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Sistayanarain A, Kunthalert D. Molecular characterization of the nonstructural 5A (NS5A) region of hepatitis C virus in Thai blood donors. Arch Microbiol 2024; 206:215. [PMID: 38619622 DOI: 10.1007/s00203-024-03950-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/16/2024]
Abstract
Direct acting antivirals (DAAs) have been developed for hepatitis C virus (HCV) therapy, and they are usually effective, however resistance to DAA regimens has also been reported to have a significant impact. Resistance associated substitutions (RASs) in the NS5A region are known to be correlated with failure of DAA therapy. HCV genotypes 3a and 1 are the most prevalent genotypes in Thailand. This study analyzed the type and frequency of RASs associated with DAA failure, focusing on the NS5A region. Serum samples of HCV genotype 3a, 1a, and 1b infection from Thai blood donors were selected. The NS5A region was amplified using reverse transcription-polymerase chain reaction (RT-PCR). A phylogenetic tree was constructed to identify the genotypes of HCV. Nucleotide sequencing and amino acid sequencing were conducted to determine the prevalence of RASs. Construction of the phylogenetic tree indicated that 29 samples were genotype 3a, 11 samples were genotype 1a, and 9 were genotype 1b. Both HCV genotypes 1a and 3a can be categorized into two subclades. Results showed that the NS5A substitutions A30V/K, A62T/V/I/M/P/S/L, and S98G were present in HCV genotype 3a. In HCV genotype 1a, only NS5A RASs H54Y was detected. NS5A amino acid substitutions Q54H and P58L were found in HCV genotype 1b. In conclusion, NS5A RASs at amino acid positions 30, 62, 54, 58, and 98 are present within HCV genotypes 3a and 1. While keeping in mind that additional information was not available on the anonymous blood donors tested in this study, these findings can contribute to understand the NS5A mutation. Further study with known patients under drug treatment is recommended.
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Affiliation(s)
- Anchalee Sistayanarain
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.
| | - Duangkamol Kunthalert
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
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Faiz S, Irfan M, Farooq S, Khan IA, Iqbal H, Wahab AT, Shakeel M, Gong P, Iftner T, Choudhary MI. Study of drug resistance-associated genetic mutations, and phylo-genetic analysis of HCV in the Province of Sindh, Pakistan. Sci Rep 2023; 13:12213. [PMID: 37500705 PMCID: PMC10374889 DOI: 10.1038/s41598-023-39339-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023] Open
Abstract
Current management of HCV infection is based on Direct-Acting Antiviral Drugs (DAAs). However, resistance-associated mutations, especially in the NS3 and NS5B regions are gradually decreasing the efficacy of DAAs. The aim of the current study was to identify such mutations in the NS3, and NS5B genes in DAAs treatment-naïve Pakistani chronic HCV 3a patients. Peripheral blood samples were collected from 233 chronic HCV 3a patients at different tertiary care hospitals in Karachi, Pakistan, between August 2020 to September 2021. PCR-amplified target regions of the NS3/NS5B gene were subjected to Sanger sequencing to identify resistance-associated mutations. Phylogenetic analysis of the identified amino acid sequences was performed using HCV3a sequences of the global population in the virus pathogen resource (VIPR) database. Sequence analysis identified five amino acid mutations, Leu36Pro, Gln41His, Gln80Lys/Arg, Ala156Tyr, and Gln168Arg in the NS3 region, and two mutations Leu159Phe and Cys316Arg in the NS5B region. Phylogenetic analysis revealed a high genetic diversity in the studied isolates. Overall, the prevalence of resistance-associated substitutions was almost similar to other geographic regions worldwide. This data could be helpful in selecting the most effective treatment regimen for HCV chronically infected people in Pakistan.
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Affiliation(s)
- Sirmast Faiz
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Irfan
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, Jamil-ur-Rahman Center for Genome Research, University of Karachi, Karachi, 75270, Pakistan
| | - Saba Farooq
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan.
| | - Ishtiaq Ahmad Khan
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, Jamil-ur-Rahman Center for Genome Research, University of Karachi, Karachi, 75270, Pakistan.
| | - Hana'a Iqbal
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan
| | - Atia-Tul Wahab
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Shakeel
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, Jamil-ur-Rahman Center for Genome Research, University of Karachi, Karachi, 75270, Pakistan
| | - Peng Gong
- Wuhan Institute of Virology, Chinese Academy of Sciences, No.44 Xiao Hong Shan, Wuhan, 430071, Hubei, China
| | - Thomas Iftner
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital and Medical Faculty, Eberhard Karls University, Tuebingen, Germany
| | - M Iqbal Choudhary
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, National Institute of Virology, University of Karachi, Karachi, 75270, Pakistan.
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, Jamil-ur-Rahman Center for Genome Research, University of Karachi, Karachi, 75270, Pakistan.
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
- Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, H.E.J. Research Institute of Chemistry, University of Karachi, Karachi, 75270, Pakistan.
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Kiattanaphon A, Vipsoongnern Y, Kunthalert D, Sistayanarain A. Partial nonstructural 3 region analysis of hepatitis C virus genotype 3a. Mol Biol Rep 2022; 49:9437-9443. [PMID: 36002650 DOI: 10.1007/s11033-022-07803-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND The hepatitis C virus (HCV) is a major cause of illness around the world. HCV genotype 3a is the most prevalent genotype in Thailand. Direct-acting antiviral (DAA) drugs are available for treatment, and these drugs target the NS3, NS5A, and NS5b proteins of HCV. However, HCV variants that are resistant to NS3 protease inhibitors have been found during treatment. This resistance can be naturally occurring or in response to treatment. The purpose of this study is to analyze the codon positions of the main mutation of the partial NS3 gene region of HCV genotype 3a. METHODS In order to detect mutations and confirm the genotype of HCV genotype 3a, the nucleotide sequencing and amino acid portion of NS3 were analyzed. RESULTS Twenty-six samples were successfully sequenced and clustered within two sub-clades defined as 3a-1 and 3a-2. Through amino acid mutation analysis, the variations were detected at codon positions 122 (3.8%), 132 (84.6%), 168 (100%), 170 (92.3%), 174 (100%), and 175 (100%). CONCLUSIONS In conclusion, mutations at positions 168, 170, 174, and 175 of the NS3 region are common within the HCV genotype 3a. This information should be useful in the development of effective anti-viral drugs that can successfully treat HCV infection.
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Affiliation(s)
- Anusorn Kiattanaphon
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | | | - Duangkamol Kunthalert
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Anchalee Sistayanarain
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.
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Frequency distribution of HCV resistance-associated variants in infected patients treated with direct-acting antivirals. Int J Infect Dis 2021; 115:171-177. [PMID: 34902582 DOI: 10.1016/j.ijid.2021.12.320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/11/2021] [Accepted: 12/05/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) is a global public health problem. Second-generation direct-acting antivirals targeting non-structural regions on the viral genome are the cornerstone for treatment of chronic infection. However, resistance-associated variants (RAVs) have been reported to be associated with therapeutic failure. The aim of this study was to assess the frequency of variants, including RAVs, in the NS3, NS5A and NS5B regions at baseline in Brazilian patients with chronic hepatitis C with HCV genotypes 1a, 1b and 3a. METHODS Serum samples from 13 patients were used to obtain viral RNA. Massively parallel sequencing was performed using genotype-specific amplicons and a panel of Ampliseq technology for all genotypes. RESULTS Several non-synonymous substitutions were detected at baseline for 11 responders and pre-/post-treatment for two non-responders. HCV genotype 3a was found to have significantly more non-synonymous substitutions than HCV genotype 1 in the NS3 and NS5A regions. Analyses were conducted using quantitative and qualitative inter- and intrapatient comparisons. Variants that confer resistance to the treatment used by the patients were found in both responders and non-responders. CONCLUSIONS A wide frequency distribution of RAVs was found at baseline, and this did not interfere with the achievement of a sustained response. Evaluation of the presence of RAVs requires additional study in order to determine clinical relevance.
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Akiyama MJ, Riback L, Reeves JD, Lie YS, Agyemang L, Norton BL, Arnsten JH, Litwin AH. Hepatitis C Resistance-Associated Substitutions Among People Who Inject Drugs Treated With Direct-Acting Antiviral-Containing Regimens. Open Forum Infect Dis 2021; 8:ofab474. [PMID: 34692891 PMCID: PMC8530260 DOI: 10.1093/ofid/ofab474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/17/2021] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND Resistance-associated substitutions (RASs) to HCV direct-acting antivirals (DAAs) can contribute to virologic failure and limit retreatment options. People who inject drugs (PWID) are at highest risk for transmission of resistant virus. We report on RASs at baseline and after virologic failure in DAA-naive and protease inhibitor-experienced PWID. METHODS We sequenced the NS3/4A, NS5A, and NS5B regions from 150 PWID with genotype 1 (GT1) viruses; 128 (85.3%) GT1a, 22 (14.7%) GT1b. RESULTS Among the 139 (92.7%) DAA-naive PWID, 85 of 139 (61.2%) had baseline RASs-67 of 139 (48.2%) in NS3 (predominantly Q80K/L); 25 of 139 (18.0%) in NS5A; and 8 of 139 (5.8%) in NS5B. Of the 11 protease inhibitor-experienced participants, 9 had baseline NS3 RASs (V36L N = 1, Q80K N = 9) and 4 had baseline NS5A RASs (M28V N = 2, H58P N = 1, A92T N = 1). Among the 11 participants who had posttreatment samples with detectable virus (7 treatment failures, 1 late relapse, 3 reinfections), 1 sofosbuvir/ledipasvir failure had a baseline H58P. Two sofosbuvir/ledipasvir-treated participants developed new NS5A mutations (Q30H, Y93H, L31M/V). Otherwise, no RASs were detected. CONCLUSIONS Our results demonstrate RAS prevalence among DAA-naive PWID is comparable to that in the general population. Only 2 of 150 (1.3%) in our longitudinal cohort developed treatment-emergent RASs. Concern for transmission of resistant virus may therefore be minimal.
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Affiliation(s)
- Matthew J Akiyama
- Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NEW YORK, USA
| | - Lindsey Riback
- Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NEW YORK, USA
| | | | - Yolanda S Lie
- Monogram Biosciences, LabCorp, South San Francisco, California, USA
| | - Linda Agyemang
- Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NEW YORK, USA
| | - Brianna L Norton
- Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NEW YORK, USA
| | - Julia H Arnsten
- Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NEW YORK, USA
| | - Alain H Litwin
- Prisma Health, Greenville, South Carolina, USA
- University of South Carolina School of Medicine, Greenville, South Carolina, USA
- Clemson University, Clemson, South Carolina, USA
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Di Stefano M, Ismail MH, Leitner T, Faleo G, Elmnan Adem SA, Elamin MOME, Eltreifi O, Alwazzeh MJ, Fiore JR, Santantonio TA. Genetic Subtypes and Natural Resistance Mutations in HCV Genotype 4 Infected Saudi Arabian Patients. Viruses 2021; 13:v13091832. [PMID: 34578414 PMCID: PMC8472952 DOI: 10.3390/v13091832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/13/2021] [Accepted: 09/10/2021] [Indexed: 12/12/2022] Open
Abstract
This study aimed to characterize the HCV genetic subtypes variability and the presence of natural occurring resistance-associated substitutions (RASs) in Saudi Arabia patients. A total of 17 GT patients were analyzed. Sequence analysis of NS3, NS5A, and NS5B regions was performed by direct sequencing, and phylogenetic analyses were used to determine genetic subtypes, RAS, and polymorphisms. Nine patients were infected by GT 4a, two with GT 4o and three with GT 4d. Two patients were infected with apparent recombinant virus (4a/4o/4a in NS3/NS5A/NS5B), and one patient was infected with a previously unknown, unclassifiable, virus of GT 4. Natural RASs were found in six patients (35%), including three infected by GT 4a, two by GT 4a/GT 4o/GT 4a, and one patient infected by an unknown, unclassifiable, virus of GT 4. In particular, NS3-RAS V170I was demonstrated in three patients, while NS5A-RASs (L28M, L30R, L28M + M31L) were detected in the remaining three patients. All patients were treated with sofosbuvir plus daclatasvir; three patients were lost to follow-up, whereas 14 patients completed the treatment. A sustained virological response (SVR) was obtained in all but one patient carrying NS3-RAS V170I who later relapsed. GT 4a is the most common subtype in this small cohort of Saudi Arabia patients infected with hepatitis C infection. Natural RASs were observed in about one-third of patients, but only one of them showed a treatment failure.
