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Echeverría N, Gámbaro F, Beaucourt S, Soñora M, Hernández N, Cristina J, Moratorio G, Moreno P. Mixed Infections Unravel Novel HCV Inter-Genotypic Recombinant Forms within the Conserved IRES Region. Viruses 2024; 16:560. [PMID: 38675902 PMCID: PMC11053413 DOI: 10.3390/v16040560] [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: 02/20/2024] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatitis C virus (HCV) remains a significant global health challenge, affecting millions of people worldwide, with chronic infection a persistent threat. Despite the advent of direct-acting antivirals (DAAs), challenges in diagnosis and treatment remain, compounded by the lack of an effective vaccine. The HCV genome, characterized by high genetic variability, consists of eight distinct genotypes and over ninety subtypes, underscoring the complex dynamics of the virus within infected individuals. This study delves into the intriguing realm of HCV genetic diversity, specifically exploring the phenomenon of mixed infections and the subsequent detection of recombinant forms within the conserved internal ribosome entry site (IRES) region. Previous studies have identified recombination as a rare event in HCV. However, our findings challenge this notion by providing the first evidence of 1a/3a (and vice versa) inter-genotypic recombination within the conserved IRES region. Utilizing advanced sequencing methods, such as deep sequencing and molecular cloning, our study reveals mixed infections involving genotypes 1a and 3a. This comprehensive approach not only confirmed the presence of mixed infections, but also identified the existence of recombinant forms not previously seen in the IRES region. The recombinant sequences, although present as low-frequency variants, open new avenues for understanding HCV evolution and adaptation.
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Affiliation(s)
- Natalia Echeverría
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (N.E.); (F.G.); (M.S.); (J.C.); (G.M.)
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Fabiana Gámbaro
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (N.E.); (F.G.); (M.S.); (J.C.); (G.M.)
| | - Stéphanie Beaucourt
- Viral Populations and Pathogenesis Laboratory, Institut Pasteur, 75015 Paris, France;
| | - Martín Soñora
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (N.E.); (F.G.); (M.S.); (J.C.); (G.M.)
- Laboratorio de Simulaciones Biomoleculares, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Nelia Hernández
- Clínica de Gastroenterología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo 11600, Uruguay;
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (N.E.); (F.G.); (M.S.); (J.C.); (G.M.)
| | - Gonzalo Moratorio
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (N.E.); (F.G.); (M.S.); (J.C.); (G.M.)
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Pilar Moreno
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; (N.E.); (F.G.); (M.S.); (J.C.); (G.M.)
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
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Jakab S, Bali K, Freytag C, Pataki A, Fehér E, Halas M, Jerzsele Á, Szabó I, Szarka K, Bálint Á, Bányai K. Deep Sequencing of Porcine Reproductive and Respiratory Syndrome Virus ORF7: A Promising Tool for Diagnostics and Epidemiologic Surveillance. Animals (Basel) 2023; 13:3223. [PMID: 37893946 PMCID: PMC10603690 DOI: 10.3390/ani13203223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major concern worldwide. Control of PRRSV is a challenging task due to various factors, including the viral diversity and variability. In this study, we evaluated an amplicon library preparation protocol targeting the ORF7 region of both PRRSV species, Betaarterivirus suid 1 and Betaarterivirus suid 2. We designed tailed primers for a two-step PCR procedure that generates ORF7-specific amplicon libraries suitable for use on Illumina sequencers. We tested the method with serum samples containing common laboratory strains and with pooled serum samples (n = 15) collected from different pig farms during 2019-2021 in Hungary. Testing spiked serum samples showed that the newly designed method is highly sensitive and detects the viral RNA even at low copy numbers (corresponding to approx. Ct 35). The ORF7 sequences were easily assembled even from clinical samples. Two different sequence variants were identified in five samples, and the Porcilis MLV vaccine strain was identified as the minor variant in four samples. An in-depth analysis of the deep sequencing results revealed numerous polymorphic sites along the ORF7 gene in a total of eight samples, and some sites (positions 12, 165, 219, 225, 315, 345, and 351) were found to be common in several clinical specimens. We conclude that amplicon deep sequencing of a highly conserved region of the PRRSV genome could support both laboratory diagnosis and epidemiologic surveillance of the disease.
