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Bajpai PS, Collignon L, Sølund C, Madsen LW, Christensen PB, Øvrehus A, Weis N, Holmbeck K, Fahnøe U, Bukh J. Full-length sequence analysis of hepatitis C virus genotype 3b strains and development of an in vivo infectious 3b cDNA clone. J Virol 2023; 97:e0092523. [PMID: 38092564 PMCID: PMC10734419 DOI: 10.1128/jvi.00925-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/27/2023] [Indexed: 12/22/2023] Open
Abstract
IMPORTANCE HCV genotype 3b is a difficult-to-treat subtype, associated with accelerated progression of liver disease and resistance to antivirals. Moreover, its prevalence has significantly increased among persons who inject drugs posing a serious risk of transmission in the general population. Thus, more genetic information and antiviral testing systems are required to develop novel therapeutic options for this genotype 3 subtype. We determined the complete genomic sequence and complexity of three genotype 3b isolates, which will be beneficial to study its biology and evolution. Furthermore, we developed a full-length in vivo infectious cDNA clone of genotype 3b and showed its robustness and genetic stability in human-liver chimeric mice. This is, to our knowledge the first reported infectious cDNA clone of HCV genotype 3b and will provide a valuable tool to evaluate antivirals and neutralizing antibodies in vivo, as well as in the development of infectious cell culture systems required for further research.
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Affiliation(s)
- Priyanka Shukla Bajpai
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura Collignon
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christina Sølund
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Lone Wulff Madsen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Peer Brehm Christensen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Anne Øvrehus
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kenn Holmbeck
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
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Adeboyejo K, King BJ, Tsoleridis T, Tarr AW, McLauchlan J, Irving WL, Ball JK, McClure CP. Hepatitis C subtyping assay failure in UK patients born in sub-Saharan Africa: Implications for global treatment and elimination. J Med Virol 2023; 95:e28178. [PMID: 36168235 PMCID: PMC10092547 DOI: 10.1002/jmv.28178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND AND AIMS: The newly developed direct-acting antivirals have revolutionized the treatment of chronic hepatitis C virus (HCV), with cure rates as high as 98% in some cohorts. Although genome sequencing has demonstrated that some subtypes of HCV naturally harbor drug resistance associated substitutions (RAS), these are often overlooked as "rarities." Furthermore, commercial subtyping assays and associated epidemiological findings are skewed towards Western cohorts and whole-genome sequencing can be problematic to deploy without significant infrastructure and training support. We thus aimed to develop a simple, robust and accurate HCV subtyping pipeline, to optimize and streamline molecular detection and sequence-based typing of diverse RAS-containing subtypes. METHODS HCV serum derived from 146 individuals, whose likely source of infection was from sub-Saharan Africa (SSA) was investigated with a novel panel of single round polymerase chain reaction (PCR) assays targeting NS5B and NS5A genomic regions. Virus subtype assignments were determined by pairwise-distance analysis and compared to both diagnostic laboratory assignments and free-to-use online typing tools. RESULTS Partial NS5A and NS5B sequences were respectively obtained from 131 to 135 HCV-positive patients born in 19 different countries from SSA but attending clinics in the UK. We determined that routine clinical diagnostic methods incorrectly subtyped 59.0% of samples, with a further 6.8% incorrectly genotyped. Of five commonly used online tools, Geno2Pheno performed most effectively in determining a subtype in agreement with pairwise distance analysis. CONCLUSION This study provides a simple low-cost pathway to accurately subtype in SSA, guide regional therapeutic choice and assist global surveillance and elimination initiatives.
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Affiliation(s)
- Kazeem Adeboyejo
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - Barnabas J King
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - Theocharis Tsoleridis
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - Alexander W Tarr
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - William L Irving
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK.,Clinical Microbiology, Nottingham University Hospitals, Nottingham, UK.,Nottingham University Hospitals, Nottingham, UK
| | - Jonathan K Ball
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
| | - C Patrick McClure
- School of Life Sciences, University of Nottingham, Nottingham, UK.,National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK.,Wolfson Centre for Global Virus Research, Nottingham, UK
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Cell Culture Studies of the Efficacy and Barrier to Resistance of Sofosbuvir-Velpatasvir and Glecaprevir-Pibrentasvir against Hepatitis C Virus Genotypes 2a, 2b, and 2c. Antimicrob Agents Chemother 2020; 64:AAC.01888-19. [PMID: 31818814 DOI: 10.1128/aac.01888-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
The introduction of highly efficient therapies with direct-acting antivirals (DAA) for patients with chronic hepatitis C virus (HCV) infection offers exceptional opportunities to globally control this deadly disease. For achieving this ambitious goal, it is essential to prevent antiviral resistance against the most optimal first-line and retreatment DAA choices. We performed independent comparisons of the efficacy and barrier to resistance of pangenotypic DAA regimens for HCV genotype 2 infections, using previously and newly developed efficient cell culture-adapted strains of subtypes 2a, 2b, and 2c. With the applied experimental cell culture conditions, combination treatment with the sofosbuvir-velpatasvir or glecaprevir-pibrentasvir DAA regimen was efficient in eradicating HCV infections; in contrast, single-drug treatments frequently led to viral escape. Sequence analysis of drug targets from recovered viruses revealed known resistance-associated substitutions (RAS) emerging in the NS3 protease or NS5A after treatment failure. These RAS were genetically stable after viral passage, and viruses with these RAS exhibited significant phenotypic resistance. After sofosbuvir treatment failure, only a genotype 2a virus harbored NS5B RAS S282T and thus had decreased susceptibility to nucleotide analogs (nucs). However, in most cases, viral escape from sofosbuvir led to other NS5B substitutions but drug susceptibility was maintained, and in one case, no changes in NS5B were detected. For a genotype 2b virus, after treatment failure with sofosbuvir-velpatasvir, the efficacy of retreatment with glecaprevir-pibrentasvir was maintained due to the high barrier to resistance and low cross-resistance of pibrentasvir. Our findings suggest the slight superiority of glecaprevir-pibrentasvir against genotype 2b in culture, which could have potential therapeutic interest meriting more definitive investigations in the clinic.
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Kiselev D, Matsvay A, Abramov I, Dedkov V, Shipulin G, Khafizov K. Current Trends in Diagnostics of Viral Infections of Unknown Etiology. Viruses 2020; 12:E211. [PMID: 32074965 PMCID: PMC7077230 DOI: 10.3390/v12020211] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022] Open
Abstract
Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.
