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Interferon lambda 4 (IFNL4) gene polymorphism is associated with spontaneous clearance of HCV in HIV-1 positive patients

Abstract

Approximately one-third of the individuals infected with human immunodeficiency virus type 1 (HIV-1) are co-infected with hepatitis C virus (HCV). Co-infected patients have an increased risk for developing end-stage liver diseases. Variants upstream of the IFNL3 gene have been associated with spontaneous and treatment-induced clearance of HCV infection. Recently, a novel polymorphism was discovered, denoted IFNL4 ΔG > TT (rs368234815), which seems to be a better predictor of spontaneous clearance than the IFNL4 rs12979860 polymorphism. We aimed to determine the prevalence of the IFNL4 ΔG > TT variants and to evaluate the association with spontaneous clearance of HCV infection in Brazilian HIV-1 patients. The IFNL4 ΔG > TT genotypes were analyzed by polymerase chain reaction followed by restriction digestion in 138 HIV-1 positive patients who had an anti-HCV positive result. Spontaneous clearance of HCV was observed in 34 individuals (24.6%). IFNL4 genotype distribution was significantly different between individuals who had spontaneous clearance and chronic HCV patients (p=0.002). The probability of spontaneous clearance of HCV infection for patients with the IFNL4 TT/TT genotype was 3.6 times higher than for patients carrying the IFNL4 ΔG allele (OR=3.63, 95% CI:1.51-8.89, p=0.001). The IFNL4 ΔG > TT polymorphism seems to be better than IFNL4 rs12979860 to predict spontaneous clearance of the HCV in Brazilian HIV-1 positive patients.

Keywords
IFNL4 genotypes; HIV/HCV co-infected patients; Spontaneous clearance

Human immunodeficiency virus type 1 (HIV-1) infects approximately 38 million people worldwide. About one-third of these individuals are also co-infected with hepatitis C virus (HCV) because of the shared transmission routes (Soriano et al., 2007Soriano V, Puoti M, Sulkowski M, Cargnel A, Benhamou Y, Peters M, Mauss S, Bräu N, Hatzakis A, Pol S, et al. (2007) Care of patients coinfected with HIV and hepatitis C virus: 2007 updated recommendations from the HCV-HIV International Panel. AIDS 21:1073-1089.; World Health Organization, 2013World Health Organization (2013) Global report epidemiology http://www.unaids.org/en/media/unaids/contentassets/documents/epidemiology/2013/gr2013/201309_epi_core_en.pdf (accessed April 15, 2014).
http://www.unaids.org/en/media/unaids/co...
). Co-infected patients have an increased risk for developing end-stage liver diseases, including cirrhosis and hepatocellular carcinoma (Soriano et al., 2013Soriano V, Vispo E, Fernandez-Montero JV, Labarga P and Barreiro P (2013) Update on HIV/HCV coinfection. Curr HIV/AIDS Rep 10:226-234.).

