The hepatitis C sequence database in Los Alamos

Kuiken, Carla; Hraber, Peter; Thurmond, Jim; Yusim, Karina

doi:10.1093/nar/gkm962

Cited by 124 publications

(143 citation statements)

References 14 publications

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“…In contrast, two or three mutations are required for genotype 2a, 4a, and 6a viruses. This holds true for other published isolates of these subtypes (66). Such differences likely translate into clinical differences, and higher treatment failure rates were observed for genotype 1a viruses, which require one nucleotide change for R155K, than for genotype 1b viruses, which require two changes (4).…”

Section: Discussionmentioning

confidence: 86%

Hepatitis C Virus Genotype 1 to 6 Protease Inhibitor Escape Variants: In Vitro Selection, Fitness, and Resistance Patterns in the Context of the Infectious Viral Life Cycle

Serre

Jensen

Ghanem

et al. 2016

Antimicrob Agents Chemother

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bHepatitis C virus (HCV) NS3 protease inhibitors (PIs) are important components of novel HCV therapy regimens. Studies of PI resistance initially focused on genotype 1. Therefore, knowledge about the determinants of PI resistance for the highly prevalent genotypes 2 to 6 remains limited. Using Huh7.5 cell culture-infectious HCV recombinants with genotype 1 to 6 NS3 protease, we identified protease positions 54, 155, and 156 as hot spots for the selection of resistance substitutions under treatment with the first licensed PIs, telaprevir and boceprevir. Treatment of a genotype 2 isolate with the newer PIs vaniprevir, faldaprevir, simeprevir, grazoprevir, paritaprevir, and deldeprevir identified positions 156 and 168 as hot spots for resistance; the Y56H substitution emerged for three newer PIs. Substitution selection also depended on the specific recombinant. The substitutions identified conferred cross-resistance to several PIs; however, most substitutions selected under telaprevir or boceprevir treatment conferred less resistance to certain newer PIs. In a single-cycle production assay, across genotypes, PI treatment primarily decreased viral replication, which was rescued by PI resistance substitutions. The substitutions identified resulted in differential effects on viral fitness, depending on the original recombinant and the substitution. Across genotypes, fitness impairment induced by resistance substitutions was due primarily to decreased replication. Most combinations of substitutions that were identified increased resistance or fitness. Combinations of resistance substitutions with fitness-compensating substitutions either rescued replication or compensated for decreased replication by increasing assembly. This comprehensive study provides insight into the selection patterns and effects of PI resistance substitutions for HCV genotypes 1 to 6 in the context of the infectious viral life cycle, which is of interest for clinical and virological HCV research. With more than 100 million chronic infections causing approximately 500,000 deaths annually, hepatitis C virus (HCV) is a major global health and economic burden (1, 2). The six epidemiologically important genotypes differ in ϳ30% of their sequence and in their sensitivity to antiviral regimens (3-6). In Europe, the Americas, Asia, and Australasia, genotypes 1, 2, and 3 are most prevalent. While genotypes 4, 5, and 6 are more restricted to specific geographical regions in Africa and Asia, they account for 20% of global HCV infections and have spread beyond these primary geographical locations (1, 2, 7).The development of directly acting antivirals (DAAs) has revolutionized HCV therapy. The main components of interferonfree regimens introduced in the clinic are inhibitors of the HCV nonstructural (NS) proteins NS3 protease (NS3P), NS5A,8,9). Even though DAA-based therapy regimens could cure most patients in clinical trials, failure rates of 5 to 10% are to be expected in real life, due primarily to the development of DAA resistance (4,8). Given the large ...

