1
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Deekshit VK, Jazeela K, Chakraborty G, Rohit A, Chakraborty A, Karunasagar I. Mismatch amplification mutation assay-polymerase chain reaction: A method of detecting fluoroquinolone resistance mechanism in bacterial pathogens. Indian J Med Res 2019; 149:146-150. [PMID: 31219078 PMCID: PMC6563742 DOI: 10.4103/ijmr.ijmr_2091_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The mismatch amplification assay is a modified version of polymerase chain reaction (PCR) that permits specific amplification of gene sequences with single base pair change. The basis of the technique relies on primer designing. The single nucleotide mismatch at the 3’ proximity of the reverse oligonucleotide primer makes Taq DNA polymerase unable to carry out extension process. Thus, the primers produce a PCR fragment in the wild type, whereas it is not possible to yield a product with a mutation at the site covered by the mismatch positions on the mismatch amplification mutation assay (MAMA) primer from any gene. The technique offers several advantages over other molecular methods, such as PCR-restriction fragment length polymorphism (RFLP) and oligonucleotide hybridization, which is routinely used in the detection of known point mutations. Since multiple point mutations in the quinolone resistance determining region play a major role in high-level fluoroquinolone resistance in Gram-negative bacteria, the MAMA-PCR technique is preferred for detecting these mutations over PCR-RFLP and sequencing technology.
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Affiliation(s)
- Vijaya Kumar Deekshit
- Division of Infectious Diseases, Nitte University Centre for Science Education & Research, Mangaluru, India
| | - Kadeeja Jazeela
- Division of Infectious Diseases, Nitte University Centre for Science Education & Research, Mangaluru, India
| | - Gunimala Chakraborty
- Division of Infectious Diseases, Nitte University Centre for Science Education & Research, Mangaluru, India
| | - Anusha Rohit
- Department of Microbiology, Madras Medical Mission, Chennai, India
| | - Anirban Chakraborty
- Division of Infectious Diseases, Nitte University Centre for Science Education & Research, Mangaluru, India
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2
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Shiha G, Soliman R, Elbasiony M, Darwish NHE, Mousa SA. Addition of Epigallocatechin Gallate 400 mg to Sofosbuvir 400 mg + Daclatisvir 60 mg With or Without Ribavirin in Treatment of Patients with Chronic Hepatitis C Improves the Safety Profile: A Pilot Study. Sci Rep 2019; 9:13593. [PMID: 31537880 PMCID: PMC6753069 DOI: 10.1038/s41598-019-49973-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 08/30/2019] [Indexed: 02/07/2023] Open
Abstract
Emergence of new molecules acting directly on the hepatitic C virus (HCV) has improved treatment outcomes. However, there is a risk of selecting viral escape mutants, so a new combination is needed using different inhibitors that target different steps of the HCV infectious cycle. Novel single tablet formulations were developed: Dactavira, composed of sofosbuvir (SOF) 400 mg/daclatisvir (DCV) 60 mg/epigallocatechin gallate (EGCG) 400 mg without ribavirin (RBV); and Dactavira plus, which includes RBV 800 mg. A randomized, open-label study was carried out on treatment-naïve non-cirrhotic (Group A, n = 50) and treatment-naïve cirrhotic (Group B, n = 22) patients with genotype 4 HCV infection. Group A was randomly assigned to receive a single daily fixed-dose (Dactavira, n = 25) or the standard of care [SOF 400 mg/DCV 60 mg] (n = 25) daily for 12 weeks. Group B was randomly assigned to receive a single daily fixed-dose (Dactavira plus, n = 11) or the standard of care + RBV 800 mg (n = 11) daily for 12 weeks. Patients receiving Dactavira or Dactavira plus had a significantly more rapid rate of viral load decline as compared to patients receiving the standard of care therapy. Sustained virological response for 12 weeks for Dactavira or Dactavira plus showed no statistically significant difference when compared to the standard of care. Also, they did not affect normal hemoglobin levels (p < 0.001) versus the standard of care. The incorporated EGCG interferes with the viral entry mechanisms, as reported by several investigators, and in turn enhances efficacy and prevents relapse as compared to the standard of care. Also, its antihemeolytic and antifibrotic activities may improve the safety and tolerability of the therapy.
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Affiliation(s)
- Gamal Shiha
- Internal Medicine Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt.,Egyptian Liver Research Institute and Hospital (ELRIAH), Mansoura, Egypt
| | - Reham Soliman
- Egyptian Liver Research Institute and Hospital (ELRIAH), Mansoura, Egypt.,Tropical Medicine Department, Faculty of Medicine, Port Said University, Port Said, Egypt
| | - Mohamed Elbasiony
- Internal Medicine Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt.,Egyptian Liver Research Institute and Hospital (ELRIAH), Mansoura, Egypt
| | - Noureldien H E Darwish
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt.,The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, USA
| | - Shaker A Mousa
- The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, USA. .,Virothera Pharmaceuticals, Rensselaer, NY, USA.
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3
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Shunmugam L, Soliman MES. Targeting HCV polymerase: a structural and dynamic perspective into the mechanism of selective covalent inhibition. RSC Adv 2018; 8:42210-42222. [PMID: 35558797 PMCID: PMC9092151 DOI: 10.1039/c8ra07346e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/30/2018] [Indexed: 12/16/2022] Open
Abstract
Background: Concerns have been raised over the emerging pandemic status of hepatitis C virus (HCV). Current available drugs lack specificity, stability and potency. The HCV NS5B RNA-dependent RNA polymerase (RdRp) is a vital component in viral replication and is often targeted in antiviral therapies. Recent experimental procedures have led to the discovery of a novel covalent RdRp inhibitor, compound 47, which selectively targets cysteine 366 of the HCV RdRp and exhibits promising pharmacokinetic outcomes. Selective covalent inhibition of HCV is, however, a highly neglected subject in the literature, that is reinforced by the lack of efficient structure-based drug design protocols. In this paper, an atomistic insight into a novel selective approach to inhibit HCV RdRp is provided. Methodology/Results: Covalent molecular dynamic analyses revealed the inhibitory mechanism of compound 47 on the RdRp. Inhibitor binding induced distinctive internal movements resulting in the disruption of normal physiological interdomain interactions. Conclusion: Compound 47 stimulates reorganization of key protein elements required for RNA transcription, thus hampering viral replication as well as disrupting the overall conformation of HCV. This study will open new lines of approach for the design of novel selective inhibitors against HCV as well as other viral families.
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Affiliation(s)
- Letitia Shunmugam
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4001 South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4001 South Africa
- School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4001 South Africa +27 (0) 31 260 7872 +27 (0) 31 260 8048
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4
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Alves da Silva R, de Souza Todão J, Kamitani FL, Silva AEB, de Carvalho-Filho RJ, Ferraz MLCG, de Carvalho IMVG. Molecular characterization of hepatitis C virus in end-stage renal disease patients under hemodialysis. J Med Virol 2017; 90:537-544. [PMID: 29064576 DOI: 10.1002/jmv.24976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 10/12/2017] [Indexed: 12/09/2022]
Abstract
New direct-acting antiviral (DAA) agents are in development or already approved for the treatment of chronic hepatitis C virus (HCV) infection. The effectiveness of these drugs is related to the previous existence of resistant variants. Certain clinical conditions can allow changes in immunological characteristics of the host and even modify genetic features of viral populations. The aim of this study was to perform HCV molecular characterization from samples of end-stage renal disease patients on hemodialysis (ESRD-HD). Nested PCR and Sanger sequencing were used to obtain genetic information from the NS5B partial region of a cohort composed by 86 treatment-naïve patients. Genomic sequences from the Los Alamos databank were employed for comparative analysis. Bioinformatics methodologies such as phylogenetic reconstructions, informational entropy, and mutation analysis were used to analyze datasets separated by geographical location, HCV genotype, and renal function status. ESRD-HD patients presented HCV genotypes 1a (n = 18), 1b (n = 16), 2a (n = 2), 2b (n = 2), and 3a (n = 4). Control subjects were infected with genotypes 1a (n = 11), 1b (n = 21), 2b (n = 4), and 3a (n = 8). Dataset phylogenetic reconstruction separated HCV subtype 1a into two distinct clades. The entropy analysis from the ESRD-HD group revealed two amino acid positions related to an epitope for cytotoxic T lymphocytes and T helper cells. Genotype 1a was found to be more diverse than subtype 1b. Also, genotype 1a ERSD-HD patients had a higher mean of amino acids changes in comparison to control group patients. The identification of specific mutations on epitopes and high genetic diversity within the NS5B HCV partial protein in hemodialysis patients can relate to host immunological features and geographical distribution patterns. This genetic diversity can affect directly the new DAA's resistance mechanisms.