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Affiliation(s)
- Szilvia Jakab
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
| | - Krisztina Bali
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
| | - Csongor Freytag
- Department of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (C.F.); (K.S.)
| | - Anna Pataki
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
| | - Enikő Fehér
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
| | | | - Ákos Jerzsele
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István u 2, H-1078 Budapest, Hungary;
| | - István Szabó
- National PRRS Eradication Committee, Keleti Károly u. 24., H-1024 Budapest, Hungary;
| | - Krisztina Szarka
- Department of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (C.F.); (K.S.)
| | - Ádám Bálint
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, H-1143 Budapest, Hungary;
| | - Krisztián Bányai
- Veterinary Medical Research Institute, Hungária krt. 21., H-1143 Budapest, Hungary; (S.J.); (K.B.); (A.P.); (E.F.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Hungária krt. 21., H-1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István u 2, H-1078 Budapest, Hungary;
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Geographic Distribution of HCV Genotypes and Efficacy of Direct-Acting Antivirals in Chronic HCV-Infected Patients in North and Northeast China: A Real-World Multicenter Study. Can J Gastroenterol Hepatol 2022; 2022:7395506. [PMID: 35531123 PMCID: PMC9076341 DOI: 10.1155/2022/7395506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To assess the geographic distribution of HCV genotypes, effectiveness, and safety of DAA treatment for HCV-infected patients in North and Northeast China. METHODS The geographic distribution of HCV genotypes was analyzed in 2162 patients recruited from April 2018 to February 2021. Sustained virologic response rates at 12 (SVR12) or 24 (SVR24) weeks posttreatment and safety were analyzed in 405 patients who completed DAA treatment according to patient baseline characteristics and treatment. RESULTS Four genotypes and six subtypes were identified as follows: 1b (1187, 54.90%), 2a (790, 36.54%), 3a/b (134, 6.20%), 6a/n (44, 2.04%), mixed genotypes (2a-6a or 2a-3a) (7, 0.32%). Overall, 99.01% patients achieved SVR12, while 98.43% achieved SVR24. All patients treated with elbasvir/grazoprevir (EBR/GZR), sofosbuvir/velpatasvir ± ribavirin (SOF/VEL ± RBV), and SOF/ledipasvir (LDV) achieved SVR12 or SVR24; 92.86% SVR12 and 95.83% SVR24 were observed in patients using SOF + RBV. SVR12 was higher in noncirrhosis versus compensated cirrhosis patients (100% vs. 97.09%, p=0.022). No severe drug-related adverse event was observed. CONCLUSIONS Genotypes 1b and 2a were dominant subtypes in North and Northeast China. The approved drug regimens EBR/GZR and SOF/LDV for subtype 1b and SOF/VEL for nongenotype 1b are the optimal effective and safety profile.