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Affiliation(s)
- Daniel Kiselev
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Alina Matsvay
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
| | - Ivan Abramov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Vladimir Dedkov
- Pasteur Institute, Federal Service on Consumers’ Rights Protection and Human Well-Being Surveillance, 197101 Saint-Petersburg, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - German Shipulin
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Kamil Khafizov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
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Le Ngoc C, Tran Thi Thanh T, Tran Thi Lan P, Nguyen Mai T, Nguyen Hoa T, Nghiem My N, Le Van T, Le Manh H, Le Thanh P, Nguyen Van Vinh C, Thwaites G, Cooke G, Heilek GM, Shikuma C, Le T, Baker S, Rahman M. Differential prevalence and geographic distribution of hepatitis C virus genotypes in acute and chronic hepatitis C patients in Vietnam. PLoS One 2019; 14:e0212734. [PMID: 30865664 PMCID: PMC6415813 DOI: 10.1371/journal.pone.0212734] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/10/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The highest burden of disease from hepatitis C virus (HCV) is found in Southeast Asia, but our understanding of the epidemiology of infection in many heavily burdened countries is still limited. In particular, there is relatively little data on acute HCV infection, the outcome of which can be influenced by both viral and host genetics which differ within the region. We studied HCV genotype and IL28B gene polymorphism in a cohort of acute HCV-infected patients in Southern Vietnam alongside two other cohorts of chronic HCV-infected patients to better understand the epidemiology of HCV infection locally and inform the development of programs for therapy with the increasing availability of directly acting antiviral therapy (DAAs). METHODS We analysed plasma samples from patients with acute and chronic HCV infection, including chronic HCV mono-infection and chronic Human Immunodeficiency Virus (HIV)-HCV coinfection, who enrolled in four epidemiological or clinical research studies. HCV infection was confirmed with RNA testing. The 5' UTR, core and NSB5 regions of HCV RNA positive samples were sequenced, and the genotype and subtype of the viral strains were determined. Host DNA from all HCV positive patients and age- and sex-matched non-HCV-infected control individuals were analysed for IL28B single nucleotide polymorphism (SNP) (rs12979860 and rs8099917). Geolocation of the patients were mapped using QGIS. RESULTS 355 HCV antibody positive patients were analysed; 54.6% (194/355) and 46.4% (161/355) were acute and chronic infections, respectively. 50.4% (81/161) and 49.6.4% (80/161) of chronic infections had HCV mono-infection and HIV-HCV coinfection, respectively. 88.7% (315/355) and 10.1% (36/355) of the patients were from southern and central regions of Vietnam, respectively. 92.4% (328/355) of patients were HCV RNA positive, including 86.1% (167/194) acute and 100% (161/161) chronic infections. Genotype could be determined in 98.4% (322/328) patients. Genotypes 1 (56.5%; 182/322) and 6 (33.9%; 109/322) predominated. Genotype 1 including genotype 1a was significantly higher in HIV-HCV coinfected patients compared to acute HCV patients [43.8% (35/80) versus 20.5% (33/167)], (p = <0.001), while genotype 6 was significantly higher in chronic HCV mono-infected patients [(44.4% (36/81) versus 20.0% (16/80)] (p = < 0.004) compared to HIV-HCV coinfected patients. The prevalence of IL28B SNP (rs12979860) homozygous CC was 86.46% (83/96) in control individuals and was significantly higher in acutely-infected compared to chronically-infected patients [93.2 (82/88) versus 76.1% (35/46)] (p = < 0.005). CONCLUSION HCV genotype 6 is highly prevalent in Vietnam and the high prevalence in treatment naïve chronic HCV patients may results from poor spontaneous clearance of acute HCV infection with genotype 6.
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Affiliation(s)
- Chau Le Ngoc
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Trinh Nguyen Mai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Trang Nguyen Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ngoc Nghiem My
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Tan Le Van
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Hung Le Manh
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Phuong Le Thanh
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Chau Nguyen Van Vinh
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | | | - Gabrielle M. Heilek
- Roche Molecular Systems, Inc., Pleasanton, California, United States of America
| | - Cecilia Shikuma
- Hawaii Center for AIDS, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Thuy Le
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Hawaii Center for AIDS, University of Hawaii at Manoa, Honolulu, HI, United States of America
- Duke University School of Medicine, Durham, NC, United States of America
| | - Stephen Baker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Motiur Rahman
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- * E-mail:
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Origin, prevalence and response to therapy of hepatitis C virus genotype 2k/1b chimeras. J Hepatol 2017; 67:680-686. [PMID: 28619439 DOI: 10.1016/j.jhep.2017.05.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/18/2017] [Accepted: 05/23/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Little is known about the epidemiology and frequency of recombinant HCV genotype 2/1 strains, which may represent a challenge for direct antiviral therapy (DAA). This study aims to identify the epidemiology and phylogeny of HCV genotype 2/1 strains and encourages genotype screening, to select the DAA-regimen that achieves the optimal sustained virologic response. METHODS Consecutive samples from HCV genotype 2 infected patients, according to commercial genotyping, from Germany, Italy and Israel were re-genotyped by Sanger-based sequencing. Virologic, epidemiological, and phylogenetic analyses including other published chimeras were performed. RESULTS Sequence analysis of 442 supposed HCV genotype 2 isolates revealed 61 (genotype 2k/1b (n=59), 2a/1b (n=1) or 2b/1a (n=1)) chimeras. No chimeras were observed in Italy, but the frequency was 14% and 25% in Germany and Israel. Treatment of viral chimera with sofosbuvir/ribavirin led to virologic relapse in 25/27 patients (93%). Nearly all patients treated with genotype 1-based DAA-regimens initially (n=8/9), or after relapse (n=13/13), achieved a sustained virologic response. Most patients with 2k/1b chimeras (88%) were originally from eight different areas of the former Soviet Union. All known 2k/1b chimeras harbour the same recombination breakpoint and build one phylogenetic cluster, while all other chimeras have different phylogenies. CONCLUSIONS The HCV genotype 2k/1b variant derives from one single recombination event most likely in the former Soviet Union, while other chimeras are unique and develop independently. A relatively high frequency has been observed along the migration flows, in Germany and Israel. In countries with little migration from the former Soviet Union the prevalence of 2k/1b chimeras is expected to be low. Treatment with sofosbuvir plus ribavirin is insufficient, but genotype 1-based regimens seem to be effective. Lay summary: The frequency of recombinant HCV is higher than expected. A novel recombinant variant (HCV genotype 2a/1b) was identified. Screening for recombinant viruses would contribute to increased response rates to direct antiviral therapy.
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Epaulard O, Signori-Schmuck A, Larrat S, Kulkarni O, Blum MG, Fusillier K, Blanc M, Leclercq P, François O, Morand P. Ultradeep sequencing of B and non-B HIV-1 subtypes: Viral diversity and drug resistance mutations before and after one month of antiretroviral therapy in naive patients. J Clin Virol 2017; 95:13-19. [PMID: 28830014 DOI: 10.1016/j.jcv.2017.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 04/06/2017] [Accepted: 07/21/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Ultradeep pyrosequencing technologies permit an assessment of the genetic diversity and the presence and frequency of minority variants in a viral population. The effect of these parameters on the outcome of highly active antiretroviral therapy (HAART) in HIV-infected patients is poorly understood. OBJECTIVES The present study used the pyrosequencing Roche 454 prototype assay to determine whether antiretroviral efficacy is correlated with viral diversity and minority drug resistance mutations in HIV-infected treatment-naive patients and to compare assay performance in B and non-B subtypes. STUDY DESIGN The study included 30 HIV-1 infected naive patients (20 with subtype non-B and 10 with subtype B). Ultradeep pyrosequencing of protease and reverse transcriptase genes was performed at baseline and 1 month after HAART initiation. Plasma HIV VL was measured at 0 and after 1, 3, and 6 months of HAART. RESULTS Pre-HAART minority drug resistance mutations were observed to NRTI in 4 patients, to NNRTI in 6 patients, and to PI in 1 patient; there was no difference in HAART-induced VL decay between patients. Pre-HAART diversity was significantly correlated with the time elapsed since HIV-1 infection diagnosis, but not with the subtype, VL, or CD4 count. Patients with an undetectable VL after 3 months of HAART had a higher pre-HAART diversity. Pre- and post-HAART diversities were not statistically different. There was no difference in assay performance between subtype B and non-B. CONCLUSIONS A high pre-HAART viral diversity might have a positive effect on the outcome of HAART. Pre-therapeutic minority drug resistance mutations are uncommon in naive patients.
