Homozygosity for HLA group 2 alleles predicts treatment failure with interferon-α and ribavirin in chronic hepatitis C virus genotype 1 infection

Interferon lambda rs368234815 ΔG/ΔG is associated with higher CD4+:CD8+ T-cell ratio in treated HIV-1 infection

BACKGROUND

The objectives of this study were to investigate the relationships between polymorphisms at the interferon lambda (IFNL) locus and CD4⁺:CD8⁺ ratio normalisation in people living with HIV (PLWH) on effective antiretroviral therapy (ART); and to examine whether these polymorphisms influence the composition of T lymphocyte compartments in long-term treated HIV-1 infection.

METHODS

A cross-sectional study in PLWH enrolled into the Mater Immunology study. We performed IFNL genotyping on stored samples and evaluated the association of IFNL single-nucleotide polymorphisms (rs368234815 and rs12979860) with CD4⁺:CD8⁺ ratio normalization (> 1) and expanded CD4⁺ and CD8⁺ T-cell subsets; CD45RO⁺CD62L⁺ (central-memory), CD45RO⁺ CD62L^-(effector-memory) and CD45RO^-CD62L⁺ (naïve), using logistic and linear regression models, respectively.

RESULTS

190 ambulatory PLWH recruited to the main study, 143 were included in the analysis (38 had no stored DNA and 9 no T-lymphocyte subpopulation). Of 143 included, the median age (IQR) was 45(39-48) years, 64% were male and 66% were of Caucasian ethnicity. Heterosexual-contact (36%), injecting drug-use (33%) and men who have sex with men (24%) were the most presented HIV-transmission risk groups. The majority of subjects (90.2%) were on ART with 79% of the cohort having an undetectable HIV-RNA (< 40 copies/ml) and the time since ART initiation was 7.5 (3.7-10.4) year. rs368234815 and rs12979860 displayed similar allelic frequencies, with minor alleles ΔG and T representing 39% and 42%, respectively, of circulating alleles. rs368234815 ΔG/ΔG minor homozygotes were significantly associated with increased odds for attaining a normalised CD4⁺:CD8⁺ ratio compared to rs368234815 T/T major homozygotes in PLWH virologically suppressed on effective ART (OR = 3.11; 95% CI [1.01:9.56]). rs368234815 ΔG/ΔG homozygosity was also significantly associated with lower levels of CD4⁺ effector memory T-cells (regression coefficient: - 7.1%, p = 0.04) and CD8⁺ naïve T-cell subsets were significantly higher in HIV-1 mono-infected PLWH with rs368234815 ΔG/ΔG (regression coefficient: + 7.2%, p = 0.04).

CONCLUSIONS

In virally-suppressed, long-term ART-treated PLWH, rs368234815 ΔG/ΔG homozygotes were more likely to have attained normalisation of their CD4⁺:CD8⁺ ratio, displayed lower CD4⁺ effector memory and higher naive CD8⁺ T-cells. Further studies are needed to replicate our findings in other, larger and more diverse cohorts and to determine the impact of IFNL genetic-variation on CD4⁺:CD8⁺ ratio normalisation and clinical outcomes in PLWH.

Association of interferon lambda polymorphisms with elevated baseline viral loads in chronic hepatitis C virus genotype 6 infection

Globally, hepatitis C virus (HCV) is one of the major causes of hepatocellular carcinoma and liver cirrhosis. For clinical decision making, genetic variation in the interferon-λ (IFNL) cluster has been utilised as a baseline predictor of natural and interferon-based treatment-induced viral clearance. In Vietnam, where HCV genotypes 1 (g1) and g6 predominate, no prior studies have been conducted investigating associations of IFNL3/4 polymorphisms with spontaneous clearance (SC) or HCV viral load (VL) in chronic infection. In this study, we have investigated the host genetic variations in IFNL loci to determine the association of IFNL3/4 polymorphisms with HCV SC and baseline VLs in a Vietnamese HCV-seropositive cohort. The majority of the cohort harboured major homozygous polymorphisms in IFNL3/4 cluster (i.e. rs12979860-CC: 82.7%; rs8099917-TT: 84.8% and rs368234815-TT/TT: 85.5%) and the SC rates in these groups were 15.8%, 16.3% and 15.7%, respectively. In the minor allele groups, the resolution rates were lower (12% in rs12979860 non-CC, 9.1% in rs8099917 non-TT and 9.5% in rs368234815 non-TT/TT). Furthermore, in individuals harbouring minor alleles, females achieved higher SC rates than males. HCV g6-infected rs12979860 major homozygous individuals had significantly higher viral loads than individuals with minor alleles (CC: 6.56 log IU/ml vs. non-CC: 5.66 log IU/ml; P = 0.021). The association between IFNL3/4 genotypes with elevated HCV VL observed in HCV g6-infected individuals may have implications for the progression of liver disease in Southeast Asian countries where this viral genotype predominates and therefore warrants further studies.