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Affiliation(s)
- Rafael Alves da Silva
- Laboratório de Hepatologia Molecular Aplicada (LHeMA), Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil.,Instituto Butantan, Laboratório de Parasitologia, São Paulo, Brazil
| | - Jardelina de Souza Todão
- Laboratório de Hepatologia Molecular Aplicada (LHeMA), Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | | | - Antonio Eduardo Benedito Silva
- Laboratório de Hepatologia Molecular Aplicada (LHeMA), Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil.,Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | - Roberto José de Carvalho-Filho
- Laboratório de Hepatologia Molecular Aplicada (LHeMA), Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil.,Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | - Maria Lucia Cardoso Gomes Ferraz
- Laboratório de Hepatologia Molecular Aplicada (LHeMA), Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil.,Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | - Isabel Maria Vicente Guedes de Carvalho
- Laboratório de Hepatologia Molecular Aplicada (LHeMA), Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil.,Instituto Butantan, Laboratório de Parasitologia, São Paulo, Brazil
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5
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Raj VS, Hundie GB, Schürch AC, Smits SL, Pas SD, Le Pogam S, Janssen HLA, de Knegt RJ, Osterhaus ADME, Najera I, Boucher CA, Haagmans BL. Identification of HCV Resistant Variants against Direct Acting Antivirals in Plasma and Liver of Treatment Naïve Patients. Sci Rep 2017; 7:4688. [PMID: 28680115 PMCID: PMC5498547 DOI: 10.1038/s41598-017-04931-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023] Open
Abstract
Current standard-of-care treatment of chronically infected hepatitis C virus (HCV) patients involves direct-acting antivirals (DAA). However, concerns exist regarding the emergence of drug -resistant variants and subsequent treatment failure. In this study, we investigate potential natural drug-resistance mutations in the NS5B gene of HCV genotype 1b from treatment-naïve patients. Population-based sequencing and 454 deep sequencing of NS5B gene were performed on plasma and liver samples obtained from 18 treatment- naïve patients. The quasispecies distribution in plasma and liver samples showed a remarkable overlap in each patient. Although unique sequences in plasma or liver were observed, in the majority of cases the most dominant sequences were shown to be identical in both compartments. Neither in plasma nor in the liver codon changes were detected at position 282 that cause resistance to nucleos(t)ide analogues. However, in 10 patients the V321I change conferring resistance to nucleos(t)ide NS5B polymerase inhibitors and in 16 patients the C316N/Y/H non-nucleoside inhibitors were found mainly in liver samples. In conclusion, 454-deep sequencing of liver and plasma compartments in treatment naïve patients provides insight into viral quasispecies and the pre-existence of some drug-resistant variants in the liver, which are not necessarily present in plasma.
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Affiliation(s)
- V Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Anita C Schürch
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Saskia L Smits
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.,Viroclinics Biosciences BV, Rotterdam, The Netherlands
| | - Suzan D Pas
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sophie Le Pogam
- Virology Discovery, Pharma Research Early Development Hoffmann La Roche, Nutley, NJ, USA
| | - Harry L A Janssen
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands.,Division of Gastroenterology, University Health Network, Toronto, Canada
| | - Rob J de Knegt
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert D M E Osterhaus
- Artemis One health, Utrecht, The Netherlands.,Center for Infection Medicine and Zoonoses Research, University of Veterinary Medicine, Hannover, Germany
| | - Isabel Najera
- Virology Discovery, Pharma Research Early Development Hoffmann La Roche, Nutley, NJ, USA
| | - Charles A Boucher
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
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6
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Elberry MH, Darwish NHE, Mousa SA. Hepatitis C virus management: potential impact of nanotechnology. Virol J 2017; 14:88. [PMID: 28464951 PMCID: PMC5414367 DOI: 10.1186/s12985-017-0753-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/19/2017] [Indexed: 12/21/2022] Open
Abstract
Around 170–200 million individuals have hepatitis C virus (HCV), which represents ~ 3% of the world population, including ~ 3–5 million people in the USA. According to the WHO regional office in the Middle East, Egypt has the highest prevalence in the world, with 7% prevalence in adults. There had been no effective vaccine for HCV; a combination of PEG-Interferon and ribavirin for at least 48 weeks was the standard therapy, but it failed in more than 40% of the patients and has a high cost and serious side effects. The recent introduction of direct-acting antivirals (DAA) resulted in major advances toward the cure of HCV. However, relapse and reduced antiviral efficacy in fibrotic, cirrhotic HCV patients in addition to some undesired effects restrain the full potential of these combinations. There is a need for new approaches for the combinations of different DAA and their targeted delivery using novel nanotechnology approaches. In this review, the role of nanoparticles as a carrier for HCV vaccines, anti-HCV combinations, and their targeted delivery are discussed.
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Affiliation(s)
- Mostafa H Elberry
- The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, 12144, USA.,National Cancer Institute, Cairo University, Cairo, Egypt
| | - Noureldien H E Darwish
- The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, 12144, USA.,Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Shaker A Mousa
- The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, 12144, USA.
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7
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Chen Q, Belmonte I, Buti M, Nieto L, Garcia-Cehic D, Gregori J, Perales C, Ordeig L, Llorens M, Soria ME, Esteban R, Esteban JI, Rodriguez-Frias F, Quer J. New real-time-PCR method to identify single point mutations in hepatitis C virus. World J Gastroenterol 2016; 22:9604-9612. [PMID: 27920481 PMCID: PMC5116604 DOI: 10.3748/wjg.v22.i43.9604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/25/2016] [Accepted: 10/10/2016] [Indexed: 02/07/2023] Open
Abstract
AIM To develop a fast, low-cost diagnostic strategy to identify single point mutations in highly variable genomes such as hepatitis C virus (HCV).
METHODS In patients with HCV infection, resistance-associated amino acid substitutions within the viral quasispecies prior to therapy can confer decreased susceptibility to direct-acting antiviral agents and lead to treatment failure and virological relapse. One such naturally occurring mutation is the Q80K substitution in the HCV-NS3 protease gene, which confers resistance to PI inhibitors, particularly simeprevir. Low-cost, highly sensitive techniques enabling routine detection of these single point mutations would be useful to identify patients at a risk of treatment failure. LightCycler methods, based on real-time PCR with sequence-specific probe hybridization, have been implemented in most diagnostic laboratories. However, this technique cannot identify single point mutations in highly variable genetic environments, such as the HCV genome. To circumvent this problem, we developed a new method to homogenize all nucleotides present in a region except the point mutation of interest.
RESULTS Using nucleotide-specific probes Q, K, and R substitutions at position 80 were clearly identified at a sensitivity of 10% (mutations present at a frequency of at least 10% were detected). The technique was successfully applied to identify the Q80K substitution in 240 HCV G1 serum samples, with performance comparable to that of direct Sanger sequencing, the current standard procedure for this purpose. The new method was then validated in a Catalonian population of 202 HCV G1-infected individuals. Q80K was detected in 14.6% of G1a patients and 0% of G1b in our setting.
CONCLUSION A fast, low-cost diagnostic strategy based on real-time PCR and fluorescence resonance energy transfer probe melting curve analysis has been successfully developed to identify single point mutations in highly variable genomes such as hepatitis C virus. This technique can be adapted to detect any single point mutation in highly variable genomes.
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8
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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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9
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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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10
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Fevery B, Thys K, Van Eygen V, Verbinnen T, Van Rossem E, Buelens A, Aerssens J, Witek J, Picchio G, De Meyer S, Lenz O. Pre-existence and Persistence of Resistant Minority Hepatitis C Virus Variants in Genotype 1-Infected Patients Treated With Simeprevir/Peginterferon/Ribavirin. Open Forum Infect Dis 2016; 3:ofw052. [PMID: 27186579 PMCID: PMC4866569 DOI: 10.1093/ofid/ofw052] [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: 12/24/2015] [Accepted: 03/04/2016] [Indexed: 01/27/2023] Open
Abstract
Deep sequencing analyses in HCV genotype 1-infected patients treated with simeprevir/peginterferon/ribavirin showed that pre-existing minority HCV variants did not impact treatment outcome and emerging resistant variants in patients failing treatment were not persisting at minority levels Background. The pre-existence of minority hepatitis C virus (HCV) variants and their impact on treatment outcome, as well as the persistence of emerging resistant variants posttreatment in patients failing treatment with simeprevir/peginterferon/ribavirin (SMV/PR), were assessed by deep sequencing (DS). Methods. Population sequencing (PS) and Illumina DS were performed on HCV genotype 1 isolates from patients treated with SMV/PR in Phase 2b (PILLAR [NCT00882908] and ASPIRE [NCT00980330]) and Phase 3 (QUEST-1 [NCT01289782], QUEST-2 [NCT01290679], and PROMISE [NCT01281839]) trials. Results. Minority polymorphisms (ie, detected pretreatment by DS only) reducing SMV activity in vitro were uncommon (3.6%, 19 of 534 patients). These SMV-resistant minority polymorphisms were detected in similar proportions of patients achieving (3.7%) and not achieving (3.3%) sustained virologic response with SMV/PR and generally did not emerge as major variants at time of failure. SMV-resistant variants emerging at time of failure were no longer detected at end of study in 69.3% and 52.0% of the patients by PS and DS, respectively. Conclusions. Minority polymorphisms did not impact outcome of SMV/PR treatment. The majority of emerging variants that became undetectable at end of study by PS were also undetectable by DS. These results suggest no added value of DS for clinical usage of SMV.
