Hepatitis C Virus, Susceptibility To

A number sign (#) is used with this entry because variation in several different genes likely influences susceptibility and resistance to hepatitis C virus (HCV) infection.

Description

HCV, which is principally transmitted by blood, infects about 3% of the world's population. HCV infection causes acute hepatitis, which is self-resolving in 20 to 50% of cases but does not confer permanent immunity. In 50 to 80% of cases, HCV infection becomes chronic and results in chronic hepatitis, cirrhosis, and hepatocellular carcinoma. As a result, HCV infection is a leading killer worldwide and the most common cause of liver failure in the U.S. HCV is opportunistic in individuals infected with human immunodeficiency virus (HIV; see 609423), approximately 25% of whom are coinfected with HCV. HCV infection is also associated with cryoglobulinemia (see 123550), a B-lymphocyte proliferative disorder (Pawlotsky, 2004; Chisari (2005); Pileri et al., 1998).

Pathogenesis

Viral Entry

Pileri et al. (1998) demonstrated that the HCV envelope protein E2 binds human CD81 (186845), a tetraspanin expressed on various cell types, including hepatocytes and B lymphocytes. Binding of E2 was mapped to the major extracellular loop of CD81. Recombinant molecules containing this loop bound HCV, and antibodies that neutralize HCV infection in vivo inhibited virus binding to CD81 in vitro.

HCV is not readily replicated in cell culture systems, making it difficult to ascertain information on cell receptors for the virus. However, several observations from studies on the role of HCV in mixed cryoglobulinemia provided some insight into HCV entry into cells. Evidence indicated that HCV and other viruses enter cells through the mediation of low density lipoprotein (LDL) receptors: by the demonstration that endocytosis of these viruses correlates with LDL receptor (LDLR; 606945) activity, by complete inhibition of detectable endocytosis by anti-LDL receptor antibody, by inhibition with anti-apolipoprotein E (APOE; 107741) and anti-apolipoprotein B (APOB; 107730) antibodies, by chemical methods abrogating lipoprotein/LDL receptor interactions, and by inhibition with the endocytosis inhibitor phenylarsine oxide. Agnello et al. (1999) provided confirmatory evidence by the lack of detectable LDL receptor on cells known to be resistant to infection by one of these viruses, bovine viral diarrheal virus (BVDV). Endocytosis via the LDL receptor was shown to be mediated by complexing of the virus to very low density lipoprotein (VLDL) or LDL, but not high density lipoprotein (HDL). Studies using LDL receptor-deficient cells or a cytolytic BVDV system indicated that the LDL receptor may be the main but not exclusive means of cell entry of these viruses.

Scarselli et al. (2002) determined that SCARB1 (601040) is a receptor for HCV glycoprotein E2. Binding between SCARB1 and E2 was found to be independent of the genotype of the viral isolate.

Pohlmann et al. (2003) showed that HCV binds to DCSIGN (CD209; 604672) and DCSIGNR (LSIGN, or CD209L; 605872) on cell membranes.

Gardner et al. (2003) provided an explanation for the hepatotropism of HCV. They demonstrated that LSIGN and DCSIGN specifically bind naturally occurring HCV present in the sera of infected individuals. Further studies demonstrated that binding is mediated by the HCV envelope glycoprotein E2 and is blocked by specific inhibitors. Thus, LSIGN represents a liver-specific receptor for HCV, and both LSIGN and DCSIGN may play important roles in HCV infection and immunity.

Entry of HCV into cells involves glycosaminoglycans and 2 host proteins, SCARB1 and CD81, that bind the viral E2 glycoprotein. However, some cell lines expressing all 3 of these factors are nonpermissive for viral entry. Using an iterative expression cloning approach, Evans et al. (2007) identified CLDN1 (603718) as essential for HCV entry. Expression of CLDN1 in some, but not all, nonpermissive cell lines allowed HCV entry, suggesting the existence of 1 or more additional HCV entry factors. Other CLDN family members failed to render nonpermissive cell lines permissive to HCV infection. Treatment with CLDN1 small interfering RNA inhibited HCV infection. Exchange of extracellular loops (EL) between CLDN1 and other CLDNs, as well as mutation analysis, showed that the N-terminal third of EL1 of CLDN1 was required for HCV entry. Treatment of cells with antibodies to CD81 or CLDN1 at different times showed that CD81 acted before CLDN1 in HCV entry. Evans et al. (2007) concluded that CLDN1 is a key factor for HCV entry and a novel target for antiviral drug development.