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Affiliation(s)
- Olivier Epaulard
- Infectious Disease Unit, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France; Team "HIV and human persistent viruses", Institut de Biologie Structurale, UMR5075 CNRS-CEA-UGA, Grenoble, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France.
| | - Anne Signori-Schmuck
- Team "HIV and human persistent viruses", Institut de Biologie Structurale, UMR5075 CNRS-CEA-UGA, Grenoble, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France; Virology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France
| | - Sylvie Larrat
- Team "HIV and human persistent viruses", Institut de Biologie Structurale, UMR5075 CNRS-CEA-UGA, Grenoble, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France; Virology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France
| | - Om Kulkarni
- Computational and Mathematical Biology, TIMC-IMAG UMR 5525 UJF-INPG-CNRS, Domaine de la Merci, 38706 La Tronche Cedex, France
| | - Michael G Blum
- Computational and Mathematical Biology, TIMC-IMAG UMR 5525 UJF-INPG-CNRS, Domaine de la Merci, 38706 La Tronche Cedex, France
| | - Katia Fusillier
- Virology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France
| | - Myriam Blanc
- Infectious Disease Unit, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France
| | - Pascale Leclercq
- Infectious Disease Unit, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France
| | - Olivier François
- Computational and Mathematical Biology, TIMC-IMAG UMR 5525 UJF-INPG-CNRS, Domaine de la Merci, 38706 La Tronche Cedex, France
| | - Patrice Morand
- Team "HIV and human persistent viruses", Institut de Biologie Structurale, UMR5075 CNRS-CEA-UGA, Grenoble, France; Fédération d'Infectiologie Multidisciplinaire de l'Arc Alpin, Université Grenoble Alpes, France; Virology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire Grenoble Alpes, CS10217, 38043 Grenoble Cedex 9, France
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Abstract
Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral WGS, this technique provides important insights into virus transmission, evolution and pathogenesis.
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Affiliation(s)
- Charlotte J. Houldcroft
- Department of Infection, UK; and the Division of Biological Anthropology, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, University of Cambridge, Cambridge CB2 3QG, UK.,
- and the Division of Biological Anthropology, University of Cambridge, Cambridge CB2 3QG, UK.,
| | - Mathew A. Beale
- Division of Infection and Immunity, University College London, London, WC1E 6BT UK
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK; and at Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.,
- and at Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.,
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SOUSA MDAC, PARANÁ R, ANDRADE LJDO. SEQUENCE SIMILARITY BETWEEN THYROID SELF-PROTEIN AND HEPATITIS C VIRUS POLYPROTEIN: possible triggering mechanism of autoimmune thyroiditis. ARQUIVOS DE GASTROENTEROLOGIA 2016; 53:185-91. [DOI: 10.1590/s0004-28032016000300012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 04/01/2016] [Indexed: 01/04/2023]
Abstract
ABSTRACT Background - Exposure to viral antigens that share amino acid sequence similar with self- antigens might trigger autoimmune diseases in genetically predisposed individuals, and the molecular mimicry theory suggests that epitope mimicry between the virus and human proteins can activate autoimmune disease. Objective - The purpose of this study is to explore the possible sequence similarity between the amino acid sequences of thyroid self-protein and hepatitis C virus proteins, using databanks of proteins and immunogenic peptides, to explain autoimmune thyroid disease. Methods - Were performed the comparisons between the amino acid sequence of the hepatitis C virus polyprotein and thyroid self-protein human, available in the database of National Center for Biotechnology Information on Basic Local Alignment Search Tool. Results - The sequence similarity was related each hepatitis C virus genotype to each thyroid antigen. The similarities between the thyroid and the viral peptides ranged from 21.0 % (31 identical residues out of 147 amino acid in the sequence) to 71.0% (5 identical residues out of 7 amino acid in the sequence). Conclusion - Bioinformatics data, suggest a possible pathogenic link between hepatitis C virus and autoimmune thyroid disease. Through of molecular mimicry is observed that sequences similarities between viral polyproteins and self-proteins thyroid could be a mechanism of induction of crossover immune response to self-antigens, with a breakdown of self-tolerance, resulting in autoimmune thyroid disease.
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Yushchuk ND, Znoyko OO, Dudina KR, Kozina AN, Kalininа OV. [The efficiency of antiviral therapy in patients with chronic -hepatitis C infected with hepatitis C virus recombinants]. TERAPEVT ARKH 2016; 88:101-105. [PMID: 27489903 DOI: 10.17116/terarkh2016886101-105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The review gives the data available in the literature in the efficiency of treatment in patients with chronic hepatitis C infected with hepatitis C virus.(HCV) recombinants, by applying various antiviral therapy regimens. The low efficiency of treatment with- pegylated interferons (PEG IFN) + ribavirin (RIB) and sofosburin (SOF) +RIB in this patient group (a sustained virologic response was achieved in 22 and 30.7%, respectively) compared with the efficiency of treatment (87-97 and 83-97%, respectively) inpatients infected with HCV genotype 2 does not allow the 2015 EASL HCV genotype 2 treatment regimens to be used in. such patients. In this connection, subtyping genotype 2 isolates by NS5B sequencing should be introduced into clinical laboratory practice to successfully detect recombinant HCVs and to enhance the efficiency of antiviral therapy.
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Affiliation(s)
- N D Yushchuk
- A.I. Evdokimov Moscow State University of Medicine and Dentistry, Ministry of Health of Russia, Moscow, Russia
| | - O O Znoyko
- A.I. Evdokimov Moscow State University of Medicine and Dentistry, Ministry of Health of Russia, Moscow, Russia
| | - K R Dudina
- A.I. Evdokimov Moscow State University of Medicine and Dentistry, Ministry of Health of Russia, Moscow, Russia
| | - A N Kozina
- A.I. Evdokimov Moscow State University of Medicine and Dentistry, Ministry of Health of Russia, Moscow, Russia
| | - O V Kalininа
- Pasteur Saint Petersburg Research Institute of Epidemiology and Microbiology, Saint Petersburg, Russia
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11
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Abstract
Antiviral drug resistance is a matter of great clinical importance that, historically, has been investigated mostly from a virological perspective. Although the proximate mechanisms of resistance can be readily uncovered using these methods, larger evolutionary trends often remain elusive. Recent interest by population geneticists in studies of antiviral resistance has spurred new metrics for evaluating mutation and recombination rates, demographic histories of transmission and compartmentalization, and selective forces incurred during viral adaptation to antiviral drug treatment. We present up-to-date summaries on antiviral resistance for a range of drugs and viral types, and review recent advances for studying their evolutionary histories. We conclude that information imparted by demographic and selective histories, as revealed through population genomic inference, is integral to assessing the evolution of antiviral resistance as it pertains to human health.