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Affiliation(s)
- Mariantonietta Di Stefano
- Department of Clinical and Experimental Medicine, Section of Infectious Diseases, University of Foggia, 71122 Foggia, Italy; (G.F.); (J.R.F.); (T.A.S.)
- Correspondence: ; Tel.: +39-338-302-2113
| | - Mona H. Ismail
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 32210, Saudi Arabia; (M.H.I.); (M.O.M.E.E.); (O.E.); (M.J.A.)
- Division of Gastroenterology, King Fahd Hospital of the University, Al-Khobar 34217, Saudi Arabia;
| | - Thomas Leitner
- Theoretical Biology & Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544, USA;
| | - Giuseppina Faleo
- Department of Clinical and Experimental Medicine, Section of Infectious Diseases, University of Foggia, 71122 Foggia, Italy; (G.F.); (J.R.F.); (T.A.S.)
| | - Saada A. Elmnan Adem
- Division of Gastroenterology, King Fahd Hospital of the University, Al-Khobar 34217, Saudi Arabia;
| | - Mohamed O. M. E. Elamin
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 32210, Saudi Arabia; (M.H.I.); (M.O.M.E.E.); (O.E.); (M.J.A.)
- Department of Biochemistry, King Fahd Hospital of the University, Al-Khobar 34217, Saudi Arabia
| | - Obeidi Eltreifi
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 32210, Saudi Arabia; (M.H.I.); (M.O.M.E.E.); (O.E.); (M.J.A.)
- Department of Microbiology and Laboratory Medicine, King Fahd Hospital of the University, Al-Khobar 34217, Saudi Arabia
| | - Marwan J. Alwazzeh
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 32210, Saudi Arabia; (M.H.I.); (M.O.M.E.E.); (O.E.); (M.J.A.)
- Infectious Disease Division, King Fahd Hospital of the University, Al-Khobar 34217, Saudi Arabia
| | - Jose R. Fiore
- Department of Clinical and Experimental Medicine, Section of Infectious Diseases, University of Foggia, 71122 Foggia, Italy; (G.F.); (J.R.F.); (T.A.S.)
| | - Teresa A. Santantonio
- Department of Clinical and Experimental Medicine, Section of Infectious Diseases, University of Foggia, 71122 Foggia, Italy; (G.F.); (J.R.F.); (T.A.S.)
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Jiang X, Lv X, Chang L, Yan Y, Ji H, Sun H, Guo F, Rodgers MA, Yin P, Wang L. Molecular characterization of hepatitis C virus for subtype determination and resistance-associated substitutions detection among Chinese voluntary blood donors. Antiviral Res 2020; 181:104871. [PMID: 32717286 DOI: 10.1016/j.antiviral.2020.104871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/28/2020] [Accepted: 07/01/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND The high prevalence of hepatitis C virus (HCV) infection and the resulting burden of the disease are significant issues to public health worldwide. Although direct-acting antiviral drugs (DAAs) with good tolerance and bioavailability are available, resistance-associated substitutions (RASs) often jeopardize the successful sustainment of virological responses in HCV treatment. High-frequency baseline RASs in treatment-naïve patients can lead to failures in DAA treatment. Clinical data on HCV RASs in patients from China are limited and require investigations. METHODS 262 HCV RNA positive plasma from Chinese blood donors were genotyped and amplified with subtype-specific primers for NS3 and NS5A regions. RASs were analyzed using Geno2pheno. The codon usage of each resistance-associated substitution was calculated for genetic barrier analysis. RESULTS The two main subtypes in mainland China were 1b and 2a, followed by subtype 6a, 3b, 3a, and 1a. In NS3 region of 1b subtype, substitutions (T54S, V55A, Y56F, Q80 K/L, S122 G/T, R117 H/C, V170I and S174A) were present in 89.7% (96/107) of the samples. Other RASs (M28L, R30Q, P58 L/S and Y93H) were observed in 22.1% (25/113) of the samples in NS5A region. A crucial RAS, Q80K, and two other mutations (S122G + V170I) was identified in the same sequence, which reduced its susceptibility to protease inhibitor ASV and resulted in resistance to SMV. In NS5A, Y93H was detected in 9.7% (11/113) of the 1b samples, leading to medium-to-high level resistance to all six commercialized NS5A inhibitors. S122G-NS3 and Y93H-NS5A occurred simultaneously in 38.1% (7/22) of the samples with mutations in both two regions. Moreover, codon usage of S122G-NS3 and Y93H-NS5A revealed that both variants had the lowest genetic barrier and required only one transition to confer resistance. CONCLUSIONS Low genetic barriers facilitated the generation of resistance mutants and threated the efficacy of DAA regimens. The baseline RASs posed a great challenge to real-world DAA application.
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Affiliation(s)
- Xinyi Jiang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China.
| | - Xiaoting Lv
- Abbott Laboratories, Research and Development, Shanghai, PR China.
| | - Le Chang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, PR China.
| | - Ying Yan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, PR China.
| | - Huimin Ji
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, PR China.
| | - Huizhen Sun
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China.
| | - Fei Guo
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, PR China.
| | - Mary A Rodgers
- Abbott Laboratories, Infectious Disease Research, Abbott Park, IL, USA.
| | - Peng Yin
- Abbott Laboratories, Infectious Disease Research, Abbott Park, IL, USA.
| | - Lunan Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China.
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Khan HU, Khan S, Shah MA, Attaullah S, Malik MA. Pre-existing resistance associated polymorphisms to NS3 protease inhibitors in treatment naïve HCV positive Pakistani patients. PLoS One 2020; 15:e0231480. [PMID: 32275694 PMCID: PMC7147739 DOI: 10.1371/journal.pone.0231480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 03/24/2020] [Indexed: 11/19/2022] Open
Abstract
Chronic Hepatitis C Virus (HCV) infection is still a major health issue especially in endemic areas where fewer direct-acting virals (DAAs) are treatment options. Some HCV variants are associated with resistance and it reduces DAAs success where pre-existing variants prevail. In this study, we investigated resistance-associated polymorphisms (RAPs) in the HCV NS3 region from DAAs naïve Pakistani patients. 277 chronic HCV treatment naïve patients infected with genotype 1a, 3a and 3b were selected from various clinical centers in the capital city of Khyber Pakhtunkhwa province Pakistan. All the patients were included in this study after taking informed consent. HCV NS3 region was amplified and Sanger sequencing was performed to analyze RAPs to NS3 protease inhibitors. Of the total 29.24% (81/277) patients had detected with known RAPs viz V36A/G/L, T54S, V55A/D/I, Q80K/R, S122G/T/R, R155K/T/I, V158I, D168T/Q, and I170V. Among HCV-1a subjects overall RAPs found were 26.09% (12/46) and most prevalent substitutions were V36A/G (10.87%, 5/46) and R155K/T/I (8.70%, 4/46). Of the total HCV-3a infected patients, 30.95% were observed with RAPS. Ammon these, the most frequent substitutions were Q80R (13.69%, 23/168) followed by V36L (18.33%, 14/168) and V55I (5.95%, 10/168). Among HCV-3b patients, 26.98% were found with RAPs and S122R and Q80R were the dominant variants detected in 17.46 (11/63) and 12.70% (8/63) patients respectively. All these substitutions were associated with Boceprevir, Simeprevir, Telaprevir, and Paritaprevir. Single substitution in one sequence was found in 18.77% (52/277) and multiple in 10.46% (29/277). More than one RAP was frequent in HCV-3a sequences. Natural RAPs are common in chronic HCV patients infected with genotype 1a, 3a and 3b, the most prevalent subtypes in Pakistan. High prevalence of HCV NS3 RAPs suggested a large scale study of the NS3 gene before the introduction of NS3 protease inhibitors in Pakistan.
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Affiliation(s)
- Hafeez Ullah Khan
- Department of Zoology, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Sanaullah Khan
- Department of Zoology, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
- * E-mail:
| | - Muhammad Akbar Shah
- Department of Medicine, Khyber Teaching Hospital, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Sobia Attaullah
- Department of Zoology, Islamia College Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Arshad Malik
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
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Baseline Amino Acid Substitutions in the NS5A ISDR and PKR Binding Domain of Hepatitis C and Different Fibrosis Levels and Levels of Development of Hepatocellular Carcinoma in Patients Treated with DAAs. Viruses 2020; 12:v12030255. [PMID: 32106574 PMCID: PMC7150791 DOI: 10.3390/v12030255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/17/2020] [Accepted: 02/22/2020] [Indexed: 02/07/2023] Open
Abstract
Variations in the interferon sensitivity-determining region (ISDR) within the NS5A region were related to the development of hepatocellular carcinoma (HCC) in patients infected with hepatitis C virus (HCV). The aim of the study was to investigate a relationship between ISDR/PKR substitutions and their association with liver fibrosis or HCC development. A total of 316 patients infected with HCV and treated with DAAs were evaluated. HCV RNA was quantified and sequenced before treatment. The liver fibrosis stage was assessed by transient elastography and equalized to METAVIR scores. Multivariate analysis showed that ≥3 substitutions in ISDR and ≥6 in PKR-bd were significantly associated with advanced fibrosis. Advanced fibrosis was observed in patients with higher substitutions in ISDR and PKR-bd. A higher correlation between advanced fibrosis and a high frequency of ≥3 substitutions in ISDR and ≥6 in PKR-bd was observed in patients infected with genotype 2c. In addition, in a higher proportion of HCC patients, advanced fibrosis (40.4% vs. 88.2%; p < 0.001) and ≥6 substitutions in PKR-bd (15.4% vs. 41.2%; p = 0.01) was observed. In conclusion, a higher number of substitutions in ISDR and PKR-bd were associated with advanced liver fibrosis, suggesting a use of like predictors for progression in the liver damage. A significantly higher number of PKR-bd substitutions was observed in HCC patients; in particular, in patients infected with HCV genotype 2c.
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Evaluating Drug Resistant Mutations to HCV NS3 Protease Inhibitors in Iranian Naïve Patients. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09957-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Nejabat N, Hosseini SY, Sarvari J, Gorzin AA, Fattahi MR, Rasoolian M. The Investigation of Drug Resistance Substitutions in NS3 Protease Sequence of Hepatitis C Virus from Non-Responder Patients. Asian Pac J Cancer Prev 2019; 20:2311-2317. [PMID: 31450900 PMCID: PMC6852801 DOI: 10.31557/apjcp.2019.20.8.2311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Indexed: 12/25/2022] Open
Abstract
Background: Even with the fantastic successes of direct-acting antivirals (DAA) in the treatment of Hepatitis C Virus (HCV) infection, natural drug resistance remains a challenging obstacle for their impacts. The data regarding protease inhibitors (PIs) resistance in Iran population are limited. The aim of this study was to investigate the variations in NS3 protease of HCV from non-responder patients. Methods: In this cross-sectional study, 14 HCV infected patients with genotype 1(N=5) and 3(N=9) who have not responded to Interferon-related regime were enrolled from Liver Clinic, Shiraz. The NS3 protease region was amplified by Nested-PCR followed by product gel extraction. Besides, some amplified protease regions were cloned into a cloning vector to improve the sensitivity of mutation detection. Both crude and cloned sequences were then introduced into sequencing. The obtained sequences were compared with the NS3 reference sequences and analyzed by Geno2pheno available software to find possible substitutions. In the end, the phylogenetic tree was constructed. Results: Among variations responsible for PIs resistance, only one out of 14 (7%) sample who was infected with genotype 1a, harbored R117C+N174S double mutation, which causes reduced susceptibility to Telaprevir. Any another resistance mutation was not found among the studied population. The most frequent substitutions were determined as I52M(N=9), S102A(N=9), S166A(8) and V170I(8) for genotype 3a, and F147S/A(4) for genotype 1. However, some uncharacterized substitutions on scored position, including I132L(N=1), I170V(N=3) and N174S(N=2) were also determined among sequences. Phylogenetic analysis demonstrated that the protease region has enough power to correctly classify enrolled samples into relevant clusters on the tree. There were 2, 3 and 9 cases of sub-genotypes 1a, 1b, and 3a, respectively. Conclusion: A low frequency of PIs resistance mutations in our HCV infected population is a hopeful point of starting these drugs in HCV infected patients.