The Role of Hepatitis C Virus Core Antigen Testing in the Era of Direct Acting Antiviral Therapies: What We Can Learn from the Protease Inhibitors

Direct-acting antiviral (DAA) therapies have revolutionised the treatment of hepatitis C virus (HCV). The financial cost of DAAs however is significant, and first generation protease inhibitors (PIs) also require frequent monitoring of viral RNA levels to guide treatment. In this context, we examined the relevance of HCV antigen testing to evaluate the potential role in monitoring virological response to HCV antiviral treatment with the PI-based triple therapies, telaprevir (TVR) and boceprevir (BOC). Chronic HCV-infected individuals (n = 152) enrolled in the Irish Hepatitis C Outcomes Research Network (ICORN) study were prospectively analysed for baseline markers and the early viral kinetics associated with SVR. The sustained virological response (SVR) rates in the cohort receiving TVR and BOC were 87.3% and 73.8%, respectively. Baseline factors associated with successful outcome in TVR therapy were age (P = 0.0098), IFNL3 genotype (P = 0.0330) and viral load (P = 0.0456). RNA level at week 4 (P = 0.0068) and viral antigen negativity at week 2 (P = 0.0359) were predictive of SVR for TVR-based therapy. In BOC therapy, prior interferon treatment (P = 0.0209) and IFNL3 genotype (P = 0.0410) were baseline predictors of SVR. Evidence of viraemia based either on viral RNA or antigen at week 4 predicted SVR in these patients. Our data showed that rapid decline of HCV antigen to negative level at week 2 in TVR treatment and <0.96 log fmol/l in BOC treatment after commencement of PI triple therapy were associated with SVR. HCV antigen measurement should be considered as a potential alternative for monitoring treatment response during DAA-based regimens.

Naturally occurring HCV NS5A/B inhibitor resistance-associated mutations to direct-acting antivirals

BACKGROUND

Direct-acting antivirals (DAAs) have significantly improved the treatment response in HCV chronic infection with higher potency and better tolerance. We established the prevalence of naturally occurring NS5A and NS5B inhibitor resistance-associated mutations (RAMs) in HCV genotype (GT)-1 chronically infected individuals in Ireland.

METHODS

In a multicentre cohort study, employing sequencing-based analysis, the presence of RAMs was determined in the HCV NS5A (n=119) and the NS5B (n=60).

RESULTS

Naturally occurring RAMs in NS5A (M28V, R30Q, L31I, P58S, E62D and Y93H) were identified in 14.3% (17/119) of cases. Notably, the major RAM Y93H was found in 15.2% (7/46) of GT-1b versus none (0/73) in GT-1a (P=0.0009). The frequency of Y93H present in IFNL3 rs12979860 CC major homozygotes (30%, 3/10) was higher than in the non-CC group (11.1%, 4/36). GT-1b-infected individuals harbouring Y93H had significantly higher viral loads than those without this mutation (P=0.006). Additionally, two novel insertions in GT-1a and GT-1b were identified in the NS5A interferon sensitivity-determining region. In NS5B, only minor pre-existing RAMs (L159F, C316N and I434M) were detected in 10% (6/60) of samples. The proportion of individuals harbouring multiple RAMs in different DAA target regions was low.

CONCLUSIONS

RAMs to novel DAAs were infrequent in the DAA-naive population in the present study. The NS5A Y93H substitution was the only significant RAM identified. Given the low frequency of multiple RAMs in NS3, NS5A and NS5B regions and the unclear impact of pre-existing Y93H on the response in combination therapies, the role of pre-treatment RAM analysis in treatment-naive individuals requires further investigation.