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Pan-Genotypic Direct-Acting Antiviral Agents for Undetermined or Mixed-Genotype Hepatitis C Infection: A Real-World Multi-Center Effectiveness Analysis. J Clin Med 2022; 11:jcm11071853. [PMID: 35407462 PMCID: PMC8999637 DOI: 10.3390/jcm11071853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
Although the pan-genotypic direct-acting antiviral regimen was approved for treating chronic hepatitis C infection regardless of the hepatitis C virus (HCV) genotype, real-world data on its effectiveness against mixed-genotype or genotype-undetermined HCV infection are scarce. We evaluated the real-world safety and efficacy of two pan-genotypic regimens (Glecaprevir/Pibrentasvir and Sofosbuvir/Velpatasvir) for HCV-infected patients with mixed or undetermined HCV genotypes from the five hospitals in the Changhua Christian Care System that commenced treatment between August 2018 and December 2020. This retrospective study evaluated the efficacy and safety of pan-genotypic direct-acting antiviral (DAA) treatment in adults with HCV infection. The primary endpoint was the sustained virological response (SVR) observed 12 weeks after completing the treatment. Altogether, 2446 HCV-infected patients received the pan-genotypic DAA regimen, 37 (1.5%) patients had mixed-genotype HCV infections and 110 (4.5%) patients had undetermined HCV genotypes. The mean age was 63 years and 55.8% of our participants were males. Nine (6.1%) patients had end-stage renal disease and three (2%) had co-existing hepatomas. We lost one patient to follow-up during treatment and one more patient after treatment. A total of four patients died. However, none of these losses were due to treatment-related side effects. The rates of SVR12 for mixed-genotype and genotype-undetermined infections were 97.1% and 96.2%, respectively, by per-protocol analyses, and 91.9% and 92.7% respectively, by intention-to-treat population analyses. Laboratory adverse events with grades ≥3 included anemia (2.5%), thrombocytopenia (2.5%), and jaundice (0.7%). Pan-genotypic DAAs are effective and well-tolerated for mixed-genotype or genotype-undetermined HCV infection real-world settings.
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5
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Bradshaw D, Bibby DF, Manso CF, Piorkowska R, Mohamed H, Ledesma J, Bubba L, Chan YT, Ngui SL, Carne S, Mbisa JL. Clinical evaluation of a Hepatitis C Virus whole-genome sequencing pipeline for genotyping and resistance testing. Clin Microbiol Infect 2021; 28:405-409. [PMID: 34245902 DOI: 10.1016/j.cmi.2021.06.042] [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: 03/03/2021] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVES We sought to evaluate clinically a hepatitis C virus (HCV) whole-genome, next-generation sequencing (NGS) pipeline that is agnostic to viral genotype. METHODS Performance of the NGS pipeline was assessed through comparison of results with Sanger sequencing (SS) of partial HCV genomes. RESULTS There was 98.7% (376/381) concordance for viral subtype between SS and NGS. The positive and negative per cent agreements for determination of resistance-associated substitutions were 97.8% (95% CI 92.5-99.4%) and 99.9% (95% CI 99.5-100.0%), respectively. The NGS pipeline was also able to detect novel subtypes, mixtures, recombinants, transiently occurring resistance mutations and distinguish re-infection with the same subtype from relapse. DISCUSSION Particular scenarios where NGS may be used include settings without universal access to pan-genotypic antiviral regimens, those infected with a 'rare' subtype or who have been failed by first-line therapy, and in cases of suspected re-infection.
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Affiliation(s)
- Daniel Bradshaw
- National Infection Service, Public Health England, London, UK.
| | - David F Bibby
- National Infection Service, Public Health England, London, UK
| | - Carmen F Manso
- National Infection Service, Public Health England, London, UK
| | | | - Hodan Mohamed
- National Infection Service, Public Health England, London, UK
| | - Juan Ledesma
- National Infection Service, Public Health England, London, UK
| | - Laura Bubba
- National Infection Service, Public Health England, London, UK
| | - Yuen T Chan
- National Infection Service, Public Health England, London, UK
| | - Siew Lin Ngui
- National Infection Service, Public Health England, London, UK
| | - Simon Carne
- National Infection Service, Public Health England, London, UK
| | - Jean L Mbisa
- National Infection Service, Public Health England, London, UK
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- National Infection Service, Public Health England, London, UK
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Byrne AS, Goudreau A, Bissonnette N, Shamputa IC, Tahlan K. Methods for Detecting Mycobacterial Mixed Strain Infections-A Systematic Review. Front Genet 2020; 11:600692. [PMID: 33408740 PMCID: PMC7779811 DOI: 10.3389/fgene.2020.600692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with multiple strains of a single pathogenic species. Known to occur in humans and animals, MSIs deserve special consideration when studying transmission dynamics, evolution, and treatment of mycobacterial diseases, notably tuberculosis in humans and paratuberculosis (or Johne's disease) in ruminants. Therefore, a systematic review was conducted to examine how MSIs are defined in the literature, how widespread the phenomenon is across the host species spectrum, and to document common methods used to detect such infections. Our search strategy identified 121 articles reporting MSIs in both humans and animals, the majority (78.5%) of which involved members of the Mycobacterium tuberculosis complex, while only a few (21.5%) examined non-tuberculous mycobacteria (NTM). In addition, MSIs exist across various host species, but most reports focused on humans due to the extensive amount of work done on tuberculosis. We reviewed the strain typing methods that allowed for MSI detection and found a few that were commonly employed but were associated with specific challenges. Our review notes the need for standardization, as some highly discriminatory methods are not adapted to distinguish between microevolution of one strain and concurrent infection with multiple strains. Further research is also warranted to examine the prevalence of NTM MSIs in both humans and animals. In addition, it is envisioned that the accurate identification and a better understanding of the distribution of MSIs in the future will lead to important information on the epidemiology and pathophysiology of mycobacterial diseases.