Zheng et al. (2007) found that, like CLDN1, CLDN6 (615798) and CLDN9 (615799) functioned as receptors for HCV entry in HCV-permissive human hepatocellular carcinoma cells. Real-time PCR showed that overexpression of either claudin in nonpermissive 293T cells conferred susceptibility to HCV entry. Mutation analysis revealed that val32, asn38, val45, and glu48 in extracellular loop-1 of CLDN9 were required for HCV infection.

Using a functional RNA interference kinase screen, Lupberger et al. (2011) identified EGFR (131550) and EPHA2 (176946) as host cofactors for HCV entry into cells. Clinically approved receptor tyrosine kinase (RTK) inhibitors (erlotinib and dasatinib) or RTK-specific antibodies impaired infection by all major HCV genotypes and viral escape variants in cell culture and in a human liver chimeric mouse model. EGFR and EPHA2 mediated HCV entry by regulating CD81-CLDN1 coreceptor associations and viral glycoprotein-dependent membrane fusion. Lupberger et al. (2011) concluded that RTKs are HCV entry cofactors and that RTK inhibitors have substantial antiviral activity that may be useful for prevention and treatment of HCV infection.

As observed with other HCV entry factors, Sainz et al. (2012) found that expression of the cholesterol-sensing receptor NPC1L1 (608010) was downregulated on a human hepatocyte cell line following HCV infection. Blocking NPC1L1 via small interfering RNA or antibody treatment reduced susceptibility to HCV infection, but not vesicular stomatitis virus infection. Treatment with the cholesterol-lowering medication ezetimibe, which antagonizes NPC1L1, also reduced susceptibility to HCV infection by directly inhibiting viral entry after receptor binding and at or before fusion. Sainz et al. (2012) concluded that NPC1L1 is an HCV cell entry factor and a potential antiviral target.

Viral Replication

See Lindenbach and Rice (2005) for a review of HCV replication.

Translation of mRNA usually requires modification of the 5-prime cap, but some viral and cellular mRNAs use a cap-independent mechanism of ribosome binding mediated by an internal ribosomal entry site (IRES). The 5-prime UTR of HCV is highly conserved in all strains and folds into an IRES that binds directly to 40S ribosome subunits. Using a ribozyme-based selection system, Kruger et al. (2000) identified EIF2-gamma (EIF2S3; 300161) and EIF2B-gamma (EIF2B3; 606273) as cellular factors involved in HCV IRES function. They validated the involvement of EIF2-gamma and EIF2B-gamma in HCV IRES-mediated translation using ribozymes directed against sites within the mRNAs of these genes.

Foy et al. (2003) showed that the HCV NS3/4A serine protease blocks phosphorylation and effector action of IRF3 (603734) to generate persistent infection. Disruption of the NS3/4A protease function by mutation or a ketoamide peptidomimetic inhibitor relieved this blockade and restored IRF3 phosphorylation after cellular challenge with an unrelated virus. Foy et al. (2003) also showed that dominant-negative or constitutively active IRF3 mutants, respectively, enhanced or suppressed HCV RNA replication in hepatoma cells. Foy et al. (2003) concluded that the NS3/4A protease represents a dual therapeutic target, the inhibition of which may both block viral replication and restore IRF3 control of HCV infection.

Wang et al. (2005) found that FBL2 (605652) forms a stable immunoprecipitable complex with the HCV NS5A protein. The FBL2-NS5A association required the CAAX motif but not the F box of FBL2. However, deletion of the F box resulted in a dominant-negative protein that inhibited HCV RNA replication when overexpressed in a hepatoma cell line. This inhibition could be overcome by NS5A coexpression. Reduction of FBL2 expression by small interfering RNA reduced HCV RNA expression by a comparable amount. Wang et al. (2005) concluded that geranylgeranylated FBL2 binds to NS5A in a reaction crucial for HCV RNA replication.

