and NS4b. Both these proteins epitope in diverse virus strains means that its use in a are released from the viral polyprotein by the NS3 prophylactic vaccine strategy remains doubtful. serine by cis cleavage at the NS3/NS4a and The most striking recent observation for E2 is its trans cleavage at the NS4a/NS4b and NS4b/NS5a putative role in obstructing the innate immune re- junction.73 NS4a is a small protein, approximately 8 68 sponse to HCV replication. The HCV envelope kd, and appears to have diverse functions, such as protein, E2, contains a sequence identical with phos- anchorage of replication complexes and a for phorylation sites of the (IFN)-inducible the NS3 protease (discussed previously).74 Currently, protein kinase (PKR), and the translation initiation there is no ascribed function for the NS4b protein, but factor, eIF2, a target of PKR. In this study, cells it likely has an integral role within HCV replication engineered to express E2 did not manifest normal complexes. kinase activity of PKR, resulting in unregulated protein synthesis and cell growth. This interaction of E2 and NS5a and NS5b PKR may be one mechanism by which HCV circum- The NS5 region of the polyprotein is composed of 2 vents the antiviral effect of interferon. major proteins, NS5a and NS5b, which are released as mature products by the action of the NS3 protease in NS2 conjunction with NS4a. The functional role of NS5a is The NS2 protein is a transmembrane protein with its currently unclear. Apart from the probable role of carboxy terminus translocated into the lumen of the NS5a in the HCV replication cycle, recent evidence (ER) while its amino terminus suggested that it may be a critical factor in determining lies in the cytosol.69 Although immunoprecipitation the susceptibility of the virus to treatment with IFN. It studies51 showed that NS2 is closely associated with the was initially reported that interferon sensitivity corre- structural proteins, the biological function of the lated with mutations within a discrete region of NS5a. majority of the NS2 protein is still unclear. Subsequently, this domain was named the IFN sensitiv- ity–determining region.75,76 Further evidence indicated that this likely occurred through a direct interaction of NS3 NS5a with the IFN-induced protein kinase, PKR, a The region coding for the NS3 protein has been the cellular mediator of IFN-induced antiviral resis- most extensively studied of the entire genome. The tance.77,78 Because PKR is a critical factor in the host NS3 protein has been shown in numerous studies to be response to IFN,79 its inactivation by NS5a may be a approximately 70 kd and to possess several diverse major mechanism by which HCV evades the host biochemical functions.70 Initial genomic analysis of immune response.80 Furthermore, restrained PKR ac- this region of the molecule showed that it could be tivity in the face of carcinogenic stress on cells infected characterized as a . Studies subsequently with HCV (e.g., hepatocytes and B lymphocytes) may showed that the NS3 protease was entirely responsible permit transformation into the malignant state.81,82 for proteolytic processing of the entire downstream The sequence of the NS5b protein is highly con- region of the viral polyprotein.71 The overall proteo- served, not only between different strains of HCV, but lytic pathway for the whole viral genome is shown in also in other RNA viruses. In particular, the amino acid Figure 3, implying that the NS3 protease mediates motif, G-D-D, is totally conserved in HCV, aviviruses, proteolysis at the NS3/NS4a, NS4a/NS4b, NS4b/ poliovirus, and tobacco mosaic virus.83 This motif is a NS5a, and NS5a/NS5b junctions to release the mature characteristic of all known RNA-dependent RNA NS3, NS4a, NS4b, NS5a, and NS5b proteins. How- polymerases (RdRp), and therefore the function of ever, there are subtle biochemical differences in the NS5b in HCV has been speculated to be the viral exact mechanism by which NS3 mediates these cleav- polymerase. The role of the viral polymerase in HCV ages. Further analysis of the NS3 protein also showed replication is to convert the single-strand genome into motifs characteristic of RNA enzymatic func- a faithful intermediate negative strand for subsequent tion (unwinding of RNA for replication and protein and repetitive production of positive strands for virion translation; Fig. 4).72 This molecule is therefore in- production (Fig. 4).74 This step in the viral replication volved in critical events of viral replication, thus cycle is responsible for the creation of quasispecies making it an attractive target for antiviral therapy. (unfaithfully reproduced genomes).84 This inefficient 402 Kenneth E. Drazan

Figure 4. Viral replication oc- curs after translation of the HCV genome from viral RNA to . Final libera- tion of the viral nonstruc- tural protein, NS5b, begins the replication process. NS5b is the viral RNA-dependent RNA polymerase, an enzyme not provided by human cells, that processes the original in- fecting viral RNA into exact copies through a negative strand intermediate. While these strands of viral RNA are produced, the NS3 protein unravels them to allow their incorporation into develop- ing viral particles containing core and envelope (E1 and E2) proteins. editing process, also present in HIV infection,85 may and the new highly conserved sequence known as the represent a ‘‘trojan horse’’ viral evasion strategy of 3ЈX tail.88 Interestingly, the poly (U) region appears to creating decoy virions or genomes for host cell defense. be extremely heterogeneous between different virus isolates and even within the same infected liver. In Ј 3 UTR contrast, the new sequence is highly conserved even A significant recent finding in the HCV area was that between the 2 most genetically divergent HCV geno- the considered 3Ј terminal region of the genome was types, 1B and 2A.88 The 3ЈUTR, like its 5Ј counter- incorrect. A number of studies suggested that the 3Ј part, is highly associated with cellular host proteins, terminus of the genome terminated in a poly (U) likely part of the virion assembly and replicase com- tract106 or, in another report,44 as a poly (A) tract. plex. However, more detailed analysis of the 5Ј end of the negative antigenomic RNA strand in infected liver cells showed the presence of a novel 98-nucleotide sequence Emerging Strategies for Therapy downstream of the presumed genomic terminus.86,87 Current approaches to the treatment of NANBH are Detailed sequence analysis of the complete new 3ЈUTR limited to the use of IFN-␣, either alone89 or in shows that it can be considered a tripartite structure combination with other agents, such as .90 The comprising the conventional 3Ј end, a poly (U) tract, efficacy of these therapies is extremely poor, and the Molecular Biology of HCV 403 posttherapy relapse rate is very high, such that sus- activity) the comingled strands for polymerase activity tained biochemical response is observed in less than and translation.100,101 Unfortunately, helicase inhibi- 20% of the patients.91 Consequently, there is an urgent tors have not reached the clinic because of toxic need for the development of novel therapeutics. The cross-reactivity with constitutively active cellular pro- antiviral effect of IFN results from both inhibition of teins. Another target for antiviral research is the NS5b viral replication92,93 and modulation of the immune protein, which functions as the viral RNA polymerase. response to viral epitopes. As recently suggested by This editing enzyme may potentially be rendered