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Yamauchi K, Maekawa S, Osawa L, Komiyama Y, Nakakuki N, Takada H, Muraoka M, Suzuki Y, Sato M, Takano S, Enomoto N. Single-molecule sequencing of the whole HCV genome revealed envelope deletions in decompensated cirrhosis associated with NS2 and NS5A mutations. J Gastroenterol 2024:10.1007/s00535-024-02146-3. [PMID: 39225750 DOI: 10.1007/s00535-024-02146-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Defective hepatitis C virus (HCV) genomes with deletion of the envelope region have been occasionally reported by short-read sequencing analyses. However, the clinical and virological details of such deletion HCV have not been fully elucidated. METHODS We developed a highly accurate single-molecule sequencing system for full-length HCV genes by combining the third-generation nanopore sequencing with rolling circle amplification (RCA) and investigated the characteristics of deletion HCV through the analysis of 21 patients chronically infected with genotype-1b HCV. RESULT In 5 of the 21 patients, a defective HCV genome with approximately 2000 bp deletion from the E1 to NS2 region was detected, with the read frequencies of 34-77%, suggesting the trans-complementation of the co-infecting complete HCV. Deletion HCV was found exclusively in decompensated cirrhosis (5/12 patients), and no deletion HCV was observed in nine compensated patients. Comparing the amino acid substitutions between the deletion and complete HCV (DAS, deletion-associated substitutions), the deletion HCV showed higher amino acid mutations in the ISDR (interferon sensitivity-determining region) in NS5A, and also in the TMS (transmembrane segment) 3 to H (helix) 2 region of NS2. CONCLUSIONS Defective HCV genome with deletion of envelope genes is associated with decompensated cirrhosis. The deletion HCV seems susceptible to innate immunity, such as endogenous interferon with NS5A mutations, escaping from acquired immunity with deletion of envelope proteins with potential modulation of replication capabilities with NS2 mutations. The relationship between these mutations and liver damage caused by HCV deletion is worth investigating.
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Affiliation(s)
- Kozue Yamauchi
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Shinya Maekawa
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan.
| | - Leona Osawa
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Yasuyuki Komiyama
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Natsuko Nakakuki
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Hitomi Takada
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Masaru Muraoka
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Yuichiro Suzuki
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Mitsuaki Sato
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Shinichi Takano
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Nobuyuki Enomoto
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
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Lapointe HR, Dong W, Dong WWY, Kirkby D, Woods C, Poon AFY, Howe AYM, Harrigan PR, Brumme CJ. Validation of a Genotype-Independent Hepatitis C Virus Near-Whole Genome Sequencing Assay. Viruses 2021; 13:v13091721. [PMID: 34578305 PMCID: PMC8473162 DOI: 10.3390/v13091721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/17/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the effectiveness of direct-acting antiviral agents in treating hepatitis C virus (HCV), cases of treatment failure have been associated with the emergence of resistance-associated substitutions. To better guide clinical decision-making, we developed and validated a near-whole-genome HCV genotype-independent next-generation sequencing strategy. HCV genotype 1-6 samples from direct-acting antiviral agent treatment-naïve and -treated HCV-infected individuals were included. Viral RNA was extracted using a NucliSens easyMAG and amplified using nested reverse transcription-polymerase chain reaction. Libraries were prepared using Nextera XT and sequenced on the Illumina MiSeq sequencing platform. Data were processed by an in-house pipeline (MiCall). Nucleotide consensus sequences were aligned to reference strain sequences for resistance-associated substitution identification and compared to NS3, NS5a, and NS5b sequence data obtained from a validated in-house assay optimized for HCV genotype 1. Sequencing success rates (defined as achieving >100-fold read coverage) approaching 90% were observed for most genotypes in samples with a viral load >5 log10 IU/mL. This genotype-independent sequencing method resulted in >99.8% nucleotide concordance with the genotype 1-optimized method, and 100% agreement in genotype assignment with paired line probe assay-based genotypes. The assay demonstrated high intra-run repeatability and inter-run reproducibility at detecting substitutions above 2% prevalence. This study highlights the performance of a freely available laboratory and bioinformatic approach for reliable HCV genotyping and resistance-associated substitution detection regardless of genotype.
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Affiliation(s)
- Hope R. Lapointe
- Department of Medicine, Division of Social Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (H.R.L.); (P.R.H.)
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Weiyan Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Winnie W. Y. Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Don Kirkby
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Conan Woods
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
| | - Art F. Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
| | - Anita Y. M. Howe
- British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada;
| | - P. Richard Harrigan
- Department of Medicine, Division of Social Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (H.R.L.); (P.R.H.)
| | - Chanson J. Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada; (W.D.); (W.W.Y.D.); (D.K.); (C.W.)