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Affiliation(s)
| | - Alex Goudreau
- Science & Health Sciences Librarian, University of New Brunswick, Saint John, NB, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Isdore Chola Shamputa
- Department of Nursing & Health Sciences, University of New Brunswick, Saint John, NB, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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Manso CF, Bibby DF, Lythgow K, Mohamed H, Myers R, Williams D, Piorkowska R, Chan YT, Bowden R, Ansari MA, Ip CLC, Barnes E, Bradshaw D, Mbisa JL. Technical Validation of a Hepatitis C Virus Whole Genome Sequencing Assay for Detection of Genotype and Antiviral Resistance in the Clinical Pathway. Front Microbiol 2020; 11:576572. [PMID: 33162957 PMCID: PMC7583327 DOI: 10.3389/fmicb.2020.576572] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/14/2020] [Indexed: 01/05/2023] Open
Abstract
Choice of direct acting antiviral (DAA) therapy for Hepatitis C Virus (HCV) in the United Kingdom and similar settings usually requires knowledge of the genotype and, in some cases, antiviral resistance (AVR) profile of the infecting virus. To determine these, most laboratories currently use Sanger technology, but next-generation sequencing (NGS) offers potential advantages in throughput and accuracy. However, NGS poses unique technical challenges, which require idiosyncratic development and technical validation approaches. This applies particularly to virology, where sequence diversity is high and the amount of starting genetic material is low, making it difficult to distinguish real data from artifacts. We describe the development and technical validation of a sequence capture-based HCV whole genome sequencing (WGS) assay to determine viral genotype and AVR profile. We use clinical samples of known subtypes and viral loads, and simulated FASTQ datasets to validate the analytical performances of both the wet laboratory and bioinformatic pipeline procedures. We show high concordance of the WGS assay compared to current "gold standard" Sanger assays. Specificity was 92.3 and 96.1% for AVR and genotyping, respectively. Discordances were due to the inability of Sanger assays to assign the correct subtype or accurately call mixed drug-resistant variants. We show high repeatability and reproducibility with >99.8% sequence similarity between sequence runs as well as high precision for variant frequency detection at >98.8% in the 95th percentile. Post-sequencing bioinformatics quality control workflows allow the accurate distinction between mixed infections, cross-contaminants and recombinant viruses at a threshold of >5% for the minority population. The sequence capture-based HCV WGS assay is more accurate than legacy AVR and genotyping assays. The assay has now been implemented in the clinical pathway of England's National Health Service HCV treatment programs, representing the first validated HCV WGS pipeline in clinical service. The data generated will additionally provide granular national-level genomic information for public health policy making and support the WHO HCV elimination strategy.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Rory Bowden
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - M. Azim Ansari
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Camilla L. C. Ip
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | | | - Jean L. Mbisa
- Public Health England, London, United Kingdom
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
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Sallam M, Batarseh R, Natsheh A, Abbadi J, Al-Fraihat E, Yaseen A, Kaddomi D, Khamees N, Mahafzah A, Şahin GÖ. An update on hepatitis C virus genotype distribution in Jordan: a 12-year retrospective study from a tertiary care teaching hospital in Amman. BMC Infect Dis 2019; 20:3. [PMID: 31892307 PMCID: PMC6938611 DOI: 10.1186/s12879-019-4735-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/24/2019] [Indexed: 11/16/2022] Open
Abstract
Background Nucleic acid hybridization (NAH) of hepatitis C virus (HCV) is a practical and reliable tool for virus genotyping. Genotype assignment is an important factor in the prediction of treatment success in chronic hepatitis C patients. The aim of this study was to determine the genotype distribution among HCV clinical isolates in Jordan between 2007 and 2018. Methods Electronic and paper-based clinical data registry records from 2007 to 2018 at the Jordan University Hospital (JUH) were retrospectively examined for individuals with HCV genotype, HCV viral load, and alanine aminotransferase (ALT) testing results. Genotype determination was based on NAH technique using the HCV 5′ untranslated region (5′ UTR) with 386 requests available from 342 unique individuals. Results A total of 263 out of 342 unique individuals (76.9%) had genotyping results available for final analysis with 259 individuals each having a single genotyping result. The most common HCV genotypes in the study were: genotype 4 (n = 142, 54.0%), genotype 1 (n = 87, 33.1%), genotype 3 (n = 16, 6.1%), genotype 2 (n = 9, 3.4%), other undetermined genotypes (n = 5, 1.9%) and mixed infections (n = 4, 1.5%). Sub-genotyping results were available for 46 individuals as follows: sub-genotype 4c/d (n = 13, 28.3%), sub-genotype 1a (n = 11, 23.9%), sub-genotype 1b (n = 10, 21.7%), sub-genotype 4a (n = 8, 17.4%), sub-genotype 3a (n = 2, 4.3%), sub-genotypes 2a/c and 4 h (n = 1, 2.2% for both). Individuals infected with genotype 1 showed higher viral load when compared to those infected with genotype 4 (p = 0.048, t-test). Younger HCV-infected individuals (< 52 years) had higher ALT levels compared to older individuals (p = 0.036, t-test). Self-reported risk factors for HCV acquisition included: history of previous surgery, invasive dental procedures, and blood transfusion, delivery at home, circumcision at home and wet cupping therapy (hijama). Conclusions High genetic diversity of HCV was found in Jordan, with genotypes 4 and 1 as the most prevalent genotypes co-circulating in the country. Potential impact of virus genotype on disease markers (viral load, ALT) was detected and needs further assessment. The study can be helpful to plan for future prevention and management of HCV infection in Jordan.
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Affiliation(s)
- Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan. .,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan. .,Department of Translational Medicine, Faculty of Medicine, Lund University, 22100, Malmö, Sweden.
| | - Rawan Batarseh
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Anas Natsheh
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Jumana Abbadi
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Esraa Al-Fraihat
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Alaa' Yaseen
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Doaa Kaddomi
- Gastroenterology and Liver Division, Department of Internal Medicine, Jordan University Hospital, Amman, 11942, Jordan
| | - Nadia Khamees
- Gastroenterology and Liver Division, Department of Internal Medicine, Jordan University Hospital, Amman, 11942, Jordan
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Gülşen Özkaya Şahin
- Department of Translational Medicine, Faculty of Medicine, Lund University, 22100, Malmö, Sweden.,Department of Clinical Microbiology, Laboratory Medicine, Skåne University Hospital, 22100, Lund, Sweden
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9
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Cuypers L, Thijssen M, Shakibzadeh A, Sabahi F, Ravanshad M, Pourkarim MR. Next-generation sequencing for the clinical management of hepatitis C virus infections: does one test fits all purposes? Crit Rev Clin Lab Sci 2019; 56:420-434. [PMID: 31317801 DOI: 10.1080/10408363.2019.1637394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
While the prospect of viral cure is higher than ever for individuals infected with the hepatitis C virus (HCV) due to ground-breaking progress in antiviral treatment, success rates are still negatively influenced by HCV's high genetic variability. This genetic diversity is represented in the circulation of various genotypes and subtypes, mixed infections, recombinant forms and the presence of numerous drug resistant variants among infected individuals. Common misclassifications by commercial genotyping assays in combination with the limitations of currently used targeted population sequencing approaches have encouraged researchers to exploit alternative methods for the clinical management of HCV infections. Next-generation sequencing (NGS), a revolutionary and powerful tool with a variety of applications in clinical virology, can characterize viral diversity and depict viral dynamics in an ultra-wide and ultra-deep manner. The level of detail it provides makes it the method of choice for the diagnosis and clinical assessment of HCV infections. The sequence library provided by NGS is of a higher magnitude and sensitivity than data generated by conventional methods. Therefore, these technologies are helpful to guide clinical practice and at the same time highly valuable for epidemiological studies. The decreasing costs of NGS to determine genotypes, mixed infections, recombinant strains and drug resistant variants will soon make it feasible to employ NGS in clinical laboratories, to assist in the daily care of patients with HCV.