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Affiliation(s)
- Kristen K Irwin
- School of Life Sciences, École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Nicholas Renzette
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jeffrey D Jensen
- School of Life Sciences, École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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12
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Trémeaux P, Caporossi A, Thélu MA, Blum M, Leroy V, Morand P, Larrat S. Hepatitis C virus whole genome sequencing: Current methods/issues and future challenges. Crit Rev Clin Lab Sci 2016; 53:341-51. [PMID: 27068766 DOI: 10.3109/10408363.2016.1163663] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Therapy for hepatitis C is currently undergoing a revolution. The arrival of new antiviral agents targeting viral proteins reinforces the need for a better knowledge of the viral strains infecting each patient. Hepatitis C virus (HCV) whole genome sequencing provides essential information for precise typing, study of the viral natural history or identification of resistance-associated variants. First performed with Sanger sequencing, the arrival of next-generation sequencing (NGS) has simplified the technical process and provided more detailed data on the nature and evolution of viral quasi-species. We will review the different techniques used for HCV complete genome sequencing and their applications, both before and after the apparition of NGS. The progress brought by new and future technologies will also be discussed, as well as the remaining difficulties, largely due to the genomic variability.
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Affiliation(s)
- Pauline Trémeaux
- a Laboratoire de Virologie , Institut de Biologie et Pathologie, CHU Grenoble-Alpes , Grenoble , France .,b Institut de Biologie Structurale (IBS), UMR 5075 CEA-CNRS-UGA , Grenoble , France
| | - Alban Caporossi
- c Centre d'investigation clinique, Santé publique, CHU Grenoble-Alpes , Grenoble , France .,d Laboratoire TIMC-IMAG , Université de Grenoble Alpes , Grenoble , France , and
| | - Marie-Ange Thélu
- e Clinique d'Hépato-gastroentérologie, Pôle Digidune, CHU Grenoble-Alpes , Grenoble , France
| | - Michael Blum
- d Laboratoire TIMC-IMAG , Université de Grenoble Alpes , Grenoble , France , and
| | - Vincent Leroy
- e Clinique d'Hépato-gastroentérologie, Pôle Digidune, CHU Grenoble-Alpes , Grenoble , France
| | - Patrice Morand
- a Laboratoire de Virologie , Institut de Biologie et Pathologie, CHU Grenoble-Alpes , Grenoble , France .,b Institut de Biologie Structurale (IBS), UMR 5075 CEA-CNRS-UGA , Grenoble , France
| | - Sylvie Larrat
- a Laboratoire de Virologie , Institut de Biologie et Pathologie, CHU Grenoble-Alpes , Grenoble , France .,b Institut de Biologie Structurale (IBS), UMR 5075 CEA-CNRS-UGA , Grenoble , France
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13
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Trémeaux P, Caporossi A, Ramière C, Santoni E, Tarbouriech N, Thélu MA, Fusillier K, Geneletti L, François O, Leroy V, Burmeister WP, André P, Morand P, Larrat S. Amplification and pyrosequencing of near-full-length hepatitis C virus for typing and monitoring antiviral resistant strains. Clin Microbiol Infect 2016; 22:460.e1-460.e10. [PMID: 26827671 DOI: 10.1016/j.cmi.2016.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/04/2016] [Accepted: 01/17/2016] [Indexed: 12/16/2022]
Abstract
Directly acting antiviral drugs have contributed considerable progress to hepatitis C virus (HCV) treatment, but they show variable activity depending on virus genotypes and subtypes. Therefore, accurate genotyping including recombinant form detection is still of major importance, as is the detection of resistance-associated mutations in case of therapeutic failure. To meet these goals, an approach to amplify the HCV near-complete genome with a single long-range PCR and sequence it with Roche GS Junior was developed. After optimization, the overall amplification success rate was 73% for usual genotypes (i.e. HCV 1a, 1b, 3a and 4a, 16/22) and 45% for recombinant forms RF_2k/1b (5/11). After pyrosequencing and subsequent de novo assembly, a near-full-length genomic consensus sequence was obtained for 19 of 21 samples. The genotype and subtype were confirmed by phylogenetic analysis for every sample, including the suspected recombinant forms. Resistance-associated mutations were detected in seven of 13 samples at baseline, in the NS3 (n = 3) or NS5A (n = 4) region. Of these samples, the treatment of one patient included daclatasvir, and that patient experienced a relapse. Virus sequences from pre- and posttreatment samples of four patients who experienced relapse after sofosbuvir-based therapy were compared: the selected variants seem too far from the NS5B catalytic site to be held responsible. Although tested on a limited set of samples and with technical improvements still necessary, this assay has proven to be successful for both genotyping and resistance-associated variant detection on several HCV types.
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Affiliation(s)
- P Trémeaux
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France; UVHCI, Grenoble, France; Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France
| | - A Caporossi
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France; Centre d'investigation clinique, Santé publique, UJF-CNRS, Grenoble, France; Laboratoire TIMC-IMAG, UMR 5525, Université de Grenoble Alpes, Grenoble, France
| | - C Ramière
- Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - E Santoni
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France
| | - N Tarbouriech
- UVHCI, Grenoble, France; Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France
| | - M-A Thélu
- Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - K Fusillier
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France
| | - L Geneletti
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France
| | - O François
- Laboratoire TIMC-IMAG, UMR 5525, Université de Grenoble Alpes, Grenoble, France
| | - V Leroy
- Service d'Hépato-Gastroentérologie, CHU de Grenoble, Grenoble, France
| | - W P Burmeister
- UVHCI, Grenoble, France; Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France
| | - P André
- Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - P Morand
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France; UVHCI, Grenoble, France; Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France
| | - S Larrat
- Laboratoire de Virologie, Institut de Biologie et Pathologie, Grenoble, France; UVHCI, Grenoble, France; Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble, France.
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14
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Karchava M, Waldenström J, Parker M, Hallack R, Sharvadze L, Gatserelia L, Chkhartishvili N, Dvali N, Dzigua L, Dolmazashvili E, Norder H, Tsertsvadze T. High incidence of the hepatitis C virus recombinant 2k/1b in Georgia: Recommendations for testing and treatment. Hepatol Res 2015; 45:1292-8. [PMID: 25689487 PMCID: PMC4787595 DOI: 10.1111/hepr.12505] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 01/23/2015] [Accepted: 02/10/2015] [Indexed: 02/06/2023]
Abstract
AIM The first hepatitis C virus (HCV) recombinant, RF2k/1b, was initially described from Russia and has since then been identified from patients in Ireland, Estonia, Uzbekistan and Cyprus. Many of these patients originated from Georgia; however, there is no information on its prevalence in Georgia or its susceptibility to antiviral treatment. METHODS We retrospectively sequenced the non-structural region 5B (NS5B) of the HCV genome in samples from 72 Georgian patients, 36 of whom had been treated with pegylated interferon and ribavirin. RESULTS The HCV genotype was determined using the Versant HCV Genotype v2 kit. Based on this typing, 32 patients (44.4%) were infected with genotype 1, 21 (29.1%) genotype 2 and 19 (26.3%) genotype 3. Partial NS5B of these strains was sequenced and analyzed for type, with concordant genotype results for all type 1 and 3 strains. Discrepant results were observed for genotyped 2 strains, with 16 (76%) having NS5B of subtype 1b. On phylogenetic analysis, 15 NS5B sequences of these strains were found in a clade formed by recombinant RF2k/1b strains. The remaining discordant sequence was found within a clade formed by 1b strains. CONCLUSION Our findings show that the RF2k/1b recombinant strain is common among Georgian patients previously assumed to be infected with genotype 2. Because genotyping is mainly performed to decide treatment strategies, there is a need to determine the genotype by analysis of at least two genomic regions in strains from Georgian patients considered infected with genotype 2 based on standard HCV genotyping methods.