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Affiliation(s)
- Nargess Nejabat
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Seyed Younes Hosseini
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Jamal Sarvari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Ali Akbar Gorzin
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Mohamad Reza Fattahi
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Rasoolian
- Department of Genetics and Molcular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Abstract
Hepatitis C virus represents a global pathogen of human health significance. In the space of less than three decades, we have witnessed the discovery of the virus, a growing understanding of the structure and biology of the viral-encoded proteins and their interaction with the host cell and the sequencing of the viral genome. Most importantly, we have moved from early therapeutic strategies aimed at crude boosting of host anti-viral immunity, limited by side effects and with poor response rates, to therapies that directly exploit our understanding of viral biology. In this review, we discuss the significance of the virus, its' discovery and outline the advances in the molecular characterisation of the virus, before setting these within the context of contemporary and emerging therapeutic strategies as well as viral resistance mechanisms.
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Tavares RCF, de Castro Amaral Feldner AC, Pinho JRR, de Mello Malta F, Carvalho-Filho RJ, Santana RAF, de Castro VFD, Dastoli GTF, Lima JC, Ferraz MLCG. Prevalence of resistance-associated substitutions to direct-acting antiviral agents in hemodialysis and renal transplant patients infected with hepatitis C virus. Infect Drug Resist 2018; 11:1993-2000. [PMID: 30464541 PMCID: PMC6208931 DOI: 10.2147/idr.s169512] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Direct-acting antiviral agents (DAAs) permit the use of interferon (IFN)-free regimens to treat hepatitis C (HCV) in patients with chronic kidney disease (CKD) on hemo-dialysis (HD) or renal transplant (RTx) recipients, with excellent response rates and safety. However, the occurrence of basal or therapy-induced resistance-associated substitutions (RASs) to DAAs can result in treatment failure. The aim of this study was to estimate the prevalence of RASs to NS3A, NS5A and NS5B inhibitors, and particularly the Q80K polymorphism, in CKD patients on HD and RTx recipients infected with HCV. Patients and methods HD and RTx patients infected with HCV-genotype 1 (GT1) were subjected to sequencing of the NS3, NS5A and NS5B regions. Results Direct sequencing of NS3 protease, NS5A and NS5B was performed in 76 patients (HD, n=37; RTx, n=39). The overall prevalence of RASs was 38.2%, but only 5.3% of the patients had mutations in more than one region. Substitutions were detected in NS3A (17.8%), NS5A (21.9%) and NS5B (8.4%). Q80K was detected in 1.5 % of the patients. Highly inhibitory RASs were uncommon (L31M, 2.6%; L159F+C316N, 2.6%). RASs were more prevalent in HCV-GT1a (42.9%) than in HCV-GT1b (32.4%), P=0.35. RASs were detected in 52.4% of treatment-naive patients and 27.8% of peg-IFN/ribavirin-experienced patients (P=0.12). The presence of RASs was associated with time of RTx (P=0.01). Conclusion The Q80K polymorphism was uncommon in our sample of HD and RTx patients. Despite the high prevalence of naturally occurring RASs, most of the substitutions detected were associated with a low level of resistance to DAAs.
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Affiliation(s)
| | | | - João Renato Rebello Pinho
- Albert Einstein Diagnostic Medicine, Albert Einstein Hospital São Paulo, SP, Brazil.,Laboratory of Tropical Gastroenterology and Hepatology "João Alves de Queiroz and Castorina Bittencourt Alves," Institute of Tropical Medicine, Department of Gastroenterology, University of São Paulo, São Paulo, SP, Brazil
| | - Fernanda de Mello Malta
- Laboratory of Tropical Gastroenterology and Hepatology "João Alves de Queiroz and Castorina Bittencourt Alves," Institute of Tropical Medicine, Department of Gastroenterology, University of São Paulo, São Paulo, SP, Brazil
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14
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Sagnelli E, Starace M, Minichini C, Pisaturo M, Macera M, Sagnelli C, Coppola N. Resistance detection and re-treatment options in hepatitis C virus-related chronic liver diseases after DAA-treatment failure. Infection 2018; 46:761-783. [DOI: 10.1007/s15010-018-1188-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022]
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15
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Fernández-Ruiz M, Polanco N, García-Santiago A, Muñoz R, Hernández AM, González E, Mercado VR, Fernández I, Aguado JM, Praga M, Andrés A. Impact of anti-HCV direct antiviral agents on graft function and immunosuppressive drug levels in kidney transplant recipients: a call to attention in the mid-term follow-up in a single-center cohort study. Transpl Int 2018; 31:887-899. [PMID: 29356211 DOI: 10.1111/tri.13118] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/27/2017] [Accepted: 01/15/2018] [Indexed: 12/16/2022]
Abstract
The medium-term impact on graft function and immunosuppressive drug pharmacokinetics of direct antiviral agents (DAAs) among hepatitis C virus (HCV)-infected kidney transplant (KT) recipients remain unclear. We compared pre- and post-treatment 12-month trajectories of estimated glomerular filtration rate (ΔeGFR) and 24-h proteinuria (Δ24-h proteinuria) in 49 recipients treated with DAAs (mostly sofosbuvir plus ledipasvir). Among evaluable patients, 66.7% and 100.0% had undetectable viral load by week 4 and end of therapy (EoT). The sustained virologic response rate at 12 weeks was 95.8%. Overall, 80.6% of patients receiving tacrolimus required dose escalation while on DAA-based therapy (median increase of 66.7%) to maintain target levels. Tacrolimus levels resulted to be higher at 12 months compared to EoT (7.8 ± 2.1 vs. 6.7 ± 2.0 ng/ml; P-value = 0.002). No changes in graft function during the course of therapy were observed. However, eGFR significantly decreased (P-value <0.001) throughout the first 12 months after EoT. Median ΔeGFR and Δ24-h over pre- and post-treatment periods were 3.9% and -6.1% (P-value = 0.002) and -5.3% and 26.2% (P-value = 0.057). Caution should be exercised when adjusting immunosuppression in HCV-infected KT recipients upon initiation of DAAs, followed by mid-term monitoring of immunosuppressive drug levels and graft function.
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Affiliation(s)
- Mario Fernández-Ruiz
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i + 12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - Natalia Polanco
- Department of Nephrology, Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i + 12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - Ana García-Santiago
- Department of Nephrology, Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i + 12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - Raquel Muñoz
- Department of Gastroenterology, Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i + 12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - Ana M Hernández
- Department of Nephrology, Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i + 12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - Esther González
- Department of Nephrology, Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i + 12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - Verónica R Mercado
- Department of Nephrology, Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i + 12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - Inmaculada Fernández
- Department of Gastroenterology, Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i + 12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - José María Aguado
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i + 12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - Manuel Praga
- Department of Nephrology, Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i + 12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - Amado Andrés
- Department of Nephrology, Hospital Universitario "12 de Octubre", Instituto de Investigación Hospital "12 de Octubre" (i + 12), School of Medicine, Universidad Complutense, Madrid, Spain
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Degasperi E, Aghemo A, Paolucci S, D'Ambrosio R, Borghi M, Perbellini R, Novazzi F, De Nicola S, Lunghi G, Baldanti F, Lampertico P. 12 weeks ombitasvir/paritaprevir-ritonavir + ribavirin achieve high SVR rates in HCV-4 patients with advanced fibrosis. Dig Liver Dis 2018; 50:703-706. [PMID: 29499903 DOI: 10.1016/j.dld.2018.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/01/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Ombitasvir/paritaprevir-ritonavir (OBT/PTV-r) plus ribavirin (RBV) for 12 weeks in hepatitis C virus (HCV) genotype 4 patients with advanced fibrosis has been only investigated in clinical trials. AIMS To assess safety and efficacy of OBT/PTV-r + RBV for 12 weeks in real-life HCV-4 patients with advanced fibrosis. METHODS HCV-4 patients with advanced fibrosis consecutively receiving OBT/PTV-r + RBV for 12 weeks in a single center were enrolled. Fibrosis was staged by transient elastography (TE) (F3: ≥10 kPa; F4 ≥11.9 kPa) or histologically. Sustained virological response (SVR) was defined as undetectable HCV-RNA 12 weeks post-treatment. RESULTS Between January 2016 and February 2017, 49 HCV-4 patients were included: median age 54 (39-72) years, 84% males, 59% Egyptians, 35% fibrosis F3 and 65% F4, all Child Pugh class A. Median RBV dose was 1200 (200-1200) mg/day. At ITT analysis, 47 (96%) patients achieved an SVR (100% at PP analysis). SVR was not affected by ancestry (Egyptian vs. Italian 97% vs. 95%, p = 1.0), fibrosis stage (F3 vs. F4 100% vs. 94%, p = .53), presence of baseline resistance associated substitutions (RASs) or RBV reduction. CONCLUSIONS We report 100% SVR with 12-weeks of OBT/PTV-r + RBV in HCV-4 patients with advanced liver disease, including compensated cirrhotics.
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Affiliation(s)
- Elisabetta Degasperi
- CRC "A. M.e A. Migliavacca" Center for Liver Disease, Division of Gastroenterology and Hepatology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy.
| | - Alessio Aghemo
- Humanitas University, Department of Biomedical Sciences, Rozzano, Milan, Italy
| | - Stefania Paolucci
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Roberta D'Ambrosio
- CRC "A. M.e A. Migliavacca" Center for Liver Disease, Division of Gastroenterology and Hepatology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Marta Borghi
- CRC "A. M.e A. Migliavacca" Center for Liver Disease, Division of Gastroenterology and Hepatology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Riccardo Perbellini
- CRC "A. M.e A. Migliavacca" Center for Liver Disease, Division of Gastroenterology and Hepatology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Federica Novazzi
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Stella De Nicola
- Hepatology and Gastroenterology Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Giovanna Lunghi
- Microbiology and Virology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Pietro Lampertico
- CRC "A. M.e A. Migliavacca" Center for Liver Disease, Division of Gastroenterology and Hepatology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
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Prevalence and distribution of hepatitis C virus genotypes in Galicia during the period 2000-2015. Enferm Infecc Microbiol Clin 2018; 37:256-259. [PMID: 29759421 DOI: 10.1016/j.eimc.2018.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/13/2018] [Accepted: 03/24/2018] [Indexed: 12/14/2022]
Abstract
INTRODUCTION We present the largest study conducted in Galicia on the prevalence and distribution of HCV genotypes/subtypes. METHODS Retrospective study collecting the total number of patients chronically infected by HCV between 2000.01.01 to 2015.12.31 in 3of the main health areas: Santiago, Pontevedra and Vigo. RESULTS We collected a total of 4469 patients. The median age was 50 years (IQR 57-45), 72,3% were men, 0,4% were coinfected with another genotype, 20,6% were coinfected with HIV and 35.2% with HBV. The main route of transmission was parenteral (83,1%), followed by unknown (15,3%), sexual (1,4%) and vertical (0,2%). The distribution of genotypes was: 62,9% HCV-1 (29,2% HCV-1a and 31,9% HCV-1b), 3,4% HCV-2, 21,0% HCV-3, 12,6% HCV-4 and 0,1% HCV-5. CONCLUSION The distribution of genotypes in Galicia shows significant differences with respect to that observed in Spain. This distribution varies with age, gender, coinfection with HIV and/or HBV, and within geographical areas.
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Paolucci S, Premoli M, Novati S, Gulminetti R, Maserati R, Barbarini G, Sacchi P, Piralla A, Sassera D, De Marco L, Girello A, Mondelli MU, Baldanti F. Baseline and Breakthrough Resistance Mutations in HCV Patients Failing DAAs. Sci Rep 2017; 7:16017. [PMID: 29167469 PMCID: PMC5700050 DOI: 10.1038/s41598-017-15987-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 10/09/2017] [Indexed: 12/19/2022] Open
Abstract
Sustained virologic response rates have increased dramatically following direct acting antiviral (DAA) therapy in chronic HCV infection. However, resistance-associated substitutions (RASs) may occur either prior to DAA or following drug exposure. The aim of this study was to determine RASs in DAA treatment-failing patients and the role of RASs in failure treatment. Six hundred and twenty HCV patients were evaluated. Direct sequencing of HCV genes was performed at breakthrough in all 31 patients failing DAAs, and in 19 baseline patients. Deep sequencing analysis was performed in 15/19 baseline patients. RASs were detected at breakthrough in 17/31 patients and at baseline in 11/19 patients, although, only 8/19 patients carried RASs associated with the prescribed regimen. Deep sequencing analysis showed RASs at baseline in 10/15 treatment-failing patients. No significant difference was observed with the Sanger sequencing. Treatment failure in the 14/31 patients without RASs was associated with suboptimal treatment. In 54.8% of treatment-failing patients one of the causes of failure might be the presence of RASs. In the majority of patients with RASs, mutations were present at baseline. Direct resistance test is advocated before treatment and at breakthrough in order to optimize retreatment regimens.