mathematical models, the major initial effect of IFN-␣ inactive by drugs that sterically alter its structure is to block virion production or release,94 but the through avid binding, compete for its viral RNA subsequent second-phase decline is believed to reflect target, or poison its substrate (nucleoside analogues). the death rate of productively infected cells, in which During viral assembly, some viral proteins require HCV-specific cytotoxic T-cell activity could be a major maturation by addition of carbohydrate or lipid mol- contributor. The mechanism of synergism provided by ecules. These sites may prove critical for the tropism of ribavirin is also unknown, but its benefit has been the mature virus or its capacity to produce infection. clearly achieved.95 The 5Ј-triphosphate metabolite of Such maturation events are termed prenylation glyco- ribavirin is believed to act as an inhibitor of the viral sylation and have been identified as a potential target RdRp. However, two other non–mutually exclusive for antiviral research.102 mechanisms of antiviral actions of ribavirin have been proposed. Inhibition of the inosine-monophosphate- dehydrogenase enzyme after phosphorylation of ribavi- Conclusion rin to ribavirin-5Ј-triphosphate may deplete intracellu- The identification of HCV as the etiologic agent of lar pools of guanosine triphosphate (similar to the NANBH is certainly the most significant recent devel- activity of mycophenolic acid). The second mechanism opment in any area of . The clinical proposed is that ribavirin inhibits the guanylyl- importance of the disease and the need to rapidly transferase by ribavirin-5Ј-triphosphate, which could identify new therapeutic approaches has resulted in interfere with the translation of cellular and viral RNA. intensive study of the molecular properties of the virus. The approach that likely will lead to novel therapies Although there are still large crevasses in our under- is that directed toward unique aspects of the viral life standing of some aspects of HCV, an aggressive pursuit 96 cycle. If one views the spectrum of HCV infection as to bridge these gaps is underway. To develop the proper a continuum from virion binding to cellular receptor armamentarium to control HCV, a durable system of on through viral replication and virion export, numer- long-term viral replication must be devised, accepted, ous theoretical opportunities exist that are currently and reproduced. Such an artificial or biologically being explored for development. After viral particle relevant system must obey important aspects of the entry, HCV RNA targets the host cell ribosome to host-viral cross-talk yet to be recorded in our patients. begin the process of viral translation. The unique The rapidity with which this translational research will mechanism by which HCV performs translation reach the clinic and blossom into useful therapy through its IRES may be a highly efficacious target for depends on the essential relationship that hepatologists sterilization of the virus. Targeted destruction of this and liver surgeons maintain and develop with those HCV domain may be achieved by antisense mol- working at the bench. 97 98 ecules or ribozymes (cleaving RNA molecules). The formidability of such a foe as HCV was astutely After the initiation of translation of viral sequences, assessed by Ali Ben Abi Taleb, son-in-law of Mahomet critical viral proteins emerge that digest the nascent and the fourth caliph, when he stated, ‘‘. . . in a single 71 polyprotein into its subunits. This proteolytic func- enemy thou hast more than enough.’’103 tion is the target of current and future protease inhibitors. Unquestionably, the emergence of protease inhibitors to the cocktail therapy of HIV has changed References the horizon for patients with acquired immunodefi- ciency syndrome. Recent progress in the proper model- 1. Lavanchy D. Hepatitis C: Public health strategies. J Hepatol ing of the HCV protease, NS3, will also lead to a 1999;31(suppl 1):146-151. 