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Affiliation(s)
- Marine Karchava
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia address
| | - Jesper Waldenström
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Monica Parker
- David Axelrod Institute, Wadsworth Center, Albany, NY, US
| | - Renee Hallack
- David Axelrod Institute, Wadsworth Center, Albany, NY, US
| | - Lali Sharvadze
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia address,Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Lana Gatserelia
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia address
| | - Nikoloz Chkhartishvili
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia address
| | - Natia Dvali
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia address
| | - Lela Dzigua
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia address
| | | | - Helene Norder
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Tengiz Tsertsvadze
- Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia address,Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
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15
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Rota PA, Bankamp B. Whole-Genome Sequencing During Measles Outbreaks. J Infect Dis 2015; 212:1529-30. [PMID: 26153410 DOI: 10.1093/infdis/jiv272] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 05/05/2015] [Indexed: 11/14/2022] Open
Affiliation(s)
- Paul A Rota
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Bettina Bankamp
- Centers for Disease Control and Prevention, Atlanta, Georgia
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16
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Hajji H, Aherfi S, Motte A, Ravaux I, Mokhtari S, Ruiz JM, Poizot-Martin I, Tourres C, Tivoli N, Gérolami R, Tamalet C, Colson P. Diversity of 1,213 hepatitis C virus NS3 protease sequences from a clinical virology laboratory database in Marseille university hospitals, southeastern France. J Med Virol 2015; 87:1921-33. [PMID: 25959702 DOI: 10.1002/jmv.24261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2015] [Indexed: 12/21/2022]
Abstract
Infection with hepatitis C virus (HCV) represents a major public health concern worldwide. Recent therapeutic advances have been considerable, HCV genotype continuing to guide therapeutic management. Since 2008, HCV genotyping in our clinical microbiology laboratory at university hospitals of Marseille, Southeastern France, has been based on NS3 protease gene population sequencing, to allow concurrent HCV genotype and protease inhibitor (PI) genotypic resistance determinations. We aimed, first, to analyze the genetic diversity of HCV NS3 protease obtained from blood samples collected between 2003 and 2013 from patients monitored at university hospitals of Marseille and detect possible atypical sequences; and, second, to identify NS3 protease amino acid patterns associated with decreased susceptibility to HCV PIs. A total of 1,213 HCV NS3 protease sequences were available in our laboratory sequence database. We implemented a strategy based on bioinformatic tools to determine whether HCV sequences are representative of our local HCV genetic diversity, or divergent. In our 2003-2012 HCV NS3 protease sequence database, we delineated 32 clusters representative of the majority HCV genetic diversity, and 61 divergent sequences. Five of these divergent sequences showed less than 85% nucleotide identity with their top GenBank hit. In addition, among the 294 sequences obtained in 2013, three were divergent relative to these 32 previously delineated clusters. Finally, we detected both natural and on-treatment genotypic resistance to HCV NS3 PIs, including a substantial prevalence of Q80K substitutions associated with decreased susceptibility to simeprevir, a second generation PI.
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Affiliation(s)
- Hind Hajji
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - Sarah Aherfi
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.,Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France
| | - Anne Motte
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - Isabelle Ravaux
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Conception, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Saadia Mokhtari
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Nord, Marseille, France
| | - Jean-Marie Ruiz
- Assistance Publique-Hôpitaux de Marseille, Hôpitaux Sud, Service de Médecine en milieu pénitentiaire, Centre pénitentiaire de Marseille, Marseille, France
| | - Isabelle Poizot-Martin
- AP-HM Sainte-Marguerite, Service d'Immuno-hématologie clinique, Marseille, France.,Aix-Marseille University, INSERM, UMR 912 (SESSTIM), Marseille, France
| | - Christian Tourres
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - Natacha Tivoli
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - René Gérolami
- Service d'Hépato-Gastro-Entérologie, Centre Hospitalo-Universitaire Conception, Marseille, France
| | - Catherine Tamalet
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.,Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France
| | - Philippe Colson
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.,Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France
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17
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Genotype- and Subtype-Independent Full-Genome Sequencing Assay for Hepatitis C Virus. J Clin Microbiol 2015; 53:2049-59. [PMID: 25878342 DOI: 10.1128/jcm.02624-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 04/09/2015] [Indexed: 01/27/2023] Open
Abstract
Hepatitis C virus (HCV) exhibits a high genetic diversity and is classified into 6 genotypes, which are further divided into 66 subtypes. Current sequencing strategies require prior knowledge of the HCV genotype and subtype for efficient amplification, making it difficult to sequence samples with a rare or unknown genotype and/or subtype. Here, we describe a subtype-independent full-genome sequencing assay based on a random amplification strategy coupled with next-generation sequencing. HCV genomes from 17 patient samples with both common subtypes (1a, 1b, 2a, 2b, and 3a) and rare subtypes (2c, 2j, 3i, 4a, 4d, 5a, 6a, 6e, and 6j) were successfully sequenced. On average, 3.7 million reads were generated per sample, with 15% showing HCV specificity. The assembled consensus sequences covered 99.3% to 100% of the HCV coding region, and the average coverage was 6,070 reads/position. The accuracy of the generated consensus sequence was estimated to be >99% based on results from in vitro HCV replicon amplification, with the same extrapolated amount of input RNA molecules as that for the patient samples. Taken together, the HCV genomes from 17 patient samples were successfully sequenced, including samples with subtypes that have limited sequence information. This method has the potential to sequence any HCV patient sample, independent of genotype or subtype. It may be especially useful in confounding cases, like those with rare subtypes, intergenotypic recombination, or multiple genotype infections, and may allow greater insight into HCV evolution, its genetic diversity, and drug resistance development.
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18
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The full-length genome sequences of nine HCV genotype 4 variants representing a new subtype 4s and eight unclassified lineages. Virology 2015; 482:111-6. [PMID: 25854865 DOI: 10.1016/j.virol.2015.03.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/09/2015] [Accepted: 03/18/2015] [Indexed: 12/23/2022]
Abstract
We characterized the full-length genomes for nine novel variants of HCV genotype 4 (HCV-4), representing a new subtype 4s and eight unclassified lineages. They were obtained from patients who resided in Canada but all had origins in Africa. An extended maximum clade credibility (MCC) tree was reconstructed after the inclusion of 30 reference sequences. It differentiated 18 assigned subtypes and 10 unclassified lineages within HCV-4. Similar analysis of 102 partial NS5B sequences resulted in another MCC tree that revealed 22 assigned subtypes (4a-4t, 4w, and 4v) and 30 unclassified lineages at the subtype level. Our study shows that HCV-4 is taxonomically complex and it displays high genetic diversity to support an African origin.