Jopling et al. (2005) found that sequestration of microRNA-122 (miR122; 609582) in liver cells resulted in marked loss of autonomously replicating HCV RNAs. Mutational analysis revealed a genetic interaction between miR122 and the 5-prime noncoding region of the HCV genome, but the interaction did not impair mRNA translation or RNA stability. Jopling et al. (2005) concluded that miR122 is likely to facilitate replication of HCV RNA and proposed that miR122 may be a target for antiviral intervention.

Using a 2-part small interfering RNA screen, followed by RT-PCR verification, Li et al. (2009) identified over 30 host genes involved in propagation of HCV. A bioinformatic metaanalysis integrated the new data with previous functional and proteomic studies to enhance the understanding of HCV pathogenesis and to suggest potential therapeutic targets.

Lanford et al. (2010) found that treatment of chronically infected chimpanzees with a locked nucleic acid-modified oligonucleotide complementary to miR122 leads to long-lasting suppression of HCV viremia, with no evidence of viral resistance or side effects in the treated animals. Furthermore, transcriptome and histologic analyses of liver biopsies demonstrated derepression of target mRNAs with miR122 seed sites, downregulation of interferon (see 147660)-regulated genes, and improvement of HCV-induced liver pathology. Lanford et al. (2010) suggested that prolonged virologic response to this agent without HCV rebound holds promise of a new antiviral therapy with a high barrier to resistance.

Using short hairpin RNA and a small molecule DGAT1 (604900) inhibitor, Herker et al. (2010) showed that DGAT1, but not DGAT2 (606983), was required for HCV infection and virus assembly. Immunofluorescence microscopy and coimmunoprecipitation experiments demonstrated that the viral core protein was retained at the endoplasmic reticulum in lipid droplets in cells treated with the DGAT1 inhibitor. Herker et al. (2010) concluded that DGAT1 is a host factor for HCV infection that binds core protein, localizes it to DGAT1-generated lipid droplets, and recruits viral RNA replication complexes for viral assembly. DGAT2-generated lipid droplets formed normally in cells treated with the DGAT1 inhibitor, suggesting that DGAT1 inhibitors may be useful as antiviral therapeutics.

Using short hairpin RNA-mediated gene silencing, Maehama et al. (2013) found that the class II phosphoinositide 3-kinase PIK3C2B (602838), but not PIK3C2A (603601) or PIK3C2G (609001), was indispensable for propagation of HCV in cells and that PIK3C2B played a role in HCV genome replication. Immunoblot analysis showed that HCV core protein bound to phosphatidylinositol 3,4-bisphosphate. Maehama et al. (2013) proposed that the phosphoinositide generated by PIK3C2B plays an indispensable role in the HCV replication cycle through binding to HCV core protein.

Majzoub et al. (2014) screened Drosophila ribosomal proteins to determine their impact on cellular viability and promotion of Dicistroviridae (DCV) virus replication. They found that knockdown of Rack1 (176981) did not affect cell viability, but that it resulted in a reduction of the DCV titer. Unlike DCV, which is dependent on an internal ribosome entry site (IRES) for translation, viruses that use cap-dependent initiation of translation were unaffected by knockdown of Rack1. Majzoub et al. (2014) found that silencing RACK1 in a human hepatocarcinoma cell line significantly impaired infection with HCV, which is dependent on an IRES, at a level comparable to those observed with silencing of the HCV host factors CD81 or CYPA (PPIA; 123840). Silencing of RACK1 did not affect liver cell proliferation or viability. The authors found that RACK1 and MIR122 regulated HCV by different mechanisms, and further mechanistic analyses suggested the involvement of EIF3J (603910) with HCV translation mediated by RACK1. Majzoub et al. (2014) concluded that RACK1 is involved in IRES-mediated translation of viruses, but that it is not required for cell viability.

