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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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2
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Zhao J, Shui J, Luo L, Ao C, Lin H, Liang Y, Wang L, Wang H, Chen H, Tang S. Identification and characterization of mixed infections of Chlamydia trachomatis via high-throughput sequencing. Front Microbiol 2022; 13:1041789. [PMID: 36439830 PMCID: PMC9687396 DOI: 10.3389/fmicb.2022.1041789] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
Precise genotyping is necessary to understand epidemiology and clinical manifestations of Chlamydia trachomatis infection with different genotypes. Next-generation high-throughput sequencing (NGHTS) has opened new frontiers in microbial genotyping, but has been clinically characterized in only a few settings. This study aimed to determine C. trachomatis genotypes in particular mixed-genotype infections and their association with clinical manifestations and to characterize the sensitivity and accuracy of NGHTS. Cervical specimens were collected from 8,087 subjects from physical examination center (PEC), assisted reproductive technology center (ART) and gynecology clinics (GC) of Chenzhou Hospital of China. The overall prevalence of C. trachomatis was 3.8% (311/8087) whereas a prevalence of 2.8, 3.7 and 4.8% was found in PEC, ART and GC, respectively. The most frequent three C. trachomatis genotypes were E (27.4%, 83/303), F (21.5%, 65/303) and J (18.2%, 55/303). Moreover, NGHTS identified 20 (6.6%, 20/303) mixed-genotype infections of C. trachomatis. Genotype G was more often observed in the subjects with pelvic inflammatory disease than genotype E (adjusted OR = 3.61, 95%CI, 1.02–12.8, p = 0.046). Mixed-genotype infection was associated with severe vaginal cleanliness (degree IV) with an adjusted OR of 5.17 (95%CI 1.03–25.9, p = 0.046) whereas mixed-genotype infection with large proportion of minor genotypes was associated with cervical squamous intraepithelial lesion (SIL) with an adjusted OR of 5.51 (95%CI 1.17–26.01, p = 0.031). Our results indicated that NGHTS is a feasible tool to identity C. trachomatis mixed-genotype infections, which may be associated with worse vaginal cleanliness and cervical SIL.
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Affiliation(s)
- Jianhui Zhao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jingwei Shui
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Lipei Luo
- Department of Clinical Microbiology Laboratory, Chenzhou No. 1 People’s Hospital, Chenzhou, China
| | - Cailing Ao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Hongqing Lin
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yuanhao Liang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Li Wang
- Department of Clinical Microbiology Laboratory, Chenzhou No. 1 People’s Hospital, Chenzhou, China
| | - Haiying Wang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Hongliang Chen
- Department of Clinical Microbiology Laboratory, Chenzhou No. 1 People’s Hospital, Chenzhou, China
- *Correspondence: Hongliang Chen, ; Shixing Tang,
| | - Shixing Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
- *Correspondence: Hongliang Chen, ; Shixing Tang,
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3
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Dopico E, Rodriguez-Frias F, Ubillos I, Rando-Segura A, Garcia-Cehic D, Gregori J, Rando-Matos Y, Solsona L, Niubó J, Esteban JI, Costa J, Martínez MJ, Quer J. Prevalence of Hepatitis C Virus Infection, Genotypes and Subtypes in Migrants from Pakistan in Barcelona, Spain. Infect Drug Resist 2022; 15:4637-4644. [PMID: 36003985 PMCID: PMC9394658 DOI: 10.2147/idr.s367715] [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: 03/28/2022] [Accepted: 07/26/2022] [Indexed: 11/23/2022] Open
Abstract
Background Hepatitis C virus (HCV) is a major cause of chronic liver infection with 71 million people infected worldwide. Pakistan has the second highest prevalence of HCV infection and more than half (52%) of Pakistani living in Spain reside in Barcelona. The aim of this study was to analyse the seroprevalence and viraemic rate and determine the genotypes and subtypes of HCV among Pakistanis living in the southern metropolitan area of Barcelona. Methods We included all Pakistani patients seeking primary healthcare in the southern metropolitan area of Barcelona from August 2011 to July 2014. Serum samples were screened for HCV antibodies. HCV viral load was determined by reverse transcription polymerase chain reaction and genotypes and subtypes were performed using Versant HCV Genotype and/or deep-sequencing. Screening for hepatitis B virus (HBV) was also carried out. Results Among 5877 Pakistani patients, 565 (9.61%) were screened for anti-HCV antibodies, with 68 (12.04%) being positive. The viral load was determined in 65, with 31 presenting active infection and the viraemic rate was 47.69% (95% confidence interval 36.02-59.62). HCV genotyping and subtyping were performed in 24 individuals. Most infections corresponded to HCV genotype 3 (91.67%), and high resolution HCV subtyping was performed in 18 samples, 16 of which presented subtype 3a. One subject presented HBV coinfection with undetectable HBV DNA. During the study period, we identified a possible case of HCV vertical transmission followed by spontaneous viraemia clearance in a chronically infected mother with a C/T IL28B genetic polymorphism. Conclusion These results suggest that general HCV screening protocols in patients from high prevalence countries, such as Pakistan, would be helpful to identify and treat active HCV infections. This could avoid further transmission and contribute to building targeted health policies for micro-elimination of HCV infection in specific communities.
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Affiliation(s)
- Eva Dopico
- Microbiology Department, Laboratori Clínic Territorial Metropolitana Sud, Hospital Universitari de Bellvitge, Institut Català de la Salut (ICS), Hospitalet de Llobregat, Barcelona, Spain.,Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Biochemistry Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Itziar Ubillos
- Laboratory Clínic Territorial Metropolitana Sud, Institut Català de la Salut (ICS), Hospitalet de Llobregat, Barcelona, Spain
| | - Ariadna Rando-Segura
- Biochemistry Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Damir Garcia-Cehic
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Josep Gregori
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Yolanda Rando-Matos
- Equip d'Atenció Primària Florida Nord, Gerència d'Àmbit d'Atenció Primària Metropolitana Sud, Institut Català de la Salut (ICS), Hospitalet de Llobregat, Barcelona, Spain.,Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
| | - Luis Solsona
- Equip d'Atenció Primària Florida Nord, Gerència d'Àmbit d'Atenció Primària Metropolitana Sud, Institut Català de la Salut (ICS), Hospitalet de Llobregat, Barcelona, Spain.,Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
| | - Jordi Niubó
- Microbiology Department, Laboratori Clínic Territorial Metropolitana Sud, Hospital Universitari de Bellvitge, Institut Català de la Salut (ICS), Hospitalet de Llobregat, Barcelona, Spain.,Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Juan Ignacio Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Josep Costa
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Microbiology Department, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Miguel J Martínez
- Microbiology Department, Hospital Clínic, University of Barcelona, Barcelona, Spain.,ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.,Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
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4
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Martínez-González B, Soria ME, Vázquez-Sirvent L, Ferrer-Orta C, Lobo-Vega R, Mínguez P, de la Fuente L, Llorens C, Soriano B, Ramos-Ruíz R, Cortón M, López-Rodríguez R, García-Crespo C, Somovilla P, Durán-Pastor A, Gallego I, de Ávila AI, Delgado S, Morán F, López-Galíndez C, Gómez J, Enjuanes L, Salar-Vidal L, Esteban-Muñoz M, Esteban J, Fernández-Roblas R, Gadea I, Ayuso C, Ruíz-Hornillos J, Verdaguer N, Domingo E, Perales C. SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations. Pathogens 2022; 11:662. [PMID: 35745516 PMCID: PMC9227345 DOI: 10.3390/pathogens11060662] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 12/23/2022] Open
Abstract
Populations of RNA viruses are composed of complex and dynamic mixtures of variant genomes that are termed mutant spectra or mutant clouds. This applies also to SARS-CoV-2, and mutations that are detected at low frequency in an infected individual can be dominant (represented in the consensus sequence) in subsequent variants of interest or variants of concern. Here we briefly review the main conclusions of our work on mutant spectrum characterization of hepatitis C virus (HCV) and SARS-CoV-2 at the nucleotide and amino acid levels and address the following two new questions derived from previous results: (i) how is the SARS-CoV-2 mutant and deletion spectrum composition in diagnostic samples, when examined at progressively lower cut-off mutant frequency values in ultra-deep sequencing; (ii) how the frequency distribution of minority amino acid substitutions in SARS-CoV-2 compares with that of HCV sampled also from infected patients. The main conclusions are the following: (i) the number of different mutations found at low frequency in SARS-CoV-2 mutant spectra increases dramatically (50- to 100-fold) as the cut-off frequency for mutation detection is lowered from 0.5% to 0.1%, and (ii) that, contrary to HCV, SARS-CoV-2 mutant spectra exhibit a deficit of intermediate frequency amino acid substitutions. The possible origin and implications of mutant spectrum differences among RNA viruses are discussed.