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Correspondence:
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Intra-host evolutionary dynamics of the hepatitis C virus among people who inject drugs. Sci Rep 2021; 11:9986. [PMID: 33976241 PMCID: PMC8113533 DOI: 10.1038/s41598-021-88132-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
Most individuals chronically infected with hepatitis C virus (HCV) are asymptomatic during the initial stages of infection and therefore the precise timing of infection is often unknown. Retrospective estimation of infection duration would improve existing surveillance data and help guide treatment. While intra-host viral diversity quantifications such as Shannon entropy have previously been utilized for estimating duration of infection, these studies characterize the viral population from only a relatively short segment of the HCV genome. In this study intra-host diversities were examined across the HCV genome in order to identify the region most reflective of time and the degree to which these estimates are influenced by high-risk activities including those associated with HCV acquisition. Shannon diversities were calculated for all regions of HCV from 78 longitudinally sampled individuals with known seroconversion timeframes. While the region of the HCV genome most accurately reflecting time resided within the NS3 gene, the gene region with the highest capacity to differentiate acute from chronic infections was identified within the NS5b region. Multivariate models predicting duration of infection from viral diversity significantly improved upon incorporation of variables associated with recent public, unsupervised drug use. These results could assist the development of strategic population treatment guidelines for high-risk individuals infected with HCV and offer insights into variables associated with a likelihood of transmission.
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Abstract
INTRODUCTION Hepatitis C virus (HCV) is divided into 7 genotypes and 67 subtypes. HCV genotype studies reflect the viral transmission patterns as well as human migration routes. In a clinical setting, HCV genotype is a baseline predictor for the sustained virological response (SVR) in chronic hepatitis C patients treated with peginterferon or some direct acting antivirals (DAAs). The Versant HCV genotype 2.0 assay has been globally used for HCV genotyping over a decade. Areas covered: The assay is based on reverse hybridization principle. It is evolved from its former versions, and the accuracy and successful genotyping/subtyping rate are substantially improved. It shows an accuracy of 99-100% for genotypes 1-6. It can also reliably identify subtypes 1a and 1b. However, the assay does not allow a high resolution for many other subtypes. Reasons for indeterminate or inaccurate genotyping/subtyping results are discussed. Expert commentary: Genotyping helps to find the most efficacious and cost-effective treatment regimen. The rapid development of anti-HCV treatment regimens, however, is greatly simplifying laboratory tests. In the near future, the need for HCV genotyping and frequent serial on-treatment HCV RNA tests will decrease along with the wide use of the more potent and pan-genotypic DAA regimens.
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Affiliation(s)
- Ruifeng Yang
- a Peking University People's Hospital, Peking University Hepatology Institute , Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases , Beijing , China
| | - Lai Wei
- a Peking University People's Hospital, Peking University Hepatology Institute , Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases , Beijing , China
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Pedersen MS, Fahnøe U, Hansen TA, Pedersen AG, Jenssen H, Bukh J, Schønning K. A near full-length open reading frame next generation sequencing assay for genotyping and identification of resistance-associated variants in hepatitis C virus. J Clin Virol 2018; 105:49-56. [PMID: 29886373 DOI: 10.1016/j.jcv.2018.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 05/22/2018] [Accepted: 05/26/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND The current treatment options for hepatitis C virus (HCV), based on direct acting antivirals (DAA), are dependent on virus genotype and previous treatment experience. Treatment failures have been associated with detection of resistance-associated substitutions (RASs) in the DAA targets of HCV, the NS3, NS5A and NS5 B proteins. OBJECTIVE To develop a next generation sequencing based method that provides genotype and detection of HCV NS3, NS5A, and NS5 B RASs without prior knowledge of sample genotype. STUDY DESIGN In total, 101 residual plasma samples from patients with HCV covering 10 different viral subtypes across 4 genotypes with viral loads of 3.84-7.61 Log IU/mL were included. All samples were de-identified and consequently prior treatment status for patients was unknown. Almost full open reading frame amplicons (∼ 9 kb) were generated using RT-PCR with a single primer set. The resulting amplicons were sequenced with high throughput sequencing and analysed using an in-house developed script for detecting RASs. RESULTS The method successfully amplified and sequenced 94% (95/101) of samples with an average coverage of 14,035; four of six failed samples were genotype 4a. Samples analysed twice yielded reproducible nucleotide frequencies across all sites. RASs were detected in 21/95 (22%) samples at a 15% threshold. The method identified one patient infected with two genotype 2b variants, and the presence of subgenomic deletion variants in 8 (8.4%) of 95 successfully sequenced samples. CONCLUSIONS The presented method may provide identification of HCV genotype, RASs detection, and detect multiple HCV infection without prior knowledge of sample genotype.