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Affiliation(s)
- Stefania Paolucci
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marta Premoli
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Stefano Novati
- Institute of Infectious Diseases, University of Pavia, Pavia, Italy
| | | | - Renato Maserati
- Institute of Infectious Diseases, University of Pavia, Pavia, Italy
| | - Giorgio Barbarini
- Division of Infectious and Tropical Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Paolo Sacchi
- Division of Infectious and Tropical Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Leone De Marco
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.,School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Alessia Girello
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mario U Mondelli
- Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy. .,Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy.
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Li Z, Chen ZW, Li H, Ren H, Hu P. Prevalence of hepatitis C virus-resistant association substitutions to direct-acting antiviral agents in treatment-naïve hepatitis C genotype 1b-infected patients in western China. Infect Drug Resist 2017; 10:377-392. [PMID: 29184422 PMCID: PMC5673042 DOI: 10.2147/idr.s146595] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Direct-acting antivirals (DAAs) against hepatitis C virus (HCV) are potent and highly efficacious. However, resistance-associated substitutions (RASs) relevant to DAAs can impair treatment effectiveness even at baseline. Moreover, the prevalence of baseline RASs in HCV genotype 1b-infected patients in western China is still unclear. Materials and methods Direct sequencing of the HCV NS3, NS5A, and NS5B regions was performed in baseline serum samples of 70 DAAs treatment-naïve HCV 1b-infected patients in western China. The sequences were analyzed with MEGA version 5.05 software. Evolutionary patterns of RASs and amino-acid covariance patterns in the NS3, NS5A, and NS5B genes were analyzed by MEGA and Cytoscape (version 3.2.1), respectively. Results The presence of at least one RAS in the NS3 region (C16S, T54S, Q80R/L, A87T, R117H, S122G, V132I, V170I) was observed in 85.48% (53 of 62) of patients, RASs in the NS5A region (L28M, R30Q, Q54H, P58S/T, Q62H/R, Y93H) were observed in 42.42% (28 of 66) of patients, and RASs in the NS5B region (N142S, A300T, C316N, A338V, S365A, L392I, M414L, I424V, A442T, V499A, S556G) were observed in 100% (44 of 44) of patients. Evolutionary patterns of RASs and amino-acid covariance patterns for the NS3, NS5A, and NS5B genes are reported. Conclusion The prevalence of RASs relevant to DAAs detected in the NS3, NS5A, and NS5B regions of HCV 1b from DAA treatment-naïve patients is high. Therefore, more attention should be paid to RASs associated with DAAs in the upcoming DAA-treatment era in China.
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Affiliation(s)
- Zhao Li
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Wei Chen
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hu Li
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Ren
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Hu
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Optimal efficacy of interferon-free HCV retreatment after protease inhibitor failure in real life. Clin Microbiol Infect 2017; 23:777.e1-777.e4. [DOI: 10.1016/j.cmi.2017.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 11/19/2022]
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21
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Martínez AP, Culasso ACA, Pérez PS, Romano V, Campos RH, Ridruejo E, García G, Di Lello FA. Polymorphisms associated with resistance to protease inhibitors in naïve patients infected with hepatitis C virus genotype 1 in Argentina: Low prevalence of Q80K. Virus Res 2017; 240:140-146. [PMID: 28837817 DOI: 10.1016/j.virusres.2017.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 12/26/2022]
Abstract
Incorporation of direct acting antivirals (DAA) in the treatment of Hepatitis C Virus (HCV) significantly increases sustained virologic response rates. However, despite the greater potency offered by these antivirals, drug resistance plays a key role in patients with failure to DAA. Nevertheless, there is no information about the prevalence of resistance-associated substitutions (RASs) in Argentina. The aim of this study was to analyze HCV variants resistant to protease inhibitors (PI) in naïve patients infected with HCV genotype 1 from Argentina. In this retrospective cross-sectional study, 103 patients infected with HCV-1 were included. Eighteen positions related with RASs were analyzed by Sanger at baseline and phylogenetic analysis was performed to determine the diversification of this samples. The analyzed RASs were present in 38 out of 103 patients (36.9%) infected with HCV-1. Patients infected with subtype HCV-1b had higher prevalence of baseline RASs than patients infected with HCV-1a [51.6% vs. 12.8%, respectively (p<0.001)]. The Q80K polymorphism was not found in HCV-1a samples, even when 51% of them belonged to cluster 1, which is associated with a high frequency of Q80K. Phylogenetic analysis showed that Argentinean samples were intermingled with sequences from other geographic regions. RASs to PI were highly prevalent and subtype dependent in treatment-naïve Argentinean patients. Surprisingly, Q80K polymorphism was not detected in our study population. The phylogenetic analysis showed no relationship between our samples and other samples from Brazil which also present a low prevalence of Q80K. This study supports the need for surveillance of resistance in patients who will be treated with DAA in each particular country since the observed RASs have very different prevalence worldwide.
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Affiliation(s)
- Alfredo P Martínez
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno "CEMIC", Ciudad Autónoma de Buenos Aires, C1425ASG Buenos Aires, Argentina
| | - Andrés C A Culasso
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Paula S Pérez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Vanesa Romano
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno "CEMIC", Ciudad Autónoma de Buenos Aires, C1425ASG Buenos Aires, Argentina
| | - Rodolfo H Campos
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ezequiel Ridruejo
- Hepatology Section, Department of Medicine, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno "CEMIC", Ciudad Autónoma de Buenos Aires, C1425ASG Buenos Aires, Argentina
| | - Gabriel García
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina
| | - Federico A Di Lello
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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A Simple but Accurate Method for Evaluating Drug-Resistance in Infectious HCVcc System. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1236801. [PMID: 28904942 PMCID: PMC5585557 DOI: 10.1155/2017/1236801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 06/23/2017] [Accepted: 07/19/2017] [Indexed: 11/21/2022]
Abstract
Use of direct-acting antivirals sometimes causes viral drug resistance, resulting in inefficiency in treated patients in real-world practice. Therefore, how to rapidly and accurately evaluate drug resistance is an urgent problem to be solved for rational use and development of antivirals in the future. Here, we aim to develop a new method by which we can evaluate easily but effectively whether a drug will still be efficient in the future treatment in infectious hepatitis C virus cell culture system. HCV-infected Huh7.5 cells were treated with drugs and the culture supernatants were replaced with fresh culture media containing the same drugs at 24 hours. The supernatants were harvested at 48 hours and incubated with naïve Huh7.5 cells. Intracellular HCV RNAs or proteins in the newly infected cells were extracted and analyzed at 48 hours or longer. Results showed that after being treated with telaprevir mutant viruses were easily detected which were resistant to telaprevir, while after being treated with sofosbuvir drug-resistant viruses did not emerge. In conclusion, the new method is simple and quick but accurate to evaluate whether a drug will be still efficient in the forthcoming therapeutic regimen and whether drug resistance will occur after long-term treatment with drugs.
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Prevalence of naturally occurring protease inhibitor resistance-associated variants in hemodialysis and renal transplant patients with hepatitis C virus infection. Eur J Gastroenterol Hepatol 2017; 29:754-758. [PMID: 28234637 DOI: 10.1097/meg.0000000000000866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Background NS3 protease inhibitors (PIs) were the first direct antiviral agents used for the treatment of hepatitis C virus. The combination of second-wave PIs with other direct antiviral agents enabled the use of interferon-free regimens for chronic kidney disease patients on dialysis and renal transplant (RTx) recipients, populations in which the use of interferon and ribavirin is limited. However, the occurrence of PI resistance-associated variants (RAVs), both baseline and induced by therapy, has resulted in the failure of many treatment strategies. Methods The aim of this study was to estimate the prevalence of PI RAVs and of the Q80K polymorphism in chronic kidney disease patients on hemodialysis and RTx recipients. Direct sequencing of the NS3 protease was performed in 67 patients (32 hemodialysis and 35 RTx).Results RAVs to PIs were detected in 18% of the patients: V55A (9%), V36L (1.5%), T54S (1.5%), S122N (1.5%), I170L (1.5%), and M175L (1.5%). Only 1.5% of the patients carried the Q80K polymorphism. The frequency of these mutations was more than two times higher in patients infected with GT1a (25%) than GT1b (9.7%) (P=0.1). The mutations were detected in 20% of treatment-naive patients and in 15.6% of peginterferon/ribavirin-experienced patients (P=0.64). Furthermore, no mutation that would confer high resistance to PIs was detected.Conclusion The Q80K polymorphism was rare in the population studied. The occurrence of RAVs was common, with predominance in GT1a. However, the variants observed were those associated with a low level of resistance to PIs, facilitating the use of these drugs in this special group of patients.
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Li Z, Zhang Y, Liu Y, Shao X, Luo Q, Cai Q, Zhao Z. Naturally occurring drug resistance associated variants to hepatitis C virus direct-acting antiviral agents in treatment-naive HCV genotype 1b-infected patients in China. Medicine (Baltimore) 2017; 96:e6830. [PMID: 28489763 PMCID: PMC5428597 DOI: 10.1097/md.0000000000006830] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The direct-acting antiviral agents (DAAs) have drastically improved the prognosis of hepatitis C virus (HCV) patients. However, the resistance-associated variants (RAVs) to DAAs may hamper treatment. There was a lack of data on the prevalence of pre-exist RAVs in Chinese HCV-infected patients. We performed nested PCR assays on 74 HCV genotype 1b-infected patients to amplify HCV viral regions of NS3, NS5A, and NS5B to investigate the prevalence of RAVs to DAAs in treatment-naive HCV genotype1b-infected patients in China. The mutations A156S, T54S, and D168Y of the NS3/4A region were found in 18.33% (11/60), 6.67% (4/60), and 1.67% (1/60) of the successfully amplified cases. Mutations Q30R, L31M, and H58P of the NS5A region were confirmed in 57.63% (34/59), 1.69%(1/59), and 86.44% (51/59) of the cases. Mutations C316N, S365A, M414L, M423I, Y448H, I482T, I482 V, V494L, P495S, and V499A of the NS5B region were detected in 100% (60/60), 3.33% (2/60), 5.88% (3/51), 1.96% (1/51), 1.96% (1/51), 5.88% (3/51), 1.96% (1/51), 3.92% (2/51), 5.88% (3/51), and 15.69% (8/51) of cases, respectively. Naturally occurring RAVs to DAAs pre-exist in treatment-naive Chinese HCV genotype 1b-infected patients and the characteristic is different from that in Europe and the United States. Clinicians should consider RAVs upon the introduction of DAA-based antiviral therapy.
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Affiliation(s)
- Zhanyi Li
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
| | - Ying Zhang
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
| | - Ying Liu
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
| | - Xiaoqiong Shao
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
| | - QiuMin Luo
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
| | - Qingxian Cai
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
| | - Zhixin Zhao
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
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Implications of hepatitis C virus subtype 1a migration patterns for virus genetic sequencing policies in Italy. BMC Evol Biol 2017; 17:70. [PMID: 28270091 PMCID: PMC5341469 DOI: 10.1186/s12862-017-0913-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 02/14/2017] [Indexed: 02/06/2023] Open
Abstract
Background In-depth phylogeographic analysis can reveal migration patterns relevant for public health planning. Here, as a model, we focused on the provenance, in the current Italian HCV subtype 1a epidemic, of the NS3 resistance-associated variant (RAV) Q80K, known to interfere with the action of NS3/4A protease inhibitor simeprevir. HCV1a migration patterns were analysed using Bayesian phylodynamic tools, capitalising on newly generated and publicly available time and geo-referenced NS3 encoding virus genetic sequence data. Results Our results showed that both immigration and local circulation fuel the current Italian HCV1a epidemic. The United States and European continental lineages dominate import into Italy, with the latter taking the lead from the 1970s onwards. Since similar migration patterns were found for Q80K and other lineages, no clear differentiation of the risk for failing simeprevir can be made between patients based on their migration and travel history. Importantly, since HCV only occasionally recombines, these results are readily transferable to the genetic sequencing policy concerning NS5A RAVs. Conclusions The patient migration and travel history cannot be used to target only part of the HCV1a infected population for drug resistance testing before start of antiviral therapy. Consequently, it may be cost-effective to expand genotyping efforts to all HCV1a infected patients eligible for simeprevir-based therapies. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0913-3) contains supplementary material, which is available to authorized users.