Host Immune Response

Gale and Foy (2005) reviewed the mechanisms by which HCV triggers, controls, and evades antiviral defenses directly within the infected hepatocyte and hepatic tissue to support HCV replication and resistance.

Bowen and Walker (2005) outlined features of successful adaptive immune responses to HCV and reviewed evasion strategies the might explain defects in humoral and cellular immunity in those individuals who develop persistent infections.

Taylor et al. (1999) studied the mechanism underlying the resistance of HCV to interferon. They demonstrated that the HCV envelope protein E2 contains a sequence identical with phosphorylation sites of the interferon-inducible protein kinase PKR (176871) and the translation initiation factor EIF2-alpha (EIF2S1; 603907), a target of PKR. E2 inhibited the kinase activity of PKR and blocked its inhibitory effect on protein synthesis and cell growth. This interaction of E2 in PKR may be one mechanism by which HCV circumvents the antiviral effect of interferon. Taylor et al. (1999) hypothesized that another potential outcome of PKR inhibition is the promotion of cell growth, which may contribute to HCV-associated hepatocellular carcinoma.

Tan et al. (1999) found that the HCV NS5A protein interacts with GRB2 (108355) and inhibits activation of ERK1 (MAPK3; 601795) and ERK2 (MAPK1; 176948) by EGF (131530). He et al. (2002) identified mutations within the C-terminal proline-rich motif of NS5A that disrupted both the binding of NS5A to GRB2 and the NS5A inhibition of EGF activation of ERK1 and ERK2. These findings indicated that the interaction between NS5A and GRB2 is direct. NS5A could also form a complex with GRB2-associated binding protein-1 (GAB1; 604439) in an EGF-dependent manner, but He et al. (2002) determined that this interaction was indirect and was dependent upon NS5A binding the p85 subunit of phosphatidylinositol 3-kinase (see 171833). The in vivo association of NS5A with p85 PI3K increased tyrosine phosphorylation of p85 PI3K. Downstream effects of the EGF-induced interaction included tyrosine phosphorylation of AKT (164730) and serine phosphorylation of BAD (603167). Both of these events would tend to inhibit apoptosis and were consistent with the antiapoptotic properties of NS5A.

Jin et al. (2000) determined that the C terminus of the HCV core protein interacts with the bZIP domain of CREB3 and can prevent the formation of nuclear CREB3 dimers. Immunofluorescence microscopy demonstrated nuclear expression of CREB3; expression shifted to the cytoplasm in the presence of HCV core protein. Jin et al. (2000) showed that HCV core protein could inactivate CREB3 function and potentiate cellular transformation.

Immune responses are rarely effective in clearing HCV, resulting in chronic HCV infection. Crotta et al. (2002) and Tseng and Klimpel (2002) showed that ligation of CD81 with either antibody or HCV E2 protein inhibited activation of natural killer (NK) cells, cytokine production, proliferation, cytolytic activity, and cytotoxic granule release; it did not inhibit activation of T or NKT cells. CD3 (see 186740)-positive T cells were stimulated by CD81 ligation. Crotta et al. (2002) determined that CD81 cross-linking blocks CD16 (146740)-mediated tyrosine phosphorylation overall and CD3Z (186780) and ERK2 phosphorylation specifically. Tseng and Klimpel (2002) concluded that NK cells differ significantly from B and T cells in their response to CD81 cross-linking. The results suggested that one mechanism whereby HCV can alter host defenses and innate immunity is via early inhibition of IFN-gamma (IFNG; 147570) production by NK cells.

Bosserhoff et al. (2003) found that HCV patients had elevated intrahepatic MIA2 (608001) expression, and the level of MIA2 expression correlated with the severity of fibrosis and inflammation.