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Section: Discussionmentioning

confidence: 86%

Hepatitis C Virus Genotype 1 to 6 Protease Inhibitor Escape Variants: In Vitro Selection, Fitness, and Resistance Patterns in the Context of the Infectious Viral Life Cycle

Serre

Jensen

Ghanem

et al. 2016

Antimicrob Agents Chemother

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“…This lack of sensitivity to telaprevir and boceprevir might be explained by V170, found for the majority of genotype 4a isolates and associated with PI resistance (alignment of 17 genotype 4a NS3P sequences deposited in the European HCV database, generated July 2015 [55], and the 2008 Web alignment from the Los Alamos HCV database [56]) (5,9). The comparatively low sensitivity of original genotype 3a recombinants to all PIs might be explained by Q168, conserved for genotype 3a, and V170, found in 3a(S52) (alignment of 28 genotype 3a NS3P sequences deposited in the European HCV database, generated July 2015 [55], and the 2008 Web alignment from the Los Alamos HCV database [56]) (5,9,10). The testing of additional genotype 2a and 3a isolates suggested that there were no major EC 50 differences for different isolates of the same genotype (Table 1; also see Fig.…”

Section: Discussionmentioning

confidence: 99%

Substitutions at NS3 Residue 155, 156, or 168 of Hepatitis C Virus Genotypes 2 to 6 Induce Complex Patterns of Protease Inhibitor Resistance

Jensen

Serre

Humes

et al. 2015

Antimicrob Agents Chemother

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Various protease inhibitors (PIs) currently are becoming available for treatment of hepatitis C virus (HCV). For genotype 1, substitutions at NS3 protease positions 155, 156, and 168 are the main determinants of PI resistance. For other genotypes, similar substitutions were selected during PI treatment but were not characterized systematically. To elucidate the impact of key PI resistance substitutions on genotypes 2 to 6, we engineered the substitutions R155A/E/G/H/K/Q/T, A156G/S/T/V, and D/Q168A/E/ G/H/N/V into HCV recombinants expressing genotype 2 to 6 proteases. We evaluated viral fitness and sensitivity to nine PIs (telaprevir, boceprevir, simeprevir, asunaprevir, vaniprevir, faldaprevir, paritaprevir, deldeprevir, and grazoprevir) in Huh7.5 cells. We found that most variants showed decreased fitness compared to that of the original viruses. Overall, R155K, A156G/S, and D/Q168A/E/H/N/V variants showed the highest fitness; however, genotype 4 position 168 variants showed strong fitness impairment. Most variants tested were resistant to several PIs. Resistance levels varied significantly depending on the specific substitution, genotype, and PI. For telaprevir and boceprevir, specific 155 and 156, but not 168, variants proved resistant. For the remaining PIs, most genotype 2, 4, 5, and 6, but not genotype 3, variants showed various resistance levels. Overall, grazoprevir (MK-5172) had the highest efficacy against original viruses and variants. This is the first comprehensive study revealing the impact of described key PI resistance substitutions on fitness and PI resistance of HCV genotypes 2 to 6. In conclusion, the studied substitutions induced resistance to a panel of clinically relevant PIs, including the newer PIs paritaprevir, deldeprevir, and grazoprevir. We discovered complex patterns of resistance, with the impact of substitutions varying from increased sensitivity to high resistance. Hepatitis C virus (HCV) chronically infects ϳ150 million people worldwide. Interferon-free treatment regimens based on direct-acting antivirals (DAAs) are currently being defined (1). Despite their high efficacy, DAA-resistant variants are expected to develop in 5 to 15% of treated patients and might be spreading in populations (1, 2). The HCV NS3 protease (NS3P) is, in association with cofactor NS4A, essential for HCV replication; furthermore, it inactivates cellular proteins mediating innate antiviral responses (3). NS3P inhibitors (PIs) are expected to be an important component of interferon-free treatment regimens (1). Telaprevir, boceprevir, simeprevir, and paritaprevir have been licensed, while several additional PIs are in the final stages of clinical development (1). For HCV, six epidemiologically important genotypes have been described, differing in ϳ30% of their sequence and in their sensitivity to antivirals (1, 4-7). In Europe and the Americas, genotype 1 is most common, followed by genotypes 2 and 3. However, worldwide, genotypes 4, 5, and 6 cause Ͼ20% of all infections and are spreading beyond their primar...