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Affiliation(s)
- Lize Cuypers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven , Leuven , Belgium
| | - Marijn Thijssen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven , Leuven , Belgium
| | - Arash Shakibzadeh
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran , Iran
| | - Farzaneh Sabahi
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran , Iran
| | - Mehrdad Ravanshad
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University , Tehran , Iran
| | - Mahmoud Reza Pourkarim
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven , Leuven , Belgium.,Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences , Shiraz , Iran.,Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine , Tehran , Iran
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10
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Fernández-Caso B, Fernández-Caballero JÁ, Chueca N, Rojo E, de Salazar A, García Buey L, Cardeñoso L, García F. Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing. Sci Rep 2019; 9:9264. [PMID: 31239457 PMCID: PMC6592891 DOI: 10.1038/s41598-019-42605-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 04/01/2019] [Indexed: 12/21/2022] Open
Abstract
Current HCV genotyping methods may have some limitations in detecting mixed infections. We aimed to determine the accuracy of genotyping and the detection of mixed-genotype infections using the Abbott-RealTime HCV Genotype II assay (Abbott-RT-PCR) in comparison with a Roche-Next Generation Sequencing assay (Roche-NGS). Plasma samples collected from 139 HCV-infected patients tested with Abbott-RT-PCR, 114 with single genotype (GT) and 25 with mixed GTs were genotyped using Roche-NGS. Roche-NGS confirmed all single GTs obtained with Abbott-RT-PCR. One case of Abbott GT 4 was found as GT 1a using Roche-NGS. Genotype 5 was confirmed using Roche-NGS in 75% cases (3 out of 4 cases). Twenty-five patients were identified as having mixed HCVinfections using Abbott-RT-PCR. The concordance between Abbott-RT-PCR and Roche-NGS was 76% (19 out of 25 cases). Three mixed-GT infections identified with the Abbott assay (two (1b + 4); one (1a + 3)) were reported as pure 1b using Roche-NGS. Very divergent results were found for the other three samples. When compared to Roche-NGS, Abbott-RT-PCR has performed excellently for the determination of patients infected with single GTs. For patients that are categorized as having a mixed infection using Abbott-RT-PCR, we recommend an NGS assay as a confirmation test.