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Affiliation(s)
| | - Kim Thys
- Janssen Discovery Sciences, Beerse , Belgium
| | | | | | | | | | | | - James Witek
- Janssen Research & Development , LLC , Titusville, New Jersey
| | - Gaston Picchio
- Janssen Research & Development , LLC , Titusville, New Jersey
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11
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Mohamed S, Bourliere M, Benali S, Oules V, Castellani P, Khiri H, Camus C, Penaranda G, Chiche L, Gonzalez D, Sayada C, Olive D, Halfon P. Clinical relevance of the HCV protease inhibitor-resistant mutant viral load assessed by ultra-deep pyrosequencing in treatment failure. J Clin Virol 2016; 78:36-43. [PMID: 26971166 DOI: 10.1016/j.jcv.2016.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 01/19/2023]
Abstract
BACKGROUND The detection of low frequency mutants in patients with hepatitis C virus (HCV) receiving direct-acting antivirals (DAAs) is still debated. The clinical relevance of the mutant viral load has not yet been evaluated. OBJECTIVES To assess the viral load of resistance associated variants (RAVs) in patients at different time points, including the baseline, virological failure and one year after the cessation of therapy. STUDY DESIGN The study included 22 patients who were previously treated with protease inhibitors (PI) (with telaprevir and boceprevir). For each patient, three time points were assessed using ultra-deep pyrosequencing (UDPS). RESULTS Baseline mutations were observed in 14/22 patients (64%). At virological failure, RAVs were detected in 18/22 patients (82%). Persistent RAVs were observed in four HCV GT 1a patients (18%). Persistence mutations were found only in HCV GT 1a patients. The baseline relative V36M, R155K, R155T and A156T mutation load of patients with persistent RAVs was significantly higher (P<0.001) than those of patients without persistent RAVs. CONCLUSION The UDPS follow-up analysis demonstrated that the presence of BOC or TLP-RAVs persist one year after therapy cessation only in HCV GT 1a patients. The relative mutant viral load should be considered prior to any PI based re-treatment. This concept of the baseline mutation viral load must be validated using current therapy and must be validated on a larger cohort.
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Affiliation(s)
- Sofiane Mohamed
- Laboratoire Alphabio, Marseille, France; CRCM, Immunity and Cancer, Inserm, U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM 105; CNRS, UMR7258, F-13009 Marseille, France
| | - Marc Bourliere
- Département d'hépato-gastroenterologie, Hôpital Saint Joseph, Marseille, France
| | - Souad Benali
- Département d'hépato-gastroenterologie, Hôpital Saint Joseph, Marseille, France
| | - Valerie Oules
- Département d'hépato-gastroenterologie, Hôpital Saint Joseph, Marseille, France
| | - Paul Castellani
- Département d'hépato-gastroenterologie, Hôpital Saint Joseph, Marseille, France
| | | | | | | | | | | | - Chalom Sayada
- Advanced Biological Laboratories (ABL), Luxembourg, Luxembourg
| | - Daniel Olive
- CRCM, Immunity and Cancer, Inserm, U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM 105; CNRS, UMR7258, F-13009 Marseille, France
| | - Philippe Halfon
- Laboratoire Alphabio, Marseille, France; Hôpital Européen, Marseille, France.
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12
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Practices of Sequencing Quality Assurance. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Gonçalves Rossi LM, Escobar-Gutierrez A, Rahal P. Multiregion deep sequencing of hepatitis C virus: An improved approach for genetic relatedness studies. INFECTION GENETICS AND EVOLUTION 2015; 38:138-145. [PMID: 26733442 DOI: 10.1016/j.meegid.2015.12.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 12/23/2015] [Accepted: 12/24/2015] [Indexed: 12/19/2022]
Abstract
Hepatitis C virus (HCV) is a major public health problem that affects more than 180 million people worldwide. Identification of HCV transmission networks is of critical importance for disease control. HCV related cases are often difficult to identify due to the characteristic long incubation period and lack of symptoms during the acute phase of the disease, making it challenging to link related cases to a common source of infection. Additionally, HCV transmission chains are difficult to trace back since viral variants from epidemiologically linked cases are genetically related but rarely identical. Genetic relatedness studies primarily rely on information obtained from the rapidly evolving HCV hypervariable region 1 (HVR1). However, in some instances, the rapid divergence of this region can lead to loss of genetic links between related isolates, which represents an important challenge for outbreak investigations and genetic relatedness studies. Sequencing of multiple and longer sub-genomic regions has been proposed as an alternative to overcome the limitations imposed by the rapid molecular evolution of the HCV HVR1. Additionally, conventional molecular approaches required to characterize the HCV intra-host genetic variation are laborious, time-consuming, and expensive while providing limited information about the composition of the viral population. Next generation sequencing (NGS) approaches enormously facilitate the characterization of the HCV intra-host population by detecting rare variants at much lower frequencies. Thus, NGS approaches using multiple sub-genomic regions should improve the characterization of the HCV intra-host population. Here, we explore the usefulness of multiregion sequencing using a NGS platform for genetic relatedness studies among HCV cases.
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Affiliation(s)
- Livia Maria Gonçalves Rossi
- Department of Biology, Institute of Bioscience, Language and Exact Science, São Paulo State University, São José do Rio Preto, Sao Paulo, Brazil; Instituto de Diagnóstico y Referencia Epidemiológicos, Mexico City, Mexico.
| | | | - Paula Rahal
- Department of Biology, Institute of Bioscience, Language and Exact Science, São Paulo State University, São José do Rio Preto, Sao Paulo, Brazil
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14
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Fourati S, Pawlotsky JM. Virologic Tools for HCV Drug Resistance Testing. Viruses 2015; 7:6346-59. [PMID: 26690198 PMCID: PMC4690865 DOI: 10.3390/v7122941] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/28/2015] [Accepted: 11/30/2015] [Indexed: 12/22/2022] Open
Abstract
Recent advances in molecular biology have led to the development of new antiviral drugs that target specific steps of the Hepatitis C Virus (HCV) lifecycle. These drugs, collectively termed direct-acting antivirals (DAAs), include non-structural (NS) HCV protein inhibitors, NS3/4A protease inhibitors, NS5B RNA-dependent RNA polymerase inhibitors (nucleotide analogues and non-nucleoside inhibitors), and NS5A inhibitors. Due to the high genetic variability of HCV, the outcome of DAA-based therapies may be altered by the selection of amino-acid substitutions located within the targeted proteins, which affect viral susceptibility to the administered compounds. At the drug developmental stage, preclinical and clinical characterization of HCV resistance to new drugs in development is mandatory. In the clinical setting, accurate diagnostic tools have become available to monitor drug resistance in patients who receive treatment with DAAs. In this review, we describe tools available to investigate drug resistance in preclinical studies, clinical trials and clinical practice.
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Affiliation(s)
- Slim Fourati
- National Reference Center for Viral Hepatitis B, C, and D; Department of Virology, Hôpital Henri Mondor, Université Paris-Est and INSERM U955, Créteil 94010, France.
| | - Jean-Michel Pawlotsky
- National Reference Center for Viral Hepatitis B, C, and D; Department of Virology, Hôpital Henri Mondor, Université Paris-Est and INSERM U955, Créteil 94010, France.