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“…All available HCV genotype 1b NS3 sequences were retrieved from the public HCV sequence database (13). Identical sequences and sequences of unknown origin were removed, and additional sequences obtained in Germany and China were added and aligned by using Geneious 7.0.6 (Biomatters, Auckland, New Zealand).…”

Section: Expansion Of Peptide-specific Cd8mentioning

confidence: 99%

Impact of Sequence Variation in a Dominant HLA-A*02-Restricted Epitope in Hepatitis C Virus on Priming and Cross-Reactivity of CD8 ⁺ T Cells

Ziegler

Skibbe

Walker

et al. 2014

J Virol

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CD8؉ T cells are an essential component of successful adaptive immune responses against hepatitis C virus (HCV). A major obstacle to vaccine design against HCV is its inherent viral sequence diversity. Here, we test the hypothesis that different sequence variants of an immunodominant CD8 ؉ T cell epitope, all binding with high affinity to HLA class I, target different T cell receptor repertoires and thereby influence the quality of the CD8 ؉ T cell response. The impacts of sequence differences in the HLA-A*02-restricted HCV NS3 1406 -1415 epitope on in vitro priming of naive CD8 ؉ T cells from seronegative donors and cross-reactivity of primed T cells with other epitope variants were characterized. Although the six epitope variants tested were all high-affinity binders to HLA-A*02:01, substantial differences in priming and cross-reactivity of CD8 ؉ T cells were observed. The variant associated with the most reproducible priming and induction of T cells with broad cross-reactivity was a genotype 1b variant (KLSAL GLNAV) that is more common in HCV isolates collected in Asia but is rare in sequences from Europe and North America. The superior immunogenicity and cross-reactivity of this relatively rare epitope variant were confirmed by using HCV-specific memory CD8 ؉ T cells from people who inject drugs, who are frequently exposed to HCV. Collectively, the data suggest that sequence differences at the epitope level between HCV isolates substantially impact CD8 ؉ T cell priming and the degree of cross-reactivity with other epitope variants. IMPORTANCEThe results have important implications for vaccine design against highly variable pathogens and suggest that evidence-based selection of the vaccine antigen sequence may improve immunogenicity and T cell cross-reactivity. Cross-reactive CD8 ؉ T cells are likely beneficial for immune control of transmitted viruses carrying epitope variants and for prevention of immune escape during acute infection. To this end, rare epitope variants and potentially even altered epitope sequences associated with priming of broadly cross-reactive T cell receptors should be considered for vaccine design and need further testing.

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The hepatitis C sequence database in Los Alamos

Cited by 124 publications

References 14 publications

Hepatitis C Virus Genotype 1 to 6 Protease Inhibitor Escape Variants: In Vitro Selection, Fitness, and Resistance Patterns in the Context of the Infectious Viral Life Cycle

Hepatitis C Virus Genotype 1 to 6 Protease Inhibitor Escape Variants: In Vitro Selection, Fitness, and Resistance Patterns in the Context of the Infectious Viral Life Cycle

Substitutions at NS3 Residue 155, 156, or 168 of Hepatitis C Virus Genotypes 2 to 6 Induce Complex Patterns of Protease Inhibitor Resistance

Impact of Sequence Variation in a Dominant HLA-A*02-Restricted Epitope in Hepatitis C Virus on Priming and Cross-Reactivity of CD8 ⁺ T Cells

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The hepatitis C sequence database in Los Alamos

Cited by 124 publications

References 14 publications

Hepatitis C Virus Genotype 1 to 6 Protease Inhibitor Escape Variants: In Vitro Selection, Fitness, and Resistance Patterns in the Context of the Infectious Viral Life Cycle

Hepatitis C Virus Genotype 1 to 6 Protease Inhibitor Escape Variants: In Vitro Selection, Fitness, and Resistance Patterns in the Context of the Infectious Viral Life Cycle

Substitutions at NS3 Residue 155, 156, or 168 of Hepatitis C Virus Genotypes 2 to 6 Induce Complex Patterns of Protease Inhibitor Resistance

Impact of Sequence Variation in a Dominant HLA-A*02-Restricted Epitope in Hepatitis C Virus on Priming and Cross-Reactivity of CD8 + T Cells

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Impact of Sequence Variation in a Dominant HLA-A*02-Restricted Epitope in Hepatitis C Virus on Priming and Cross-Reactivity of CD8 ⁺ T Cells