Genome-wide association studies (GWAS) identified single nucleotide polymorphisms upstream of interferon-λ3 gene (IFNL3; formerly known as IL28B), strongly associated with spontaneous and treatment-induced clearance of HCV infection (Ge et al., 2009Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV, Urban TJ, Heinzen EL, Qiu P, Bertelsen AH, Muir AJ, et al. (2009) Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature 461:399-401.; Suppiah et al., 2009Suppiah V, Moldovan M, Ahlenstiel G, Berg T, Weltman M, Abate ML, Bassendine M, Spengler U, Dore GJ, Powell E, et al. (2009) IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy. Nat Genet 41:1100-1104.; Tanaka et al., 2009Tanaka Y, Nishida N, Sugiyama M, Kurosaki M, Matsuura K, Sakamoto N, Nakagawa M, Korenaga M, Hino K, Hige S, et al. (2009) Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C. Nat Genet 41:1105-1109.; Rauch et al., 2010Rauch A, Kutalik Z, Descombes P, Cai T, Di Iulio J, Mueller T, Bochud M, Battegay M, Bernasconi E, Borovicka J, et al. (2010) Genetic variation in IL28B is associated with chronic hepatitis C and treatment failure: A genome-wide association study. Gastroenterology 138:1338-1345.). The IFNL3 gene, located on chromosome 19, encodes interferon-λ3 protein, a cytokine which has antiviral properties in vitro and in vivo (Hou et al., 2009Hou W, Wang X, Ye L, Zhou L, Yang ZQ, Riedel E and Ho WZ (2009) Lambda interferon inhibits human immune deficiency virus type 1 infection of macrophages. J Virol 83:3834-3842.) through activation of the JAK-STAT pathway and up-regulation of interferon-stimulated genes (ISGs) (Zhou et al., 2007Zhou Z, Hamming O, Ank N, Paludan S, Nielsen AL and Hartmann R (2007) Type II interferon (IFN) induces a type I IFN-like response in a restricted subset of cells through signaling pathway and the mitogen-actived protein kinases. J Virol 81:7749-7758.). Several studies confirmed the significant association between the CC genotype of the rs12979860 polymorphism (located approximately 3Kb upstream of IFNL3) and spontaneous and treatment-induced clearance of HCV infection in both HCV mono-infected and HIV/HCV co-infected patients (Matsuura et al., 2014Matsuura K, Watanabe T and Tanaka Y (2014) Role of IL28B for chronic hepatitis C treatment toward personalized medicine. J Gastroenterol Hepatol 29:241-249.). However, it was not clear how the genotypes of the rs12979860 polymorphism affect the interferon signaling pathways (Balagopal et al., 2010Balagopal A, Thomas DL and Thio CL (2010) IL28B and the control of hepatitis C infection. Gastroenterology 139:1865-1876.; Prokunina-Olsson et al., 2013Prokunina-Olsson L, Muchmore B, Tang W, Pfeiffer RM, Park H, Dickensheets H, Hergott D, Porter-Gill P, Mumy A, Kohaar I, et al. (2013). A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. Nat Genet 45:164-171.). Recently, the IFNL4 gene was discovered. It is controlled by a dinucleotide polymorphism, denoted IFNL4 ΔG > TT (rs368234815; c.65_66delAAinsC; p. Glu22AlafsTer25) and located in exon 1 of IFNL4. The IFNL4 ΔG allele creates a novel gene which encodes the interferon-λ4 protein, moderately similar to interferon-λ3. The alternative allele IFNL4 TT does not create this protein. IFNL4 ΔG > TT was identified in high linkage disequilibrium with rs12979860, now more properly called IFNL4 rs12979860 because of its location within intron 1 of IFNL4 (Prokunina-Olsson et al., 2013Prokunina-Olsson L, Muchmore B, Tang W, Pfeiffer RM, Park H, Dickensheets H, Hergott D, Porter-Gill P, Mumy A, Kohaar I, et al. (2013). A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. Nat Genet 45:164-171.; O'Brien et al., 2014O'Brien TR, Prokunina-Olsson L and Donnelly RP (2014) IFN-λ4: The paradoxical new member of the interferon lambda family. J Interferon Cytokine Res 34:829-838.). IFNL4 ΔG > TT seems to be a better predictor of HCV clearance than IFNL4 rs12979860, mainly in individuals of African ancestry (Prokunina-Olsson et al., 2013Prokunina-Olsson L, Muchmore B, Tang W, Pfeiffer RM, Park H, Dickensheets H, Hergott D, Porter-Gill P, Mumy A, Kohaar I, et al. (2013). A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. Nat Genet 45:164-171.; Bibert et al., 2013Bibert S, Roger T, Calandra T, Bochud M, Cerny A, Semmo N, Duong FH, Gerlach T, Malinverni R, Moradpour D, et al. (2013) IL28B expression depends on a novel TT/-G polymorphism which improves HCV clearance prediction. J Exp Med 210:1109-1116.; O'Brien et al., 2014O'Brien TR, Prokunina-Olsson L and Donnelly RP (2014) IFN-λ4: The paradoxical new member of the interferon lambda family. J Interferon Cytokine Res 34:829-838.). The present study aimed to determine the prevalence of the IFNL4 ΔG > TT variants and to evaluate the association with spontaneous clearance of HCV infection in Brazilian HIV-1 positive patients.