99 2. Berenguer M, Wright T. Hepatitis C and liver transplantation. rationale drug design of prospective compounds. Gut 1999;45:159-163. Critical to replication of the viral RNA is the need for 3. Davis G. Anticipated mortality of hepatitis C and impact on one of the HCV proteins, NS3, to unwind (helicase treatment [abstract]. Hepatology 1998;28:390A. 404 Kenneth E. Drazan

4. Choo QL, Kuo G, Weiner AJ, Bradley LRDW, Houghton M. 21. Eren R, Lubin I, Terkieltaub D, Ben-Moshe O, Zauberman A, Isolation of a cDNA clone derived from a blood-borne non-A Uhlmann R, et al. Human monoclonal antibodies specific to non-B viral hepatitis genome. Science 1989;244:359-362. generated in a human/mouse radiation 5. Kuo G, Choo Q-L, Alter HJ, Gitnick GL, Redeker AG, Purcell chimera: The Trimera system. 1998;2:154-161. RH, et al. An assay for circulating antibodies to a major 22. Bradley DW, McCaustland KA, Krawczynski K, Spelbring J, etiologic virus of human non-A, non-B hepatitis. Science Humphrey C, Cook EH. Hepatitis C virus: Buoyant density of 1989;244:362-364. the factor VIII-derived isolate in sucrose. J Med Virol 1991;34: 6. Saito I, Miyamura T, Ohbayashi A, Harada H, Katayama T, 206-210. Kikuchi S, et al. Hepatitis C virus infection is associated with 23. He LF, Alling D, Popkin T, Shapiro M, Alter HJ, Purcell RH. the development of hepatocellular carcinoma. Proc Natl Acad Determining the size of non-A, non-B hepatitis virus by SciUSA1990;87:6547-6549. filtration. J Infect Dis 1987;156:636-640. 7. El-Serag H, Mason A. Rising incidence of hepatocellular 24. Hijikata M, Shimizu YK, Kato H, Iwamoto A, Shih JW, Alter carcinoma in the United States. N Engl J Med 1999;340:745. HJ, et al. Equilibrium centrifugation studies of hepatitis C 8. Dhillon AP, Dusheiko GM. Pathology of hepatitis C virus virus: Evidence for circulating immune complexes. J Virol infection. Histopathology 1995;26:297-309. 1993;67:1953-1958. 9. Ito T, Mukaigawa J, Zuo J, Hirabayashi Y, Mitamura K, Yasui 25. Thomssen R, Bonk S, Propfe C, Heermann K-H, Kochel HG, K. Cultivation of hepatitis C in primary culture Uy A. Association of hepatitis C virus in human sera with from patients with chronic hepatitis C results in release of high b-lipoprotein. Med Microbiol Immunol 1992;181:293-300. titre infectious virus. J Gen Virol 1996;77:1043-1055. 26. Prince AM, Huima-Byron T, Parker TS, Levine DM. Visualiza- 10. Zignego AL, Macchia D, Monti M, Thiers V, Muzzetti M, tion of hepatitis C virions and putative defective interfering Foschi M, et al. Infection of peripheral mononuclear blood particles isolated from low-density lipoproteins. J Viral Hepat cells by hepatitis C virus. J Hepatol 1992;15:382-386. 1996;3:11-17. 11. Bertolini L, Iacovacci S, Ponzetto A, Gorini G, Battaglia M, 27. Kaito M, Watanabe S, Tsukiyama-Kohara K, Yamaguchi K, Carloni G. The human bone marrow-derived B cell line CE, Kobayashi Y, Konishi M, et al. Hepatitis C virus particle susceptible to hepatitis C virus infection. Res Virol 1993;144: detected by immunoelectron microscopic study. J Gen Virol 281-285. 1994;75:1755-1760. 12. Shimizu YK, Iwamoto A, Hijikata M, Purcell RH, Yoshikura 28. Agnello V. The etiology of mixed associated H. Evidence for in vitro replication of hepatitis C virus genome with hepatitis C virus infection. Scand J Immunol 1995;42:179- in a human T-cell line. Proc Natl Acad SciUSA1992;89:5477- 184. 5481. 