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Affiliation(s)
- M S Pedersen
- Department of Microbiology, Copenhagen University Hospital, Hvidovre, Denmark; Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, And Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark; Department of Science and Environment, Roskilde University, Denmark
| | - U Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, And Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - T A Hansen
- Department of Microbiology, Copenhagen University Hospital, Hvidovre, Denmark
| | - A G Pedersen
- DTU Bioinformatics, Technical University of Denmark, Denmark
| | - H Jenssen
- Department of Science and Environment, Roskilde University, Denmark
| | - J Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, And Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - K Schønning
- Department of Microbiology, Copenhagen University Hospital, Hvidovre, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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6
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Walker A, Bergmann M, Camdereli J, Kaiser R, Lübke N, Timm J. A genotype independent, full-genome reverse-transcription protocol for HCV genotyping and resistance testing. J Clin Virol 2017; 91:42-48. [DOI: 10.1016/j.jcv.2017.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/31/2017] [Accepted: 04/06/2017] [Indexed: 12/13/2022]
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7
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Marques BLC, do Espírito-Santo MP, Marques VA, Miguel JC, da Silva EF, Villela-Nogueira CA, Lewis-Ximenez LL, Lampe E, Villar LM. Evaluation of dried blood spot samples for hepatitis C virus detection and quantification. J Clin Virol 2016; 82:139-144. [PMID: 27497191 DOI: 10.1016/j.jcv.2016.07.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Dried blood spots (DBS) could be an excellent alternative for HCV diagnosis, since it is less invasive and can be stored and transported without refrigeration. OBJECTIVES The aim of this study was to optimize quantitative and qualitative methods for HCV detection in DBS. STUDY DESIGN DBS and serum samples were collected from 99 subjects (59 anti-HCV/HCV RNA positive and 40 seronegative samples). Seven extraction methods and different PCR parameters were evaluated in DBS samples in the quantitative RT-PCR (qRT-PCR) developed to amplify the 5' noncoding region of HCV. A qualitative PCR for amplification of NS5B region of HCV was also valued and the nested-PCR sequenced. RESULTS The qRT-PCR showed good correlation to commercial assay for HCV viral measurement in serum. To quantify HCV RNA in DBS, it was necessary to increase reverse transcriptase and cDNA concentration. HCV RNA quantification in DBS demonstrated sensitivity of 65.9%, 100% of specificity and kappa statistic of 0.65. The median viral load of DBS samples was 5.38 log10 copies/ml (minimum value=1.76 and maximum value=10.48 log10 copies/ml). HCV RNA was detected in NS5B regions and nucleotide sequences obtained in 43 serum and 11 DBS samples. The presence of the same subtype was observed in paired serum and DBS samples. CONCLUSIONS In this study, it was possible to demonstrate that, despite the low sensitivity, the optimized protocol was able to determine the viral load, as well as, the infecting HCV genotype, validating the usefulness of DBS for viral load determination and molecular epidemiology studies of HCV.
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Affiliation(s)
| | | | - Vanessa Alves Marques
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | | | | | | | | | - Elisabeth Lampe
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Livia Melo Villar
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
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8
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Hézode C, Chevaliez S, Scoazec G, Soulier A, Varaut A, Bouvier-Alias M, Ruiz I, Roudot-Thoraval F, Mallat A, Féray C, Pawlotsky JM. Retreatment with sofosbuvir and simeprevir of patients with hepatitis C virus genotype 1 or 4 who previously failed a daclatasvir-containing regimen. Hepatology 2016; 63:1809-16. [PMID: 26853230 DOI: 10.1002/hep.28491] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/10/2016] [Accepted: 02/05/2016] [Indexed: 01/01/2023]
Abstract
UNLABELLED Failure to achieve sustained virological response (SVR) with hepatitis C virus (HCV) direct-acting antiviral-based regimens is commonly associated with emergence of resistance-associated variants (RAVs). To avoid cross-resistance, recent guidelines recommend that patients who have failed on nonstructural protein 5A (NS5A) inhibitors should be retreated with sofosbuvir (SOF; NS5B inhibitor) combined with simeprevir (SIM; protease inhibitor [PI]); however, supporting evidence is lacking. This "real-world" study comprised patients who had failed to achieve SVR on previous NS5A-based therapy with daclatasvir (DCV) plus pegylated interferon (Peg-IFN) and ribavirin (RBV), with (n = 3) or without (n = 13) asunaprevir (ASV; PI). All 16 patients were retreated for 12 weeks with SOF plus SIM, without RBV. Antiviral efficacy was evaluated using the primary endpoint of SVR12 (SVR 12 weeks post-treatment); on-treatment response was also assessed. Patients (N = 16; 13 male; mean age: 54 years [range, 43-73]) were chronically infected with HCV genotype (GT) 1 (1a, n = 11; 1b, n = 3) or 4 (n = 2); they had advanced fibrosis or compensated cirrhosis (FibroScan, 9.6-70 kPa; cirrhosis, n = 9); median baseline HCV-RNA level was 1.38 × 10(6) IU/mL. No patient discontinued treatment because of adverse events or virological failure. All patients achieved HCV RNA below lower limit of quantification (<12 IU/mL) by end of treatment (EOT) and 10 of 16 had a rapid response (week 4). SVR12 was achieved by 14 of 16 patients; the remaining 2 relapsed by 4 weeks post-EOT (both were GT 1a infected with cirrhosis; 1 had previously failed DCV-ASV plus Peg-IFN and RBV). Presence of SIM RAVs/polymorphisms (R155K and Q80K) at study baseline did not predict retreatment failure. CONCLUSION Our findings support the concept of retreating NS5A inhibitor failures with SOF combined with SIM. However, the most difficult-to-cure patients may need more than 12 weeks of treatment and/or the addition of RBV. (Hepatology 2016;63:1809-1816).