Okamoto et al. (2014) noted that the TLR3 (603029)-TICAM1 (607601) pathway is essential for production of type III interferon (e.g., IFNL1; 607403) in response to HCV infection. Using Ips1 (MAVS; 609676)-knockout mice, they showed that Ips1 was essential for production of type III interferons by mouse hepatocytes and Cd8-positive dendritic cells in response to cytoplasmic HCV RNA. In turn, type III interferons induced expression of Rigi (DDX58; 609631), but not Tlr3, in dendritic cells and augmented production of type III interferon, but not activation of natural killer cells. In addition, both Ifna and Ifnl3 (607402) induced the cytoplasmic antiviral proteins Isg20 (604533), Mx1 (147150), and RNase L (RNASEL; 180435). Okamoto et al. (2014) concluded that multiple mechanisms, including an IPS1-dependent pathway, are involved in type III interferon production in response to HCV RNA, and that these lead to the expression of cytoplasmic antiviral proteins.

Lin et al. (2014) noted that MCPIP1 (ZC3H12A; 610562), as an RNase, targets viral RNA and has antiviral activity. They found that infection of a hepatoma cell line with HCV induced MCPIP1 expression. Expression of MCPIP1 was higher in liver tissue from patients with chronic HCV infection compared with those without chronic infection. Knockdown of MCPIP1 expression enhanced HCV replication and HCV-mediated expression of proinflammatory cytokines, such as TNF (191160), IL6 (147620), and MCP1 (CCL2; 158105). In contrast, overexpression of MCPIP1 significantly inhibited HCV replication and proinflammatory cytokine expression. Mutation analysis indicated that disruption of the RNA-binding and oligomerization abilities, as well as the RNase activity, of MCPIP1, but not the deubiquitinase activity, impaired its inhibitory activity against HCV replication. Immunocytochemical analysis demonstrated MCPIP1 colocalization with HCV RNA. A replication-defective HCV mutant was susceptible to MCPIP1-mediated RNA degradation. Lin et al. (2014) proposed that MCPIP1 suppresses HCV replication and HCV-induced proinflammatory responses.

Kim et al. (2016) observed upregulation of SCOTIN (SHISA5; 607290) expression in Huh7 human hepatocellular carcinoma cells treated with the antiviral cytokine IFNB (147640), but not in cells treated with the inflammatory cytokines IL1B (147720) or IL6. Overexpression of SCOTIN restricted HCV replication and virion production. SCOTIN also promoted autophagosomal degradation of the ER-localized HCV protein NS5A. SCOTIN suppressed HCV replication through autophagy, but it did not directly alter the general autophagy process. SCOTIN bound NS5A via its transmembrane/proline-rich domain, colocalized with LC3 (MAP1LC3A; 601242) in autophagosomes, and was itself degraded through the autophagy process. Kim et al. (2016) concluded that IFNB-induced SCOTIN recruits HCV NS5A to autophagosomes for degradation, thereby restricting HCV replication.

Molecular Genetics

Variation in Genes Involved in Viral Entry

Price et al. (2006) evaluated APOE genotypes in 420 Northern Europeans with evidence of HCV exposure. Both APOE2 (107741.0001) and APOE4 (107741.0016) alleles were associated with reduced likelihood of chronic HCV infection, and no APOE2 homozygotes were HCV seropositive. Price et al. (2006) concluded that APOE2 and APOE4 alleles favor HCV clearance.

Variation in Genes Involved in Host Immune Response

Thursz et al. (1999) studied the distribution of MHC class II alleles in 85 patients with self-limiting HCV infection versus 170 matched patients with persistent infection. They found that self-limiting HCV infection was associated with HLA-DRB1*1101 (see HLA-DRB1; 142857), with an odds ratio (OR) of 2.14, and HLA-DQB1*0301 (see HLA-DQB1; 604305), with an OR of 2.22. Persistent HCV infection was associated with HLA-DRB1*0701, with an OR of 2.04, and HLA-DRB4*0101, with an OR of 2.38. Thursz et al. (1999) confirmed their results with a second-stage study of 52 patients with self-limiting infection versus 152 with persistent infection.