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15
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Echeverría N, Moratorio G, Cristina J, Moreno P. Hepatitis C virus genetic variability and evolution. World J Hepatol 2015; 7:831-845. [PMID: 25937861 PMCID: PMC4411526 DOI: 10.4254/wjh.v7.i6.831] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/22/2014] [Accepted: 02/11/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) has infected over 170 million people worldwide and creates a huge disease burden due to chronic, progressive liver disease. HCV is a single-stranded, positive sense, RNA virus, member of the Flaviviridae family. The high error rate of RNA-dependent RNA polymerase and the pressure exerted by the host immune system, has driven the evolution of HCV into 7 different genotypes and more than 67 subtypes. HCV evolves by means of different mechanisms of genetic variation. On the one hand, its high mutation rates generate the production of a large number of different but closely related viral variants during infection, usually referred to as a quasispecies. The great quasispecies variability of HCV has also therapeutic implications since the continuous generation and selection of resistant or fitter variants within the quasispecies spectrum might allow viruses to escape control by antiviral drugs. On the other hand HCV exploits recombination to ensure its survival. This enormous viral diversity together with some host factors has made it difficult to control viral dispersal. Current treatment options involve pegylated interferon-α and ribavirin as dual therapy or in combination with a direct-acting antiviral drug, depending on the country. Despite all the efforts put into antiviral therapy studies, eradication of the virus or the development of a preventive vaccine has been unsuccessful so far. This review focuses on current available data reported to date on the genetic mechanisms driving the molecular evolution of HCV populations and its relation with the antiviral therapies designed to control HCV infection.
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16
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Rossi LMG, Escobar-Gutierrez A, Rahal P. Advanced molecular surveillance of hepatitis C virus. Viruses 2015; 7:1153-88. [PMID: 25781918 PMCID: PMC4379565 DOI: 10.3390/v7031153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/05/2015] [Accepted: 02/20/2015] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) infection is an important public health problem worldwide. HCV exploits complex molecular mechanisms, which result in a high degree of intrahost genetic heterogeneity. This high degree of variability represents a challenge for the accurate establishment of genetic relatedness between cases and complicates the identification of sources of infection. Tracking HCV infections is crucial for the elucidation of routes of transmission in a variety of settings. Therefore, implementation of HCV advanced molecular surveillance (AMS) is essential for disease control. Accounting for virulence is also important for HCV AMS and both viral and host factors contribute to the disease outcome. Therefore, HCV AMS requires the incorporation of host factors as an integral component of the algorithms used to monitor disease occurrence. Importantly, implementation of comprehensive global databases and data mining are also needed for the proper study of the mechanisms responsible for HCV transmission. Here, we review molecular aspects associated with HCV transmission, as well as the most recent technological advances used for virus and host characterization. Additionally, the cornerstone discoveries that have defined the pathway for viral characterization are presented and the importance of implementing advanced HCV molecular surveillance is highlighted.
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Affiliation(s)
- Livia Maria Gonçalves Rossi
- Department of Biology, Institute of Bioscience, Language and Exact Science, Sao Paulo State University, Sao Jose do Rio Preto, SP 15054-000, Brazil.
| | | | - Paula Rahal
- Department of Biology, Institute of Bioscience, Language and Exact Science, Sao Paulo State University, Sao Jose do Rio Preto, SP 15054-000, Brazil.
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17
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Preciado MV, Valva P, Escobar-Gutierrez A, Rahal P, Ruiz-Tovar K, Yamasaki L, Vazquez-Chacon C, Martinez-Guarneros A, Carpio-Pedroza JC, Fonseca-Coronado S, Cruz-Rivera M. Hepatitis C virus molecular evolution: Transmission, disease progression and antiviral therapy. World J Gastroenterol 2014; 20:15992-16013. [PMID: 25473152 PMCID: PMC4239486 DOI: 10.3748/wjg.v20.i43.15992] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/22/2014] [Accepted: 08/28/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) infection represents an important public health problem worldwide. Reduction of HCV morbidity and mortality is a current challenge owned to several viral and host factors. Virus molecular evolution plays an important role in HCV transmission, disease progression and therapy outcome. The high degree of genetic heterogeneity characteristic of HCV is a key element for the rapid adaptation of the intrahost viral population to different selection pressures (e.g., host immune responses and antiviral therapy). HCV molecular evolution is shaped by different mechanisms including a high mutation rate, genetic bottlenecks, genetic drift, recombination, temporal variations and compartmentalization. These evolutionary processes constantly rearrange the composition of the HCV intrahost population in a staging manner. Remarkable advances in the understanding of the molecular mechanism controlling HCV replication have facilitated the development of a plethora of direct-acting antiviral agents against HCV. As a result, superior sustained viral responses have been attained. The rapidly evolving field of anti-HCV therapy is expected to broad its landscape even further with newer, more potent antivirals, bringing us one step closer to the interferon-free era.
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18
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ur Rehman I, Vaughan G, Purdy MA, Xia GL, Forbi JC, Rossi LMG, Butt S, Idrees M, Khudyakov YE. Genetic history of hepatitis C virus in Pakistan. INFECTION GENETICS AND EVOLUTION 2014; 27:318-24. [PMID: 25131452 DOI: 10.1016/j.meegid.2014.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/26/2014] [Accepted: 08/05/2014] [Indexed: 12/13/2022]
Abstract
Hepatitis C virus (HCV) genotype 3a accounts for ∼80% of HCV infections in Pakistan, where ∼10 million people are HCV-infected. Here, we report analysis of the genetic heterogeneity of HCV NS3 and NS5b subgenomic regions from genotype 3a variants obtained from Pakistan. Phylogenetic analyses showed that Pakistani genotype 3a variants were as genetically diverse as global variants, with extensive intermixing. Bayesian estimates showed that the most recent ancestor for genotype 3a in Pakistan was last extant in ∼1896-1914 C.E. (range: 1851-1932). This genotype experienced a population expansion starting from ∼1905 to ∼1970 after which the effective population leveled. Death/birth models suggest that HCV 3a has reached saturating diversity with decreasing turnover rate and positive extinction. Taken together, these observations are consistent with a long and complex history of HCV 3a infection in Pakistan.
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Affiliation(s)
- Irshad ur Rehman
- National Centre of Excellence in Molecular Biology, Division of Molecular Virology and Molecular Diagnostics, University of the Punjab, Genome Center for Molecular Diagnosis & Research, Lahore, Pakistan
| | - Gilberto Vaughan
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Michael A Purdy
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Guo-liang Xia
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joseph C Forbi
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Livia Maria Gonçalves Rossi
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA; Department of Biology, Institute of Bioscience, Language and Exact Science, São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Sadia Butt
- National Centre of Excellence in Molecular Biology, Division of Molecular Virology and Molecular Diagnostics, University of the Punjab, Genome Center for Molecular Diagnosis & Research, Lahore, Pakistan
| | - Muhammad Idrees
- National Centre of Excellence in Molecular Biology, Division of Molecular Virology and Molecular Diagnostics, University of the Punjab, Genome Center for Molecular Diagnosis & Research, Lahore, Pakistan
| | - Yury E Khudyakov
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA
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19
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Applegate TL, Gaudieri S, Plauzolles A, Chopra A, Grebely J, Lucas M, Hellard M, Luciani F, Dore GJ, Matthews GV. Naturally occurring dominant drug resistance mutations occur infrequently in the setting of recently acquired hepatitis C. Antivir Ther 2014; 20:199-208. [PMID: 25105742 DOI: 10.3851/imp2821] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Direct-acting antivirals (DAAs) are predicted to transform hepatitis C therapy, yet little is known about the prevalence of naturally occurring resistance mutations in recently acquired HCV. This study aimed to determine the prevalence and frequency of drug resistance mutations in the viral quasispecies among HIV-positive and -negative individuals with recent HCV. METHODS The NS3 protease, NS5A and NS5B polymerase genes were amplified from 50 genotype 1a participants of the Australian Trial in Acute Hepatitis C. Amino acid variations at sites known to be associated with possible drug resistance were analysed by ultra-deep pyrosequencing. RESULTS A total of 12% of individuals harboured dominant resistance mutations, while 36% demonstrated non-dominant resistant variants below that detectable by bulk sequencing (that is, <20%) but above a threshold of 1%. Resistance variants (<1%) were observed at most sites associated with DAA resistance from all classes, with the exception of sofosbuvir. CONCLUSIONS Dominant resistant mutations were uncommonly observed in the setting of recent HCV. However, low-level mutations to all DAA classes were observed by deep sequencing at the majority of sites and in most individuals. The significance of these variants and impact on future treatment options remains to be determined. Clinicaltrials.gov NCT00192569.