29. Shimizu YP,Purcell RH, Yoshikura H. Correlation between the 13. Iacovacci S, Sargiacomo M, Parolini I, Ponzetto A, Peschle C, infectivity of hepatitis C virus in vivo and its infectivity in Carloni G. Replication and multiplication of hepatitis C virus vitro. Proc Natl Acad SciUSA1993;90:6037-6041. genome in human foetal liver cells. Res Virol 1993;144:275- 30. Brown M, Goldstein J. A receptor-mediated pathway for 279. cholesterol homeostasis. Science 1986;232:34-47. 14. Lanford RE, Sureau C, Jacob JR, White R, Fuerst TR. 31. Brown M, Herz J, Goldstein J. Calcium cages, acid baths and Demonstration of in vitro infection of chimpanzee hepatocytes recycling receptors. Nature 1997;388:629-630. with hepatitis C virus using strand-specific RT-PCR. 1994;202:606-614. 32. Hofer FG, Gruenberger M, Kowalski H, Machat H, Huettinger M, Kuechler E, Blaas D. Members of the low-density lipopro- 15. Sun BGM, Feitelson MA. Evidence for consistent HCV tein receptor family mediate cell entry of a minor group cold replication in HepG2 cells. In: Liang TJ, Alter HJ (ed). Sixth virus.ProcNatlAcadSciUSA1994;91:1839-1842. International Symposium on Hepatitis C and Related Viruses: Molecular Virology and Pathogenesis, Bethesda, MD, March 33. Bates P, Young J, Varmus H. A receptor for subgroup A 16-19, 1999. sarcoma virus is related to the low-density lipoprotein receptor. 16. Mizutani T, Kato N, Saito S, Ikeda M, Sugiyama K, Shimo- Cell 1993;74:1043-1051. tohno K. Characterization of hepatitis C virus replication in 34. Seipp SM, Mueller HM, Pfaff E, Stremmel W, Theilmann L, cloned cells obtained from a human T-cell leukaemia virus type Goeser T. Establishment of persistent hepatitis C virus infec- I infected cell line, MT-2. J Virol 1996;70:7219-7223. tion and replication in vitro. J Gen Virol 1997;78:2467-2477. 17. Sugiyama K, Kato N, Mizutani T, Ikeda M, Tanaka T, 35. Levy ST,Todd SC, Maecker HT. CD81 (TAPA-1): A molecule Shimotohmo K. Genetic analysis of the hepatitis C virus involved in signal transduction and in the (HCV) genome from HCV-infected human T-cells. J Gen immune system. Ann Rev Immunol 1998;16:89-101. Virol 1997;78:329-336. 36. Pileri PU, Uematsu Y, Campagnoli S, Galli G, Falugi F, 18. Bradley D, Maynard J, Popper H, Cook EH, Ebert JW, Petracca R, Weiner AJ, et al. Binding of hepatitis C virus to McCaustland KA, et al. Posttransfusion non-A, non-B hepati- CD81. Science 1998;282:938-941. tis, physicochemical properties of two distinct agents. J Infect 37. Flint M, Maidens C, Loomis-Price LD, Shotten C, Levy S, Dis 1983;148:254-265. Barclay WS, et al. Characterization of hepatitis C virus E2 19. Barry CWS, Mocarski E, Brown P. Analysis of host viral glycoprotein interaction with a putative cellular receptor, interactions in CMV using cDNA microarray. 25th CD81. J Virol 1999;72:6235-6244. Annual Meeting of the American Society of Transplant 38. Agnello V. The etiology and pathophysiology of mixed cryo- Surgeons, Chicago, IL, May 12-17, 1999. globulinemia secondary to hepatitis C virus infection. Springer 20. Xie ZC, Riezu-Boj JI, Lasarte JJ, Guillen J, Su JH, Civeira MP, Semin Immunopathol 1997;19:111-129. Prieto J. Transmission of hepatitis C virus infection to tree 39. Dammacco FG, Gatti P, Sansonno D. Hepatitis C virus shrews. Virology 1998;244:513-520. infection, mixed cryoglobulinemia, and non-Hodgkin’s lym- Molecular Biology of HCV 405

phoma: An emerging picture. Leuk Lymphoma 1998;31:463- protein inhibits human immunodeficiency virus type 1 replica- 476. tion. Virus Res 1996;45:87-92. 40. Maecker HL, Levy ST. Normal lymphocyte development but 58. Ray RB, Steele R, Meyer K, Ray R. Transcriptional repression delayed humoral immune response in CD81-null mice. J Exp of P53 promoter by hepatitis C virus core protein. J Biol Chem Med 1997;185:1505-1510. 1997;272:10983-10986. 