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Paolucci S, Premoli M, Ludovisi S, Mondelli MU, Baldanti F. HCV intergenotype 2k/1b recombinant detected in a DAA-treated patient in Italy. Antivir Ther 2017; 22:365-368. [PMID: 28085002 DOI: 10.3851/imp3130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2017] [Indexed: 10/20/2022]
Abstract
Direct-acting antiviral (DAA) combinations are potent and effective drugs currently recommended for treatment of chronic HCV infection. Difficult to treat genotypes are the most important predictors of treatment failure. We report a case of DAA treatment failure in an HCV-infected patient carrying a recombinant genotype 2k/1b. This strain, first isolated from a Russian patient in 2002, has now been observed for the first time in Italy.
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Affiliation(s)
- Stefania Paolucci
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marta Premoli
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Serena Ludovisi
- Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mario U Mondelli
- Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
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Cao Y, Bao Y, Xia W, Wu H, Wei F, Zhang Y, Zhang R, Xu X. Resistance-associated mutations to HCV protease inhibitors naturally pre-existed in HIV/HCV coinfected, treatment-naïve patients. Clin Res Hepatol Gastroenterol 2016; 40:597-604. [PMID: 27016893 DOI: 10.1016/j.clinre.2016.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 12/01/2015] [Accepted: 02/17/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND OBJECTIVE Presently, it has been approved to treat hepatitis C virus (HCV) infection with protease inhibitors (PIs). In the present study, we aimed to illustrate the natural prevalence of HCV NS3/4A PI resistance mutations in HIV/HCV coinfected, treatment-naïve patients. METHODS Population sequence analysis of the NS3/4A protease was conducted in 96 HIV/HCV coinfected, treatment-naïve patients. RESULTS Complete HCV NS3/4A sequence information was obtained from 70 (72.92%) samples, including 68 patients (97.14%) with genotype 1b and 2 patients (2.86%) with genotype 2a. A total of 21 patients (30.88%) of the 68 patients with HCV genotype 1b showed amino acid substitutions associated with HCV PI resistance. Mutation F43S was observed in 1.47% of patients with genotype 1b. The mutations of T54S, Q80K/R, R155K, A156G and D168A/E/G were found in 4.41%, 1.47%/1.47%, 2.94%, 23.53% and 1.47%/1.47%/1.47% of patients with genotype 1b, respectively. In addition, 4.41% of patients with genotype 1b showed double mutations in the NS3 region. The multiple mutations of Q80R+R155K+D168G and Q80K+R155K+A156G+D168A were detected in 1.47% and 1.47% of patients with HCV genotype 1b, respectively. CONCLUSIONS The most predominant HCV genotype was 1b in patients with HIV/HCV coinfection. Naturally occurring mutations resistant to HCV PIs (simeprevir, vaniprevir, boceprevir, telaprevir, asunaprevir and paritaprevir) pre-existed in patients with HIV/HCV genotype 1b coinfection. The effects of baseline PI resistance on treatment outcome should be further analyzed.
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Affiliation(s)
- Ying Cao
- Department of Infectious Diseases, Peking University First Hospital, Peking University Health Science Center, No. 8 Xishiku Street, Xicheng District, Beijing, China
| | - Yi Bao
- Department of Infectious Diseases, Peking University First Hospital, Peking University Health Science Center, No. 8 Xishiku Street, Xicheng District, Beijing, China; Department of Neurology, Shiyan Taihe Hospital, Shiyan, Hubei Province, China
| | - Wei Xia
- Department of Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Hao Wu
- Department of Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Feili Wei
- Department of Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yu Zhang
- Department of Infectious Diseases, Peking University First Hospital, Peking University Health Science Center, No. 8 Xishiku Street, Xicheng District, Beijing, China
| | - Renwen Zhang
- Department of Infectious Diseases, Peking University First Hospital, Peking University Health Science Center, No. 8 Xishiku Street, Xicheng District, Beijing, China
| | - Xiaoyuan Xu
- Department of Infectious Diseases, Peking University First Hospital, Peking University Health Science Center, No. 8 Xishiku Street, Xicheng District, Beijing, China.
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El Kassas M, Elbaz T, Hafez E, Esmat G. Safety of direct antiviral agents in the management of hepatitis C. Expert Opin Drug Saf 2016; 15:1643-1652. [PMID: 27661100 DOI: 10.1080/14740338.2017.1240781] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Hepatitis C virus is a hepatotropic virus that generally leads to chronic hepatitis and various harmful sequelae. The lone standard of treatment has been pegylated interferon and ribavirin, which produces a modest response and many side effects. However, a new era of management was declared with the introduction of various directly acting antiviral agents. Areas covered: Recent direct antiviral agents (DAAs) primarily target the non-structural proteins of the virus and affect its replication. These agents successfully achieve a sustained virologic response. However, some serious side effects were reported, which may or may not be drug-related effects. Important drug-drug interactions were also reported. The treating physician should be reasonably familiar with these effects. We review the safety profile of these agents in the management of HCV. Expert opinion: Cautious concomitant drug intake is necessary for the new HCV therapies. Future HCV management will depend on interferon-free and likely ribavirin-free regimens. The co-administration of direct antiviral agents of different classes increases the probability of side effects and drug-drug interactions.
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Affiliation(s)
- Mohamed El Kassas
- a Endemic Medicine Department, Faculty of Medicine , Helwan University , Cairo , Egypt
| | - Tamer Elbaz
- b Endemic Hepatogastroenterology, Faculty of Medicine , Cairo University , Cairo , Egypt
| | - Enas Hafez
- c Clinical Pharmacy Unit , New Cairo Viral Hepatitis Treatment Unit , Cairo , Egypt
| | - Gamal Esmat
- b Endemic Hepatogastroenterology, Faculty of Medicine , Cairo University , Cairo , Egypt
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Echeverría N, Betancour G, Gámbaro F, Hernández N, López P, Chiodi D, Sánchez A, Boschi S, Fajardo A, Sóñora M, Moratorio G, Cristina J, Moreno P. Naturally occurring NS3 resistance-associated variants in hepatitis C virus genotype 1: Their relevance for developing countries. Virus Res 2016; 223:140-6. [PMID: 27449600 DOI: 10.1016/j.virusres.2016.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 01/20/2023]
Abstract
Hepatitis C virus (HCV) is a major cause of global morbidity and mortality, with an estimated 130-150 million infected individuals worldwide. HCV is a leading cause of chronic liver diseases including cirrhosis and hepatocellular carcinoma. Current treatment options in developing countries involve pegylated interferon-α and ribavirin as dual therapy or in combination with one or more direct-acting antiviral agents (DAA). The emergence of resistance-associated variants (RAVs) after treatment reveals the great variability of this virus leading to a great difficulty in developing effective antiviral strategies. Baseline RAVs detected in DAA treatment-naïve HCV-infected patients could be of great importance for clinical management and outcome prediction. Although the frequency of naturally occurring HCV NS3 protease inhibitor mutations has been addressed in many countries, there are only a few reports on their prevalence in South America. In this study, we investigated the presence of RAVs in the HCV NS3 serine protease region by analysing a cohort of Uruguayan patients with chronic hepatitis C who had not been treated with any DAAs and compare them with the results found for other South American countries. The results of these studies revealed that naturally occurring mutations conferring resistance to NS3 inhibitors exist in a substantial proportion of Uruguayan treatment-naïve patients infected with HCV genotype 1 enrolled in these studies. The identification of these baseline RAVs could be of great importance for patients' management and outcome prediction in developing countries.
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Affiliation(s)
- Natalia Echeverría
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Gabriela Betancour
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Fabiana Gámbaro
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Nelia Hernández
- Clínica de Gastroenterología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
| | - Pablo López
- Clínica de Gastroenterología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
| | - Daniela Chiodi
- Clínica de Gastroenterología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
| | - Adriana Sánchez
- Clínica de Gastroenterología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay
| | - Susana Boschi
- Laboratorio de Biología Molecular, Asociación Española, Palmar 1465, Montevideo, Uruguay, Uruguay
| | - Alvaro Fajardo
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Martín Sóñora
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Gonzalo Moratorio
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Pilar Moreno
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay.
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Esposito I, Trinks J, Soriano V. Hepatitis C virus resistance to the new direct-acting antivirals. Expert Opin Drug Metab Toxicol 2016; 12:1197-209. [PMID: 27384079 DOI: 10.1080/17425255.2016.1209484] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The treatment of hepatitis C virus (HCV) infection has dramatically improved in recent years with the widespread use of interferon-free combination regimens. Despite the high sustained virological response (SVR) rates (over 90%) obtained with direct-acting antivirals (DAAs), drug resistance has emerged as a potential challenge. The high replication rate of HCV and the low fidelity of its RNA polymerase result in a high degree of genetic variability in the HCV population, which ultimately explains the rapid selection of drug resistance associated variants (RAVs). AREAS COVERED Results from clinical trials and real-world experience have both provided important information on the rate and clinical significance of RAVs. They can be present in treatment-naive patients as natural polymorphisms although more frequently they are selected upon treatment failure. In patients engaged in high-risk behaviors, RAVs can be transmitted. EXPERT OPINION Although DAA failures generally occur in less than 10% of treated chronic hepatitis C patients, selection of drug resistance is the rule in most cases. HCV re-treatment options are available, but first-line therapeutic strategies should be optimized to efficiently prevent DAA failure due to baseline HCV resistance. Considerable progress is being made and next-generation DAAs are coming with pangenotypic activity and higher resistance barrier.
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Affiliation(s)
- Isabella Esposito
- a Infectious Diseases Unit , IdiPAZ & La Paz University Hospital , Madrid , Spain
| | - Julieta Trinks
- b Instituto de Ciencias Básicas y Medicina Experimental (ICBME) , Instituto Universitario del Hospital Italiano de Buenos Aires , Buenos Aires , Argentina.,c Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Buenos Aires , Argentina
| | - Vicente Soriano
- a Infectious Diseases Unit , IdiPAZ & La Paz University Hospital , Madrid , Spain
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Zhou K, Liang Z, Wang C, Hu F, Ning C, Lan Y, Tang X, Tucker JD, Cai W. Natural Polymorphisms Conferring Resistance to HCV Protease and Polymerase Inhibitors in Treatment-Naïve HIV/HCV Co-Infected Patients in China. PLoS One 2016; 11:e0157438. [PMID: 27341031 PMCID: PMC4920402 DOI: 10.1371/journal.pone.0157438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 05/31/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The advent of direct-acting agents (DAAs) has improved treatment of HCV in HIV co-infection, but may be limited by primary drug resistance. This study reports the prevalence of natural polymorphisms conferring resistance to NS3/4A protease inhibitors and NS5B polymerase inhibitors in treatment-naïve HIV/HCV co-infected individuals in China. METHODS Population based NS3/4A sequencing was completed for 778 treatment-naïve HIV/HCV co-infected patients from twelve provinces. NS3 sequences were amplified by nested PCR using in-house primers for genotypes 1-6. NS5B sequencing was completed for genotyping in 350 sequences. Resistance-associated variants (RAVs) were identified in positions associated with HCV resistance. RESULTS Overall, 72.8% (566/778) of all HCV sequences had at least one RAV associated with HCV NS3/4A protease inhibitor resistance. Variants were found in 3.6% (7/193) of genotype 1, 100% (23/23) of genotype 2, 100% (237/237) of genotype 3 and 92% (299/325) of genotype 6 sequences. The Q80K variant was present in 98.4% of genotype 6a sequences. High-level RAVs were rare, occurring in only 0.8% of patients. 93% (64/69) patients with genotype 1b also carried the C316N variant associated with NS5B low-level resistance. CONCLUSIONS The low frequency of high-level RAVs associated with primary HCV DAA resistance among all genotypes in HIV/HCV co-infected patients is encouraging. Further phenotypic studies and clinical research are needed.