The study was performed with HIV-1 positive patients from a cross-sectional study conducted previously (July 2008 to January 2009) in a reference outpatient treatment center for HIV testing and AIDS treatment in Canoas (Rio Grande do Sul, Brazil). A total of 580 adult patients (aged ≥ 18 years) were consecutively enrolled, and 57 refused to participate in the study. Socio-demographic and clinical variables of the studied sample were described previously (Lunge et al., 2012Lunge VR, Da Rocha DB, Béria JU, Tietzmann DC, Stein AT and Simon D (2012) IL28B polymorphism associated with spontaneous clearance of hepatitis C infection in a Southern Brazilian HIV type 1 population. AIDS Res Hum Retrov 28:215-219.; Simon et al., 2014Simon D, Michita RT, Béria JU, Tietzmann DC, Stein AT and Lunge VR (2014) Alcohol misuse and illicit drug use are associated with HCV/HIV co-infection. Epidemiol Infect 142:2616-2623.). All study participants signed an informed consent form. The study was approved by the Research Ethics Committee of the Universidade Luterana do Brasil (process 139H/2007).

Blood samples were collected by venipuncture in 5 mL tubes, using ethylenediamitetraacetic acid (EDTA) as anticoagulant, and centrifuged for plasma and cell separation. All plasma samples were submitted to anti-HCV and HCV-RNA detection, as described previously (Lunge et al., 2012Lunge VR, Da Rocha DB, Béria JU, Tietzmann DC, Stein AT and Simon D (2012) IL28B polymorphism associated with spontaneous clearance of hepatitis C infection in a Southern Brazilian HIV type 1 population. AIDS Res Hum Retrov 28:215-219.). The viral genotype was identified in all HCV-RNA positive samples. Spontaneous HCV clearance was defined as HCV seropositivity and negative HCV RNA results (< 50 UI/ml) without any hepatitis C specific treatment (either interferon or interferon and ribavirin).

IFNL4 genotyping was performed in all patients with a positive result for anti-HCV. Total DNA of each clinical sample was purified by a standard silica-based procedure (Boom et al., 1990Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM and van der Noordaa J (1990) Rapid and simple method for purification of nucleic acids. J Clin Microbiol 28:495-503.). IFNL4 genotypes were determined by polymerase chain reaction (PCR) using primers (5'-GCCTGCTGCAGAAGCAGAGAT-3' and R 5'-GCTCCAGCGAGCGGTAGTG-3') described previously (Prokunina-Olsson et al., 2013Prokunina-Olsson L, Muchmore B, Tang W, Pfeiffer RM, Park H, Dickensheets H, Hergott D, Porter-Gill P, Mumy A, Kohaar I, et al. (2013). A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. Nat Genet 45:164-171.). The amplification mixture consisted of ultrapure distilled water (DNase and RNase free), 10 mM Tris-HCl, pH 8.5, 50 mM KCl, 0.75 mM MgCl2, 0.0625 mM of deoxynucleoside triphosphates, 0.25 μM of each primer, 1 U of Taq DNA polymerase (Cenbiot Enzimas, Brazil) and 20-100 ng of DNA. All reactions were performed with the following cycling parameters: 1 cycle at 94 °C for 3 min followed by 35 cycles at 94 °C for 10 s, 61 °C for 30 s and 72 °C for 30 s, followed by a final extension step at 72 °C for 5 min. The amplified DNA was digested for restriction fragment length polymorphism (RFLP) analysis using ApeK I restriction enzyme according the manufacturer instructions (New England Biolabs). Digested fragments were separated by electrophoresis on a 10% polyacrylamide gel stained with silver nitrate. The IFNL4 TT allele presented three fragments (of 92, 32 and 5 bp, respectively), while the IFNL4 ΔG allele presented four fragments (of 75, 32, 16 and 5 bp, respectively). PCR amplified products of the three IFNL4 genotypes were sequenced to validate the PCR-RFLP assay results.