41. Houghton M (ed). Hepatitis C viruses (ed 3). Philadelphia: 59. Matsumoto M, Hsieh T-Y, Zhu N, Vanarsdale T, Hwang SB, Lippincott-Raven, 1996. Jeng K-S, et al. Hepatitis C virus core protein interacts with the 42. Bukh J, Miller RH, Purcell RH. Genetic heterogeneity of cytoplasmic tail of lymphotoxin-␤ receptor. J Virol 1997;71: hepatitis C virus: Quasispecies and genotypes. Semin Liver Dis 1301-1309. 1995;15:41-63. 60. Barba G, Harper F, Harada T, Kohara M, Goulinet S, 43. Han JH, Shyamala V, Richman KH, Brauer MJ, Irvine B, Matsuura Y, et al. Hepatitis C virus core protein shows a Urdea MS, et al. Characterization of the terminal regions of cytoplasmic localization and associates to cellular lipid storage hepatitis C viral RNA: Identification of conserved sequences in droplets. Proc Natl Acad SciUSA1997;94:1200-1205. the 5Ј and poly(A) tails at the 3Ј end. Proc 61. Weiner A, Brauer M, Rosenblatt J, Richman KH, Tung J, NatlAcadSciUSA1991;88:1711-1715. Crawford K, et al. Variable and hypervariable domains are 44. Tsukiyama-Kohara K, Iizuka N, Kohara M, Nomoto A. found in the regions of HCV corresponding to the flavivirus Internal ribosomal entry site within hepatitis C virus RNA. J envelope and NS1 proteins and the pestivirus envelope Virol 1992;66:1476-1483. glycoproteins. Virology 1991;180:842-848. 45. Brown EA, Zhang H, Ping L-H, Lemon SM. Secondary 62. Rosa D, Campagnoli S, Moretto C, Guenzi E, Cousens L, structure of the 5Ј nontranslated regions of the hepatitis C Chin M, et al. A quantitative test to estimate neutralizing virus and pestivirus genomic . Nucleic Acids Res 1992; antibodies to the hepatitis C virus: Cytofluorometric assess- 20:5041-5045. ment of envelope glycoprotein 2 binding to target cells. Proc 46. Bukh J, Purcell RH, Miller RH. Sequence analysis of the 5Ј NatlAcadSciUSA1996;93:1759-1763. non-coding region of hepatitis C virus. Proc Natl Acad Sci U S 63. Kumar U, Brown J, Monjardino J, Thomas HC. Sequence A 1992;89:4942-4946. variation in the large envelope glycoprotein (E2/NS1) of 47. Furione MS, Simoncini L, Gatti M, Baldanti F, Grazia Revello hepatitis C virus during chronic infection. J Infect Dis M, Gerna G. HCV genotyping by three methods: Analysis of 1993;167:726-730. discordant results based on sequencing. J Clin Virol 1999;13: 64. Kumar U, Monjardino J, Thomas HC. Hypervariable region 121-130. of hepatitis C virus envelope glycoprotein (E2/NS1) in an 48. Lemon SM, Honda M. Internal ribosome entry sites within agammaglobulinemic patient. Gastroenterology 1994;106: the RNA genomes of hepatitis C virus and other flaviviruses. 1072-1075. Semin Virol 1997;8:274-289. 65. Zibert A, Schreier E, Roggendorf M. Antibodies in human sera 49. Sachs AB, Sarnow P, Hentze MW. Starting at the beginning, specific to hypervariable region 1 of hepatitis C virus block middle and end: Translation initiation in eukaryotes. Cell viral attachment. Virology 1995;208:653-661. 1997;89:831-838. 66. Shimizu YK, Igarashi H, Kiyohara T, Cabezon T, Farci P, 50. Lai MMC. Cellular factors in the transcription and regulation Purcell RHY. A hyperimmune serum against a synthetic of viral RNA genomes: A parallel to DNA-dependent RNA peptide corresponding to the hypervariable region 1 of hepati- transcription. Virology 1998;244:1-12. tis C virus can prevent viral infection in cell cultures. Virology 51. Grakoui A, McCourt DW, Wychowski C, Feinstone SM, Rice 1996;223:409-412. CM. Characterization of the hepatitis C virus-encoded serine 67. Farci P, Shimoda A, Wong D, Cabezon T, De Gioannis D, proteinase: Determination of proteinase-dependent polypro- Strazzera A, et al. Prevention of hepatitis C virus infection in tein cleavage sites. J Virol 1993;67:2832-2843. chimpanzees by hyperimmune serum against the hypervariable 52. Hijikata MK, Kato N, Ootsuyama Y, Nakagawa M, Shimo- region 1 of the envelope 2 protein. Proc Natl Acad SciUSA tohno K. Gene mapping of the putative structural region of the 1996;93:15394-15399. hepatitis