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20
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de Carvalho IMVG, Alves R, de Souza PAVM, da Silva EF, Mazo D, Carrilho FJ, Queiroz ATL, Pessoa MG. Protease inhibitor resistance mutations in untreated Brazilian patients infected with HCV: novel insights about targeted genotyping approaches. J Med Virol 2014; 86:1714-21. [PMID: 25042789 DOI: 10.1002/jmv.24015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2014] [Indexed: 12/11/2022]
Abstract
Several new direct-acting antiviral (DAA) drugs are being developed or are already approved for the treatment of chronic hepatitis C virus (HCV) infection. HCV variants presenting drug-resistant phenotypes were observed both in vitro and during clinical trials. The aim of this study was to characterize amino acid changes at positions previously associated with resistance in the NS3 protease in untreated Brazilian patients infected with HCV genotypes 1a and 1b. Plasma samples from 171 untreated Brazilian patients infected with HCV were obtained from the Department of Gastroenterology of Clinics Hospital (HCFMUSP) in São Paulo, Brazil. Nested PCR and Sanger sequencing were used to obtain genetic information on the NS3 protein. Bioinformatics was used to confirm subtype information and analyze frequencies of resistance mutations. The results from the genotype analysis using non-NS3 targeted methods were at variance with those obtained from the NS3 protease phylogenetic analyses. It was found that 7.4% of patients infected with HCV genotype 1a showed the resistance-associated mutations V36L, T54S, Q80K, and R155K, while 5.1% of patients infected with HCV genotype 1b had the resistance-associated mutations V36L, Q41R, T54S, and D168S. Notably, codons at positions 80 and 155 differed between samples from Brazilian patient used in this study and global isolates. The present study demonstrates that genotyping methods targeting the NS3 protein showed a difference of results when compared to mainstream methodologies (INNO-LiPA and polymerase sequencing). The resistance mutations present in untreated patients infected with HCV and codon composition bias by geographical location warrant closer examination.
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Affiliation(s)
- Isabel M V G de Carvalho
- Viral Imunology, Butantan Institute, Avenida Doutor Vital Brasil, São Paulo, Brazil; Applied Molecular Hepatology Laboratory (LHeMA), Hepatitis Sector, Gastroenterology Division, São Paulo Federal University, São Paulo, Brazil
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21
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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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22
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Gonçalves Rossi LM, Rahal P. Challenges in molecular epidemiology of hepatitis C virus. J Clin Virol 2014; 60:174-6. [DOI: 10.1016/j.jcv.2014.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 03/18/2014] [Accepted: 03/21/2014] [Indexed: 02/07/2023]
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Li S, Duan X, Li Y, Liu B, McGilvray I, Chen L. MicroRNA-130a inhibits HCV replication by restoring the innate immune response. J Viral Hepat 2014; 21:121-8. [PMID: 24383925 DOI: 10.1111/jvh.12131] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/01/2013] [Indexed: 12/15/2022]
Abstract
Hepatitis C virus (HCV) infection is a major cause of chronic hepatitis and hepatocellular carcinoma. Currently pegylated interferon (IFN) combined with ribavirin remains the best therapeutic approach, although patients infected with HCV genotype I may benefit from adding protease inhibitors as 'triple therapy'. MicroRNAs (miRNAs) are endogenous small noncoding RNAs that regulate gene expression and have recently been shown to play an important role in human innate immune response and as an antiviral in chimpanzees. We studied the effect of miR-130a on the HCV replication. We found that miR-130a significantly inhibits HCV replication in both HCV replicon and J6-/JFH1-infected cells. Over expression of miR-130a upregulated the expression of type I IFN (IFN-α/IFN -β), ISG15, USP18 and MxA, which are involved in innate immune response and decreased expression of miR-122, a well-defined miRNA promoting HCV production. In conclusion, miR-130a inhibits HCV replication/production by restoring host innate immune responses and/or downregulating pro-HCV miR-122. miR-130a might be a potential drug target by modulating host innate immune responses to combat HCV infection.
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Affiliation(s)
- S Li
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
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24
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Ninomiya M, Ueno Y, Shimosegawa T. Application of deep sequence technology in hepatology. Hepatol Res 2014; 44:141-8. [PMID: 23905712 DOI: 10.1111/hepr.12214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 07/02/2013] [Accepted: 07/25/2013] [Indexed: 02/08/2023]
Abstract
Deep sequencing technologies are currently cutting edge, and are opening fascinating opportunities in biomedicine, producing over 100-times more data compared to the conventional capillary sequencers based on the Sanger method. Next-generation sequencing (NGS) is now generally defined as the sequencing technology that, by employing parallel sequencing processes, producing thousands or millions of sequence reads simultaneously. Since the GS20 was released as the first NGS sequencer on the market by 454 Life Sciences, the competition in the development of the new sequencers has become intense. In this review, we describe the current deep sequencing systems and discuss the application of advanced technologies in the field of hepatology.
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Affiliation(s)
- Masashi Ninomiya
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai
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PCR-based in vitro synthesis of hepatitis C virus NS3 protease for rapid phenotypic resistance testing of protease inhibitors. J Clin Microbiol 2014; 52:1139-45. [PMID: 24452171 DOI: 10.1128/jcm.03257-13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Protease inhibitors (PIs) targeting the hepatitis C virus (HCV) NS3 protease, such as telaprevir, have significantly improved the sustained virologic response (SVR) rates of HCV genotype 1 antiviral therapy. Given the expanding antiviral therapy regimen, fast HCV PI resistance assays are urgently needed. In this view, we have developed a novel phenotypic resistance test for HCV PIs based on in vitro synthesis of patient-derived HCV NS3 protease and subsequent enzymatic testing in a fluorescent readout. The enzymatically active HCV NS3 proteases were synthesized from PCR-derived templates by an Escherichia coli S30 extract system. Tests of the protease genes with known mutations for telaprevir resistance showed that the phenotypic resistance test was fast, with a total turnaround time of <10 h, and was fully in agreement with the previous resistance results. The initial tests with 38 treatment-naive serum samples showed that the method was significantly less laborious and faster than currently available phenotypic resistance assays of HCV NS3 PIs.
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Escobar-Gutiérrez A, Soudeyns H, Larouche A, Carpio-Pedroza JC, Martinez-Guarneros A, Vazquez-Chacon CA, Fonseca-Coronado S, Yamasaki LHT, Ruiz-Tovar K, Cruz-Rivera M. Vertical transmission of hepatitis C virus: a tale of multiple outcomes. INFECTION GENETICS AND EVOLUTION 2013; 20:465-70. [PMID: 24140559 DOI: 10.1016/j.meegid.2013.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 10/06/2013] [Accepted: 10/08/2013] [Indexed: 12/15/2022]
Abstract
Globally, hepatitis C virus (HCV) infection affects approximately 130 million people and 3 million new infections occur annually. HCV is also recognized as an important cause of chronic liver disease in children. The absence of proofreading properties of the HCV RNA polymerase leads to a highly error prone replication process, allowing HCV to escape host immune response. The adaptive nature of HCV evolution dictates the outcome of the disease in many ways. Here, we investigated the molecular evolution of HCV in three unrelated children who acquired chronic HCV infection as a result of mother-to-child transmission, two of whom were also coinfected with HIV-1. The persistence of discrete HCV variants and their population structure were assessed using median joining network and Bayesian approaches. While patterns of viral evolution clearly differed between subjects, immune system dysfunction related to HIV coinfection or persistent HCV seronegativity stand as potential mechanisms to explain the lack of molecular evolution observed in these three cases. In contrast, treatment of HCV infection with PegIFN, which did not lead to sustained virologic responses in all 3 cases, was not associated with commensurate variations in the complexity of the variant spectrum. Finally, the differences in the degree of divergence suggest that the mode of transmission of the virus was not the main factor driving viral evolution.
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Franco S, Casadellà M, Noguera-Julian M, Clotet B, Tural C, Paredes R, Martinez MA. No detection of the NS5B S282T mutation in treatment-naïve genotype 1 HCV/HIV-1 coinfected patients using deep sequencing. J Clin Virol 2013; 58:726-9. [PMID: 24140031 DOI: 10.1016/j.jcv.2013.09.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 09/03/2013] [Accepted: 09/24/2013] [Indexed: 12/17/2022]
Abstract
BACKGROUND The S282T mutation is the main variant described associated with resistance to nucleos(t)ide analogues hepatitis C virus (HCV) NS5B polymerase inhibitors. OBJECTIVE We aimed here to investigate whether this substitution pre-existed in treatment naive HCV/HIV-1 coinfected patients. STUDY DESIGN NS5B polymerase deep sequencing was performed at a median coverage per base of 4471 in 16 patient samples. RESULTS No S282T variant was detected in the 16 analyzed samples. CONCLUSION This finding is in agreement with the high genetic barrier of nucleoside analogues NS5B polymerase inhibitors and the clinical efficacy of these compounds.