Data were expressed as mean and standard deviation (± S.D.) or frequency percentage (%). Variables were compared between groups using Student's t-test or the nonparametric Mann-Whitney test for categorical variables, and the chi-square test for qualitative variables. Allele frequencies were obtained by direct counting of alleles. Allele and genotype frequencies were compared between groups using the chi-square test. The linkage disequilibrium between IFNL4 ΔG > TT and IFNL4 rs12979860 polymorphisms was calculated using the CubeX program (Gaunt et al., 2007Gaunt TR, Rodríguez S and Day IN (2007) Cubic exact solutions for the estimation of pairwise haplotype frequencies: Implications for linkage disequilibrium analyses and a web tool ‘CubeX'. BMC Bioinform 8:e428.). All tests were two-tailed and P < 0.05 values were considered statistically significant.

Out of 580 HIV-1 positive patients originally included in this study, 138 (23.8%) patients had an HCV-positive result. Sociodemographic traits, risk factor for HIV-1, and clinical characteristics of HIV-1/HCV co-infected patients are presented in Table 1. The mean age of this group of HCV-positive patients was 41.7 ± 9.5 years, and 62.3% were men. Spontaneous clearance of the HCV infection was observed in 34 individuals (24.6%). HCV genotype analysis in the chronically infected individuals showed that 63 (60.6%) patients had genotype 1, 5 (4.8%) had 2 genotype, and 36 (34.6%) had genotype 3. The mean log10 HCV-RNA was 6.8 ± 0.7, 6.9 ± 0.3, and 6.6 ± 0.9 IU/ml for HCV genotypes 1, 2, and 3, respectively (p=0.14). The IFNL4 genotypes were not associated with HCV viral load.

Table 1
Socio-demographic and clinical characteristics of the HIV/HCV co-infected study population.

Allele and genotype frequencies of the IFNL4 ΔG > TT polymorphism in the HIV-1/HCV co-infected patients are presented in Table 2. The IFNL4 ΔG allele frequency was 37%. The genotypic frequencies are in Hardy-Weinberg equilibrium for the total sample. A significant difference was observed between HCV chronic infected patients and individuals with spontaneous clearance (p=0.002). The probability of spontaneous resolution of the HCV infection in patients with IFNL4 TT/TT genotype was 3.6 higher than for patients carrying ΔG allele (OR = 3.63, 95% CI: 1.51-8.89; p=0.001). The distribution of IFNL4 ΔG > TT genotypes in comparison to IFNL4 rs12979860 genotypes is shown in Table 3. The variants are in strong linkage disequilibrium (D' = 0.883; r2 = 0.733).

Table 2
Allele and genotype frequencies of the rs368234815 IFNL4 gene polymorphism in the study population.
Table 3
The IFNL4 rs368234815 and rs12979860 genotypes in the study population.