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Affiliation(s)
- Christophe Hézode
- Department of Hepatology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Stéphane Chevaliez
- INSERM U955, Créteil, France.,National Reference Center for Viral Hepatitis B, C and Delta, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Giovanna Scoazec
- Department of Hepatology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Alexandre Soulier
- INSERM U955, Créteil, France.,National Reference Center for Viral Hepatitis B, C and Delta, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Anne Varaut
- Department of Hepatology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Magali Bouvier-Alias
- INSERM U955, Créteil, France.,National Reference Center for Viral Hepatitis B, C and Delta, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Isaac Ruiz
- INSERM U955, Créteil, France.,National Reference Center for Viral Hepatitis B, C and Delta, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Françoise Roudot-Thoraval
- Department of Hepatology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Ariane Mallat
- Department of Hepatology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Cyrille Féray
- Department of Hepatology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.,INSERM U955, Créteil, France
| | - Jean-Michel Pawlotsky
- INSERM U955, Créteil, France.,National Reference Center for Viral Hepatitis B, C and Delta, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
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Trémeaux P, Caporossi A, Thélu MA, Blum M, Leroy V, Morand P, Larrat S. Hepatitis C virus whole genome sequencing: Current methods/issues and future challenges. Crit Rev Clin Lab Sci 2016; 53:341-51. [PMID: 27068766 DOI: 10.3109/10408363.2016.1163663] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Therapy for hepatitis C is currently undergoing a revolution. The arrival of new antiviral agents targeting viral proteins reinforces the need for a better knowledge of the viral strains infecting each patient. Hepatitis C virus (HCV) whole genome sequencing provides essential information for precise typing, study of the viral natural history or identification of resistance-associated variants. First performed with Sanger sequencing, the arrival of next-generation sequencing (NGS) has simplified the technical process and provided more detailed data on the nature and evolution of viral quasi-species. We will review the different techniques used for HCV complete genome sequencing and their applications, both before and after the apparition of NGS. The progress brought by new and future technologies will also be discussed, as well as the remaining difficulties, largely due to the genomic variability.
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Affiliation(s)
- Pauline Trémeaux
- a Laboratoire de Virologie , Institut de Biologie et Pathologie, CHU Grenoble-Alpes , Grenoble , France .,b Institut de Biologie Structurale (IBS), UMR 5075 CEA-CNRS-UGA , Grenoble , France
| | - Alban Caporossi
- c Centre d'investigation clinique, Santé publique, CHU Grenoble-Alpes , Grenoble , France .,d Laboratoire TIMC-IMAG , Université de Grenoble Alpes , Grenoble , France , and
| | - Marie-Ange Thélu
- e Clinique d'Hépato-gastroentérologie, Pôle Digidune, CHU Grenoble-Alpes , Grenoble , France
| | - Michael Blum
- d Laboratoire TIMC-IMAG , Université de Grenoble Alpes , Grenoble , France , and
| | - Vincent Leroy
- e Clinique d'Hépato-gastroentérologie, Pôle Digidune, CHU Grenoble-Alpes , Grenoble , France
| | - Patrice Morand
- a Laboratoire de Virologie , Institut de Biologie et Pathologie, CHU Grenoble-Alpes , Grenoble , France .,b Institut de Biologie Structurale (IBS), UMR 5075 CEA-CNRS-UGA , Grenoble , France
| | - Sylvie Larrat
- a Laboratoire de Virologie , Institut de Biologie et Pathologie, CHU Grenoble-Alpes , Grenoble , France .,b Institut de Biologie Structurale (IBS), UMR 5075 CEA-CNRS-UGA , Grenoble , France
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10
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Naidoo A, Parboosing R, Moodley P. Real-time polymerase chain reaction optimised for hepatitis C virus detection in dried blood spots from HIV-exposed infants, KwaZulu-Natal, South Africa. Afr J Lab Med 2016; 5:269. [PMID: 28879101 PMCID: PMC5436390 DOI: 10.4102/ajlm.v5i1.269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/08/2016] [Indexed: 01/24/2023] Open
Abstract
Background There is a paucity of data on the prevalence of hepatitis C virus (HCV) in children, particularly in sub-Saharan Africa. A major obstacle in resource-limited settings for polymerase chain reaction (PCR) testing is the necessity for specimen transportation and storage at low temperatures. There are numerous recent studies of using real-time HCV PCR for diagnosis and screening of plasma and serum, but few have looked at using dried blood spot (DBS) specimens. Objectives The aim of this study was to optimise a real-time HCV PCR method to detect HCV RNA from infant DBS specimens for use as a tool for HCV surveillance in KwaZulu-Natal, South Africa. Method The LightCycler® 2.0 instrument was used for the HCV PCR using the LightCycler® RNA Master SYBR Green I kit. Template volume, primer concentration and primer annealing temperatures were optimised and the method was used on 179 DBS specimens from HIV-exposed infants in KwaZulu-Natal. Results Primer concentrations adjusted to 0.25 µM and a template volume of 10 µL improved the PCR amplification. Primer annealing temperatures lowered from 65 °C to 58 °C resulted in higher quantities of amplified PCR product. The limit of detection of the optimised HCV PCR assay was between 1200 IU/mL and 3580 IU/mL of HCV RNA. HCV was not detected in any of the 179 DBS specimens. Conclusion The optimised real-time HCV PCR on infant DBS specimens performed well, but HCV was not found in this surveillance study. HIV infection may have little impact on the vertical transmission of HCV in this region.