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19
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Aherfi S, Glazunova O, Borentain P, Botta-Fridlund D, Chiche L, Bregigeon S, Motte A, Tamalet C, Colson P. Hepatitis C virus of subtype 2l in Marseille, southeastern France. Intervirology 2015; 58:6-13. [PMID: 25592333 DOI: 10.1159/000369015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The rate of eradication of chronic hepatitis C considerably increases with direct-acting antiviral agents, particularly hepatitis C virus (HCV) polymerase inhibitors. While implementing full-length HCV NS5B polymerase sequencing in our clinical microbiology laboratory, we identified atypical HCV sequences, classified as subtype 2l, from 2 patients. HCV-2l NS5B polymerase sequences were detected from 5 and 14 additional patients by screening our laboratory hepatitis virus sequence database and the NCBI GenBank sequence database. Phylogenetic analyses show unambiguously that all HCV-2l sequences are clustered apart from HCV 2 non-l sequences, which compose a second cluster. Mean (±SD) nucleotide identity between near full-length NS5B fragments of subtype 2l was 93.4 ± 0.8% (range: 92.4-95.1). Of note, all HCV-2l sequences obtained in our laboratory and in other centers were from serum samples collected in France. Analysis of the HCV-2l NS5B polymerase amino acid sequences at 30 positions critical for interaction with or resistance to HCV polymerase inhibitors showed specific patterns.
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Affiliation(s)
- Sarah Aherfi
- URMITE UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Aix-Marseille University, Marseille, France
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20
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Quer J, Gregori J, Rodríguez-Frias F, Buti M, Madejon A, Perez-del-Pulgar S, Garcia-Cehic D, Casillas R, Blasi M, Homs M, Tabernero D, Alvarez-Tejado M, Muñoz JM, Cubero M, Caballero A, del Campo JA, Domingo E, Belmonte I, Nieto L, Lens S, Muñoz-de-Rueda P, Sanz-Cameno P, Sauleda S, Bes M, Gomez J, Briones C, Perales C, Sheldon J, Castells L, Viladomiu L, Salmeron J, Ruiz-Extremera A, Quiles-Pérez R, Moreno-Otero R, López-Rodríguez R, Allende H, Romero-Gómez M, Guardia J, Esteban R, Garcia-Samaniego J, Forns X, Esteban JI. High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods. J Clin Microbiol 2015; 53:219-26. [PMID: 25378574 PMCID: PMC4290919 DOI: 10.1128/jcm.02093-14] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) is classified into seven major genotypes and 67 subtypes. Recent studies have shown that in HCV genotype 1-infected patients, response rates to regimens containing direct-acting antivirals (DAAs) are subtype dependent. Currently available genotyping methods have limited subtyping accuracy. We have evaluated the performance of a deep-sequencing-based HCV subtyping assay, developed for the 454/GS-Junior platform, in comparison with those of two commercial assays (Versant HCV genotype 2.0 and Abbott Real-time HCV Genotype II) and using direct NS5B sequencing as a gold standard (direct sequencing), in 114 clinical specimens previously tested by first-generation hybridization assay (82 genotype 1 and 32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 calling by population Sanger sequencing (69% 1b, 31% 1a) in 81 specimens and identified a mixed-subtype infection (1b/3a/1a) in one sample. Similarly, among the 32 previously indeterminate specimens, identical genotype and subtype results were obtained by direct and deep sequencing in all but four samples with dual infection. In contrast, both Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II failed subtype 1 calling in 13 (16%) samples each and were unable to identify the HCV genotype and/or subtype in more than half of the non-genotype 1 samples. We concluded that deep sequencing is more efficient for HCV subtyping than currently available methods and allows qualitative identification of mixed infections and may be more helpful with respect to informing treatment strategies with new DAA-containing regimens across all HCV subtypes.
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Affiliation(s)
- Josep Quer
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep Gregori
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Roche Diagnostics SL, Barcelona, Spain
| | - Francisco Rodríguez-Frias
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - Maria Buti
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Antonio Madejon
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital La Paz-Carlos III, Madrid, Spain
| | - Sofia Perez-del-Pulgar
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Rosario Casillas
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - Maria Blasi
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - Maria Homs
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | | | | | - Maria Cubero
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Andrea Caballero
- Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - Jose Antonio del Campo
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital Universitario Virgen de Valme, Seville, Spain
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Irene Belmonte
- Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - Leonardo Nieto
- Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - Sabela Lens
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Paloma Muñoz-de-Rueda
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital San Cecilio, Granada, Spain
| | - Paloma Sanz-Cameno
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital de la Princesa, Madrid, Spain
| | - Silvia Sauleda
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Banc de Sang i de Teixits, Institut Català de la Salut, Barcelona, Spain
| | - Marta Bes
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Banc de Sang i de Teixits, Institut Català de la Salut, Barcelona, Spain
| | - Jordi Gomez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain CSIC, Instituto de Parasitología y Biomedicina López Neyra, Granada, Spain
| | - Carlos Briones
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Celia Perales
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Julie Sheldon
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Lluis Castells
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Lluis Viladomiu
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Salmeron
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital San Cecilio, Granada, Spain
| | - Angela Ruiz-Extremera
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital San Cecilio, Granada, Spain
| | - Rosa Quiles-Pérez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital San Cecilio, Granada, Spain
| | - Ricardo Moreno-Otero
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital de la Princesa, Madrid, Spain
| | - Rosario López-Rodríguez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital de la Princesa, Madrid, Spain
| | - Helena Allende
- Pathological Anatomy Department, VHIR-HUVH, Barcelona, Spain
| | - Manuel Romero-Gómez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital Universitario Virgen de Valme, Seville, Spain
| | - Jaume Guardia
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rafael Esteban
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Javier Garcia-Samaniego
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital La Paz-Carlos III, Madrid, Spain
| | - Xavier Forns
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain
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21
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Li C, Yuan M, Lu L, Lu T, Xia W, Pham VH, Vo AXD, Nguyen MH, Abe K. The genetic diversity and evolutionary history of hepatitis C virus in Vietnam. Virology 2014; 468-470:197-206. [PMID: 25193655 DOI: 10.1016/j.virol.2014.07.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 12/21/2022]
Abstract
Vietnam has a unique history in association with foreign countries, which may have resulted in multiple introductions of the alien HCV strains to mix with those indigenous ones. In this study, we characterized the HCV sequences in Core-E1 and NS5B regions from 236 Vietnamese individuals. We identified multiple HCV lineages; 6a, 6 e, 6h, 6k, 6l, 6 o, 6p, and two novel variants may represent the indigenous strains; 1a was probably introduced from the US; 1b and 2a possibly originated in East Asia; while 2i, 2j, and 2m were likely brought by French explorers. We inferred the evolutionary history for four major subtypes: 1a, 1b, 6a, and 6 e. The obtained Bayesian Skyline Plots (BSPs) consistently showed the rapid HCV population growth from 1955 to 1963 until 1984 or after, corresponding to the era of the Vietnam War. We also estimated HCV growth rates and reconstructed phylogeographic trees for comparing subtypes 1a, 1b, and HCV-2.