Previous studies demonstrated that the IFNL4 rs12979860 polymorphism was significantly associated with spontaneous clearance and response to therapy in HCV infected patients (Ge et al., 2009Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV, Urban TJ, Heinzen EL, Qiu P, Bertelsen AH, Muir AJ, et al. (2009) Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature 461:399-401.; McCarthy et al., 2010McCarthy JJ, Li JH, Thompson A, Suchindran S, Lao XQ, Patel K, Tillmann HL, Muir AJ and McHutchison JG (2010) Replicated association between an IL28B gene variant and a sustained response to pegylated interferon and ribavirina. Gastroenterology 138:2307-2314.). However, recent studies reported that the IFNL4 ΔG > TT polymorphism has a better prediction value than IFNL4 rs12979860. The IFNL4 ΔG > TT polymorphism has been proposed as a candidate to provide a causal link between variants nearby IFNL3 or within IFNL4 and spontaneous clearance of the HCV, thus solving some confusing results (Covolo et al., 2014Covolo L, Bibert S, Donato F, Bochud PY, Lagging M, Negro F and Fattovich G (2014) The novel ss469415590 variant predicts virological response to therapy in patients with chronic hepatitis C virus type 1 infection. Aliment Pharmacol Ther 39:322-330.). In the present study we observed that the genotype distribution was significantly different between HCV chronic infection patients and individuals who had spontaneous clearance. There was an association between the IFNL4 TT/TT genotype of the IFNL4 ΔG > TT polymorphism and spontaneous clearance. In our previous study, the HIV-1/ HCV co-infected group presenting the CC genotype of the IFNL4 rs12979860 polymorphism had a 2.8 times higher probability for spontaneous clearance than the other genotypes (Lunge et al., 2012Lunge VR, Da Rocha DB, Béria JU, Tietzmann DC, Stein AT and Simon D (2012) IL28B polymorphism associated with spontaneous clearance of hepatitis C infection in a Southern Brazilian HIV type 1 population. AIDS Res Hum Retrov 28:215-219.). The current results now showed that patients with the IFNL4 TT/TT genotype had a 3.6 times higher probability for spontaneous HCV clearance than patients carrying the ΔG allele. Our finding is in agreement with other studies that investigated the association of the IFNL4 ΔG > TT polymorphism with impaired spontaneous or treatment-induced clearance of HCV in HIV-1 infected patients. A cohort of 207 patients treated with interferon was investigated and the IFNL4 ΔG > TT polymorphism was a better predictor of treatment failure than IFNL4 rs12979860 (Franco et al., 2014Franco S, Aparicio E, Parera M, Clotet B, Tural C and Martinez MA (2014) IFNL4 ss469415590 variant is a better predictor than ILF3 (IL28B) rs12979860 of pegylated interferon-alpha/ribavirin therapy failure in hepatitis C virus/HIV-1 coinfected patients. AIDS 28:133-136.). Similar results were found in an analysis of 890 HIV-1/HCV co-infected women. HCV clearance was three-fold higher in black women with the IFNL4 TT/TT genotype than in those with TT/ΔG or ΔG/ΔG genotypes (Aka et al., 2014Aka PV, Kuniholm MH, Pfeiffer RM, Wang AS, Tang W, Chen S, Astemborski J, Plankey M, Villacres MC, Peters MG, et al. (2014) Association of the IFNL4-ΔG allele with impaired spontaneous clearance of hepatitis C virus. J Infect Dis 209:350-354.). However, another study that analyzed 206 HIV/HCV co-infected patients and 162 HCV mono-infected patients found that the IFNL4 ΔG > TT polymorphism was strongly associated with the response to interferon/ribavirin therapy in mono-infected patients, but not in co-infected ones (Krämer et al., 2013Krämer B, Nischalke HD, Boesecke C, Ingiliz P, Voigt E, Mauss S, Stellbrink HJ, Baumgarten A, Rockstroh JK, Spengler U, et al. (2013) Variation in IFNL4 genotype and response to interferon-based therapy of hepatitis C in HIV-positive patients with acute and chronic hepatitis C. AIDS 27:2817-1819.).

Other groups have studied this polymorphism in HCV mono-infected patients only. In a Swiss cohort of 540 HCV patients, the IFNL4 ΔG > TT polymorphism was a better predictor of HCV clearance than IFNL4 rs12979860 (Bibert et al., 2013Bibert S, Roger T, Calandra T, Bochud M, Cerny A, Semmo N, Duong FH, Gerlach T, Malinverni R, Moradpour D, et al. (2013) IL28B expression depends on a novel TT/-G polymorphism which improves HCV clearance prediction. J Exp Med 210:1109-1116.). Interestingly, these authors attributed the effect of the IFNL4 ΔG variant to reduced expression of IFNL3 and interferon-γ-inducible protein-10 (IP-10). In Italian patients, the IFNL4 ΔG > TT polymorphism was significantly associated with a marker for ISG activation (IP-10), but with regard to spontaneous and treatment-induced clearance, IFNL4 ΔG > TT had a predictive value similar to IFNL4 rs12979860 (Covolo et al., 2014Covolo L, Bibert S, Donato F, Bochud PY, Lagging M, Negro F and Fattovich G (2014) The novel ss469415590 variant predicts virological response to therapy in patients with chronic hepatitis C virus type 1 infection. Aliment Pharmacol Ther 39:322-330.). Two other studies also reported similar predictive values of IFNL4 ΔG > TT and IFNL4 rs12979860 polymorphisms (Keshvari et al., 2014Keshvari M, Pouryasin A, Behnara B, Sharafi H, Hajarizadeh B and Alavian SM (2014) Letter: The rs12979860 and ss469415590 polymorphisms are in strong linkage disequilibrium in Caucasian patients with chronic hepatitis C. Aliment Pharmacol Ther 39:343.; Stättermayer et al., 2014Stättermayer AF, Strass R, Maieron A, Rutter K, Stauber R, Strasser M, Beinhardt S, Datz C, Scherzer TM, Steindl-Munda P, et al. (2014) Polymorphisms of interferon-λ4 and IL28B - effects on treatment response to interferon/ribavirin in patients with chronic hepatitis C. Aliment Pharmacol Ther 39:104-111.). Nonetheless if, as reported, one accepts the argument that IFNL4 is a functional polymorphism in the process of HCV clearance, then it would make sense to include IFNL4 ΔG > TT genotyping in clinical decisions (Keshvari et al., 2014Keshvari M, Pouryasin A, Behnara B, Sharafi H, Hajarizadeh B and Alavian SM (2014) Letter: The rs12979860 and ss469415590 polymorphisms are in strong linkage disequilibrium in Caucasian patients with chronic hepatitis C. Aliment Pharmacol Ther 39:343.).