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Affiliation(s)
- Sandra Franco
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
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Capobianchi MR, Giombini E, Rozera G. Next-generation sequencing technology in clinical virology. Clin Microbiol Infect 2013; 19:15-22. [PMID: 23279287 DOI: 10.1111/1469-0691.12056] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/17/2012] [Accepted: 09/22/2012] [Indexed: 12/18/2022]
Abstract
Recent advances in nucleic acid sequencing technologies, referred to as 'next-generation' sequencing (NGS), have produced a true revolution and opened new perspectives for research and diagnostic applications, owing to the high speed and throughput of data generation. So far, NGS has been applied to metagenomics-based strategies for the discovery of novel viruses and the characterization of viral communities. Additional applications include whole viral genome sequencing, detection of viral genome variability, and the study of viral dynamics. These applications are particularly suitable for viruses such as human immunodeficiency virus, hepatitis B virus, and hepatitis C virus, whose error-prone replication machinery, combined with the high replication rate, results, in each infected individual, in the formation of many genetically related viral variants referred to as quasi-species. The viral quasi-species, in turn, represents the substrate for the selective pressure exerted by the immune system or by antiviral drugs. With traditional approaches, it is difficult to detect and quantify minority genomes present in viral quasi-species that, in fact, may have biological and clinical relevance. NGS provides, for each patient, a dataset of clonal sequences that is some order of magnitude higher than those obtained with conventional approaches. Hence, NGS is an extremely powerful tool with which to investigate previously inaccessible aspects of viral dynamics, such as the contribution of different viral reservoirs to replicating virus in the course of the natural history of the infection, co-receptor usage in minority viral populations harboured by different cell lineages, the dynamics of development of drug resistance, and the re-emergence of hidden genomes after treatment interruptions. The diagnostic application of NGS is just around the corner.
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Affiliation(s)
- M R Capobianchi
- National Institute for Infectious Diseases 'L. Spallanzani', Rome, Italy.
| | - E Giombini
- National Institute for Infectious Diseases 'L. Spallanzani', Rome, Italy
| | - G Rozera
- National Institute for Infectious Diseases 'L. Spallanzani', Rome, Italy
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Molecular epidemiology of viral diseases in the era of next generation sequencing. J Clin Virol 2013; 57:378-80. [PMID: 23726419 DOI: 10.1016/j.jcv.2013.04.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 12/17/2022]
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Ultradeep pyrosequencing of hepatitis C virus hypervariable region 1 in quasispecies analysis. BIOMED RESEARCH INTERNATIONAL 2013; 2013:626083. [PMID: 23710455 PMCID: PMC3655449 DOI: 10.1155/2013/626083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 02/12/2013] [Indexed: 12/17/2022]
Abstract
Genetic variability of hepatitis C virus (HCV) determines pathogenesis of infection, including viral persistence and resistance to treatment. The aim of the present study was to characterize HCV genetic heterogeneity within a hypervariable region 1 (HVR1) of a chronically infected patient by ultradeep 454 sequencing strategy. Three independent sequencing error correction methods were applied. First correction method (Method I) implemented cut-off for genetic variants present in less than 1%. In the second method (Method II), a condition to call a variant was bidirectional coverage of sequencing reads. Third method (Method III) used Short Read Assembly into Haplotypes (ShoRAH) program. After the application of these three different algorithms, HVR1 population consisted of 8, 40, and 186 genetic haplotypes. The most sensitive method was ShoRAH, allowing to reconstruct haplotypes constituting as little as 0.013% of the population. The most abundant genetic variant constituted only 10.5%. Seventeen haplotypes were present in a frequency above 1%, and there was wide dispersion of the population into very sparse haplotypes. Our results indicate that HCV HVR1 heterogeneity and quasispecies population structure may be reconstructed by ultradeep sequencing. However, credible analysis requires proper reconstruction methods, which would distinguish sequencing error from real variability in vivo.
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Multicenter quality control of hepatitis C virus protease inhibitor resistance genotyping. J Clin Microbiol 2013; 51:1428-33. [PMID: 23426922 DOI: 10.1128/jcm.03032-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hepatitis C virus (HCV) protease inhibitor resistance-associated substitutions are selected during triple-therapy breakthrough. This multicenter quality control study evaluated the expertise of 23 French laboratories in HCV protease inhibitor resistance genotyping. A panel of 12 well-defined blinded samples comprising two wild-type HCV strains, nine transcripts from synthetic NS3 mutant samples or from clinical strains, and one HCV RNA-negative sample was provided to the participating laboratories. The results showed that any laboratory with expertise in sequencing techniques should be able to provide reliable HCV protease inhibitor resistance genotyping. Only a 0.7% error rate was reported for the amino acid sites studied. The accuracy of substitution identification ranged from 75% to 100%, depending on the laboratory. Incorrect results were mainly related to the methodology used. The results could be improved by changing the primers and modifying the process in order to avoid cross-contamination. This study underlines the value of quality control programs for viral resistance genotyping, which is required prior to launching observational collaborative multicenter studies on HCV resistance to direct-acting antiviral agents.
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Cento V, Landonio S, De Luca F, Di Maio VC, Micheli V, Mirabelli C, Niero F, Magni C, Rizzardini G, Perno CF, Ceccherini-Silberstein F. A boceprevir failure in a patient infected with HCV genotype 1g: importance and limitations of virus genotyping prior to HCV protease-inhibitor-based therapy. Antivir Ther 2013; 18:645-8. [PMID: 23411358 DOI: 10.3851/imp2529] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2012] [Indexed: 01/12/2023]
Abstract
A patient classified as HCV-1a-positive by both LiPA Siemens 2.0 and Abbott RealTime HCV Genotype II was instead found to be infected with HCV-1g, as determined by phylogenetic analysis of NS3 sequences. HCV-1g NS3 sequences available to date naturally harbour the resistance substitution T54S, plus P131S and L135F changes, located in the highly conserved NS3 positions within the boceprevir-binding site, as determined by structural modelling. HCV-1g NS3 sequences show some similarities to HCV-4 and are poorly responsive to interferon/ribavirin and to boceprevir/telaprevir; this patient was also a null-responder to boceprevir treatment. Baseline genotypic resistance testing may provide crucial information for the management of first-generation protease-inhibitor-based regimens, including both HCV genotype/subtype and natural resistance.
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Affiliation(s)
- Valeria Cento
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
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Dynamics of resistance mutations to NS3 protease inhibitors in a cohort of Brazilian patients chronically infected with hepatitis C virus (genotype 1) treated with pegylated interferon and ribavirin: a prospective longitudinal study. Virol J 2013; 10:57. [PMID: 23409973 PMCID: PMC3599441 DOI: 10.1186/1743-422x-10-57] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 02/11/2013] [Indexed: 01/24/2023] Open
Abstract
Abstract About sixty thousand new cases of Hepatitis C virus (HCV) infection are recorded in Brazil each year. These cases are currently treated with pegylated interferon (PEG-IFN) and ribavirin (RBV) with an overall success rate of 50%. New compounds for anti-HCV therapy targeted to the HCV NS3 protease are being developed and some already form the components of licensed therapies. Mapping NS3 protease resistance mutations to protease inhibitors or anti-viral drug candidates is important to direct anti-HCV drug treatment. Methods Sequence analysis of the HCV NS3 protease was conducted in a group of 68 chronically infected patients harboring the HCV genotype 1. The patients were sampled before, during and after a course of PEG-IFN-RBV treatment. Results Resistance mutations to the protease inhibitors, Boceprevir and Telaprevir were identified in HCV isolated from three patients (4.4%); the viral sequences contained at least one of the following mutations: V36L, T54S and V55A. In one sustained virological responder, the T54S mutation appeared during the course of PEG-IFN and RBV therapy. In contrast, V36L and V55A mutations were identified in virus isolated from one relapsing patient before, during, and after treatment, whereas the T54S mutation was identified in virus isolated from one non-responding patient, before and during the treatment course. Conclusions The incidence and persistence of protease resistance mutations occurring in HCV from chronically infected patients in Brazil should be considered when using protease inhibitors to treat HCV disease. In addition, patients treated with the current therapy (PEG-IFN and RBV) that are relapsing or are non-responders should be considered candidates for protease inhibitor therapy.
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Salvatierra K, Fareleski S, Forcada A, López-Labrador FX. Hepatitis C virus resistance to new specifically-targeted antiviral therapy: A public health perspective. World J Virol 2013; 2:6-15. [PMID: 24175225 PMCID: PMC3785043 DOI: 10.5501/wjv.v2.i1.6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Revised: 12/30/2012] [Accepted: 01/17/2013] [Indexed: 02/05/2023] Open
Abstract
Until very recently, treatment for chronic hepatitis C virus (HCV) infection has been based on the combination of two non-viral specific drugs: pegylated interferon-α and ribavirin, which is effective in, overall, about 40%-50% of cases. To improve the response to treatment, novel drugs have been designed to specifically block viral proteins. Multiple compounds are under development, and the approval for clinical use of the first of such direct-acting antivirals in 2011 (Telaprevir and Boceprevir), represents a milestone in HCV treatment. HCV therapeutics is entering a new expanding era, and a highly-effective cure is envisioned for the first time since the discovery of the virus in 1989. However, any antiviral treatment may be limited by the capacity of the virus to overcome the selective pressure of new drugs, generating antiviral resistance. Here, we try to provide a basic overview of new treatments, HCV resistance to new antivirals and some considerations derived from a Public Health perspective, using HCV resistance to protease and polymerase inhibitors as examples.