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Affiliation(s)
- Brenda Martínez-González
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
| | - María Eugenia Soria
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Lucía Vázquez-Sirvent
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Cristina Ferrer-Orta
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, 08028 Barcelona, Spain; (C.F.-O.); (N.V.)
| | - Rebeca Lobo-Vega
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Pablo Mínguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (P.M.); (L.d.l.F.); (M.C.); (R.L.-R.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Lorena de la Fuente
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (P.M.); (L.d.l.F.); (M.C.); (R.L.-R.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Carlos Llorens
- Biotechvana, “Scientific Park”, Universidad de Valencia, 46980 Valencia, Spain; (C.L.); (B.S.)
| | - Beatriz Soriano
- Biotechvana, “Scientific Park”, Universidad de Valencia, 46980 Valencia, Spain; (C.L.); (B.S.)
| | - Ricardo Ramos-Ruíz
- Unidad de Genómica, “Scientific Park of Madrid”, Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Marta Cortón
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (P.M.); (L.d.l.F.); (M.C.); (R.L.-R.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rosario López-Rodríguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (P.M.); (L.d.l.F.); (M.C.); (R.L.-R.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Pilar Somovilla
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Antoni Durán-Pastor
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
| | - Isabel Gallego
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Ana Isabel de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Soledad Delgado
- Departamento de Sistemas Informáticos, Escuela Técnica Superior de Ingeniería de Sistemas Informáticos (ETSISI), Universidad Politécnica de Madrid, 28031 Madrid, Spain;
| | - Federico Morán
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid, 28005 Madrid, Spain;
| | - Cecilio López-Galíndez
- Unidad de Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28222 Madrid, Spain;
| | - Jordi Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, 18016 Granada, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Llanos Salar-Vidal
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Mario Esteban-Muñoz
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Jaime Esteban
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Ricardo Fernández-Roblas
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (P.M.); (L.d.l.F.); (M.C.); (R.L.-R.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Javier Ruíz-Hornillos
- Allergy Unit, Hospital Infanta Elena, Valdemoro, 28342 Madrid, Spain;
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, 28223 Madrid, Spain
| | - Nuria Verdaguer
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, 08028 Barcelona, Spain; (C.F.-O.); (N.V.)
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Celia Perales
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
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Quer J, Colomer-Castell S, Campos C, Andrés C, Piñana M, Cortese MF, González-Sánchez A, Garcia-Cehic D, Ibáñez M, Pumarola T, Rodríguez-Frías F, Antón A, Tabernero D. Next-Generation Sequencing for Confronting Virus Pandemics. Viruses 2022; 14:v14030600. [PMID: 35337007 PMCID: PMC8950049 DOI: 10.3390/v14030600] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Virus pandemics have happened, are happening and will happen again. In recent decades, the rate of zoonotic viral spillover into humans has accelerated, mirroring the expansion of our global footprint and travel network, including the expansion of viral vectors and the destruction of natural spaces, bringing humans closer to wild animals. Once viral cross-species transmission to humans occurs, transmission cannot be stopped by cement walls but by developing barriers based on knowledge that can prevent or reduce the effects of any pandemic. Controlling a local transmission affecting few individuals is more efficient that confronting a community outbreak in which infections cannot be traced. Genetic detection, identification, and characterization of infectious agents using next-generation sequencing (NGS) has been proven to be a powerful tool allowing for the development of fast PCR-based molecular assays, the rapid development of vaccines based on mRNA and DNA, the identification of outbreaks, transmission dynamics and spill-over events, the detection of new variants and treatment of vaccine resistance mutations, the development of direct-acting antiviral drugs, the discovery of relevant minority variants to improve knowledge of the viral life cycle, strengths and weaknesses, the potential for becoming dominant to take appropriate preventive measures, and the discovery of new routes of viral transmission.
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Affiliation(s)
- Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence: (J.Q.); (A.A.)
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Cristina Andrés
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Maria Piñana
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Maria Francesca Cortese
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Clinical Biochemistry Research Group, Biochemistry Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Alejandra González-Sánchez
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Marta Ibáñez
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
| | - Tomàs Pumarola
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
- Clinical Biochemistry Research Group, Biochemistry Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Andrés Antón
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence: (J.Q.); (A.A.)
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Microbiology Departments, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
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Liu C, Liu C, Su T, Tseng T, Chen P, Kao J. Sofosbuvir/velpatasvir or glecaprevir/pibrentasvir for treating patients with hepatitis C virus reinfection following direct‐acting antiviral‐induced sustained virologic response. ADVANCES IN DIGESTIVE MEDICINE 2022. [DOI: 10.1002/aid2.13302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Chen‐Hua Liu
- Department of Internal Medicine National Taiwan University Hospital Taipei Taiwan
- Hepatitis Research Center National Taiwan University Hospital Taipei Taiwan
- Department of Internal Medicine National Taiwan University Hospital, Yun‐Lin Branch Yunlin Taiwan
| | - Chun‐Jen Liu
- Department of Internal Medicine National Taiwan University Hospital Taipei Taiwan
- Hepatitis Research Center National Taiwan University Hospital Taipei Taiwan
- Graduate Institute of Clinical Medicine National Taiwan University College of Medicine Taipei Taiwan
| | - Tung‐Hung Su
- Department of Internal Medicine National Taiwan University Hospital Taipei Taiwan
- Hepatitis Research Center National Taiwan University Hospital Taipei Taiwan
| | - Tai‐Chung Tseng
- Department of Internal Medicine National Taiwan University Hospital Taipei Taiwan
- Hepatitis Research Center National Taiwan University Hospital Taipei Taiwan
- Department of Medical Research National Taiwan University Hospital Taipei Taiwan
| | - Pei‐Jer Chen
- Department of Internal Medicine National Taiwan University Hospital Taipei Taiwan
- Hepatitis Research Center National Taiwan University Hospital Taipei Taiwan
- Graduate Institute of Clinical Medicine National Taiwan University College of Medicine Taipei Taiwan
| | - Jia‐Horng Kao
- Department of Internal Medicine National Taiwan University Hospital Taipei Taiwan
- Hepatitis Research Center National Taiwan University Hospital Taipei Taiwan
- Graduate Institute of Clinical Medicine National Taiwan University College of Medicine Taipei Taiwan
- Department of Medical Research National Taiwan University Hospital Taipei Taiwan
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7
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Adaptive Immune Responses, Immune Escape and Immune-Mediated Pathogenesis during HDV Infection. Viruses 2022; 14:v14020198. [PMID: 35215790 PMCID: PMC8880046 DOI: 10.3390/v14020198] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/13/2022] Open
Abstract
The hepatitis delta virus (HDV) is the smallest known human virus, yet it causes great harm to patients co-infected with hepatitis B virus (HBV). As a satellite virus of HBV, HDV requires the surface antigen of HBV (HBsAg) for sufficient viral packaging and spread. The special circumstance of co-infection, albeit only one partner depends on the other, raises many virological, immunological, and pathophysiological questions. In the last years, breakthroughs were made in understanding the adaptive immune response, in particular, virus-specific CD4+ and CD8+ T cells, in self-limited versus persistent HBV/HDV co-infection. Indeed, the mechanisms of CD8+ T cell failure in persistent HBV/HDV co-infection include viral escape and T cell exhaustion, and mimic those in other persistent human viral infections, such as hepatitis C virus (HCV), human immunodeficiency virus (HIV), and HBV mono-infection. However, compared to these larger viruses, the small HDV has perfectly adapted to evade recognition by CD8+ T cells restricted by common human leukocyte antigen (HLA) class I alleles. Furthermore, accelerated progression towards liver cirrhosis in persistent HBV/HDV co-infection was attributed to an increased immune-mediated pathology, either caused by innate pathways initiated by the interferon (IFN) system or triggered by misguided and dysfunctional T cells. These new insights into HDV-specific adaptive immunity will be discussed in this review and put into context with known well-described aspects in HBV, HCV, and HIV infections.