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Affiliation(s)
- Belén Fernández-Caso
- Servicio de Microbiologia, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa, Madrid, Spain
| | - Jose Ángel Fernández-Caballero
- Unidad de Gestión Clinica de Microbiologia, Hospital Universitario San Cecilio; Instituto de Investigación Biosanitaria ibs.Granada; Red de Investigación en SIDA, RD16/0025/0040, Granada, Spain
| | - Natalia Chueca
- Unidad de Gestión Clinica de Microbiologia, Hospital Universitario San Cecilio; Instituto de Investigación Biosanitaria ibs.Granada; Red de Investigación en SIDA, RD16/0025/0040, Granada, Spain
| | - Eukene Rojo
- Servicio de Aparato Digestivo - Unidad de Hepatologia, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa, Madrid, Spain
| | - Adolfo de Salazar
- Unidad de Gestión Clinica de Microbiologia, Hospital Universitario San Cecilio; Instituto de Investigación Biosanitaria ibs.Granada; Red de Investigación en SIDA, RD16/0025/0040, Granada, Spain
| | - Luisa García Buey
- Servicio de Aparato Digestivo - Unidad de Hepatologia, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa, Madrid, Spain
| | - Laura Cardeñoso
- Servicio de Microbiologia, Hospital Universitario de La Princesa; Instituto de Investigacion Sanitaria La Princesa, Madrid, Spain
| | - Federico García
- Unidad de Gestión Clinica de Microbiologia, Hospital Universitario San Cecilio; Instituto de Investigación Biosanitaria ibs.Granada; Red de Investigación en SIDA, RD16/0025/0040, Granada, Spain.
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11
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Hayashi K, Tachi K, Shimizu Y, Nagano K, Ishizu Y, Kuzuya T, Honda T, Ishigami M, Hirooka Y, Hattori M, Goto H. The Prevalence of Mixed Hepatitis C Virus Genotype Infection and Its Effect on the Response to Direct-Acting Antivirals Therapy. Intervirology 2019; 62:23-29. [PMID: 31207601 DOI: 10.1159/000499691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/15/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The incidence of mixed hepatitis C virus (HCV) genotype infection is variable, and a few reports exist regarding the efficacy of direct-acting antivirals (DAA) therapy for mixed genotype. We aimed to investigate the prevalence of mixed genotype and its impact on the virologic response to DAA therapy. METHODS A total of 365 patients with chronic HCV infection who completed antiviral therapy were recruited. Nested polymerase chain reaction with universal and specific primers of genotypes 1b and 2 and direct sequencing were used for HCV genotyping. RESULTS Direct sequencing with universal primers defined genotypes 1b (n = 230), 2a (n = 95), and 2b (n = 40). Direct sequencing of genotype 2 was performed in patients with genotype 1b, and direct sequencing of genotype 1b in patients with genotype 2. Four patients with genotype 1b underwent amplification for genotype 2, and direct sequencing identified genotypes 1b (n = 1), 2a (n = 1), and 2b (n = 2). None with genotype 2 underwent amplification for genotype 1b. Three cases were confirmed to have mixed genotype. CONCLUSIONS Mixed genotype was rare, and hence the impact of mixed genotype on treatment outcome with DAA therapy is expected to be minimal.
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Affiliation(s)
- Kazuhiko Hayashi
- Department of Gastroenterology and Hepatology, Federation of National Public Service Personnel Mutual Aid Associations Meijo Hospital, Nagoya, Japan, .,Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan,
| | - Kosuke Tachi
- Department of Gastroenterology and Hepatology, Federation of National Public Service Personnel Mutual Aid Associations Meijo Hospital, Nagoya, Japan
| | - Yuko Shimizu
- Department of Gastroenterology and Hepatology, Federation of National Public Service Personnel Mutual Aid Associations Meijo Hospital, Nagoya, Japan
| | - Kenichi Nagano
- Department of Gastroenterology and Hepatology, Federation of National Public Service Personnel Mutual Aid Associations Meijo Hospital, Nagoya, Japan
| | - Yoji Ishizu
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Teiji Kuzuya
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Honda
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masatoshi Ishigami
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiki Hirooka
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masashi Hattori
- Department of Gastroenterology, Yamashita Hospital, Ichinomiya, Japan
| | - Hidemi Goto