Khakoo et al. (2004) demonstrated that genes encoding the inhibitory NK cell receptor KIR2DL3 (604938) and its HLA-C group-1 (HLA-C1; see 142840) ligand directly influence resolution of HCV infection. This effect was observed in Caucasians and African Americans with expected low infectious doses of HCV but not in those with high-dose exposure, in whom the innate immune response was likely overwhelmed. The frequency of individuals with 2 copies of HLA-C1 alleles was higher in the group that had resolved infection (37.5%) relative to those with persistent infection (29.9%) (OR = 1.40, p = 0.01). The reciprocal association of 2 HLA-C2 alleles with viral persistence was also observed. Khakoo et al. (2004) concluded that inhibitory NK cell interactions are important in determining antiviral immunity and that diminished inhibitory responses confer protection against HCV.

Goulding et al. (2005) genotyped 283 Irish women exposed to HCV genotype-1b from a single donor for CCR5 (601373), CCR2 (601267), and CCL5 (187011) polymorphisms. They found that CCR5 delta-32 (601373.0001) heterozygotes showed significantly higher spontaneous clearance of HCV compared with wildtype CCR5 homozygotes. In addition, the authors observed a trend toward lower hepatic inflammation scores in CCR5 delta-32 heterozygotes compared with wildtype CCR5 homozygotes. No significant relationships were found with CCR2 or CCL5.

The 77C-G SNP in exon 4 of CD45 (151460.0001) alters CD45 (151460) splicing and has been associated with autoimmune and infectious diseases. Dawes et al. (2006) found that there were twice as many 77C-G heterozygotes among HCV-infected patients than in a healthy UK control population; no 77C-G homozygotes were observed in either group. In addition, there were twice as many 77C-G heterozygotes among chronic HCV carriers than in individuals who resolved HCV infection. FACs and immunoblot analyses showed that lymphocytes, particularly CD8 (see 186910)-positive T cells, from 77C-G heterozygotes had a significantly increased proportion of CD45RA-positive cells compared with controls. Individuals heterozygous for 77C-G also showed more rapid dephosphorylation tyr505 of LCK (153390) after in vitro stimulation. Transgenic mice with Cd45 expression mimicking that in human 77C-G heterozygotes had an altered Cd8 cell phenotype and more rapid proliferative responses and Lck activation, as in humans. Dawes et al. (2006) concluded that 77C-G heterozygotes have an altered T-cell phenotype and greater susceptibility to HCV infection and severe HCV-induced fibrosis.

Variation Influencing Response to Therapy

Huang et al. (2007) genotyped 8 SNPs spanning the entire 5.4-kb IFNG gene in 2 large cohorts of HCV-positive patients, one consisting of IFNA (147660)-treated patients, and the other consisting of intravenous drug users who had spontaneously cleared HCV infection or who had chronic HCV infection. One SNP, a C-to-G change at position -764 (147570.0004; rs2069707) in the proximal promoter region next to the binding motif for HSF1 (140580), was significantly associated with sustained virologic response to IFNA therapy in the first cohort and with spontaneous recovery in the second cohort. Luciferase reporter and EMSA analyses showed that the -764G allele had 2- to 3-fold higher promoter activity and stronger binding affinity for HSF1 than the -764C allele. Huang et al. (2007) concluded that the -764C-G SNP is functionally important in determining viral clearance and treatment response in HCV-infected patients.

The recommended treatment for chronic HCV infection involves a 48-week course of pegylated interferon-alpha-2b or -alpha-2a (see IFNA2; 147562) combined with ribavirin (RVN). However, many patients are not cured by treatment, and patients of European ancestry have a significantly higher probability of being cured than patients of African ancestry. Ge et al. (2009) performed a genomewide association study on more than 1,600 individuals chronically infected with HCV who were participating in a clinical treatment trial. They identified a SNP 3 kb upstream of the IL28B gene (IFNL3; 607402), rs12979860, that was strongly associated with sustained virologic response (SVR), defined as the absence of detectable virus at the end of follow-up evaluation. The CC genotype of rs12979860 was associated with an approximately 2-fold greater rate of SVR compared with the TT genotype, both among patients of European ancestry (P of 1.06 x 10(-25)) and African Americans (P of 2.06 x 10(-3)). Because the CC genotype was substantially more frequent in European than African populations, Ge et al. (2009) estimated that rs12979860 could explain approximately half of the difference in SVR between African Americans and patients of European ancestry. They sequenced the IL28B gene in 96 individuals and identified 2 variants that were highly associated with rs12979860: a G-C SNP 37 bp upstream of the translation initiation codon (rs28416183), and a nonsynonymous coding SNP that produces a lys70-to-arg (K70R) substitution (rs8103142). Ge et al. (2009) could not resolve which, if any, of these 3 SNPs was uniquely responsible for the association with SVR and suggested that functional studies were needed.