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Llorens-Revull M, Gregori J, Dopazo C, Rodriguez-Frías F, Garcia-Cehic D, Soria ME, Chen Q, Rando A, Perales C, Esteban JI, Quer J, Bilbao I. Study of Quasispecies Complexity and Liver Damage Progression after Liver Transplantation in Hepatitis C Virus Infected Patients. Genes (Basel) 2021; 12:genes12111731. [PMID: 34828337 PMCID: PMC8625210 DOI: 10.3390/genes12111731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023] Open
Abstract
Cirrhosis derived from chronic hepatitis C virus (HCV) infection is still a common indication for liver transplantation (LT). Reinfection of the engrafted liver is universal in patients with detectable viral RNA at the time of transplant and causes fast progression of cirrhosis (within 5 years) in around one-third of these patients. To prevent damage to the liver graft, effective direct-acting antiviral (DAA) therapy is required as soon as possible. However, because of post-LT clinical instability, it is difficult to determine the optimal time to start DAAs with a low risk of complications. Evaluate changes in quasispecies complexity following LT and seek a predictive index of fast liver damage progression to determine the timing of DAA initiation. HCV genomes isolated from pre-LT and 15-day post-LT serum samples of ten patients, who underwent orthotopic LT, were quantified and sequenced using a next-generation sequencing platform. Sequence alignments, phylogenetic trees, quasispecies complexity measures, biostatistics analyses, adjusted R2 values, and analysis of variance (ANOVA) were carried out. Three different patterns of reinfection were observed (viral bottlenecking, conserved pre-LT population, and mixed populations), suggesting that bottlenecking or homogenization of the viral population is not a generalized effect after liver graft reinfection. None of the quasispecies complexity measures predicted the future degree of liver damage. Higher and more uniform viral load (VL) values were observed in all pre-LT samples, but values were more dispersed in post-LT samples. However, VL increased significantly from the pre-LT to 15-day post-LT samples in patients with advanced fibrosis at 1-year post-LT, suggesting that a VL increase on day 15 may be a predictor of fast liver fibrosis progression. HCV kinetics after LT differ between patients and are not fibrosis-dependent. Higher VL at day 15 post-LT versus pre-LT samples may predict fast liver fibrosis progression.
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Affiliation(s)
- Meritxell Llorens-Revull
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Biochemistry, Molecular Biology, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Roche Diagnostics SL, Avinguda de la Generalitat, 171-173, 08174 Sant Cugat del Vallès, Spain
| | - Cristina Dopazo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Hepatobiliopancreatic Surgery and Transplant Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Francisco Rodriguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Biochemistry, Molecular Biology, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
| | - Maria Eugenia Soria
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
| | - Qian Chen
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
| | - Ariadna Rando
- Biochemistry and Microbiology Departments, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Celia Perales
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
| | - Juan Ignacio Esteban
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Medicine, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.L.-R.); (J.G.); (D.G.-C.); (M.E.S.); (Q.C.); (C.P.); (J.I.E.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Biochemistry, Molecular Biology, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence: or
| | - Itxarone Bilbao
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain; (C.D.); (F.R.-F.); (I.B.)
- Hepatobiliopancreatic Surgery and Transplant Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Surgery, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
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Garcia-Cehic D, Rando A, Rodriguez-Frias F, Gregori J, Costa JG, Carrión JA, Macenlle R, Pamplona J, Castro-Iglesias A, Cañizares A, Tabernero D, Campos C, Buti M, Esteban JI, Quer J. Resistance-associated substitutions after sofosbuvir/velpatasvir/voxilaprevir triple therapy failure. J Viral Hepat 2021; 28:1319-1324. [PMID: 33720484 DOI: 10.1111/jvh.13497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 02/05/2023]
Abstract
Direct-acting antivirals (DAAs) resolve chronic HCV infection in >95% of patients, but a small percentage do not respond to DAA-based therapy. These may be difficult to treat because of resistance-associated substitutions (RAS) emerging after treatment failure. Triple therapy with sofosbuvir (SOF)/velpatasvir (VEL)/voxilaprevir (VOX) is the recommended retreatment after DAA-based failure. However, in rare cases, failure to triple therapy occurs, and there is little information characterizing the viruses that relapse. To determine the RAS profile after failing SOF/VEL/VOX, and seek suitable alternatives for retreatment, samples from 5 patients were analysed using MiSeq Illumina deep sequencing before and after triple therapy. All patients were men, aged 59-78 years, 2 HCV genotype (G) 1b and 3 G3a. The most prevalent NS3 substitutions after SOF/VEL/VOX failure were Y56F and A166T. Four patients had the NS5A RAS, Y93H, after triple failure, and Y93H was observed in both G1b patients before retreatment and after SOF/ledipasvir failure. In 2 G3a patients, Y93H appeared at triple failure, and on the other G3a, A30K persisted in 100% of viral genomes. Finally, G1b patients showed C316N in NS5B, associated with SOF failure, but G3a patients had no known NS5B substitutions. HCV RAS analysis identified the following substitutions present at higher rates after triple failure: Y56F in NS3 (G1b), A166T in NS3 (G3a), A30K or Y93H in NS5A, and C316N in NS5B (G1b). A RAS-based salvage treatment (SOF + glecaprevir/pibrentasvir + RBV) was successfully used in one G3a patient.