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Affiliation(s)
- Kali Zhou
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
- University of California San Francisco, Department of Medicine, Division of Gastroenterology, 513 Parnassus Avenue, Room S-357, San Francisco, California, 94143-0538 United States of America
| | - Zhiwei Liang
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
| | - Charles Wang
- UNC-Project – China, Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, 130 Mason Farm Rd., 2nd Floor, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, 27599-3368, United States of America
- Brown University School of Medicine, Department of Medicine, Division of Gastroenterology 593 Eddy Street, APC 406, Providence, Rhode Island, 02903, United States of America
| | - Fengyu Hu
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
| | - Chuanyi Ning
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
- UNC-Project – China, Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, 130 Mason Farm Rd., 2nd Floor, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, 27599-3368, United States of America
| | - Yun Lan
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
| | - Xiaoping Tang
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
| | - Joseph D. Tucker
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
- UNC-Project – China, Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, 130 Mason Farm Rd., 2nd Floor, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, 27599-3368, United States of America
| | - Weiping Cai
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
- * E-mail:
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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. Antimicrob Agents Chemother 2016; 60:3563-78. [PMID: 27021330 DOI: 10.1128/aac.02929-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/21/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatitis 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.
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Cao Y, Zhang Y, Bao Y, Zhang R, Zhang X, Xia W, Wu H, Xu X. Naturally occurring hepatitis C virus protease inhibitors resistance-associated mutations among chronic hepatitis C genotype 1b patients with or without HIV co-infection. Hepatol Res 2016; 46:552-8. [PMID: 26355704 DOI: 10.1111/hepr.12590] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/23/2015] [Accepted: 09/07/2015] [Indexed: 12/13/2022]
Abstract
UNLABELLED The aim of this study was to measure the frequency of natural mutations in hepatitis C virus (HCV) mono-infected and HIV/HCV co-infected protease inhibitor (PI)-naive patients. METHODS Population sequence of the non-structural (NS)3 protease gene was evaluated in 90 HCV mono-infected and 96 HIV/HCV co-infected PI treatment-naive patients. The natural prevalence of PI resistance mutations in both groups was compared. RESULTS Complete HCV genotype 1b NS3 sequence information was obtained for 152 (81.72%) samples. Seven sequences (8.33%) of the 84 HCV mono-infected patients and 21 sequences (30.88%) of the 68 HIV/HCV co-infected patients showed amino acid substitutions associated with HCV PI resistance. There was a significant difference in the natural prevalence of PI resistance mutations between these two groups (P = 0.000). The mutations T54S, R117H and N174F were observed in 1.19%, 5.95% and 1.19% of HCV mono-infected patients. The mutations F43S, T54S, Q80K/R, R155K, A156G/V, D168A/E/G and V170A were found in 1.47%, 4.41%, 1.47%/1.47%, 2.94%, 23.53%/1.47%, 1.47%/1.47%/1.47% and 1.47% of HIV/HCV co-infected patients, respectively. In addition, the combination mutations in the NS3 region were detected only in HIV/HCV genotype 1b co-infected patients. CONCLUSION Naturally occurring HCV PI resistance mutations existed in HCV mono-infected and HIV/HCV co-infected genotype 1b PI-naive patients. HIV co-infection was associated with a greater frequency of PI resistance mutations. The impact of HIV infection on baseline HCV PI resistance mutations and treatment outcome in chronic hepatitis C (CHC) patients should be further analyzed.
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Affiliation(s)
- Ying Cao
- Department of Infectious Diseases, Peking University First Hospital, Peking University Health Science Center, Beijing, China
| | - Yu Zhang
- Department of Infectious Diseases, Peking University First Hospital, Peking University Health Science Center, Beijing, China
| | - Yi Bao
- Department of Neurology, Shiyan Taihe Hospital, Shiyan, China
| | - Renwen Zhang
- Department of Infectious Diseases, Peking University First Hospital, Peking University Health Science Center, Beijing, China
| | - Xiaxia Zhang
- Department of Infectious Diseases, Peking University First Hospital, Peking University Health Science Center, Beijing, China
| | - Wei Xia
- Department of Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Hao Wu
- Department of Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xiaoyuan Xu
- Department of Infectious Diseases, Peking University First Hospital, Peking University Health Science Center, Beijing, China
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Patiño-Galindo JÁ, Salvatierra K, González-Candelas F, López-Labrador FX. Comprehensive Screening for Naturally Occurring Hepatitis C Virus Resistance to Direct-Acting Antivirals in the NS3, NS5A, and NS5B Genes in Worldwide Isolates of Viral Genotypes 1 to 6. Antimicrob Agents Chemother 2016; 60:2402-16. [PMID: 26856832 PMCID: PMC4808155 DOI: 10.1128/aac.02776-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/01/2016] [Indexed: 01/06/2023] Open
Abstract
There is no comprehensive study available on the natural hepatitis C virus (HCV) polymorphism in sites associated with resistance including all viral genotypes which may present variable susceptibilities to particular direct-acting antivirals (DAAs). This study aimed to analyze the frequencies, genetic barriers, and evolutionary histories of naturally occurring resistance-associated variants (RAVs) in the six main HCV genotypes. A comprehensive analysis of up to 103 RAVs was performed in 2,901, 2,216, and 1,344 HCV isolates for the NS3, NS5A, and NS5B genes, respectively. We report significant intergenotypic differences in the frequencies of natural RAVs for these three HCV genes. In addition, we found a low genetic barrier for the generation of new RAVs, irrespective of the viral genotype. Furthermore, in 1,126 HCV genomes, including sequences spanning the three genes, haplotype analysis revealed a remarkably high frequency of viruses carrying more than one natural RAV to DAAs (53% of HCV-1a, 28.5% of HCV-1b, 67.1% of HCV-6, and 100% of genotype 2, 3, 4, and 5 haplotypes). With the exception of HCV-1a, the most prevalent haplotypes showed RAVs in at least two different viral genes. Finally, evolutionary analyses revealed that, while most natural RAVs appeared recently, others have been efficiently transmitted over time and cluster in well-supported clades. In summary, and despite the observed high efficacy of DAA-based regimens, we show that naturally occurring RAVs are common in all HCV genotypes and that there is an overall low genetic barrier for the selection of resistance mutations. There is a need for natural DAA resistance profiling specific for each HCV genotype.
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Affiliation(s)
- Juan Ángel Patiño-Galindo
- Joint Unit in Infection and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain CIBER-ESP (Centro de Investigación Biomédica en Epidemiología y Salud Publica), Instituto de Salud Carlos III, Madrid, Spain
| | - Karina Salvatierra
- Joint Unit in Genomics and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain Virology Laboratory, Genomics and Health Area, FISABIO-Public Health, Generalitat Valenciana, Valencia, Spain
| | - Fernando González-Candelas
- Joint Unit in Infection and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain CIBER-ESP (Centro de Investigación Biomédica en Epidemiología y Salud Publica), Instituto de Salud Carlos III, Madrid, Spain
| | - F Xavier López-Labrador
- Joint Unit in Infection and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain Joint Unit in Genomics and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain Virology Laboratory, Genomics and Health Area, FISABIO-Public Health, Generalitat Valenciana, Valencia, Spain CIBER-ESP (Centro de Investigación Biomédica en Epidemiología y Salud Publica), Instituto de Salud Carlos III, Madrid, Spain
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CD36 is a co-receptor for hepatitis C virus E1 protein attachment. Sci Rep 2016; 6:21808. [PMID: 26898231 PMCID: PMC4761891 DOI: 10.1038/srep21808] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 01/08/2016] [Indexed: 02/06/2023] Open
Abstract
The cluster of differentiation 36 (CD36) is a membrane protein related to lipid metabolism. We show that HCV infection in vitro increased CD36 expression in either surface or soluble form. HCV attachment was facilitated through a direct interaction between CD36 and HCV E1 protein, causing enhanced entry and replication. The HCV co-receptor effect of CD36 was independent of that of SR-BI. CD36 monoclonal antibodies neutralized the effect of CD36 and reduced HCV replication. CD36 inhibitor sulfo-N-succinimidyl oleate (SSO), which directly bound CD36 but not SR-BI, significantly interrupted HCV entry, and therefore inhibited HCV replication. SSO’s antiviral effect was seen only in HCV but not in other viruses. SSO in combination with known anti-HCV drugs showed additional inhibition against HCV. SSO was considerably safe in mice. Conclusively, CD36 interacts with HCV E1 and might be a co-receptor specific for HCV entry; thus, CD36 could be a potential drug target against HCV.
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36
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Fernandes TDA, Manvar D, Domingos JLO, Basu A, Nichols DB, Kaushik-Basu N, Costa PRR. 5-Carba-pterocarpens: A new scaffold with anti-HCV activity. Eur J Med Chem 2016; 112:33-38. [PMID: 26874742 DOI: 10.1016/j.ejmech.2016.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 01/01/2023]
Abstract
The synthesis of a series of 5-carba-pterocarpens derivatives involving the cyclization of α-aryl-α-tetralones is described. Several compounds demonstrated potent activity and selectivity in vitro against HCV replicon reporter cells. The best profile in Huh7/Rep-Feo1b replicon reporter cells was observed with 2h (EC50 = 5.5 μM/SI = 20), while 2e was the most active in Huh7.5-FGR-JC1-Rluc2A replicon reporter cells (EC50 = 1.5 μM/SI = 70). Hydroxy groups at A- and D-rings are essential for anti-HCV activity, and substitutions in the A-ring at positions 3 and 4 resulted in enhanced activity of the compounds.
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Affiliation(s)
- Talita de A Fernandes
- Laboratório de Química Bioorgânica, Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco H, Ilha da Cidade Universitária, 21941-590 Rio de Janeiro, RJ, Brazil
| | - Dinesh Manvar
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers-The State University of New Jersey, 185 South Orange Avenue, New Jersey 07103, USA
| | - Jorge L O Domingos
- Departamento de Química Orgânica, Centro de Tecnologia e Ciências, Universidade do Estado do Rio de Janeiro, Rua São Francisco Xavier 524, Pav. Haroldo Lisboa da Cunha - s 406 - Maracanã, 20550-900 Rio de Janeiro, RJ, Brazil
| | - Amartya Basu
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers-The State University of New Jersey, 185 South Orange Avenue, New Jersey 07103, USA
| | - Daniel Brian Nichols
- Department of Biological Sciences, Seton Hall University, 400 South Orange Avenue, New Jersey, 07079, USA
| | - Neerja Kaushik-Basu
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers-The State University of New Jersey, 185 South Orange Avenue, New Jersey 07103, USA.
| | - Paulo R R Costa
- Laboratório de Química Bioorgânica, Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco H, Ilha da Cidade Universitária, 21941-590 Rio de Janeiro, RJ, Brazil.
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Bagaglio S, Uberti-Foppa C, Messina E, Merli M, Hasson H, Andolina A, Galli A, Lazzarin A, Morsica G. Distribution of natural resistance to NS3 protease inhibitors in hepatitis C genotype 1a separated into clades 1 and 2 and in genotype 1b of HIV-infected patients. Clin Microbiol Infect 2015; 22:386.e1-386.e3. [PMID: 26706617 DOI: 10.1016/j.cmi.2015.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 10/15/2015] [Accepted: 12/05/2015] [Indexed: 10/22/2022]
Abstract
Naturally occurring resistance-associated variants (RAVs) within the protease domain of hepatitis C virus (HCV) genotype (G) 1a separated into clades 1 and 2, and G1b were investigated in 59 HIV/HCV coinfected patients. RAVs were detected in 10/23 G1a/clade 1 and 1/19 G1b (p 0.0059). A similar frequency of RAVs was found when comparing G1a/clade 2 and G1b (p 0.1672). A cross-resistance to the macrocyclic compounds simeprevir and paritaprevir was detected in two G1a/clade 2 and 1 G1b sequences and none of G1a/clade 1 sequences. The simultaneous characterization of subtype and natural RAVs by population analysis of the NS3 domain by may add important information for anti-HCV treatment strategies including protease inhibitors.