Studies reported that IFNL4 ΔG > TT and IFNL4 rs12979860 polymorphisms are in linkage disequilibrium, but this association varies according to ethnic group. The IFNL4 ΔG allele is completely correlated with the unfavorable IFNL4 rs12979860 T allele in Asians (r2 = 1.00) and highly so in Europeans (r2 = 0.92). However, in Africans, this correlation is only moderate (r2 = 0.71). The IFNL4 ΔG > TT polymorphism has been highly associated with HCV clearance in individuals of African ancestry, with the IFNL4 ΔG allele being better than the IFNL4 rs12979860 T allele in predicting impaired clearance and treatment failure in HCV infection (Prokunina-Olsson et al., 2013Prokunina-Olsson L, Muchmore B, Tang W, Pfeiffer RM, Park H, Dickensheets H, Hergott D, Porter-Gill P, Mumy A, Kohaar I, et al. (2013). A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. Nat Genet 45:164-171.). The allele frequencies of both polymorphisms also differ according to ethnic groups. According to the HapMap project (Prokunina-Olsson et al., 2013Prokunina-Olsson L, Muchmore B, Tang W, Pfeiffer RM, Park H, Dickensheets H, Hergott D, Porter-Gill P, Mumy A, Kohaar I, et al. (2013). A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. Nat Genet 45:164-171.; Franco et al., 2014Franco S, Aparicio E, Parera M, Clotet B, Tural C and Martinez MA (2014) IFNL4 ss469415590 variant is a better predictor than ILF3 (IL28B) rs12979860 of pegylated interferon-alpha/ribavirin therapy failure in hepatitis C virus/HIV-1 coinfected patients. AIDS 28:133-136.), the frequencies for the IFNL4 ΔG allele are 7% in Asians, 32% in Europeans, and 78% in Africans. The Brazilian population is remarkably heterogeneous, which reflect its history of extensive admixture, mainly from Europeans, Africans and Amerindians (Cavalcante et al., 2011Cavalcante LN, Abe-Sandes K, Angelo AL, Machado TM, Lemaire DC, Mendes CM, Pinho JR, Malta F, Lyra LG and Lyra AC (2011) IL28B polymorphisms are markers of therapy response and are influenced by genetic ancestry in chronic hepatitis C patients from an admixed population. Liver Int 32:476-486.). In this regard, the present study comprised a sample of individuals of mixed ancestry, but the majority (59.4%) of the subjects self-reported skin color as white. The frequency of IFNL4 ΔG > TT polymorphism in the Brazilian populations is not known yet. Our study found a frequency of 37% for the IFNL4 ΔG allele, which is associated with impaired HCV clearance. The frequency of the IFNL4 ΔG allele in our study was similar to that reported in Swiss (38%) (Bibert et al., 2013Bibert S, Roger T, Calandra T, Bochud M, Cerny A, Semmo N, Duong FH, Gerlach T, Malinverni R, Moradpour D, et al. (2013) IL28B expression depends on a novel TT/-G polymorphism which improves HCV clearance prediction. J Exp Med 210:1109-1116.) and European (32%) (Franco et al., 2014Franco S, Aparicio E, Parera M, Clotet B, Tural C and Martinez MA (2014) IFNL4 ss469415590 variant is a better predictor than ILF3 (IL28B) rs12979860 of pegylated interferon-alpha/ribavirin therapy failure in hepatitis C virus/HIV-1 coinfected patients. AIDS 28:133-136.) cohorts.