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Affiliation(s)
- Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Ariadna Rando
- Biochemistry and Microbiology Departments, Vall d'Hebron Institut de Recerca (VHIR, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Departments, Vall d'Hebron Institut de Recerca (VHIR, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics SL, Sant Cugat del Vallès, Barcelona, Spain
| | - Juan Garcia Costa
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - José Antonio Carrión
- Liver Section, Gastroenterology Department, Hospital del Mar, Parc de Salur Mar, Barcelona, Spain
| | - Ramiro Macenlle
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - Javier Pamplona
- Gastroenterology Department, Hospital de Santa Caterina, Salt. Girona, Spain
| | | | - Angelina Cañizares
- Microbiology Department, Institut de Investigación Biomédica de a Coruña (INIBIC) - Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Departments, Vall d'Hebron Institut de Recerca (VHIR, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maria Buti
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
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10
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Antuori A, Montoya V, Piñeyro D, Sumoy L, Joy J, Krajden M, González-Gómez S, Folch C, Casabona J, Matas L, Colom J, Saludes V, Martró E. Characterization of Acute HCV Infection and Transmission Networks in People Who Currently Inject Drugs in Catalonia: Usefulness of Dried Blood Spots. Hepatology 2021; 74:591-606. [PMID: 33609288 DOI: 10.1002/hep.31757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND AND AIMS Accurate identification of recent HCV infections is critical for tracing the extent and mechanisms of ongoing transmission. We aimed to validate dried blood spot (DBS) samples for the assessment of Hepatitis C virus (HCV) genetic diversity and to determine epidemiological parameters including incidence, determinants of acute infection, and phylogenetic clustering in people who inject drugs (PWID). APPROACH AND RESULTS HCV nonstructural protein 5B next-generation sequencing was performed from plasma and/or DBS in 220 viremic PWID from the HepCdetect II study. No significant differences were found in consensus sequences or Shannon entropy (SE) intrahost diversity estimate between paired plasma/DBS specimens. SE values were used to identify acute infections with 93.3% sensitivity (95% CI, 0.81-1.06) and 95.0% specificity (95% CI, 0.88-1.02) in a set of well-defined controls. An acute HCV infection (either primary infection or reinfection) was detected in 13.5% of viremic participants and was associated with age ≤30 years (OR, 8.09), injecting less than daily (OR, 4.35), ≤5 years of injected drug use (OR, 3.43), sharing cocaine snorting straws (OR, 2.89), and being unaware of their HCV status (OR, 3.62). Annualized HCV incidence was estimated between 31 and 59/100 person-years. On phylogenetic analysis, 46.8% of viremic cases were part of a transmission pair or cluster; age ≤30 years (OR, 6.16), acute infection (OR, 5.73), and infection with subtype 1a (OR, 4.78) were independently associated with this condition. CONCLUSIONS The results obtained from plasma and DBS characterize PWID with acute infection and those involved in ongoing HCV transmission and allow estimating incidence from cross-sectional data. This information is critical for the design and assessment of targeted harm reduction programs and test-and-treat interventions and to facilitate monitoring of HCV elimination in this key population.
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Affiliation(s)
- Adrián Antuori
- Microbiology DepartmentLaboratori Clínic Metropolitana NordHospital Universitari Germans Trias i PujolInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolBadalonaSpain
- Genetics and Microbiology DepartmentUniversitat Autònoma de BarcelonaBellaterraSpain
| | | | - David Piñeyro
- High Content Genomics & Bioinformatics UnitInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolProgram of Predictive and Personalized Medicine of CancerBadalonaSpain
| | - Lauro Sumoy
- High Content Genomics & Bioinformatics UnitInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolProgram of Predictive and Personalized Medicine of CancerBadalonaSpain
| | - Jeffrey Joy
- BC Centre for Excellence in HIVVancouverBCCanada
- Department of MedicineUniversity of British ColumbiaVancouverBCCanada
| | - Mel Krajden
- Public Health LaboratoryHepatitis-Clinical Prevention Services British Columbia Centre for Disease ControlVancouverBCCanada
| | - Sara González-Gómez
- Microbiology DepartmentLaboratori Clínic Metropolitana NordHospital Universitari Germans Trias i PujolInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolBadalonaSpain
| | - Cinta Folch
- Centre for Epidemiological Studies on Sexually Transmitted Infections and HIV/AIDS of CataloniaPublic Health Agency of CataloniaBadalonaSpain
- Group 27Biomedical Research Networking Centre in Epidemiology and Public HealthInstituto de Salud Carlos IIIMadridSpain
| | - Jordi Casabona
- Centre for Epidemiological Studies on Sexually Transmitted Infections and HIV/AIDS of CataloniaPublic Health Agency of CataloniaBadalonaSpain
- Group 27Biomedical Research Networking Centre in Epidemiology and Public HealthInstituto de Salud Carlos IIIMadridSpain
| | - Lurdes Matas
- Microbiology DepartmentLaboratori Clínic Metropolitana NordHospital Universitari Germans Trias i PujolInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolBadalonaSpain
- Genetics and Microbiology DepartmentUniversitat Autònoma de BarcelonaBellaterraSpain
- Group 27Biomedical Research Networking Centre in Epidemiology and Public HealthInstituto de Salud Carlos IIIMadridSpain
| | - Joan Colom
- Programme for Prevention, Control and Treatment of HIVSTIs and Viral HepatitisPublic Health Agency of CataloniaBarcelonaSpain
| | - Verónica Saludes
- Microbiology DepartmentLaboratori Clínic Metropolitana NordHospital Universitari Germans Trias i PujolInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolBadalonaSpain
- Genetics and Microbiology DepartmentUniversitat Autònoma de BarcelonaBellaterraSpain
- Group 27Biomedical Research Networking Centre in Epidemiology and Public HealthInstituto de Salud Carlos IIIMadridSpain
| | - Elisa Martró
- Microbiology DepartmentLaboratori Clínic Metropolitana NordHospital Universitari Germans Trias i PujolInstitut d'Investigació en Ciències de la Salut Germans Trias i PujolBadalonaSpain
- Genetics and Microbiology DepartmentUniversitat Autònoma de BarcelonaBellaterraSpain
- Group 27Biomedical Research Networking Centre in Epidemiology and Public HealthInstituto de Salud Carlos IIIMadridSpain
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11
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Velásquez-Orozco F, Rando-Segura A, Martínez-Camprecios J, Salmeron P, Najarro-Centeno A, Esteban À, Quer J, Buti M, Pumarola-Suñe T, Rodríguez-Frías F. Utility of the Cobas ® Plasma Separation Card as a Sample Collection Device for Serological and Virological Diagnosis of Hepatitis C Virus Infection. Diagnostics (Basel) 2021; 11:diagnostics11030473. [PMID: 33800211 PMCID: PMC7998864 DOI: 10.3390/diagnostics11030473] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023] Open
Abstract
Diagnosis and clinical management of people infected with hepatitis C virus (HCV) relies on results from a combination of serological and virological tests. The aim of this study was to compare the performance of dried plasma spots (DPS), prepared using the cobas® Plasma Separation Card (PSC), to plasma and serum from venipuncture, for HCV diagnosis. We carried out a prospective study using DPS and paired plasma or serum samples. Serum and DPS samples were analyzed by immunoassay using Elecsys® Anti-HCV II (Roche). Plasma and DPS samples were analyzed using the cobas® HCV viral load and cobas® HCV genotyping tests (Roche). All DPS samples that had high anti-HCV antibody titers in serum were also antibody-positive, as were five of eight samples with moderate titers. Eight samples with low titers in serum were negative with DPS. Among 80 samples with plasma HCV viral loads between 61.5 and 2.2 × 108 IU/mL, 74 were RNA-positive in DPS. The mean viral load difference between plasma and DPS was 2.65 log10 IU/mL. The performance of DPS for detection of serological and virological markers of hepatitis C virus infection was comparable to that of the conventional specimen types. However, the limits of detection were higher for DPS.
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Affiliation(s)
- Fernando Velásquez-Orozco
- Department of Microbiology, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (F.V.-O.); (P.S.); (T.P.-S.)
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
| | - Ariadna Rando-Segura
- Department of Microbiology, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (F.V.-O.); (P.S.); (T.P.-S.)
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Liver Pathology Unit, Department of Microbiology and Biochemistry, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (A.N.-C.); (À.E.)
- Correspondence:
| | - Joan Martínez-Camprecios
- Department of Internal Medicine, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (J.M.-C.); (M.B.)
| | - Paula Salmeron
- Department of Microbiology, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (F.V.-O.); (P.S.); (T.P.-S.)
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
| | - Adrián Najarro-Centeno
- Liver Pathology Unit, Department of Microbiology and Biochemistry, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (A.N.-C.); (À.E.)
- Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hberon Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
- Department of Biochemistry, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Àngels Esteban
- Liver Pathology Unit, Department of Microbiology and Biochemistry, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (A.N.-C.); (À.E.)
- Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hberon Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
- Department of Biochemistry, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Josep Quer
- Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hberon Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - María Buti
- Department of Internal Medicine, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (J.M.-C.); (M.B.)
- Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hberon Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
- CIBER de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Avenida de Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Tomás Pumarola-Suñe
- Department of Microbiology, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (F.V.-O.); (P.S.); (T.P.-S.)
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
| | - Francisco Rodríguez-Frías
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Liver Pathology Unit, Department of Microbiology and Biochemistry, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (A.N.-C.); (À.E.)
- Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hberon Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
- Department of Biochemistry, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- CIBER de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Avenida de Monforte de Lemos 3-5, 28029 Madrid, Spain
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12
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Mostafa AM, Saafan HA, Al-Tawashi AS, Kasem MH, Alaa AM, Eltobgy MM, Moubarak AS, Gharib MM, Awwad MA, Omar HM, El-Derany MO. Interleukin-17 haplotyping predicts hepatocellular carcinoma in sofosbuvir, pegylated interferon-alpha-2a & ribavirin treated chronic hepatitis C patients. Virus Res 2020; 292:198226. [PMID: 33171166 DOI: 10.1016/j.virusres.2020.198226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/22/2020] [Accepted: 11/04/2020] [Indexed: 02/07/2023]
Abstract
Suspect has been directed towards some direct acting antivirals (DAAs) due to their reported association with hepatocellular carcinoma (HCC) development in chronic hepatitis C (CHC) patients. The mechanisms behind HCC development, following CHC treatment, were not well understood and may be linked to genetic variabilities in different patients which affect several cytokine productions involved in angiogenesis and inflammation. Of these variabilities, is the genetic polymorphisms in the interleukin-17 (IL-17) A receptor gene. Being an important pleiotropic cytokine, this study aimed to investigate the association between haplotypes in IL-17A receptor rs2275913 and rs3819024 and development of HCC in CHC patients treated with either triple therapy (sofosbuvir (SOF), pegylated interferon-alpha-2a (Peg-IFNα-2a) & ribavirin(RBV)) or with dual therapy (Peg-IFNα-2a&RBV). A cohort of 100 CHC patients was recruited in this study. Samples were tested for single nucleotide polymorphism (SNPs) in IL-17A receptor (rs2275913 and rs3819024) using TaqMan Genotyping assay. Our results showed that the presence of G-G haplotype in IL-17A (rs2275913& rs3819024) is inversely associated with HCC development in patients receiving triple therapy. While, high serum AFP levels are directly associated with HCC development in patients receiving triple therapy. However, in patients receiving dual therapy, HCC development was only associated with high serum alpha fetoprotein (AFP) levels and was not correlated to any specific allele in our studied SNPs. Such results highlight the importance of IL17A receptor gene haplotyping in the prediction of HCC development in patients receiving triple therapy. These results will aid in performing tailored, personalized strategy for CHC treatment.
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Affiliation(s)
- Ahmed M Mostafa
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Hesham A Saafan
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Badr University, Cairo, Egypt
| | - Ahmed S Al-Tawashi
- Drug Design Program, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Muhannad H Kasem
- Drug Design Program, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Ahmed M Alaa
- Drug Design Program, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mahmoud M Eltobgy
- Drug Design Program, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Ahmed S Moubarak
- Drug Design Program, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Manar M Gharib
- Drug Design Program, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohamed A Awwad
- Drug Design Program, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Hazem M Omar
- Radiology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Marwa O El-Derany
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.
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13
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Aziz H, Fatima S, Faheem M. Indeterminate Prediction of Hepatitis C Virus Genotype by Commercial Real-Time Polymerase Chain Reaction Assay Resolving by Sequencing to Avoid the Consequence of Inaccurate Typing. Viral Immunol 2020; 33:507-513. [PMID: 32429831 DOI: 10.1089/vim.2019.0162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pakistan is ranked second highest after Egypt in hepatitis C virus (HCV) infection. Accurate typing is mandatory to be compliant with the World Health Organization strategy to eliminate HCV infection in 2030. We characterized the HCV genotypes using Abbott real-time polymerase chain reaction assay and indeterminate samples were sequenced. We also investigated the distribution of HCV genotype among different age groups and gender in chronic HCV patients. One thousand thirteen samples were tested for HCV genotyping using Abbott real-time HCV genotyping assay. RNA extraction from plasma was done using the m2000sp platform. The amplification and detection of genotypes was done on m2000rt instrument. The lower limit of detection assay is 500 IU/mL. The indeterminate genotypes were analyzed by sequencing of the NS5B region. We found genotype 1 in 1.68%, genotype 1b in 0.89%, genotype 1a in 0.79%, genotype 2 in 0.6, genotype 3 in 94.37%, genotype 4 in 0.4%, genotype 5 in 0.09%, and indeterminate genotype result were found in 1.18%. Abbott assay could not identify 12 samples of genotype 3 (1.18%) and gave the indeterminate result. It also fails to assign some of the samples of genotype 1 into 1a and 1b. The indeterminate genotypes were resolved by sequencing followed by phylogenetic analysis. Genotype 3 is the predominant genotype and significantly higher in females as compared with males. Genotype 1a is more common in males than in females. Indeterminate HCV genotypes on sequencing analysis identify as genotype 3a and likewise subtype of genotype1 as 1a.
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Affiliation(s)
- Hafsa Aziz
- Nuclear Medicine, Oncology, and Radiotherapy Institute, Islamabad, Pakistan
| | - Shazia Fatima
- Nuclear Medicine, Oncology, and Radiotherapy Institute, Islamabad, Pakistan
| | - Mohammad Faheem
- Nuclear Medicine, Oncology, and Radiotherapy Institute, Islamabad, Pakistan
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14
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D'Andrea L, Pérez-Rodríguez FJ, de Castellarnau M, Guix S, Ribes E, Quer J, Gregori J, Bosch A, Pintó RM. The Critical Role of Codon Composition on the Translation Efficiency Robustness of the Hepatitis A Virus Capsid. Genome Biol Evol 2020; 11:2439-2456. [PMID: 31290967 PMCID: PMC6735747 DOI: 10.1093/gbe/evz146] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 12/13/2022] Open
Abstract
Hepatoviruses show an intriguing deviated codon usage, suggesting an evolutionary signature. Abundant and rare codons in the cellular genome are scarce in the human hepatitis A virus (HAV) genome, while intermediately abundant host codons are abundant in the virus. Genotype–phenotype maps, or fitness landscapes, are a means of representing a genotype position in sequence space and uncovering how genotype relates to phenotype and fitness. Using genotype–phenotype maps of the translation efficiency, we have shown the critical role of the HAV capsid codon composition in regulating translation and determining its robustness. Adaptation to an environmental perturbation such as the artificial induction of cellular shutoff—not naturally occurring in HAV infection—involved movements in the sequence space and dramatic changes of the translation efficiency. Capsid rare codons, including abundant and rare codons of the cellular genome, slowed down the translation efficiency in conditions of no cellular shutoff. In contrast, rare capsid codons that are abundant in the cellular genome were efficiently translated in conditions of shutoff. Capsid regions very rich in slowly translated codons adapt to shutoff through sequence space movements from positions with highly robust translation to others with diminished translation robustness. These movements paralleled decreases of the capsid physical and biological robustness, and resulted in the diversification of capsid phenotypes. The deviated codon usage of extant hepatoviruses compared with that of their hosts may suggest the occurrence of a virus ancestor with an optimized codon usage with respect to an unknown ancient host.