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Affiliation(s)
- Chunhua Li
- Department of pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Manqiong Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen, Fujian, 361102, PR China
| | - Ling Lu
- Department of pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, Kansas City, KS, United States of America.
| | - Teng Lu
- Department of pathology and Laboratory Medicine, Center for Viral Oncology, University of Kansas Medical Center, Kansas City, KS, United States of America; University of Southern California, Los Angeles, CA, United States of America
| | - Wenjie Xia
- Guangzhou Blood Center, Guangzhou, Guangdong, China
| | - Van H Pham
- Center for Molecular Biomedicine, School of Medicine, University of Medicine and Pharmacy in Ho Chi Minh City, Ho Chi Minh City, Vietnam; Molecular Diagnostic Section, The NK-BIOTEK Laboratory, Ho Chi Minh City, Vietnam
| | - An X D Vo
- Molecular Diagnostic Section, The NK-BIOTEK Laboratory, Ho Chi Minh City, Vietnam
| | - Mindie H Nguyen
- Division of Gastroenterology and Hepatology, Stanford University Medical Center, Palo Alto, CA, United States of America
| | - Kenji Abe
- Center for Molecular Biomedicine, School of Medicine, University of Medicine and Pharmacy in Ho Chi Minh City, Ho Chi Minh City, Vietnam; Molecular Diagnostic Section, The NK-BIOTEK Laboratory, Ho Chi Minh City, Vietnam; Department of Pathology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
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22
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Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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23
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Li C, Lu L, Murphy DG, Negro F, Okamoto H. Origin of hepatitis C virus genotype 3 in Africa as estimated through an evolutionary analysis of the full-length genomes of nine subtypes, including the newly sequenced 3d and 3e. J Gen Virol 2014; 95:1677-1688. [PMID: 24795446 DOI: 10.1099/vir.0.065128-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We characterized the full-length genomes of nine hepatitis C virus genotype 3 (HCV-3) isolates: QC7, QC8, QC9, QC10, QC34, QC88, NE145, NE274 and 811. To the best of our knowledge, NE274 and NE145 were the first full-length genomes for confirming the provisionally assigned subtypes 3d and 3e, respectively, whereas 811 represented the first HCV-3 isolate that had its extreme 3' UTR terminus sequenced. Based on these full-length genomes, together with 42 references representing eight assigned subtypes and an unclassified variant of HCV-3, and 10 sequences of six other genotypes, a timescaled phylogenetic tree was reconstructed after an evolutionary analysis using a coalescent Bayesian procedure. The results indicated that subtypes 3a, 3d and 3e formed a subset with a common ancestor dated to ~202.89 [95% highest posterior density (HPD): 160.11, 264.6] years ago. The analysis of all of the HCV-3 sequences as a single lineage resulted in the dating of the divergence time to ~457.81 (95% HPD: 350.62, 587.53) years ago, whereas the common ancestor of all of the seven HCV genotypes dated to ~780.86 (95% HPD: 592.15, 1021.34) years ago. As subtype 3h and the unclassified variant were relatives, and represented the oldest HCV-3 lineages with origins in Africa and the Middle East, these findings may indicate the ancestral origin of HCV-3 in Africa. We speculate that the ancestral HCV-3 strains may have been brought to South Asia from Africa by land and/or across the sea to result in its indigenous circulation in that region. The spread was estimated to have occurred in the era after Vasco da Gama had completed his expeditions by sailing along the eastern coast of Africa to India. However, before this era, Arabians had practised slave trading from Africa to the Middle East and South Asia for centuries, which may have mediated the earliest spread of HCV-3.
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Affiliation(s)
- Chunhua Li
- Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Ling Lu
- Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Donald G Murphy
- Institut national de santé publique du Québec, Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - Francesco Negro
- Divisions of Gastroenterology and Hepatology and of Clinical pathology, University Hospitals, Geneva, Switzerland
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
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24
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Smith DB, Bukh J, Kuiken C, Muerhoff AS, Rice CM, Stapleton JT, Simmonds P. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology 2014; 59:318-27. [PMID: 24115039 PMCID: PMC4063340 DOI: 10.1002/hep.26744] [Citation(s) in RCA: 924] [Impact Index Per Article: 92.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 08/29/2013] [Indexed: 12/11/2022]
Abstract
UNLABELLED The 2005 consensus proposal for the classification of hepatitis C virus (HCV) presented an agreed and uniform nomenclature for HCV variants and the criteria for their assignment into genotypes and subtypes. Since its publication, the available dataset of HCV sequences has vastly expanded through advancement in nucleotide sequencing technologies and an increasing focus on the role of HCV genetic variation in disease and treatment outcomes. The current study represents a major update to the previous consensus HCV classification, incorporating additional sequence information derived from over 1,300 (near-)complete genome sequences of HCV available on public databases in May 2013. Analysis resolved several nomenclature conflicts between genotype designations and using consensus criteria created a classification of HCV into seven confirmed genotypes and 67 subtypes. There are 21 additional complete coding region sequences of unassigned subtype. The study additionally describes the development of a Web resource hosted by the International Committee for Taxonomy of Viruses (ICTV) that maintains and regularly updates tables of reference isolates, accession numbers, and annotated alignments (http://talk.ictvonline.org/links/hcv/hcv-classification.htm). The Flaviviridae Study Group urges those who need to check or propose new genotypes or subtypes of HCV to contact the Study Group in advance of publication to avoid nomenclature conflicts appearing in the literature. While the criteria for assigning genotypes and subtypes remain unchanged from previous consensus proposals, changes are proposed in the assignment of provisional subtypes, subtype numbering beyond "w," and the nomenclature of intergenotypic recombinant. CONCLUSION This study represents an important reference point for the consensus classification of HCV variants that will be of value to researchers working in clinical and basic science fields.
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Affiliation(s)
- Donald B Smith
- Centre for Immunity, Infection and Evolution, University of EdinburghScotland, UK
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, and Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of CopenhagenDenmark
| | - Carla Kuiken
- Theoretical Biology and Biophysics group, Los Alamos National LaboratoryLos Alamos, NM, USA
| | | | - Charles M Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller UniversityNew York, NY, USA
| | - Jack T Stapleton
- Medical Service, Iowa City Veterans Affairs Medical Center, Departments of Internal Medicine and Microbiology, University of IowaIowa City, IA, USA
| | - Peter Simmonds
- Centre for Immunity, Infection and Evolution, University of EdinburghScotland, UK
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Markussen T, Sindre H, Jonassen CM, Tengs T, Kristoffersen AB, Ramsell J, Numanovic S, Hjortaas MJ, Christiansen DH, Dale OB, Falk K. Ultra-deep pyrosequencing of partial surface protein genes from infectious Salmon Anaemia virus (ISAV) suggest novel mechanisms involved in transition to virulence. PLoS One 2013; 8:e81571. [PMID: 24303056 PMCID: PMC3841194 DOI: 10.1371/journal.pone.0081571] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 10/14/2013] [Indexed: 11/22/2022] Open
Abstract
Uncultivable HPR0 strains of infectious salmon anaemia viruses (ISAVs) infecting gills are non-virulent putative precursors of virulent ISAVs (vISAVs) causing systemic disease in farmed Atlantic salmon (Salmo salar). The transition to virulence involves two molecular events, a deletion in the highly polymorphic region (HPR) of the hemagglutinin-esterase (HE) gene and a Q266→L266 substitution or insertion next to the putative cleavage site (R267) in the fusion protein (F). We have performed ultra-deep pyrosequencing (UDPS) of these gene regions from healthy fish positive for HPR0 virus carrying full-length HPR sampled in a screening program, and a vISAV strain from an ISA outbreak at the same farming site three weeks later, and compared the mutant spectra. As the UDPS data shows the presence of both HE genotypes at both sampling times, and the outbreak strain was unlikely to be directly related to the HPR0 strain, this is the first report of a double infection with HPR0s and vISAVs. For F amplicon reads, mutation frequencies generating L266 codons in screening samples and Q266 codons in outbreak samples were not higher than at any random site. We suggest quasispecies heterogeneity as well as RNA structural properties are linked to transition to virulence. More specifically, a mechanism where selected single point mutations in the full-length HPR alter the RNA structure facilitating single- or sequential deletions in this region is proposed. The data provides stronger support for the deletion hypothesis, as opposed to recombination, as the responsible mechanism for generating the sequence deletions in HE.