Certain limitations must be considered in this study. First, the statistical power to detect differences was limited due to small sample size, which prevented us to perform a multivariate analysis. Second, it was not possible to identify the time of infection for the two viruses (HCV and HIV-1) and to clarify the precise relation between HIV-1 infection and HCV clearance.

To investigate factors that influence spontaneous clearance of HCV, as well as clearance induced by IFN-based treatment is important to understand the natural history of infection and establish new insights about treatment strategies. It has been reported that IFNL4 polymorphisms are associated with treatment outcomes based on direct-acting antivirals (DAAs) (Chu et al., 2012Chu TW, Kulkarni R, Gane EJ, Roberts SK, Stedman C, Angus PW, Ritchie B, Lu XY, Ipe D, Lopatin U, et al. (2012) Effect of IL28B genotype on early viral kinetics during interferon-free treatment of patients with chronic hepatitis C. Gastroenterology 142:790-795.; Zeuzem et al., 2013Zeuzem S, Soriano V, Asselah T, Bronowicki J-P, Lohse AW, Mullhaupt B, Schuchmann M, Bourliere M, Buti M, Roberts SK, et al. (2013) Faldaprevir and deleobuvir for HCV genotype 1 infection. N Engl J Med 369:630-639.; Meissner et al., 2014Meissner EG, Bon D, Prokunina-Olsson L, Tang W, Masur H, O'Brien TR, Herrmann E, Kottilil S and Osinusi A (2014) IFNL4-ΔG genotype is associated with slower viral clearance in hepatitis C, genotype-1 patients treated with sofosbuvir and ribavirin. J Infect Dis 209:1700-1704.). However, IFN-free DAA treatments allow high cure rates, but come with matching high price tags (The Lancet, 2014The Lancet (2014) Only just the beginning of the end of hepatitis C. Lancet 383:281.). In this sense, IFNL4 genotyping could to be useful tool before and until global access to DAA can be achieved, helping to prioritize DAA treatment.

In conclusion, our findings suggest that the IFNL4 ΔG > TT polymorphism of the IFNL4 gene seems to be better than IFNL4 rs12979860 to predict spontaneous clearance of the HCV in HIV-1 positive patients.

Acknowledgments

The authors would like to thank the patients and staff of the Specialized Service (SAE) and Testing and Counseling Center (CTA) of Canoas, RS, for their collaboration in the development of this study. The project was funded by the Brazilian Ministry of Health, Secretaria de Vigilância em Saúde (Department of Health Surveillance), Programa Nacional de Doenças Sexualmente Transmissíveis e Aids (MS/SVS/PN-DST/AIDS – Brazilian Program of Sexually Transmitted Diseases and AIDS – Cooperation Term 282/07), through the International Technical Cooperation Project AD/BRA/03/H34, established between the Brazilian government and the United Nations Office on Drugs and Crime (UNODC).

References

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  • Bibert S, Roger T, Calandra T, Bochud M, Cerny A, Semmo N, Duong FH, Gerlach T, Malinverni R, Moradpour D, et al. (2013) IL28B expression depends on a novel TT/-G polymorphism which improves HCV clearance prediction. J Exp Med 210:1109-1116.
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  • Chu TW, Kulkarni R, Gane EJ, Roberts SK, Stedman C, Angus PW, Ritchie B, Lu XY, Ipe D, Lopatin U, et al. (2012) Effect of IL28B genotype on early viral kinetics during interferon-free treatment of patients with chronic hepatitis C. Gastroenterology 142:790-795.
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Internet resources

  • Associate Editor: Maria Luiza Petzl-Erler

Publication Dates

  • Publication in this collection
    25 July 2016
  • Date of issue
    Jul-Sep 2016

History

  • Received
    21 Apr 2015
  • Accepted
    14 Jan 2016
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