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Affiliation(s)
- Lucía D'Andrea
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Spain
| | - Francisco-Javier Pérez-Rodríguez
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Spain
| | - Montserrat de Castellarnau
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Spain
| | - Enric Ribes
- Enteric Virus Laboratory, Department of Cell Biology, Physiology and Immunology, School of Biology, University of Barcelona, Spain
| | - Josep Quer
- Liver Unit, Internal Medicine, Hepatic Diseases Laboratory, Vall d'Hebron Research Institute-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain.,Centre of the Biomedical Research Network (CIBER) for Hepatic and Digestive Diseases (CIBERehd), Instituto de Salud Carlos III
| | - Josep Gregori
- Liver Unit, Internal Medicine, Hepatic Diseases Laboratory, Vall d'Hebron Research Institute-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain.,Roche Diagnostics SL, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Spain
| | - Rosa M Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Spain
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15
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Chen Q, Perales C, Soria ME, García-Cehic D, Gregori J, Rodríguez-Frías F, Buti M, Crespo J, Calleja JL, Tabernero D, Vila M, Lázaro F, Rando-Segura A, Nieto-Aponte L, Llorens-Revull M, Cortese MF, Fernandez-Alonso I, Castellote J, Niubó J, Imaz A, Xiol X, Castells L, Riveiro-Barciela M, Llaneras J, Navarro J, Vargas-Blasco V, Augustin S, Conde I, Rubín Á, Prieto M, Torras X, Margall N, Forns X, Mariño Z, Lens S, Bonacci M, Pérez-Del-Pulgar S, Londoño MC, García-Buey ML, Sanz-Cameno P, Morillas R, Martró E, Saludes V, Masnou-Ridaura H, Salmerón J, Quíles R, Carrión JA, Forné M, Rosinach M, Fernández I, García-Samaniego J, Madejón A, Castillo-Grau P, López-Núñez C, Ferri MJ, Durández R, Sáez-Royuela F, Diago M, Gimeno C, Medina R, Buenestado J, Bernet A, Turnes J, Trigo-Daporta M, Hernández-Guerra M, Delgado-Blanco M, Cañizares A, Arenas JI, Gomez-Alonso MJ, Rodríguez M, Deig E, Olivé G, Río OD, Cabezas J, Quiñones I, Roget M, Montoliu S, García-Costa J, Force L, Blanch S, Miralbés M, López-de-Goicoechea MJ, García-Flores A, Saumoy M, Casanovas T, Baliellas C, Gilabert P, Martin-Cardona A, Roca R, Barenys M, Villaverde J, Salord S, Camps B, Silvan di Yacovo M, Ocaña I, Sauleda S, Bes M, Carbonell J, Vargas-Accarino E, Ruzo SP, Guerrero-Murillo M, Von Massow G, Costafreda MI, López RM, González-Moreno L, Real Y, Acero-Fernández D, Viroles S, Pamplona X, Cairó M, Ocete MD, Macías-Sánchez JF, Estébanez A, Quer JC, Mena-de-Cea Á, Otero A, Castro-Iglesias Á, Suárez F, Vázquez Á, Vieito D, López-Calvo S, Vázquez-Rodríguez P, Martínez-Cerezo FJ, Rodríguez R, Macenlle R, Cachero A, Mereish G, Mora-Moruny C, Fábregas S, Sacristán B, Albillos A, Sánchez-Ruano JJ, Baluja-Pino R, Fernández-Fernández J, González-Portela C, García-Martin C, Sánchez-Antolín G, Andrade RJ, Simón MA, Pascasio JM, Romero-Gómez M, Antonio Del-Campo J, Domingo E, Esteban R, Esteban JI, Quer J. Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure. Antiviral Res 2020; 174:104694. [PMID: 31857134 DOI: 10.1016/j.antiviral.2019.104694] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 10/24/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
A percentage of hepatitis C virus (HCV)-infected patients fail direct acting antiviral (DAA)-based treatment regimens, often because of drug resistance-associated substitutions (RAS). The aim of this study was to characterize the resistance profile of a large cohort of patients failing DAA-based treatments, and investigate the relationship between HCV subtype and failure, as an aid to optimizing management of these patients. A new, standardized HCV-RAS testing protocol based on deep sequencing was designed and applied to 220 previously subtyped samples from patients failing DAA treatment, collected in 39 Spanish hospitals. The majority had received DAA-based interferon (IFN) α-free regimens; 79% had failed sofosbuvir-containing therapy. Genomic regions encoding the nonstructural protein (NS) 3, NS5A, and NS5B (DAA target regions) were analyzed using subtype-specific primers. Viral subtype distribution was as follows: genotype (G) 1, 62.7%; G3a, 21.4%; G4d, 12.3%; G2, 1.8%; and mixed infections 1.8%. Overall, 88.6% of patients carried at least 1 RAS, and 19% carried RAS at frequencies below 20% in the mutant spectrum. There were no differences in RAS selection between treatments with and without ribavirin. Regardless of the treatment received, each HCV subtype showed specific types of RAS. Of note, no RAS were detected in the target proteins of 18.6% of patients failing treatment, and 30.4% of patients had RAS in proteins that were not targets of the inhibitors they received. HCV patients failing DAA therapy showed a high diversity of RAS. Ribavirin use did not influence the type or number of RAS at failure. The subtype-specific pattern of RAS emergence underscores the importance of accurate HCV subtyping. The frequency of "extra-target" RAS suggests the need for RAS screening in all three DAA target regions.
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Affiliation(s)
- Qian Chen
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - María Eugenia Soria
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Damir García-Cehic
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Gregori
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Roche Diagnostics SL, Sant Cugat del Valles, Barcelona, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - María Buti
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Crespo
- Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - Marta Vila
- Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - Fernando Lázaro
- Microbiology Department, Hospital Universitario La Paz, Madrid, Spain
| | | | | | - Meritxell Llorens-Revull
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Irati Fernandez-Alonso
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - José Castellote
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Jordi Niubó
- Microbiology Department, Hospital Universitari de Bellvitge, Barcelona
| | - Arkaitz Imaz
- HIV and STI Unit, Infectious Diseases Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Xavier Xiol
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Lluís Castells
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Mar Riveiro-Barciela
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Llaneras
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Víctor Vargas-Blasco
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Salvador Augustin
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Conde
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Ángel Rubín
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Martín Prieto
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Xavier Torras
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Microbiology Department, Hospital Universitari Santa Creu i Sant Pau, Barcelona, Spain
| | - Nuria Margall
- Digestive Pathology Unit, Hospital Universitari Santa Creu i Sant Pau, Barcelona, Spain
| | - Xavier Forns
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Zoe Mariño
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Sabela Lens
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Martin Bonacci
- Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Sofía Pérez-Del-Pulgar
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Maria Carlota Londoño
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | | | | | - Rosa Morillas
- Liver Unit, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Elisa Martró
- Microbiology Department, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Institut de Recerca Germans Trias i Pujol (IGTP), Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Verónica Saludes
- Microbiology Department, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Institut de Recerca Germans Trias i Pujol (IGTP), Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | | | - Javier Salmerón
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Complejo Hospitalario de Granada, Granada, Spain
| | - Rosa Quíles
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Complejo Hospitalario de Granada, Granada, Spain
| | - José Antonio Carrión
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Parc de Salut Mar - Hospital del Mar, Barcelona, Spain
| | - Montserrat Forné
- Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain
| | - Mercè Rosinach
- Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain
| | | | - Javier García-Samaniego
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain
| | - Antonio Madejón
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain
| | - Pilar Castillo-Grau
- Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain
| | - Carme López-Núñez
- Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - María José Ferri
- Clinical Laboratory, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Rosa Durández
- Laboratori Territorial - Hospital Santa Caterina, Girona, Spain
| | - Federico Sáez-Royuela
- Gastroenterology and Hepatology Depart., Hospital Universitario de Burgos, Burgos, Spain
| | - Moisés Diago
- Liver Unit, Hospital General de Valencia, Valencia, Spain
| | | | - Rafael Medina
- Microbiology Unit, Hospital General de Valencia, Valencia, Spain
| | - Juan Buenestado
- Medicine Department-Medical School, Hospital Univ. Arnau de Vilanova, Lleida, Spain
| | - Albert Bernet
- Microbiology Department, Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Juan Turnes