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Affiliation(s)
- Anneta Naidoo
- Department of Virology, Nelson R Mandela School of Medicine, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa.,National Health Laboratory Services, Inkosi Albert Luthuli Central Hospital, Durban, KwaZulu-Natal, South Africa
| | - Raveen Parboosing
- Department of Virology, Nelson R Mandela School of Medicine, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa.,National Health Laboratory Services, Inkosi Albert Luthuli Central Hospital, Durban, KwaZulu-Natal, South Africa
| | - Pravi Moodley
- Department of Virology, Nelson R Mandela School of Medicine, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa.,National Health Laboratory Services, Inkosi Albert Luthuli Central Hospital, Durban, KwaZulu-Natal, South Africa
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11
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Bull RA, Eltahla AA, Rodrigo C, Koekkoek SM, Walker M, Pirozyan MR, Betz-Stablein B, Toepfer A, Laird M, Oh S, Heiner C, Maher L, Schinkel J, Lloyd AR, Luciani F. A method for near full-length amplification and sequencing for six hepatitis C virus genotypes. BMC Genomics 2016; 17:247. [PMID: 26988550 PMCID: PMC4797172 DOI: 10.1186/s12864-016-2575-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/08/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) is a rapidly evolving RNA virus that has been classified into seven genotypes. All HCV genotypes cause chronic hepatitis, which ultimately leads to liver diseases such as cirrhosis. The genotypes are unevenly distributed across the globe, with genotypes 1 and 3 being the most prevalent. Until recently, molecular epidemiological studies of HCV evolution within the host and at the population level have been limited to the analyses of partial viral genome segments, as it has been technically challenging to amplify and sequence the full-length of the 9.6 kb HCV genome. Although recent improvements have been made in full genome sequencing methodologies, these protocols are still either limited to a specific genotype or cost-inefficient. RESULTS In this study we describe a genotype-specific protocol for the amplification and sequencing of the near-full length genome of all six major HCV genotypes. We applied this protocol to 122 HCV positive clinical samples, and had a successful genome amplification rate of 90%, when the viral load was greater than 15,000 IU/ml. The assay was shown to have a detection limit of 1-3 cDNA copies per reaction. The method was tested with both Illumina and PacBio single molecule, real-time (SMRT) sequencing technologies. Illumina sequencing resulted in deep coverage and allowed detection of rare variants as well as HCV co-infection with multiple genotypes. The application of the method with PacBio RS resulted in sequence reads greater than 9 kb that covered the near full-length HCV amplicon in a single read and enabled analysis of the near full-length quasispecies. CONCLUSIONS The protocol described herein can be utilised for rapid amplification and sequencing of the near-full length HCV genome in a cost efficient manner suitable for a wide range of applications.
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Affiliation(s)
- Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, 2052, Australia.
| | - Auda A Eltahla
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, 2052, Australia
| | - Chaturaka Rodrigo
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, 2052, Australia
| | - Sylvie M Koekkoek
- Department of Medical Microbiology, Section of Clinical Virology, Academic Medical Center, Public Health Service, Amsterdam, The Netherlands
| | - Melanie Walker
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, 2052, Australia
| | - Mehdi R Pirozyan
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, 2052, Australia
| | - Brigid Betz-Stablein
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, 2052, Australia
| | | | | | - Steve Oh
- Pacific Biosciences, Menlo Park, CA, USA
| | | | - Lisa Maher
- The Kirby Institute, University of New South Wales, Sydney, Australia
| | - Janke Schinkel
- Department of Medical Microbiology, Section of Clinical Virology, Academic Medical Center, Public Health Service, Amsterdam, The Netherlands
| | - Andrew R Lloyd
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, 2052, Australia
| | - Fabio Luciani
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, 2052, Australia
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12
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Trémeaux P, Caporossi A, Ramière C, Santoni E, Tarbouriech N, Thélu MA, Fusillier K, Geneletti L, François O, Leroy V, Burmeister WP, André P, Morand P, Larrat S. Amplification and pyrosequencing of near-full-length hepatitis C virus for typing and monitoring antiviral resistant strains. Clin Microbiol Infect 2016; 22:460.e1-460.e10. [PMID: 26827671 DOI: 10.1016/j.cmi.2016.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/04/2016] [Accepted: 01/17/2016] [Indexed: 12/16/2022]
Abstract
Directly acting antiviral drugs have contributed considerable progress to hepatitis C virus (HCV) treatment, but they show variable activity depending on virus genotypes and subtypes. Therefore, accurate genotyping including recombinant form detection is still of major importance, as is the detection of resistance-associated mutations in case of therapeutic failure. To meet these goals, an approach to amplify the HCV near-complete genome with a single long-range PCR and sequence it with Roche GS Junior was developed. After optimization, the overall amplification success rate was 73% for usual genotypes (i.e. HCV 1a, 1b, 3a and 4a, 16/22) and 45% for recombinant forms RF_2k/1b (5/11). After pyrosequencing and subsequent de novo assembly, a near-full-length genomic consensus sequence was obtained for 19 of 21 samples. The genotype and subtype were confirmed by phylogenetic analysis for every sample, including the suspected recombinant forms. Resistance-associated mutations were detected in seven of 13 samples at baseline, in the NS3 (n = 3) or NS5A (n = 4) region. Of these samples, the treatment of one patient included daclatasvir, and that patient experienced a relapse. Virus sequences from pre- and posttreatment samples of four patients who experienced relapse after sofosbuvir-based therapy were compared: the selected variants seem too far from the NS5B catalytic site to be held responsible. Although tested on a limited set of samples and with technical improvements still necessary, this assay has proven to be successful for both genotyping and resistance-associated variant detection on several HCV types.