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Affiliation(s)
- Turhan Markussen
- Department of Laboratory Services, Norwegian Veterinary Institute, Oslo, Norway
- * E-mail:
| | - Hilde Sindre
- Department of Laboratory Services, Norwegian Veterinary Institute, Oslo, Norway
| | | | - Torstein Tengs
- Department of Laboratory Services, Norwegian Veterinary Institute, Oslo, Norway
| | | | - Jon Ramsell
- Department of Laboratory Services, Norwegian Veterinary Institute, Oslo, Norway
| | - Sanela Numanovic
- Department of Laboratory Services, Norwegian Veterinary Institute, Oslo, Norway
| | - Monika J. Hjortaas
- Department of Laboratory Services, Norwegian Veterinary Institute, Oslo, Norway
| | - Debes H. Christiansen
- National Reference Laboratory for Fish Diseases, Food and Veterinary Authority, Torshavn, Faroe Islands
| | - Ole Bendik Dale
- Department of Laboratory Services, Norwegian Veterinary Institute, Oslo, Norway
| | - Knut Falk
- Department of Health Surveillance, Norwegian Veterinary Institute, Oslo, Norway
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26
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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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27
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Bartolini B, Giombini E, Zaccaro P, Selleri M, Rozera G, Abbate I, Comandini UV, Ippolito G, Solmone M, Capobianchi MR. Extent of HCV NS3 protease variability and resistance-associated mutations assessed by next generation sequencing in HCV monoinfected and HIV/HCV coinfected patients. Virus Res 2013; 177:205-8. [PMID: 23954579 DOI: 10.1016/j.virusres.2013.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 02/07/2023]
Abstract
HCV quasispecies variability represents the background for the selection of mutations and for the development of drug resistance. Natural aminoacid changes in NS3, associated with reduced protease inhibitor susceptibility, have been observed in treatment-naïve patients. Massively parallel sequencing has been used to analyze NS3 quasispecies in patients infected with HCV genotype 1, naive to anti-HCV treatment, with/without HIV-coinfection, to establish the genetic heterogeneity and the presence of amino acid substitutions at positions responsible for drug resistance. Genomes carrying substitutions represented either predominant or minority components of viral quasispecies, and were observed in 85.7% of patients. Multiple substitutions, frequently associated on the same haplotype, were observed in 46.4% of patients. High resistance combinations were not detected, neither on the same genome, nor in the whole quasispecies. Heterogeneity of HCV NS3 was lower in HIV-coinfected as compared to HCV-monoinfected patients, but factors underlying this difference remain to be established. Although the relevance of naturally occurring mutations with respect of resistance development and probability of success of direct acting antivirals is questioned, UDPS may be beneficial to help understanding viral dynamics, providing high resolution view of viral diversity.
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Affiliation(s)
- Barbara Bartolini
- "L. Spallanzani" National Institute for Infectious Diseases, Via Portuense 292, 00149 Rome, Italy
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28
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Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases. Nat Rev Drug Discov 2013; 12:447-64. [PMID: 23722347 DOI: 10.1038/nrd4010] [Citation(s) in RCA: 812] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleoside analogues have been in clinical use for almost 50 years and have become cornerstones of treatment for patients with cancer or viral infections. The approval of several additional drugs over the past decade demonstrates that this family still possesses strong potential. Here, we review new nucleoside analogues and associated compounds that are currently in preclinical or clinical development for the treatment of cancer and viral infections, and that aim to provide increased response rates and reduced side effects. We also highlight the different approaches used in the development of these drugs and the potential of personalized therapy.
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Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases. NATURE REVIEWS. DRUG DISCOVERY 2013. [PMID: 23722347 DOI: 10.1038/nrd4010]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleoside analogues have been in clinical use for almost 50 years and have become cornerstones of treatment for patients with cancer or viral infections. The approval of several additional drugs over the past decade demonstrates that this family still possesses strong potential. Here, we review new nucleoside analogues and associated compounds that are currently in preclinical or clinical development for the treatment of cancer and viral infections, and that aim to provide increased response rates and reduced side effects. We also highlight the different approaches used in the development of these drugs and the potential of personalized therapy.
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Comparison of pyrosequencing, Sanger sequencing, and melting curve analysis for detection of low-frequency macrolide-resistant mycoplasma pneumoniae quasispecies in respiratory specimens. J Clin Microbiol 2013; 51:2592-8. [PMID: 23720793 DOI: 10.1128/jcm.00785-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Macrolide-resistant Mycoplasma pneumoniae (MRMP) is emerging worldwide and has been associated with treatment failure. In this study, we used pyrosequencing to detect low-frequency MRMP quasispecies in respiratory specimens, and we compared the findings with those obtained by Sanger sequencing and SimpleProbe PCR coupled with a melting curve analysis (SimpleProbe PCR). Sanger sequencing, SimpleProbe PCR, and pyrosequencing were successfully performed for 96.7% (88/91), 96.7% (88/91), and 93.4% (85/91) of the M. pneumoniae-positive specimens, respectively. The A-to-G transition at position 2063 was the only mutation identified. Pyrosequencing identified A2063G MRMP quasispecies populations in 78.8% (67/88) of the specimens. Only 38.8% (26/67) of these specimens with the A2063G quasispecies detected by pyrosequencing were found to be A2063G quasispecies by Sanger sequencing or SimpleProbe PCR. The specimens that could be detected by SimpleProbe PCR and Sanger sequencing had higher frequencies of MRMP quasispecies (51% to 100%) than those that could not be detected by those two methods (1% to 44%). SimpleProbe PCR correctly categorized all specimens that were identified as wild type or mutant by Sanger sequencing. The clinical characteristics of the patients were not significantly different when they were grouped by the presence or absence of MRMP quasispecies, while patients with MRMP identified by Sanger sequencing more often required a switch from macrolides to an alternative M. pneumoniae-targeted therapy. The clinical significance of mutant quasispecies should be investigated further with larger patient populations and with specimens obtained before and after macrolide therapy.
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