To address the role of rs12979860 in HCV clearance, Thomas et al. (2009) genotyped 1,008 people from 6 independent HCV cohorts. The frequency of the C allele was greater in individuals of European than those of African ancestry in both HCV clearance (P of 3 x 10(-10)) and persistence (P of 1 x 10(-21)) groups. However, the frequency of the C allele versus the T allele was much greater in the clearance group in both ethnic groups, with frequencies of 80.3% versus 66.7%, respectively, in individuals of European ancestry (P of 7 x 10(-8)) and 56.2% versus 37%, respectively, in individuals of African ancestry (P of 1 x 10(-5)). Patients with the CC genotype were 3 times more likely to clear HCV relative to patients with CT and TT genotypes combined (OR of 0.33, P = 10(-12) for combined ethnic groups), and the protective effect of the C allele seemed to be recessive. The protective effect of the C allele was independent of human immunodeficiency virus and hepatitis B virus surface antigen status, route of HCV acquisition, and other known host genetic factors. Genotyping of populations worldwide showed that the C allele was nearly fixed throughout east Asia, had an intermediate frequency in Europe, and was a minor allele in Africa. The frequencies in Central and South America were also intermediate, suggesting selective pressure since migration from Asia. Thomas et al. (2009) noted that rs12979860 is in strong linkage disequilibrium with a nonsynonymous coding SNP, rs8103142, that could alter the function of IL28B and explain the association, but that tests for functional differences were needed to define the biologic mechanism. Thomas et al. (2009) concluded that rs12979860 is associated with both HCV treatment response and with natural clearance of HCV.

Prokunina-Olsson et al. (2013) found that ss469415590, a dinucleotide frameshift variant that 'creates' the IFNL4 gene (615090), was in high linkage disequilibrium with rs12979860, a genetic marker strongly associated with HCV clearance. They showed that the delT/G allele of ss469415590 was even more strongly correlated with poor response to pegylated IFNA/ribavirin treatment of chronic HCV than the T allele of rs12979860 in individuals of African ancestry. Prokunina-Olsson et al. (2013) proposed that IFNL4 induces weak expression of ISGs, providing an antiviral response that lowers the HCV load, but that it also reduces responses to type I and type III IFNs that are necessary for efficient HCV clearance.

To identify genetic variants associated with HCV treatment response, Suppiah et al. (2009) conducted a genomewide association study of SVR to PEG-IFN-alpha/RBV combination therapy in 293 Australian individuals with genotype 1 chronic hepatitis C, with validation in an independent replication cohort consisting of 555 individuals. They reported an association to SVR with the SNP rs8099917 (combined P = 9.25 x 10(-9), OR = 1.98, 95% CI = 1.57-2.52), within the gene region encoding IL28B. IL28B contributes to viral resistance and is known to be upregulated by interferons and by RNA virus infection. Suppiah et al. (2009) concluded that their data suggested that host genetics may be useful for the prediction of drug response, and supported the investigation of the role of IL28B in the treatment of HCV and in other diseases treated with IFNA.