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Affiliation(s)
- P Trémeaux
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France; UVHCI, Grenoble, France; Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France
| | - A Caporossi
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France; Centre d'investigation clinique, Santé publique, UJF-CNRS, Grenoble, France; Laboratoire TIMC-IMAG, UMR 5525, Université de Grenoble Alpes, Grenoble, France
| | - C Ramière
- Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - E Santoni
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France
| | - N Tarbouriech
- UVHCI, Grenoble, France; Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France
| | - M-A Thélu
- Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - K Fusillier
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France
| | - L Geneletti
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France
| | - O François
- Laboratoire TIMC-IMAG, UMR 5525, Université de Grenoble Alpes, Grenoble, France
| | - V Leroy
- Service d'Hépato-Gastroentérologie, CHU de Grenoble, Grenoble, France
| | - W P Burmeister
- UVHCI, Grenoble, France; Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France
| | - P André
- Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - P Morand
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France; UVHCI, Grenoble, France; Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France
| | - S Larrat
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France; UVHCI, Grenoble, France; Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France.
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13
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Lamoury FMJ, Jacka B, Bartlett S, Bull RA, Wong A, Amin J, Schinkel J, Poon AF, Matthews GV, Grebely J, Dore GJ, Applegate TL. The Influence of Hepatitis C Virus Genetic Region on Phylogenetic Clustering Analysis. PLoS One 2015; 10:e0131437. [PMID: 26192190 PMCID: PMC4507989 DOI: 10.1371/journal.pone.0131437] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/01/2015] [Indexed: 02/06/2023] Open
Abstract
Sequencing is important for understanding the molecular epidemiology and viral evolution of hepatitis C virus (HCV) infection. To date, there is little standardisation among sequencing protocols, in-part due to the high genetic diversity that is observed within HCV. This study aimed to develop a novel, practical sequencing protocol that covered both conserved and variable regions of the viral genome and assess the influence of each subregion, sequence concatenation and unrelated reference sequences on phylogenetic clustering analysis. The Core to the hypervariable region 1 (HVR1) of envelope-2 (E2) and non-structural-5B (NS5B) regions of the HCV genome were amplified and sequenced from participants from the Australian Trial in Acute Hepatitis C (ATAHC), a prospective study of the natural history and treatment of recent HCV infection. Phylogenetic trees were constructed using a general time-reversible substitution model and sensitivity analyses were completed for every subregion. Pairwise distance, genetic distance and bootstrap support were computed to assess the impact of HCV region on clustering results as measured by the identification and percentage of participants falling within all clusters, cluster size, average patristic distance, and bootstrap value. The Robinson-Foulds metrics was also used to compare phylogenetic trees among the different HCV regions. Our results demonstrated that the genomic region of HCV analysed influenced phylogenetic tree topology and clustering results. The HCV Core region alone was not suitable for clustering analysis; NS5B concatenation, the inclusion of reference sequences and removal of HVR1 all influenced clustering outcome. The Core-E2 region, which represented the highest genetic diversity and longest sequence length in this study, provides an ideal method for clustering analysis to address a range of molecular epidemiological questions.
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Affiliation(s)
- François M. J. Lamoury
- The Kirby Institute, University of New South Wales Australia, Sydney, Australia
- * E-mail:
| | - Brendan Jacka
- The Kirby Institute, University of New South Wales Australia, Sydney, Australia
| | - Sofia Bartlett
- The Kirby Institute, University of New South Wales Australia, Sydney, Australia
| | - Rowena A. Bull
- Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales Australia, Sydney, Australia
| | - Arthur Wong
- The Kirby Institute, University of New South Wales Australia, Sydney, Australia
| | - Janaki Amin
- The Kirby Institute, University of New South Wales Australia, Sydney, Australia
| | - Janke Schinkel
- Academic Medical Centre, Department of Medical Microbiology, Section of Clinical Virology, Amsterdam, The Netherlands
| | - Art F. Poon
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Gail V. Matthews
- The Kirby Institute, University of New South Wales Australia, Sydney, Australia
| | - Jason Grebely
- The Kirby Institute, University of New South Wales Australia, Sydney, Australia
| | - Gregory J. Dore
- The Kirby Institute, University of New South Wales Australia, Sydney, Australia
- HIV/Immunology/Infectious Diseases Clinical Services Unit, St Vincent’s Hospital, Sydney, Australia
| | - Tanya L. Applegate
- The Kirby Institute, University of New South Wales Australia, Sydney, Australia
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14
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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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15
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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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16
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Ho CKY, Welkers MRA, Thomas XV, Sullivan JC, Kieffer TL, Reesink HW, Rebers SPH, de Jong MD, Schinkel J, Molenkamp R. A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants. J Virol Methods 2015; 219:28-37. [PMID: 25818622 DOI: 10.1016/j.jviromet.2015.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 01/09/2023]
Abstract
We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were used to compare the consensus sequence, average pairwise distance, normalized Shannon entropy, phylogenetic tree topology and the number and frequency of variants derived from both sequencing techniques. In general, a good concordance was observed between both techniques for the majority of datasets. Discordant results were observed for 5 out of 39 clonal and 454 datasets, which could be attributed to primer-related selective amplification used for clonal sequencing. Both 454 and clonal datasets consisted of a few major variants and a large number of low-frequency variants. Telaprevir resistance-associated variants were observed in low frequencies and were detected more often by 454. We conclude that performance of 454 and clonal sequencing is comparable for the characterization of intra-host virus populations. Not surprisingly, 454 is superior for the detection of low frequency resistance-associated variants. However, despite the greater coverage, 454 failed to detect some low frequency variants detected by clonal sequencing.