- Gastroenterology and Hepatology Department, Instituto de Investigación Sanitaria Galicia Sur (IISGS) - Complejo Hospitalario de Pontevedra, Pontevedra, Spain
| | - Matilde Trigo-Daporta
- Microbiology and Parasitology Department, Complejo Hospitalario de Pontevedra, Pontevedra, Spain
| | | | | | - Angelina Cañizares
- Microbiology Department, Institut de Investigación Biomédica de a Coruña (INIBIC) - Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | | | | | - Manuel Rodríguez
- Gastroenterology Depart., Central University Hospital of Asturias (HUCA), Oviedo, Spain
| | | | - Gemma Olivé
- Sant Jaume de Calella County Hospital, Barcelona, Spain
| | - Oscar Del Río
- Sant Jaume de Calella County Hospital, Barcelona, Spain
| | - Joaquín Cabezas
- Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Ildefonso Quiñones
- Gastroenterology Department, Dr Negrin University Hospital of Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Mercè Roget
- Liver Unit, Consorci Sanitari de Terrassa - Hospital de Terrassa, Terrassa, Spain
| | - Silvia Montoliu
- Gastroenterology Unit, Joan XXIII University Hospital, Tarragona, Spain
| | - Juan García-Costa
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | | | - Silvia Blanch
- Hospital Universitari Sant Pau i Santa Tecla, Tarragona, Spain
| | - Miguel Miralbés
- Gastroenterology Department, Hospital Universitari Santa Maria de Lleida, Lleida, Spain
| | | | | | - María Saumoy
- HIV and STI Unit, Infectious Diseases Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Teresa Casanovas
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Carme Baliellas
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Pau Gilabert
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | | | - Rosa Roca
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Mercè Barenys
- Liver Unit, Hospital de Viladecans, Barcelona, Spain
| | - Joana Villaverde
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Silvia Salord
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Blau Camps
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | | | - Imma Ocaña
- Infectious Disease Unit, HUVH, Barcelona, Spain
| | - Silvia Sauleda
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Marta Bes
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Judit Carbonell
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Elena Vargas-Accarino
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Sofía P Ruzo
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Mercedes Guerrero-Murillo
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Georg Von Massow
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - María Isabel Costafreda
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Rosa Maria López
- Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | | | - Yolanda Real
- Liver Unit, Hospital Universitario La Princesa, Madrid, Spain
| | | | - Silvia Viroles
- Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Xavier Pamplona
- Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Mireia Cairó
- Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain
| | | | | | - Angel Estébanez
- Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Joan Carles Quer
- Gastroenterology Unit, Joan XXIII University Hospital, Tarragona, Spain
| | - Álvaro Mena-de-Cea
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - Alejandra Otero
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | | | - Francisco Suárez
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - Ángeles Vázquez
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - David Vieito
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - Soledad López-Calvo
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | | | | | - Raúl Rodríguez
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - Ramiro Macenlle
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - Alba Cachero
- Liver Unit, Hospital d'Igualada, Barcelona, Spain
| | | | | | - Silvia Fábregas
- Fundació Salut Empordà - Hospital de Figueres, Girona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | - Manolo Romero-Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario Virgen de Valme, Seville, Spain
| | - José Antonio Del-Campo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario Virgen de Valme, Seville, Spain
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Centro de Biología Molecular "Severo Ochoa" (CBMSO), Universidad Autónoma de Madrid, Madrid, Spain
| | - Rafael Esteban
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
| | - Josep Quer
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
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16
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Bhebhe L, Anderson M, Souda S, Choga WT, Zumbika E, Shaver ZM, Mbangiwa T, Phinius BB, Banda CC, Melamu P, Musonda RM, Essex M, Blackard JT, Moyo S, Gaseitsiwe S. Molecular characterization of hepatitis C virus in liver disease patients in Botswana: a retrospective cross-sectional study. BMC Infect Dis 2019; 19:875. [PMID: 31640596 PMCID: PMC6805647 DOI: 10.1186/s12879-019-4514-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/26/2019] [Indexed: 12/11/2022] Open
Abstract
Background Hepatitis C virus (HCV) infection is a major cause of chronic liver disease globally. Direct acting antivirals (DAAs) have proven effective in curing HCV. However, the current standard of care (SOC) in Botswana remains PEGylated interferon-α (IFN-α) with ribavirin. Several mutations have been reported to confer resistance to interferon-based treatments. Therefore, there is a need to determine HCV genotypes in Botswana, as these data will guide new treatment guidelines and understanding of HCV epidemiology in Botswana. Methods This was a retrospective cross-sectional pilot study utilizing plasma obtained from 55 participants from Princess Marina Hospital in Gaborone, Botswana. The partial core region of HCV was amplified, and genotypes were determined using phylogenetic analysis. Results Four genotype 5a and two genotype 4v sequences were identified. Two significant mutations – K10Q and R70Q – were observed in genotype 5a sequences and have been associated with increased risk of hepatocellular carcinoma (HCC), while R70Q confers resistance to interferon-based treatments. Conclusion Genotypes 5a and 4v are circulating in Botswana. The presence of mutations in genotype 5 suggests that some patients may not respond to IFN-based regimens. The information obtained in this study, in addition to the World health organization (WHO) recommendations, can be utilized by policy makers to implement DAAs as the new SOC for HCV treatment in Botswana.
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Affiliation(s)
- Lynnette Bhebhe
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana.,Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Motswedi Anderson
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana
| | - Sajini Souda
- Department of Pathology, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana.,Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Edward Zumbika
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Zachary M Shaver
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana
| | - Tshepiso Mbangiwa
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana.,Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Bonolo B Phinius
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana
| | - Chabeni C Banda
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana
| | - Pinkie Melamu
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana
| | - Rosemary M Musonda
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jason T Blackard
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Research Laboratory, Gaborone, Botswana. .,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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17
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Uribe-Noguez LA, Mata-Marín JA, Ocaña-Mondragón A, Pompa-Mera EN, Ribas-Aparicio RM, Arroyo-Anduiza CI, Gomez-Torres ME, Chaparro-Sánchez A, Gaytán-Martínez J, Mauss S. Comparison of direct sequencing of the NS5B region with the Versant HCV genotype 2.0 assay for genotyping of viral isolates in Mexico. J Infect Chemother 2019; 26:205-210. [PMID: 31537472 DOI: 10.1016/j.jiac.2019.08.009] [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: 04/27/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) infection affects an estimated 71 million people worldwide. HCV is classified into eight genotypes and >70 subtypes. Determination of HCV genotype is important for selection of type and duration of antiviral therapy, and genotype is also a predictor of treatment response. The most commonly used HCV genotyping method in clinical laboratories is a hybridization-based line probe assay (LiPA; Versant HCV Genotype 2.0). However, these methods have a lack of specificity in genotype identification and subtype assignment. Here, we compared the performance of Versant HCV Genotype 2.0 with the gold standard direct sequencing of the NS5B region, in 97 samples from Mexican patients. We found a genotypic concordance of 63.9% between these methods. While 68 samples (70%) were classified into HCV genotype 1 (GT1) by NS5B sequencing, it was not true for 17 samples (17.5%), which were not match HCV subtype by LiPA. Furthermore, nine of the 33 samples classified by NS5B sequencing as GT1a were not identified by LiPA. Use of direct sequencing could improve selection of the optimal therapy, avoid possible failures of therapy and avoid high costs resulting from incorrect genotyping tests in settings without broad access to pangenotypic regimens.