C virus genome by in vitro processing analysis. J Virol 68. Taylor DR, Shi ST, Romano PR, Barber GN, Lai MM. 1991;67:4665-4671. Inhibition of the interferon-inducible protein kinase PKR by 53. Hijikata MM, Mizushima H, Tanji Y, Komoda Y, Hirowatari HCV E2 protein. Science 1999;285:107-110. Y, Akagi T, Kato N, et al. Proteolytic processing and membrane 69. Santolini E, Pacini L, Fipaldini C, Migliaccio G, La Monica N. association of putative nonstructural proteins of hepatitis C The NS2 protein of hepatitis C virus is a transmembrane virus.ProcNatlAcadSciUSA1993;90:10773-10777. polypeptide. J Virol 1995;69:7461-7471. 54. Santolini E, Migliaccio G, La Monica N. Biosynthesis and 70. Kwong AK, Kim JL, Rao G, Lipovsek D, Raybuck SA. biochemical properties of the hepatitis C virus core protein. J Hepatitis C virus NS3/4A protease. Antiviral Res 1999;41:67- Virol 1994;68:3631-3641. 84. 55. Large M, Kittleson D, Hahn Y. Suppression of host immune 71. Gallinari PB, Brennan D, Nardi C, Brunetti M, Tomei L, response by the core protein of hepatitis C virus: Implications Steinku¨hler C, De Francesco R. Multiple enzymatic activities for hepatitis C virus persistence. J Immunol 1999;162:931- associated with recombinant NS3 protein of hepatitis C virus. 938. J Virol 1998;72:6758-6769. 56. Shih CM, Lo SJ, Miyamura T, Chen SY, Lee YW. Suppression 72. Tai CLCW, Chen DS, Hwang LH. The helicase activity of hepatitis B virus expression and replication by hepatitis C associated with hepatitis C virus nonstructural protein 3 virus core protein in Huh-7 cells. J Virol 1993;67:5823-5832. (NS3). J Virol 1996;70:8477-8484. 57. Srinivas R, Ray R, Meyer K, Ray R. Hepatitis C virus core 73. Hahm BH, Han DS, Back SH, Song OK, Cho MJ, Kim CJ, 406 Kenneth E. Drazan

Shimotohno K, Jang SK. NS3-4A of hepatitis C virus is a therapy with ribavirin and interferon alpha in interferon alpha chymotrypsin-like protease. J Virol 1995;69:2534-2539. relapsers and non-responders: Italian experience. J Hepatol 74. Rice CM. Flaviviridae: The viruses and their replication (ed 3). 1995;23:13-15. Philadelphia: Lippincott-Raven, 1996. 91. Lindsay KL. Therapy of hepatitis C: Overview. Hepatology 75. Enomoto N, Sakuma I, Asahina Y, Kurosaki M, Murakami T, 1997;26:715-755. Yamamoto C, et al. Comparison of full-length sequences of 92. Castelli JW, Wood KA, Youle RJ. The 2-5A system in viral interferon-sensitive and resistant hepatitis C virus 1b. Sensitiv- infection and apoptosis. Biomed Pharmacother 1998;52:386- ity to interferon is conferred with amino acid and substitutions 390. in the NS5A gene. J Clin Invest 1995;96:224-230. 93. Jacobs BL, Langland JO. When two strands are better than 76. Enomoto N, Sakuma I, Asahina Y, Kurosaki M, Murakami T, one: The mediators and modulators of the cellular responses to Yamamoto C, et al. Mutations in the nonstructural protein double-stranded RNA. Virology 1996;219:339-349. NS5A gene and response to interferon in patients with chronic 94. Neumann A, Lam N, Dahari H, Gretch DR, Wiley TE, hepatitis C virus 1b infection. N Engl J Med 1996;334:77-81. Layden TJ, et al. Hepatitis C viral dynamics in vivo and the 77. Gale MJ, Korth MJ, Tang NM, Tau SL, Hopkins DA, Dever antiviral efficacy of interferon alfa therapy. Science 1998;282: TE, et al. Evidence that hepatitis C virus resistance to 103-107. interferon is mediated through repression of the PKR protein 95. Glue P. The clinical pharmacology of ribavirin. Semin Liver kinase by the nonstructural 5A protein. Virology 1997;230:217- Dis 1999;19:17-24. 227. 96. Jones P. Strategies for discovery. Antiviral Chem 78. Gale MJ, Blakeley CM, Kwieciszewski B, Tan S-L, Dossett M, Chemother 1998;9:283-297. Tang NM, et al. Control of PKR protein kinase by the hepatitis 97. Brown-Driver VE, Eto T, Lesnik E, Anderson KP, Hanecak C virus nonstructural 5A protein: Molecular mechanisms of RC. Inhibition of translation of hepatitis C virus RNA by kinase regulation. Mol Cell Biol 1998;18:5208-5218. 