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Affiliation(s)
- Cynthia K Y Ho
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Matthijs R A Welkers
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Xiomara V Thomas
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - James C Sullivan
- Department of Infectious Diseases, Vertex Pharmaceuticals Incorporated, Cambridge, MA 02139, USA.
| | - Tara L Kieffer
- Department of Infectious Diseases, Vertex Pharmaceuticals Incorporated, Cambridge, MA 02139, USA.
| | - Henk W Reesink
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam 1104 AZ, The Netherlands.
| | - Sjoerd P H Rebers
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Janke Schinkel
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Richard Molenkamp
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
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17
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Dierynck I, Ghys A, Witek J, Luo D, Janssen K, Daems B, Picchio G, Buti M, De Meyer S. Incidence of virological failure and emergence of resistance with twice-daily vs every 8-h administration of telaprevir in the OPTIMIZE study. J Viral Hepat 2014; 21:835-42. [PMID: 25402544 DOI: 10.1111/jvh.12347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/23/2014] [Indexed: 12/20/2022]
Abstract
The OPTIMIZE study demonstrated noninferior efficacy between telaprevir (TVR) twice daily (bid) vs every 8-h (q8h) administration. This analysis compared the selective pressure of both dosing regimens by characterisation of the hepatitis C virus (HCV) variants emerging in genotype 1 (G1) HCV-infected patients who did not achieve sustained virological response (SVR). HCV NS3•4A population sequencing was performed at baseline and time of failure (viral breakthrough, stopping rule or relapse). TVR-resistant variants were classified by fold change in inhibitory concentration (IC50 ). Baseline TVR-resistance was low (<5%) and did not preclude achieving SVR in either arm. The proportion of patients with TVR-resistant variants at time of failure was similar in the bid (15%) and q8h (17%) dosing arms. The majority of variants and virological failures occurred in G1a patients, and mutations V36M, R155K and R155T (G1a), and V36A, T54A and A156S (G1b) were significantly enriched in both treatment arms. The number and type of emerging TVR-resistant variants in non-SVR patients were comparable between treatment arms and were consistent with previous observations. No differences in viral resistance profiles were observed between TVR-based treatment arms in non-SVR patients, indicating a similar selective pressure of TVR bid and q8h dosing.
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Affiliation(s)
- I Dierynck
- Janssen Infectious Diseases BVBA, Beerse, Belgium
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18
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Cuypers L, Snoeck J, Vrancken B, Kerremans L, Vuagniaux G, Verbeeck J, Nevens F, Camacho RJ, Vandamme AM, Van Dooren S. A near-full length genotypic assay for HCV1b. J Virol Methods 2014; 209:126-35. [PMID: 25245140 DOI: 10.1016/j.jviromet.2014.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 08/29/2014] [Accepted: 09/09/2014] [Indexed: 02/05/2023]
Abstract
A near-full genome genotypic assay for HCV1b was developed, which may prove useful to investigate antiviral drug resistance, given new combination therapies for HCV1 infection. The assay consists of three partially overlapping PCRs followed by Sanger population or Illumina next-generation sequencing. Seventy-seven therapy-naïve samples, spanning the entire diversity range of currently known HCV1b, were used for optimization of PCRs, of which ten were sequenced using Sanger and of these ten, four using Illumina. The median detection limits for the three regions, 5'UTR-NS2, E2-NS5A and NS4B-NS5B, were 570, 5670 and 56,670 IU/ml respectively. The number of Illumina reads mapped varied according to the software used, Segminator II being the best performing (81%). Consensus Illumina and Sanger sequencing results accord largely (0.013% major discordances). Differences were due almost exclusively to a larger number of ambiguities (presumably minority variants) scored by Illumina (1.50% minor discordances). The assay is easy to perform in an equipped laboratory; nevertheless, it was difficult to reach high sensitivity and reproducibility, due to the high genetic viral variability. This assay proved to be suitable for detecting drug resistance mutations and can also be used for epidemiological research, even though only a limited set of samples was used for validation.
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Affiliation(s)
- Lize Cuypers
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
| | - Joke Snoeck
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Bram Vrancken
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Lien Kerremans
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Grégoire Vuagniaux
- Debiopharm SA, Che. Messidor 5-7, P.O. Box 5911, 1002 Lausanne, Switzerland
| | - Jannick Verbeeck
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Frederik Nevens
- Department of Hepatology, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Ricardo J Camacho
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium; Centro de Malária e Outras Doencas Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium; Centro de Malária e Outras Doencas Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Sonia Van Dooren
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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Genotypic and phenotypic analyses of hepatitis C virus variants observed in clinical studies of VX-222, a nonnucleoside NS5B polymerase inhibitor. Antimicrob Agents Chemother 2014; 58:5456-65. [PMID: 24982088 DOI: 10.1128/aac.03052-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
VX-222, a thiophene-2-carboxylic acid derivative, is a selective nonnucleoside inhibitor of the hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase. In phase 1 and 2 clinical studies, VX-222 demonstrated effective antiviral efficacy, with substantial reductions in plasma HCV RNA in patients chronically infected with genotype 1 HCV. To characterize the potential for selection of VX-222-resistant variants in HCV-infected patients, the HCV NS5B gene was sequenced at baseline and during and after 3 days of VX-222 dosing (monotherapy) in a phase 1 study. Variants with the substitutions L419C/I/M/P/S/V, R422K, M423I/T/V, I482L/N/T, A486S/T/V, and V494A were selected during VX-222 dosing, and their levels declined over time after the end of dosing. Phenotypic analysis of these variants was conducted using HCV replicons carrying site-directed mutations. Of the 17 variants, 14 showed reduced susceptibility to VX-222 compared with the wild type, with the L419C/S and R422K variants having higher levels of resistance (>200-fold) than the rest of the variants (6.8- to 76-fold). The M423I and A486S variants remained susceptible to VX-222. The 50% effective concentration (EC50) for the L419P variant could not be obtained due to the poor replication of this replicon. The majority of the variants (15/17) were less fit than the wild type. A subset of the variants, predominately the L419S and R422K variants, were observed when the efficacy and safety of VX-222- and telaprevir-based regimens given for 12 weeks were investigated in genotype 1 HCV-infected patients in a phase 2 study. The NS3 and NS5B variants selected during the dual combination therapy showed reduced susceptibility to both telaprevir and VX-222 and had a lower replication capacity than the wild type. The phase 1b study has the ClinicalTrials.gov identifier NCT00911963, and the phase 2a study has ClinicalTrials.gov identifier NCT01080222.