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Affiliation(s)
- S Bagaglio
- Department of Infectious Diseases, Scientific Institute Ospedale San Raffaele, Italy; Vita-Salute University, Milan, Italy.
| | - C Uberti-Foppa
- Department of Infectious Diseases, Scientific Institute Ospedale San Raffaele, Italy
| | - E Messina
- Department of Infectious Diseases, Scientific Institute Ospedale San Raffaele, Italy
| | - M Merli
- Department of Infectious Diseases, Scientific Institute Ospedale San Raffaele, Italy
| | - H Hasson
- Department of Infectious Diseases, Scientific Institute Ospedale San Raffaele, Italy
| | - A Andolina
- Department of Infectious Diseases, Scientific Institute Ospedale San Raffaele, Italy
| | - A Galli
- Department of Infectious Diseases, Scientific Institute Ospedale San Raffaele, Italy
| | - A Lazzarin
- Department of Infectious Diseases, Scientific Institute Ospedale San Raffaele, Italy; Vita-Salute University, Milan, Italy
| | - G Morsica
- Department of Infectious Diseases, Scientific Institute Ospedale San Raffaele, Italy
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Costantino A, Spada E, Equestre M, Bruni R, Tritarelli E, Coppola N, Sagnelli C, Sagnelli E, Ciccaglione AR. Naturally occurring mutations associated with resistance to HCV NS5B polymerase and NS3 protease inhibitors in treatment-naïve patients with chronic hepatitis C. Virol J 2015; 12:186. [PMID: 26577836 PMCID: PMC4650141 DOI: 10.1186/s12985-015-0414-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/30/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The detection of baseline resistance mutations to new direct-acting antivirals (DAAs) in HCV chronically infected treatment-naïve patients could be important for their management and outcome prevision. In this study, we investigated the presence of mutations, which have been previously reported to be associated with resistance to DAAs in HCV polymerase (NS5B) and HCV protease (NS3) regions, in sera of treatment-naïve patients. FINDINGS HCV RNA from 152 naïve patients (84 % Italian and 16 % immigrants from various countries) infected with different HCV genotypes (21,1a; 21, 1b; 2, 2a; 60, 2c; 22, 3a; 25, 4d and 1, 4k) was evaluated for sequence analysis. Amplification and sequencing of fragments in the NS5B (nt 8256-8640) and NS3 (nt 3420-3960) regions of HCV genome were carried out for 152 and 28 patients, respectively. The polymorphism C316N/H in NS5B region, associated with resistance to sofosbuvir, was detected in 9 of the 21 (43 %) analysed sequences from genotype 1b-infected patients. Naturally occurring mutations V36L, and M175L in the NS3 protease region were observed in 100 % of patients infected with subtype 2c and 4. CONCLUSION A relevant proportion of treatment naïve genotype 1b infected patients evaluated in this study harboured N316 polymorphism and might poorly respond to sofosbuvir treatment. As sofosbuvir has been approved for treatment of HCV chronic infection in USA and Europe including Italy, pre-treatment testing for N316 polymorphism on genotype 1b naïve patients should be considered for this drug.
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Affiliation(s)
- Angela Costantino
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161, Rome, Italy.
| | - Enea Spada
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161, Rome, Italy.
| | - Michele Equestre
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome, Italy.
| | - Roberto Bruni
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161, Rome, Italy.
| | - Elena Tritarelli
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161, Rome, Italy.
| | - Nicola Coppola
- Department of Mental Health and Public Medicine, Section of Infectious diseases, Second University of Naples, Naples, Italy.
| | - Caterina Sagnelli
- Department of Experimental Medicine and Surgery F. Magrassi and A. Lanzara, Second University of Naples, Naples, Italy.
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious diseases, Second University of Naples, Naples, Italy.
| | - Anna Rita Ciccaglione
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Viral Hepatitis Unit, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161, Rome, Italy.
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Lontok E, Harrington P, Howe A, Kieffer T, Lennerstrand J, Lenz O, McPhee F, Mo H, Parkin N, Pilot-Matias T, Miller V. Hepatitis C virus drug resistance-associated substitutions: State of the art summary. Hepatology 2015; 62:1623-32. [PMID: 26095927 DOI: 10.1002/hep.27934] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 06/06/2015] [Indexed: 12/12/2022]
Abstract
UNLABELLED Hepatitis C virus (HCV) drug development has resulted in treatment regimens composed of interferon-free, all-oral combinations of direct-acting antivirals. While the new regimens are potent and highly efficacious, the full clinical impact of HCV drug resistance, its implications for retreatment, and the potential role of baseline resistance testing remain critical research and clinical questions. In this report, we discuss the viral proteins targeted by HCV direct-acting antivirals and summarize clinically relevant resistance data for compounds that have been approved or are currently in phase 3 clinical trials. CONCLUSION This report provides a comprehensive, systematic review of all resistance information available from sponsors' trials as a tool to inform the HCV drug development field.
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Affiliation(s)
- Erik Lontok
- Forum for Collaborative HIV Research, University of California at Berkeley, Washington, DC
| | - Patrick Harrington
- Center for Drug Evaluation and Research, Office of Antimicrobial Products, Division of Antiviral Products, US Food and Drug Administration, Silver Spring, MD
| | - Anita Howe
- Merck Research Laboratories, West Point, PA
| | | | | | - Oliver Lenz
- Janssen Infectious Diseases, Beerse, Belgium
| | - Fiona McPhee
- Bristol-Myers Squibb Research and Development, Wallingford, CT
| | | | | | | | - Veronica Miller
- Forum for Collaborative HIV Research, University of California at Berkeley, Washington, DC
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Afrasiabi M, Hosseini SY, Yaghobi R, Fattahi MR, Ardebili M, Khodadad M. Analysis of Naturally Occurring Resistant Mutations to Hepatitis C Virus NS3 Protease Inhibitors: A Preliminary Study in South of Iran. Jundishapur J Microbiol 2015; 8:e24965. [PMID: 26587218 PMCID: PMC4644313 DOI: 10.5812/jjm.24965] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/03/2015] [Accepted: 02/28/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Exploring the rate of naturally occurring NS3 protease mutants in HCV infected population is influential in the future therapeutic approaches. OBJECTIVES This study explored naturally occurring resistant mutations to protease inhibitors in a pilot study. PATIENTS AND METHODS We analyzed NS3 gene sequences in 7 HCV infected patients, referred to the central liver center, south of Iran. The protease domain was amplified by PCR followed by product extraction. Amplified NS3 genes were cloned by TA/cloning system. For each patient, clonal-sequencing was performed to improve mutation detection sensitivity. Then, the obtained sequences were compared with the reference sequences and final phylogenic tree was constructed. Afterwards, the sequences were studied to investigate point mutations. RESULTS Phylogenetic analysis between reference and amplified sequences demonstrated high similarity of all sequences with genotype 1. Interestingly, crucial protease resistant mutations were detected in V36 and R155 positions in one patient's sequence. Checking different clones of this patient confirmed V36L, as the dominant mutation while R155K was detected only in a few cases. CONCLUSIONS As revealed, naturally occurring resistant mutations, especially R155K in protease sequence were identified in 1 out of the 7 patients, so the rate of such mutations is estimated to be high. It seems that checking HCV patients before protease inhibitor treatment are necessary in the region.
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Affiliation(s)
- Mozhgan Afrasiabi
- Gastroenterohepatology Research Center (GEHRC), Shiraz University of Medical Sciences, Shiraz, IR Iran
| | - Seyed Younes Hosseini
- Gastroenterohepatology Research Center (GEHRC), Shiraz University of Medical Sciences, Shiraz, IR Iran
- Corresponding authors: Seyed Younes Hosseini, Gastroenterohepatology Research Center (GEHRC), Shiraz University of Medical Sciences, Shiraz, IR Iran. Tel: +98-7116125860, Fax: +98-7116474263, E-mail: ; Ramin Yaghoubi, Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran, E-mail:
| | - Ramin Yaghobi
- Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran
- Corresponding authors: Seyed Younes Hosseini, Gastroenterohepatology Research Center (GEHRC), Shiraz University of Medical Sciences, Shiraz, IR Iran. Tel: +98-7116125860, Fax: +98-7116474263, E-mail: ; Ramin Yaghoubi, Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran, E-mail:
| | - Mohammad-Reza Fattahi
- Gastroenterohepatology Research Center (GEHRC), Shiraz University of Medical Sciences, Shiraz, IR Iran
| | - Maryam Ardebili
- Gastroenterohepatology Research Center (GEHRC), Shiraz University of Medical Sciences, Shiraz, IR Iran
| | - Mahboobeh Khodadad
- Gastroenterohepatology Research Center (GEHRC), Shiraz University of Medical Sciences, Shiraz, IR Iran
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Bonsall D, Ansari MA, Ip C, Trebes A, Brown A, Klenerman P, Buck D, Piazza P, Barnes E, Bowden R. ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens. F1000Res 2015; 4:1062. [PMID: 27092241 PMCID: PMC4821293 DOI: 10.12688/f1000research.7111.1] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/08/2015] [Indexed: 12/22/2022] Open
Abstract
The routine availability of high-depth virus sequence data would allow the sensitive detection of resistance-associated variants that can jeopardize HIV or hepatitis C virus (HCV) treatment. We introduce ve-SEQ, a high-throughput method for sequence-specific enrichment and characterization of whole-virus genomes at up to 20% divergence from a reference sequence and 1,000-fold greater sensitivity than direct sequencing. The extreme genetic diversity of HCV led us to implement an algorithm for the efficient design of panels of oligonucleotide probes to capture any sequence among a defined set of targets without detectable bias. ve-SEQ enables efficient detection and sequencing of any HCV genome, including mixtures and intra-host variants, in a single experiment, with greater tolerance of sequence diversity than standard amplification methods and greater sensitivity than metagenomic sequencing, features that are directly applicable to other pathogens or arbitrary groups of target organisms, allowing the combination of sensitive detection with sequencing in many settings.
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Affiliation(s)
- David Bonsall
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX1 4BH, UK
| | - M Azim Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX1 4BH, UK.,Oxford Martin School, University of Oxford, Oxford, OX1 4BH, UK
| | - Camilla Ip
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX1 4BH, UK
| | - Amy Trebes
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX1 4BH, UK
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX1 4BH, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX1 4BH, UK.,National Institute for Health Research Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - David Buck
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX1 4BH, UK
| | | | - Paolo Piazza
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX1 4BH, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX1 4BH, UK.,National Institute for Health Research Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Rory Bowden
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX1 4BH, UK
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42
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Substitutions at NS3 Residue 155, 156, or 168 of Hepatitis C Virus Genotypes 2 to 6 Induce Complex Patterns of Protease Inhibitor Resistance. Antimicrob Agents Chemother 2015; 59:7426-36. [PMID: 26392503 DOI: 10.1128/aac.01953-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 09/10/2015] [Indexed: 01/14/2023] Open
Abstract
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.
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Paolucci S, Fiorina L, Mariani B, Landini V, Gulminetti R, Novati S, Maserati R, Barbarini G, Bruno R, Baldanti F. Development and persistence of DAA resistance associated mutations in patients failing HCV treatment. J Clin Virol 2015; 72:114-8. [PMID: 26489401 DOI: 10.1016/j.jcv.2015.08.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND Direct-acting antiviral agents (DAAs) combined with pegylated-interferon (PegIFN) and ribavirin (RBV) are still a standard treatment in patients with genotype 1HCV infection. However, virologic response could be impaired by baseline or early selection of resistant HCV strains. OBJECTIVES The aim of this study was to determine the onset and persistence of resistance-associated mutations (RAMs) in the NS3 and NS5B genes of DAA-naïve patients failing treatment. STUDY DESIGN Direct sequencing of HCV NS3 was performed in 49 DAA-naïve patients with HCV genotype 1 infection. RESULTS Eight out of 23 patients (34.7%) failed PegIFN/RBV/telaprevir during the 12-weeks of therapy. Treatment failure was associated with the development of RAMs at amino-acids 36,54,80 and 155 of the HCV protease in 6/8 patients (75%). Among patients treated with PegIFN/RBV/boceprevir treatment, 4/18 (22.2%) failed therapy. Of these, 2 (50%) carried virus strains which developed a RAM at amino-acids 54 and 155. Among HCV strains with RAMs, 7 belonged to genotype 1a and 1 to 1b. Finally, in 6/10 (60%) patients, drug-resistant variants could still be detected for up to 3-7 months after stopping therapy. CONCLUSIONS A higher rate (p=0.49) of treatment failure was observed in patients receiving telaprevir- compared to the boceprevir-based combination. In addition, compared with genotype 1b, genotype 1a was associated with higher rates (p=0.01) of treatment failure due to virus resistant strains. Resistance testing at baseline and during DAA treatment should be taken into consideration when treating patients with new HCV combination therapies.