Tanaka et al. (2009) reported a genomewide association study to null virologic response (NVR) in the treatment of patients with hepatitis C virus genotype 1 within a Japanese population. Tanaka et al. (2009) found 2 SNPs near the gene IL28B on chromosome 19 to be strongly associated with NVR (rs12980275, P = 1.93 x 10(-13), and rs8099917, P = 3.11 x 10(-15)). Tanaka et al. (2009) replicated these associations in an independent cohort (combined P values, 2.84 x 10(-27) (OR = 17.7; 95% CI = 10.0-31.3) and 2.68 x 10(-32) (OR = 27.1; 95% CI = 14.6-50.3), respectively). These SNPs were also associated with SVR (rs12980275, P = 3.99 x 10(-24), and rs8099917, P = 1.11 x 10(-27)). In further fine mapping of the region, 7 SNPs located in the IL28B region showed the most significant associations (P = 5.52 x 10(-28) to 2.68 x 10(-32); OR = 22.3-27.1). Real-time quantitative PCR assays in peripheral blood mononuclear cells showed lower IL28B expression levels in individuals carrying the minor alleles (P = 0.015).

Chronic hepatitis C virus infection is treated with a combination of pegylated interferon-alpha and ribavirin. One of the most important side effects is ribavirin-induced hemolytic anemia, which affects most patients and is severe enough to require dose modification in up to 15% of patients. Fellay et al. (2010) showed that genetic variants leading to inosine triphosphatase deficiency, a condition not thought to be clinically important, protect against hemolytic anemia in hepatitis C-infected patients receiving ribavirin. The association between the ITPA gene variants with protection against anemia was identified by an association between the SNP rs6051702 with a genomewide P value of 1.1 x 10(-45) among European-Americans. This SNP was in linkage disequilibrium with 2 less common alleles within ITPA, a P32T mutation (rs1127354, 147520.0001) and a splice site variant (rs7270101, 147520.0002).

Among 304 patients with hepatitis C who were treated with ribavirin, Thompson et al. (2010) found that the minor allele of the ITPA SNPs rs1127354 and rs7270101 were significantly associated with protection against hemoglobin (Hb) reduction at week 4 (p = 3.1 x 10(-13) and p = 1.3 x 10(-3), respectively). Combining the variants into the ITPase deficiency variable according to the severity of enzyme deficiency strengthened the association (p = 2.4 x 10(-18)). The ITPase deficiency variable was associated with lower rates of anemia over the entire treatment period (48 weeks); however, no association with sustained virologic response was observed. The findings replicated those of Fellay et al. (2010) in an independent cohort.

By sequencing the putative regulatory region upstream of IL28B, Bibert et al. (2013) identified a novel polymorphism, which they called TT/-G, in which a T deletion (rs67272382) occurs adjacent to a T-to-G substitution (rs74597329) at positions 39739154 and 39739155 on chromosome 19 (build 37.1). Analysis of cohorts of patients with chronic HCV infection and patients with spontaneous HCV clearance showed strong linkage disequilibrium between rs12979860 and the TT/-G polymorphism, with equivalent minor allele frequencies of 0.38. Analysis of individuals discordant at these SNPs revealed that TT/-G was a better marker than rs12979860 for HCV clearance and showed that the -G allele was associated with reduced clearance, regardless of viral genotype. Stimulation of peripheral blood mononuclear cells from individuals with different combinations of the polymorphisms with polyinosine-polycytidylic acid determined that IL28B and IP10 (CXCL10; 147310), but not TNF (191160), mRNA expression was driven by the presence of 1 or 2 mutant -G alleles of TT/-G, but not by rs12979860. Bibert et al. (2013) proposed that there is a strong link between the mutant -G allele of TT/-G, reduced expression of IL28B and IP10, and HCV treatment failure.

By measuring expression of IFNL1 (607403) and IFNLR1 (607404) in 122 liver biopsies of patients with chronic hepatitis C and 53 controls, Duong et al. (2014) found that expression of IFNLR1, but not IFNL1, was associated with IFNL3 genotype. In 30 primary human hepatocyte (PHH) samples, IFNLR1 expression was low unless induced by IFNA, and IFNA-induced IFNLR1 expression was stronger in PHHs carrying the minor IFNL3 allele. In chronic hepatitis C liver biopsies, there was a strong association of high IFNLR1 expression with elevated ISG expression, with IFNL3 minor alleles, and with nonresponse to pegylated IFNA and ribavirin. Duong et al. (2014) concluded that these findings explain the link between IFNL3 genotype and treatment nonresponse.