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Affiliation(s)
- Karina Salvatierra
- Karina Salvatierra, Sabrina Fareleski, F Xavier López-Labrador, Joint Unit in Genomics and Health, Centre for Public Health Research, Public Health Department, Generalitat Valenciana/Institut Cavanilles, University of Valencia, 46020 Valencia, Spain
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Cruz-Rivera M, Carpio-Pedroza JC, Escobar-Gutiérrez A, Lozano D, Vergara-Castaneda A, Rivera-Osorio P, Martinez-Guarneros A, Chacon CAV, Fonseca-Coronado S, Vaughan G. Rapid hepatitis C virus divergence among chronically infected individuals. J Clin Microbiol 2013; 51:629-32. [PMID: 23224093 PMCID: PMC3553878 DOI: 10.1128/jcm.03042-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 11/26/2012] [Indexed: 12/17/2022] Open
Abstract
Here, we analyze the viral divergence among hepatitis C virus (HCV) chronic cases infected with genotype 1. The intrahost viral evolution was assessed by deep sequencing using the 454 Genome Sequencer platform. The results showed a rapid nucleotide sequence divergence. This notorious short-term viral evolution is of the utmost importance for the study of HCV transmission, because direct links between related samples were virtually lost. Thus, rapid divergence of HCV significantly affects genetic relatedness studies and outbreak investigations.
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Affiliation(s)
- Mayra Cruz-Rivera
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | - Daniela Lozano
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | | | | | | | - Salvador Fonseca-Coronado
- Laboratorio de Inmunobiología de Enfermedades Infecciosas, Unidad de Investigación Multidisciplinaria, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, Mexico
| | - Gilberto Vaughan
- Instituto de Diagnóstico y Referencia Epidemiológicos, Mexico City, Mexico
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Boceprevir: a protease inhibitor for the treatment of hepatitis C. Clin Ther 2012; 34:2021-38. [PMID: 22975763 DOI: 10.1016/j.clinthera.2012.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 08/17/2012] [Indexed: 02/07/2023]
Abstract
BACKGROUND Boceprevir is a protease inhibitor indicated for the treatment of chronic hepatitis C virus (HCV) genotype 1 infection in combination with peginterferon and ribavirin for treatment-naive patients and those who previously failed to improve with interferon and ribavirin treatment. OBJECTIVE This article provides an overview of the mechanism of action, pharmacologic and pharmacokinetic properties, clinical efficacy, and tolerability of boceprevir. METHODS Relevant information was identified through a search of PubMed (1990-July 2012), EMBASE (1990-July 2012), International Pharmaceutical Abstracts (1970-July 2012), and Google Scholar using the key words boceprevir, SCH 503034, non-structural protein 3 (NS3) serine protease inhibitor, and direct-acting antiviral agent (DAA). Additional information was obtained from the US Food and Drug Administration's Web site, review of the reference lists of identified articles, and posters and abstracts from scientific meetings. RESULTS Clinical efficacy of boceprevir was assessed in 2 Phase III trials, Serine Protease Inhibitor Therapy-2 (SPRINT-2) for treatment-naive patients and Retreatment with HCV Serine Protease Inhibitor Boceprevir and PegIntron/Rebetol 2 (RESPOND-2) for treatment-experienced patients. In SPRINT-2, patients were randomized to receive peginterferon + ribavirin (PR) or peginterferon + ribavirin + boceprevir (PRB); duration of boceprevir therapy varied from 24, 32, to 44 weeks on the basis of HCV RNA results. The primary endpoint was achievement of sustained virologic response (SVR; lower limit of detection, 9.3 IU/mL). The addition of boceprevir was shown to be superior, with overall SVR rates ranging from 63% to 66% compared with 38% with PR (P < 0.001). Results of SVR in SPRINT-2 were also reorganized to monitor SVRs in black and non-black patients. Treatment-experienced patients were assessed in RESPOND-2; however, null responders were excluded. Patients were again randomized to PR or PRB; duration of boceprevir therapy varied from 32 to 44 weeks on the basis of HCV RNA results. SVR was significantly higher in patients receiving boceprevir (59%-66% vs 21% with PR; P < 0.001). This benefit was seen in both previous nonresponders (SVR, 40%-52% vs 7% with PR), as well as previous relapsers (SVR, 69%-75% vs 29% with PR). Importantly, SVR could be attained with a shortened course of therapy in almost one half of all treated patients in SPRINT-2 (44%) and RESPOND-2 (46%). CONCLUSIONS Boceprevir was well tolerated in clinical trials and a welcomed addition to our HCV armamentarium.
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Beerenwinkel N, Günthard HF, Roth V, Metzner KJ. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data. Front Microbiol 2012; 3:329. [PMID: 22973268 PMCID: PMC3438994 DOI: 10.3389/fmicb.2012.00329] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/24/2012] [Indexed: 12/17/2022] Open
Abstract
Many viruses, including the clinically relevant RNA viruses HIV (human immunodeficiency virus) and HCV (hepatitis C virus), exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing (NGS) technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different NGS platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants (SNVs) to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of NGS to estimate viral diversity.
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Affiliation(s)
- Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH ZurichBasel, Switzerland
- Swiss Institute of BioinformaticsBasel, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of ZurichZurich, Switzerland
| | - Volker Roth
- Department of Mathematics and Computer Science, University of BaselBasel, Switzerland
| | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of ZurichZurich, Switzerland
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Young AM, Crosby RA, Oser CB, Leukefeld CG, Stephens DB, Havens JR. Hepatitis C viremia and genotype distribution among a sample of nonmedical prescription drug users exposed to HCV in rural Appalachia. J Med Virol 2012; 84:1376-87. [PMID: 22825816 PMCID: PMC3571688 DOI: 10.1002/jmv.23252] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Research has demonstrated that hepatitis C (HCV) genotype distribution varies geographically and demographically. This exploratory study examines HCV viremia, viral concentration, and genotype distribution among anti-HCV positive, rural Appalachian nonmedical prescription drug users. The study population was randomly selected from a pool of 200 anti-HCV positive participants in a longitudinal study. Those randomly chosen were representative of the overall pool in terms of demographics, drug use, and other risk behaviors. Participants were tested serologically for HCV RNA, viral concentration, and genotype, and interview-administered questionnaires examined behavioral and demographic characteristics. Of the 81 participants, 69% tested RNA positive, 59% of which had viral loads exceeding 800,000 IU/ml. Approximately 66% of the RNA positive sample had genotype 1a; types 2b (16%) and 3a (13%) were less common. RNA positive participants were not significantly different than RNA negative participants demographically or behaviorally. Likewise, with the exception of education, genotype 1 participants were not significantly different than those with genotype 2 or 3. The prevalence of active HCV infection highlights a need for prevention and treatment in this population. However, the predominance of genotype 1 may present challenges due to its association with decreased responsiveness to drug treatment, although the novel class of direct-acting antivirals such as telaprevir and boceprevir offer new hope in this regard. The prevalence of genotype 1 may also foreshadow heightened burden of hepatocellular carcinoma and elevated healthcare expenditures. More research is needed to characterize HCV infection and genotype in this population.
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Affiliation(s)
- April M Young
- Department of Behavioral Sciences and Health Education, Emory University Rollins School of Public Health, Atlanta, Georgia 30322, USA.
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Abundant drug-resistant NS3 mutants detected by deep sequencing in hepatitis C virus-infected patients undergoing NS3 protease inhibitor monotherapy. J Clin Microbiol 2012; 50:3267-74. [PMID: 22837328 DOI: 10.1128/jcm.00838-12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The high genetic variation of hepatitis C virus (HCV) results in rapid selection of drug resistance mutations (DRMs) during monotherapy with direct-acting antivirals (DAAs). It has been proposed that each possible single mutant preexists in infected individuals; however, the levels of preexisting DRMs are too low to be directly quantified in most patients using current techniques. In this study, we evaluated the presence of DRMs in HCV-infected patients treated with the HCV protease inhibitors GS-9256 or GS-9451 as monotherapy using deep sequencing in 137 longitudinal samples from 45 patients. Software was developed to analyze deep-sequencing results with an assay cutoff of 0.25%. No NS3 DRMs that confer resistance to GS-9256 and GS-9451 (R155K, A156T, and D168V/E) were observed in 33 baseline samples at >0.25%. In contrast, these and other substitutions at NS3 positions 155, 156, and 168 were detected in 19/27 patients at day 2 (24 h) and 21/21 at day 4 (84 h) of monotherapy but not in placebo-treated patients. Based on the DRM growth kinetics during drug treatment, pretreated NS3 mutations at amino acids 155, 156, and 168 were estimated on average at 0.025% and 0.015% per genotype 1a and 1b HCV-infected patients, respectively. Relative fitness of the DRM viruses was shown to be significantly lower than the wild type. Deep-sequencing analyses of NS3 protease inhibitor-treated HCV-infected patients suggest a limit of HCV viral load suppression of 3.6 to 3.8 log(10) with NS3 protease inhibitor monotherapy that does not suppress the identified preexisting NS3 DRMs and thus a need for a combination therapy.