2-modified antisense oligonucleotides. Antisense Nucleic Acid 79. Williams B. Role of the double-stranded RNA-activated Drug Dev 1999;9:145-154. protein kinase (PKR) in cell regulation. Biochem Soc Trans 98. Lieber AH, He CY, Polyak SJ, Gretch DR, Barr D, Kay MA. 1997;25:509-513. Elimination of hepatitis C virus RNA in infected human 80. Gale MJK, Korth MJ, Katze MG. Repression of the PKR hepatocytes by adenovirus-mediated expression of ribozymes. J protein kinase by the hepatitis C virus NS5A protein: A Virol 1996;70:8782-8791. potential mechanism of interferon resistance. Clin Diagn Virol 99. Kim JL, Morgenstern KA, Lin C, Fox T, Dwyer MO, Landro 1998;10:157-162. JA, et al. Crystal structure of the hepatitis C virus NS3 protease 81. Jagus R, Joshi B, Barber GN. PKR, apoptosis and cancer. Int J domain complexed with a synthetic NS4A cofactor peptide. Biochem Cell Biol 1999;31:128-138. Cell 1996;87:343-355. 82. Clemens MJ, Bommer UA. Translational control: The cancer 100. Kim DW, Gwack Y, Han JH, Choe J. C-terminal domain of connection. Int J Biochem Cell Biol 1999;31:1-23. the hepatitis C virus NS3 protein contains an RNA helicase 83. Kamer G, Argos P. Primary structural comparison of RNA- activity. Biochem Biophys Res Commun 1995;215:160-166. dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res 1984;12:7269-7282. 101. Kanai A, Tanabe K, Kohara M. Poly(U) binding activity of 84. Oh JW, Ito T, Lai MM. A recombinant hepatitis C virus hepatitis C virus NS3 protein, a putative RNA helicase. FEBS RNA-dependent RNA polymerase capable of copying the Lett 1995;376:221-224. full-length viral RNA. J Virol 1999;73:7694-7702. 102. Glenn JM, Marsters JC Jr, Greenberg HB. Use of a prenylation 85. Berkhout B. HIV-1 evolution under pressure of protease inhibitor as a novel antiviral agent. J Virol 1998;72:9303- inhibitors: Climbing the stairs of viral fitness. J Biomed Sci 9306. 1999;6:298-305. 103. Bartlett J. Familiar quotations: A collection of passages, 86. Tanaka T, Kato N, Cho M-J, Sugiyama K, Shimotohno K. phrases, and proverbs traced to their sources in ancient and Structure of the 3Ј terminus of the hepatitis C virus genome. J modern literature (ed 9). Boston: Little, Brown, 1901. Virol 1996;70:3307-3312. 104. Lohmann V, Korner F, Koch J, Herian U, Theilmann L, 87. Kolykhalov AA, Feinstone SM, Rice CM. Identification of a Bartenschlager R. Replication of subgenomic hepatitis C virus highly conserved sequence element at the 3Ј terminus of RNAs in a hepatoma cell line. Science 1999;285:110-113. hepatitis C virus genome RNA. J Virol 1996;70:3363-3371. 105. Galun E. The Trimera Mouse System: A model for HCV 88. Yanagi M, St Claire M, Emerson SU, Purcell RH, Bukh J. In infection and evaluation of antiviral drugs. In: Liang TJ, Alter vivo analysis of the 3Ј untranslated region of the hepatitis C HJ, eds. Seventh International Symposium on Hepatitis C and virus after in vitro mutagenesis of an infectious cDNA clone. Related Viruses: Molecular Virology and Pathogenesis. At- ProcNatlAcadSciUSA1999;96:2291-2295. lanta, GA, April 9-13, 2000. 89. Davis GL, Balart LA, Schiff EL, Lindsay K, Bodenheimer HC, 106. Okamato H, Okada S, Sugiyama Y, Kurai K, Iizuka H, Perrillo H, et al. Treatment of chronic hepatitis C with Machida A, et al. Nucleotide sequence of the genomic RNA of recombinant interferon-alfa. A multicenter randomized con- hepatitis C virus isolated from a human carrier: Comparison trolled trial. N Engl J Med 1989;321:1501-1506. with reported isolates for conserved and divergent regions. J 90. Brillanti S, Miglioli M, Barbara L. Combination antiviral Gen Virol 1991;72:2697-2704.