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Affiliation(s)
- Stefania Paolucci
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
| | - Loretta Fiorina
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
| | - Bianca Mariani
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
| | - Viviana Landini
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
| | - Roberto Gulminetti
- Institute of Infectious Diseases, University of Pavia, 27100, Pavia, Italy
| | - Stefano Novati
- Institute of Infectious Diseases, University of Pavia, 27100, Pavia, Italy
| | - Renato Maserati
- Institute of Infectious Diseases, University of Pavia, 27100, Pavia, Italy
| | - Giorgio Barbarini
- Division of Infectious and Tropical Diseases, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
| | - Raffaele Bruno
- Division of Infectious and Tropical Diseases, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100, Pavia, Italy.
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Development and Validation of Two Screening Assays for the Hepatitis C Virus NS3 Q80K Polymorphism Associated with Reduced Response to Combination Treatment Regimens Containing Simeprevir. J Clin Microbiol 2015; 53:2942-50. [PMID: 26135875 DOI: 10.1128/jcm.00650-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/26/2015] [Indexed: 01/03/2023] Open
Abstract
Persons with hepatitis C virus (HCV) genotype 1a (GT1a) infections harboring a baseline Q80K polymorphism in nonstructural protein 3 (NS3) have a reduced virologic response to simeprevir in combination with pegylated interferon-alfa and ribavirin. We aimed to develop, validate, and freely disseminate an NS3 clinical sequencing assay to detect the Q80K polymorphism and potentially other HCV NS3 drug resistance mutations. HCV RNA was extracted from frozen plasma using a NucliSENS easyMAG automated nucleic acid extractor, amplified by nested reverse transcription-PCR, and sequenced using Sanger and/or next-generation (MiSeq) methods. Sanger chromatograms were analyzed using in-house software (RECall), and nucleotide mixtures were called automatically. MiSeq reads were iteratively mapped to the H77 reference genome, and consensus NS3 sequences were generated with nucleotides present at >20% called as mixtures. The accuracy, precision, and sensitivity for detecting the Q80K polymorphism were assessed in 70 samples previously sequenced by an external laboratory. A comparison of the sequences generated by the Sanger and MiSeq methods with those determined by an external lab revealed >98.5% nucleotide sequence concordance and zero discordant calls of the Q80K polymorphism. The results were both highly repeatable and reproducible (>99.7% nucleotide concordance and 100% Q80K concordance). The limits of detection (>2 and ∼5 log10 IU/ml for the Sanger and MiSeq assays, respectively) are sufficiently low to allow genotyping in nearly all chronically infected treatment-naive persons. No systematic bias in the under- or overamplification of minority variants was observed. Coinfection with other viruses (e.g., HIV and hepatitis B virus [HBV]) did not affect the assay results. The two independent HCV NS3 sequencing assays with the automated analysis procedures described here are useful tools to screen for the Q80K polymorphism and other HCV protease inhibitor drug resistance mutations.
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Silva T, Cortes Martins H, Coutinho R, Leitão E, Silva R, Pádua E. Molecular characterization of hepatitis C virus for determination of subtypes and detection of resistance mutations to protease inhibitors in a group of intravenous drug users co-infected with HIV. J Med Virol 2015; 87:1549-57. [DOI: 10.1002/jmv.24213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Tânia Silva
- Department of Infectious Diseases; National Reference Laboratory of HIV and Hepatitis B and C; National Institute of Health; Lisbon Portugal
| | - Helena Cortes Martins
- Department of Infectious Diseases; National Reference Laboratory of HIV and Hepatitis B and C; National Institute of Health; Lisbon Portugal
| | - Rodrigo Coutinho
- Support office for Drug Addicts; Association of Ares do Pinhal; Lisboa Portugal
| | - Emília Leitão
- Support office for Drug Addicts; Association of Ares do Pinhal; Lisboa Portugal
| | - Rui Silva
- Support office for Drug Addicts; Association of Ares do Pinhal; Lisboa Portugal
| | - Elizabeth Pádua
- Department of Infectious Diseases; National Reference Laboratory of HIV and Hepatitis B and C; National Institute of Health; Lisbon Portugal
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Nguyen LT, Gray E, Dean J, Carr M, Connell J, De Gascun C, Nguyen LA, O'Leary A, Bergin C, Hall W, Norris S. Baseline prevalence and emergence of protease inhibitor resistance mutations following treatment in chronic HCV genotype-1-infected individuals. Antivir Ther 2015; 20:865-9. [PMID: 25920764 DOI: 10.3851/imp2964] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND The HCV NS3/4A serine protease inhibitors (PIs) boceprevir (BOC), telaprevir (TVR) and simeprevir (SMV) are approved for treatment of chronic hepatitis C infection in combination with pegylated interferon and ribavirin. The present study investigated the prevalence of HCV NS3 drug resistance mutations (DRMs) associated with HCV genotype-1-infected individuals at baseline and in viral breakthrough following BOC and TVR treatment. METHODS HCV genotype-1-infected individuals were enrolled in a multicentre, prospective outcomes study. The HCV NS3 viral protease was analysed for DRMs at baseline (n=164) and at viral breakthrough (n=18) following BOC/TVR treatment. RESULTS Viral NS3 protease subtype analysis showed 65.2% (107/164) were HCV subtype-1a and 34.8% (57/164) were HCV subtype-1b infections. Naturally occurring PI DRMs in NS3 (V36L, T54S, V55A, Q80K/R and I132V) were identified in 57.3% (94/164) cases at baseline. The NS3 Q80K polymorphism was found in 43/107 (40.2%) of HCV subtype-1a and exclusively in clade 1 (43/82; 52.4%) versus clade 2 viruses (0/25; 0%, P<10(-6)). The pretreatment I132V variant was found in 78.9% (45/57) of subtype-1b. Of 18 patients who had viral breakthrough, the majority was subtype-1a (77.8%, 14/18). BOC/TVR-associated DRMs were detected in 94.4% (17/18), of which 64.7% (11/17) emerged on-treatment. CONCLUSIONS To ensure the most appropriate direct-acting antiviral-based treatment regimen is employed, baseline reporting of clade and resistance mutations for HCV subtype-1a using nucleotide sequence-based analysis is warranted prior to commencement of therapy.
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Affiliation(s)
- Linh Thuy Nguyen
- Ireland Vietnam Blood-Borne Virus Initiative (IVVI), Dublin, Ireland and Hanoi, Vietnam.
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Naturally Occurring Resistance-Associated Variants of Hepatitis C Virus Protease Inhibitors in Poor Responders to Pegylated Interferon-Ribavirin. J Clin Microbiol 2015; 53:2195-202. [PMID: 25926499 DOI: 10.1128/jcm.03633-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/23/2015] [Indexed: 11/20/2022] Open
Abstract
The pretherapeutic presence of protease inhibitor (PI) resistance-associated variants (RAVs) has not been shown to be predictive of triple-therapy outcomes in treatment-naive patients. However, they may influence the outcome in patients with less effective pegylated interferon (pegIFN)-ribavirin (RBV) backbones. Using hepatitis C virus (HCV) population sequence analysis, we retrospectively investigated the prevalence of baseline nonstructural 3 (NS3) RAVs in a multicenter cohort of poor IFN-RBV responders (i.e., prior null responders or patients with a viral load decrease of <1 log IU/ml during the pegIFN-RBV lead-in phase). The impact of the presence of these RAVs on the outcome of triple therapy was studied. Among 282 patients, the prevalances (95% confidence intervals) of baseline RAVs ranged from 5.7% (3.3% to 9.0%) to 22.0% (17.3% to 27.3%), depending to the algorithm used. Among mutations conferring a >3-fold shift in 50% inhibitory concentration (IC50) for telaprevir or boceprevir, T54S was the most frequently detected mutation (3.9%), followed by A156T, R155K (0.7%), V36M, and V55A (0.35%). Mutations were more frequently found in patients infected with genotype 1a (7.5 to 23.6%) than 1b (3.3 to 19.8%) (P = 0.03). No other sociodemographic or viroclinical characteristic was significantly associated with a higher prevalence of RAVs. No obvious effect of baseline RAVs on viral load was observed. In this cohort of poor responders to IFN-RBV, no link was found with a sustained virological response to triple therapy, regardless of the algorithm used for the detection of mutations. Based on a cross-study comparison, baseline RAVs are not more frequent in poor IFN-RBV responders than in treatment-naive patients and, even in these difficult-to-treat patients, this study demonstrates no impact on treatment outcome, arguing against resistance analysis prior to treatment.
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Discovery of the 2-phenyl-4,5,6,7-Tetrahydro-1H-indole as a novel anti-hepatitis C virus targeting scaffold. Eur J Med Chem 2015; 96:250-8. [PMID: 25890075 DOI: 10.1016/j.ejmech.2015.04.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 01/12/2023]
Abstract
Although all-oral direct-acting antiviral (DAA) therapy for hepatitis C virus (HCV) treatment is now a reality, today's HCV drugs are expensive, and more affordable drugs are still urgently needed. In this work, we report the identification of the 2-phenyl-4,5,6,7-Tetrahydro-1H-indole chemical scaffold that inhibits cellular replication of HCV genotype 1b and 2a subgenomic replicons. The anti-HCV genotype 1b and 2a profiling and effects on cell viability of a selected representative set of derivatives as well as their chemical synthesis are described herein. The most potent compound 39 displayed EC50 values of 7.9 and 2.6 μM in genotype 1b and 2a, respectively. Biochemical assays showed that derivative 39 had no effect on HCV NS5B polymerase, NS3 helicase, IRES mediated translation and selected host factors. Thus, future work will involve both the chemical optimization and target identification of 2-phenyl-4,5,6,7-Tetrahydro-1H-indoles as new anti-HCV agents.
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No correspondence between resistance mutations in the HCV-NS3 protease at baseline and early telaprevir-based triple therapy. BBA CLINICAL 2015; 3:146-51. [PMID: 26674563 PMCID: PMC4661554 DOI: 10.1016/j.bbacli.2015.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 02/06/2023]
Abstract
Direct-acting antiviral (DAA)-based therapy is the new standard treatment for chronic hepatitis C virus (HCV) infection. However, protease inhibitor (PI)-resistant viral variants have been often described. This study aimed to examine HCV-NS3 protease variants at baseline and at 4 weeks under triple therapy. To this end, we analyzed the presence of variants in HCV-NS3 protease region from peripheral blood samples of 16 patients infected with HCV-1 at baseline and at 4 weeks of combined therapy with telaprevir, pegylated interferon, and ribavirin, using next-generation sequencing. Several variants with synonymous and non-synonymous amino acid substitutions were detected at both time points. Variants detected at low frequency corresponded to 74% (HCV-1a) and 35% (HCV-1b) of non-synonymous substitutions. We found nine PI-resistance-associated variants (V36A, T54S, V55I, Q80K, Q80R, V107I, I132V, D168E, M175L) in HCV-NS3 of 10 patients. There was no correspondence of resistance-associated variant profile between baseline and at 4 weeks. Moreover, these resistance variants at baseline and short-term treatment are not good predictors of outcome under triple therapy. Our study also shows a large number of others minor and major non-synonymous variants in HCV-NS3 early in telaprevir-based therapy that can be important for further drug resistance association studies with newly developed PI agents. HCV-NS3 protease variants were analyzed at baseline and 4 weeks of triple therapy. Synonymous and non-synonymous variants, even at low frequency, were detected. Nine PI resistance mutations were identified in 10/16 patients in both time points. There was no correspondence between resistance mutation at baseline and 4 weeks. We provide a comprehensive databank of non-synonymous variants in HCV-NS3.
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An update on the management of chronic hepatitis C: 2015 Consensus guidelines from the Canadian Association for the Study of the Liver. Can J Gastroenterol Hepatol 2015; 29:19-34. [PMID: 25585348 PMCID: PMC4334064 DOI: 10.1155/2015/692408] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Chronic hepatitis C remains a significant medical and economic burden in Canada, affecting nearly 1% of the population. Since the last Canadian consensus conference on the management of chronic hepatitis C, major advances have occurred that warrant a review of recommended management approaches for these patients. Specifically, direct-acting antiviral agents with dramatically improved rates of virological clearance compared with standard therapy have been developed and interferon-free, all-oral antiviral regimens have been approved. In light of this new evidence, an update to the 2012 Canadian Association for the Study of the Liver consensus guidelines on the management of hepatitis C was produced. The present document reviews the epidemiology of hepatitis C in Canada, preferred diagnostic testing approaches and recommendations for the treatment of chronically infected patients with the newly approved antiviral agents, including those who have previously failed peginterferon and ribavirin-based therapy. In addition, recommendations are made regarding approaches to reducing the burden of hepatitis C in Canada.
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