- Department of Gastroenterology and Hepatology, Federation of National Public Service Personnel Mutual Aid Associations Meijo Hospital, Nagoya, Japan.,Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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12
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Abdel Ghaffar TY, El Naghi S, Abdel Gawad M, Helmy S, Abdel Ghaffar A, Yousef M, Moafy M. Safety and efficacy of combined sofosbuvir/daclatasvir treatment of children and adolescents with chronic hepatitis C Genotype 4. J Viral Hepat 2019; 26:263-270. [PMID: 30380158 DOI: 10.1111/jvh.13032] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/03/2018] [Indexed: 12/16/2022]
Abstract
Direct-acting antivirals have become available for treating chronic HCV (hepatitis C virus) infection in adults and, recently, in children at least 12 years old. Our aim was to investigate the safety and efficacy of combined sofosbuvir (SOF)/daclatasvir (DCV) for HCV Genotype 4 in children aged 8 to 18 years or weighing 17 kg or more. A total of 40 chronic HCV-infected, treatment-naïve children with well compensated livers were recruited from two sites. Patients received combined therapy of SOF (400 mg/d for patients weighing greater than 45 kg; 200 mg/d for patients weighing 17 to 45 kg) and DCV (60 mg/d for patients weighing greater than 45 kg; 30 mg/d for patients weighing 17 to 45 kg) for 12 weeks. They were followed up regularly by clinical examination and laboratory tests during treatment (weekly in the first month then monthly to the end of treatment), every 3 months for 6 months post-treatment, and at 48 weeks post-treatment. In our cohort, which included 45% of children below the age of 12 years (72.5% genotype 4 and 27.5% mixed genotype 4 and 1), end of treatment response (ETR) was 97.5%. Sustained virologic response for weeks 12 and 24 post-treatment (SVR12 and SVR24) were 97.5% and 95%, respectively, on an intention to treat basis, and 100% and 100% for those who completed the study protocol. Observed side effects were mild and none required drug cessation. Combined SOF/DCV was found to be effective and safe for treating HCV Genotype 4-infected children, 8 years of age and above.
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Affiliation(s)
- Tawhida Y Abdel Ghaffar
- Yassin Abdel Ghaffar Charity Center for Liver Disease and Research, Cairo, Egypt.,Department of Pediatrics, Ain Shams University, Cairo, Egypt
| | - Suzan El Naghi
- Yassin Abdel Ghaffar Charity Center for Liver Disease and Research, Cairo, Egypt.,Department of Pediatrics, National Hepatology & Tropical Medicine Research Institute, Cairo, Egypt
| | | | - Sarah Helmy
- Yassin Abdel Ghaffar Charity Center for Liver Disease and Research, Cairo, Egypt
| | | | | | - Mohamad Moafy
- Department of Pediatrics, Ain Shams University, Cairo, Egypt
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13
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Abstract
INTRODUCTION Hepatitis C virus (HCV) is divided into 7 genotypes and 67 subtypes. HCV genotype studies reflect the viral transmission patterns as well as human migration routes. In a clinical setting, HCV genotype is a baseline predictor for the sustained virological response (SVR) in chronic hepatitis C patients treated with peginterferon or some direct acting antivirals (DAAs). The Versant HCV genotype 2.0 assay has been globally used for HCV genotyping over a decade. Areas covered: The assay is based on reverse hybridization principle. It is evolved from its former versions, and the accuracy and successful genotyping/subtyping rate are substantially improved. It shows an accuracy of 99-100% for genotypes 1-6. It can also reliably identify subtypes 1a and 1b. However, the assay does not allow a high resolution for many other subtypes. Reasons for indeterminate or inaccurate genotyping/subtyping results are discussed. Expert commentary: Genotyping helps to find the most efficacious and cost-effective treatment regimen. The rapid development of anti-HCV treatment regimens, however, is greatly simplifying laboratory tests. In the near future, the need for HCV genotyping and frequent serial on-treatment HCV RNA tests will decrease along with the wide use of the more potent and pan-genotypic DAA regimens.
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Affiliation(s)
- Ruifeng Yang
- a Peking University People's Hospital, Peking University Hepatology Institute , Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases , Beijing , China
| | - Lai Wei
- a Peking University People's Hospital, Peking University Hepatology Institute , Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases , Beijing , China
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