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Shiryaev SA, Cheltsov AV, Strongin AY. Probing of exosites leads to novel inhibitor scaffolds of HCV NS3/4A proteinase. PLoS One 2012; 7:e40029. [PMID: 22768327 PMCID: PMC3388044 DOI: 10.1371/journal.pone.0040029] [Citation(s) in RCA: 4] [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: 12/13/2011] [Accepted: 06/01/2012] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Hepatitis C is a treatment-resistant disease affecting millions of people worldwide. The hepatitis C virus (HCV) genome is a single-stranded RNA molecule. After infection of the host cell, viral RNA is translated into a polyprotein that is cleaved by host and viral proteinases into functional, structural and non-structural, viral proteins. Cleavage of the polyprotein involves the viral NS3/4A proteinase, a proven drug target. HCV mutates as it replicates and, as a result, multiple emerging quasispecies become rapidly resistant to anti-virals, including NS3/4A inhibitors. METHODOLOGY/PRINCIPAL FINDINGS To circumvent drug resistance and complement the existing anti-virals, NS3/4A inhibitors, which are additional and distinct from the FDA-approved telaprevir and boceprevir α-ketoamide inhibitors, are required. To test potential new avenues for inhibitor development, we have probed several distinct exosites of NS3/4A which are either outside of or partially overlapping with the active site groove of the proteinase. For this purpose, we employed virtual ligand screening using the 275,000 compound library of the Developmental Therapeutics Program (NCI/NIH) and the X-ray crystal structure of NS3/4A as a ligand source and a target, respectively. As a result, we identified several novel, previously uncharacterized, nanomolar range inhibitory scaffolds, which suppressed of the NS3/4A activity in vitro and replication of a sub-genomic HCV RNA replicon with a luciferase reporter in human hepatocarcinoma cells. The binding sites of these novel inhibitors do not significantly overlap with those of α-ketoamides. As a result, the most common resistant mutations, including V36M, R155K, A156T, D168A and V170A, did not considerably diminish the inhibitory potency of certain novel inhibitor scaffolds we identified. CONCLUSIONS/SIGNIFICANCE Overall, the further optimization of both the in silico strategy and software platform we developed and lead compounds we identified may lead to advances in novel anti-virals.
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Affiliation(s)
- Sergey A. Shiryaev
- Inflammatory and Infectious Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Anton V. Cheltsov
- R&D Department, Q-MOL L.L.C., San Diego, California, United States of America
- * E-mail: (AVC) (AC); (AYS) (AS)
| | - Alex Y. Strongin
- Inflammatory and Infectious Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- * E-mail: (AVC) (AC); (AYS) (AS)
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Besse B, Coste-Burel M, Bourgeois N, Feray C, Imbert-Marcille BM, André-Garnier E. Genotyping and resistance profile of hepatitis C (HCV) genotypes 1-6 by sequencing the NS3 protease region using a single optimized sensitive method. J Virol Methods 2012; 185:94-100. [PMID: 22728274 DOI: 10.1016/j.jviromet.2012.06.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 06/04/2012] [Accepted: 06/13/2012] [Indexed: 12/21/2022]
Abstract
The objective was to develop a method of NS3 gene sequencing that allowed simultaneous genotyping and protease inhibitor (PI) resistance profiling of HCV genotypes 1-6. To validate the use of a unique RT-PCR for genotypes 1-6 and evaluate its sensitivity, the NS3 protease region was amplified from 140 plasma samples from patients infected with HCV without previous PI therapy. In parallel, NS5b sequences were obtained. Amplification of NS3 was successful in 139/140 samples (99%). For the 135 samples with both NS5b and NS3 sequencing results, phylogenetic analysis showed concordance of genotypes with a bootstrap >90% for each cluster. PI resistance mutations were analyzed using the Geno2pheno [hcv] v1.0 tool. For the 63 genotype 1 (G1) Nantes clinical strains, 12 (19%) presented a natural resistance mutation. This proportion was higher (p<0.05) than that observed in a sample of 374 G1 reference sequences. This significant difference was observed only in subtype 1b (n=7; 25% against n=19; 8%). In conclusion, this tool allows determination of both HCV genotype and identification of PI-resistance mutations. It can be used to detect pre-existing resistance mutations in NS3 before treatment and follow the emergence of resistant viruses during therapy.
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Affiliation(s)
- Bernard Besse
- Laboratoire de Virologie, CHU Hôtel Dieu Nantes, UNAM, EA4271, Nantes, France
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Birdsell DN, Pearson T, Price EP, Hornstra HM, Nera RD, Stone N, Gruendike J, Kaufman EL, Pettus AH, Hurbon AN, Buchhagen JL, Harms NJ, Chanturia G, Gyuranecz M, Wagner DM, Keim PS. Melt analysis of mismatch amplification mutation assays (Melt-MAMA): a functional study of a cost-effective SNP genotyping assay in bacterial models. PLoS One 2012; 7:e32866. [PMID: 22438886 PMCID: PMC3306377 DOI: 10.1371/journal.pone.0032866] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 02/01/2012] [Indexed: 11/18/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are abundant in genomes of all species and biologically informative markers extensively used across broad scientific disciplines. Newly identified SNP markers are publicly available at an ever-increasing rate due to advancements in sequencing technologies. Efficient, cost-effective SNP genotyping methods to screen sample populations are in great demand in well-equipped laboratories, but also in developing world situations. Dual Probe TaqMan assays are robust but can be cost-prohibitive and require specialized equipment. The Mismatch Amplification Mutation Assay, coupled with melt analysis (Melt-MAMA), is flexible, efficient and cost-effective. However, Melt-MAMA traditionally suffers from high rates of assay design failures and knowledge gaps on assay robustness and sensitivity. In this study, we identified strategies that improved the success of Melt-MAMA. We examined the performance of 185 Melt-MAMAs across eight different pathogens using various optimization parameters. We evaluated the effects of genome size and %GC content on assay development. When used collectively, specific strategies markedly improved the rate of successful assays at the first design attempt from ∼50% to ∼80%. We observed that Melt-MAMA accurately genotypes across a broad DNA range (∼100 ng to ∼0.1 pg). Genomic size and %GC content influence the rate of successful assay design in an independent manner. Finally, we demonstrated the versatility of these assays by the creation of a duplex Melt-MAMA real-time PCR (two SNPs) and conversion to a size-based genotyping system, which uses agarose gel electrophoresis. Melt-MAMA is comparable to Dual Probe TaqMan assays in terms of design success rate and accuracy. Although sensitivity is less robust than Dual Probe TaqMan assays, Melt-MAMA is superior in terms of cost-effectiveness, speed of development and versatility. We detail the parameters most important for the successful application of Melt-MAMA, which should prove useful to the wider scientific community.
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Affiliation(s)
- Dawn N. Birdsell
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Talima Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erin P. Price
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heidie M. Hornstra
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Roxanne D. Nera
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nathan Stone
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey Gruendike
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Emily L. Kaufman
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Amanda H. Pettus
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Audriana N. Hurbon
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jordan L. Buchhagen
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - N. Jane Harms
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Gvantsa Chanturia
- National Center for Disease Control and Public Health and Ilia State University, Tbilisi, Georgia, United States of America
| | - Miklos Gyuranecz
- Veterinary Medical Research Institute, Hungarian Academy of Sciences, Budapest, Hungary
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul S. Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- * E-mail:
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Identification of hepatitis C virus transmission using a next-generation sequencing approach. J Clin Microbiol 2012; 50:1461-3. [PMID: 22301026 DOI: 10.1128/jcm.00005-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Here, we describe a transmission event of hepatitis C virus (HCV) among injection drug users. Next-generation sequencing (NGS) was used to assess the intrahost viral genetic variation. Deep amplicon sequencing of HCV hypervariable region 1 allowed for a detailed analysis of the structure of the viral population. Establishment of the genetic relatedness between cases was accomplished by phylogenetic analysis. NGS is a powerful tool with applications in molecular epidemiology studies and outbreak investigations.
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