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20
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Dierynck I, Thys K, Ghys A, Sullivan JC, Kieffer TL, Aerssens J, Picchio G, De Meyer S. Deep-sequencing analysis of the gene encoding the hepatitis C virus nonstructural 3-4A protease confirms a low prevalence of telaprevir-resistant variants at baseline and the end of the REALIZE study. J Infect Dis 2014; 210:1871-80. [PMID: 24943725 DOI: 10.1093/infdis/jiu340] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Population sequencing (PS) has shown that telaprevir-resistant variants are not typically detectable at baseline (prevalence, ≤5% of patients), and most variants present at the time of treatment failure are no longer detectable at the end of the study. METHODS To gain insight into the evolution of telaprevir-resistant variants, their baseline prevalence and persistence after treatment was investigated using a more sensitive, deep-sequencing (DS) technique in a large number of treatment-experienced patients from the REALIZE study who were infected with hepatitis C virus genotype 1. RESULTS Before treatment initiation, telaprevir-resistant variants (T54A, T54S, or R155K in 1%-2% of the viral population) were detected by DS in a fraction (2%) of patients for whom PS failed to detect resistance; these variants were not necessarily detected at the time of treatment failure. Of 49 patients in whom telaprevir-resistant variants were detected by PS at the time of treatment failure but not at the end of the study, DS revealed the presence of variants (V36A/L/M, T54S, or R155K in 1%-36% of the viral population) in 16 patients (33%) at the end of the study. CONCLUSIONS Similar to PS findings, DS analysis revealed that the frequency of telaprevir-resistant variants before treatment was also low, and variants detected at the time of treatment failure were no longer detectable in the majority of patients during follow-up.
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Affiliation(s)
| | - Kim Thys
- Janssen Infectious Diseases, Beerse, Belgium
| | - Anne Ghys
- Janssen Infectious Diseases, Beerse, Belgium
| | | | | | | | - Gaston Picchio
- Janssen Research and Development, Titusville, New Jersey
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Sullivan JC, De Meyer S, Bartels DJ, Dierynck I, Zhang EZ, Spanks J, Tigges AM, Ghys A, Dorrian J, Adda N, Martin EC, Beumont M, Jacobson IM, Sherman KE, Zeuzem S, Picchio G, Kieffer TL. Evolution of treatment-emergent resistant variants in telaprevir phase 3 clinical trials. Clin Infect Dis 2013; 57:221-9. [PMID: 23575197 DOI: 10.1093/cid/cit226] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Telaprevir (TVR), a hepatitis C virus (HCV) NS3/4A protease inhibitor, has been approved to treat genotype 1 HCV. To understand the clinical impact of TVR-resistant variants, we analyzed samples from patients in phase 3 clinical trials to determine the frequency and retention of TVR-resistant variants in patients who did not achieve sustained virologic response (SVR). METHODS A total of 1797 patients were treated with TVR. Resistant variants (V36A/G/I/L/M, T54A/S, I132V [subtype 1a only], R155G/K/T/M, A156F/N/S/T/V, and D168N) were identified after treatment failure and at visits thereafter, by direct (population) sequencing of the NS3/4A region. Kaplan-Meier analysis was used to determine median time to loss of these variants. RESULTS Resistant variants were observed in 77% (299/388) of patients who did not achieve SVR. Resistance occurred more commonly in subtype 1a (86%; 232/269) than subtype 1b infections (56%; 67/119). After treatment failure, 355 patients had at least 1 follow-up visit (median follow-up period: 9.6 months). Of patients with resistance at time of failure and at least 1 follow-up visit, 60% (153/254) lost resistance. Kaplan-Meier analysis, including all patients with any sequence data after treatment failure, indicated that median time to wild type was 10.6 months (95% confidence interval [CI], 9.47-12.20) in subtype 1a and 0.9 months (95% CI, 0.00-2.07) in subtype 1b infections. CONCLUSIONS After failure to achieve SVR with TVR-based treatment, resistant variants are observed in most patients. However, presumably due to the lower fitness of those variants, they tend to be replaced with wild-type virus over time.
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