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Affiliation(s)
- Luis Antonio Uribe-Noguez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico; Departamento de Microbiología, Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, IPN, Mexico City, Mexico; Centro de Simulación Médica, Facultad Mexicana de Medicina, Universidad La Salle, Mexico City, Mexico.
| | - José Antonio Mata-Marín
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Alicia Ocaña-Mondragón
- Laboratorio Central de Epidemiología, División de Laboratorios de Vigilancia e Investigación Epidemiológica, CMN "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Ericka Nelly Pompa-Mera
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, IPN, Mexico City, Mexico
| | - Carla Ileana Arroyo-Anduiza
- Departamento de Patología Clínica, Banco Central de Sangre, CMN "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - María Elena Gomez-Torres
- Laboratorio de Urgencias, Hospital de Infectología, Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Alberto Chaparro-Sánchez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Jesus Gaytán-Martínez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Stefan Mauss
- Center for HIV and Hepatogastroenterology, Duesseldorf, Germany
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18
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Amer F, Yousif MM, Hammad NM, Garcia-Cehic D, Gregori J, Rando-Segura A, Nieto-Aponte L, Esteban JI, Rodriguez-Frias F, Quer J. Deep-sequencing study of HCV G4a resistance-associated substitutions in Egyptian patients failing DAA treatment. Infect Drug Resist 2019; 12:2799-2807. [PMID: 31571936 PMCID: PMC6750843 DOI: 10.2147/idr.s214735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/23/2019] [Indexed: 02/05/2023] Open
Abstract
PURPOSE To study resistance-associated substitutions using next-generation sequencing in Egyptian hepatitis C virus-infected patients failing direct-acting antiviral treatment. METHODS The current study describes three cases of treatment failure in patients referred to Zagazig Viral Hepatitis Treatment Center (ZVHTC), Sharkia Governorate, Egypt. RAS were identified and characterized using deep sequencing. The first patient had breakthrough while receiving a daclatasvir (DCV)+sofosbuvir (SOF) regimen, patient 2 relapsed after treatment with DCV+SOF+ribavirin (RBV), and patient 3 relapsed after DCV+SOF therapy. A serum sample was collected from each patient at failure and sent to Vall d'Hebron Research Institute at Hospital Universitari Vall d'Hebron in Barcelona (Spain) for deep-sequencing study to identify and characterize the RAS present in the samples. RESULTS The following were identified: L28M, L30S and L28M+L30S in patient 1, L30R in patient 2, and R155C, D168E, L28M, L30H, L30S, L28M+L30H, and L28M+L30S in patient 3. CONCLUSION To the best of our knowledge, this is the first report from Egypt of patients failing DAA-based therapy, describing the associated RAS. This information will be of help to understand the natural history of HCV in Egyptian patients and guide the proper choice of retreatment protocols.
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Affiliation(s)
- Fatma Amer
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Medical College, Zagazig University, Zagazig, Egypt
| | - Monkez M Yousif
- Internal Medicine Department , Faculty of Medicine, Medical College, Zagazig University, Zagazig, Egypt
| | - Noha M Hammad
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Medical College, Zagazig University, Zagazig, Egypt
| | - Damir Garcia-Cehic
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona08035, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid28029, Spain
| | - Josep Gregori
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona08035, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid28029, Spain
- Business Development Department, Roche Diagnostics SL, Sant Cugat del Vallès, Barcelona08174, Spain
| | - Ariadna Rando-Segura
- Liver Pathology Unit, Department of Biochemistry and Microbiology, HUVH, Barcelona08035, Spain
| | - Leonardo Nieto-Aponte
- Liver Pathology Unit, Department of Biochemistry and Microbiology, HUVH, Barcelona08035, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona08035, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid28029, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid28029, Spain
- Liver Pathology Unit, Department of Biochemistry and Microbiology, HUVH, Barcelona08035, Spain
| | - Josep Quer
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d’Hebron (HUVH), Barcelona08035, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid28029, Spain
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19
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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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20
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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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21
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Abstract
Introduction: The improvement of number of people diagnosed with hepatitis C virus (HCV) infection is crucial to reach the WHO objectives for eliminating viral hepatitis by 2030. Alternatives to classical HCV virological tests using serum or plasma taken from venous puncture including point-of-care (POC) tests and dried blood spot (DBS) are being considered for HCV screening, diagnosis, and monitoring. Reflex nucleic acid testing and HCV core antigen test have the potential to simplify diagnostic algorithm, increase diagnosis and facilitate linkage to care. Areas covered: This review examines strategies for the improvement of HCV testing and diagnosis including alternatives to classical HCV virological tests and approaches for simplified diagnostic algorithms. Expert opinion: Serological and molecular POC tests are now available for HCV antibody and HCV RNA detections in less than 20 and 60, respectively. DBS offers the main advantage to store desiccated blood that can be easily transported to reference centers where state-of-the-art molecular and serological diagnostic tests are used. Simplifications of diagnostic algorithms are urgently needed to enhance HCV testing, linkage to care and treatment.
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Affiliation(s)
- Stéphane Chevaliez
- a National Reference Center for Viral Hepatitis B, C and delta, Department of Virology, Hôpital Henri Mondor , Université Paris-Est , Créteil , France.,b INSERM U955 , Créteil , France
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22
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Saludes V, Antuori A, Reinhardt B, Viciana I, Clavijo E, Schreiber L, Tenenbaum M, Rodriguez-Frias F, Quer J, Matas L, Martró E. Reliable resolution of ambiguous hepatitis C virus genotype 1 results with the Abbott HCV Genotype Plus RUO assay. Sci Rep 2019; 9:3678. [PMID: 30842623 PMCID: PMC6403303 DOI: 10.1038/s41598-019-40099-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/27/2018] [Indexed: 12/19/2022] Open
Abstract
Accurate subtyping of hepatitis C virus genotype 1 (HCV-1) remains clinically and epidemiologically relevant. The Abbott HCV Genotype Plus RUO (GT Plus) assay, targeting the core region, was evaluated as a reflex test to resolve ambiguous HCV-1 results in a challenging sample collection. 198 HCV-1 specimens were analysed with GT Plus (38 specimens with and 160 without subtype assigned by the Abbott RealTime Genotype II (GT II) assay targeting the 5'NC and NS5B regions). Sanger sequencing of the core and/or NS5B regions were performed in 127 specimens without subtype assignment by GT II, with "not detected" results by GT Plus, or with mixed genotypes/subtypes. The remaining GT Plus results were compared to LiPA 2.0 (n = 45) or just to GT II results if concordant (n = 26). GT Plus successfully assigned the subtype in 142/160 (88.8%) samples. "Not detected" results indicated other HCV-1 subtypes/genotypes or mismatches in the core region in subtype 1b. The subtyping concordance between GT Plus and either sequencing or LiPA was 98.6% (140/142). Therefore, combined use of GT II and GT Plus assays represents a reliable and simple approach which considerably reduced the number of ambiguous HCV-1 results and enabled a successful subtyping of 98.9% of all HCV-1 samples.
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Affiliation(s)
- V Saludes
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol; Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - A Antuori
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol; Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Badalona, Spain
| | | | - I Viciana
- Microbiology Service, Hospital Virgen de la Victoria, Málaga, Spain
| | - E Clavijo
- Microbiology Service, Hospital Virgen de la Victoria, Málaga, Spain
| | | | | | - F Rodriguez-Frias
- Liver Pathology Lab, Biochemistry and Microbiology Department, University Hospital Vall d'Hebron, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - J Quer
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Liver Diseases-Viral Hepatitis, Vall d'Hebron Institute of Research (VHIR-HUVH), Barcelona, Spain
| | - L Matas
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol; Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Badalona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - E Martró
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol; Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Badalona, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.
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23
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Olmstead AD, Montoya V, Chui CK, Dong W, Joy JB, Tai V, Poon AFY, Nguyen T, Brumme CJ, Martinello M, Matthews GV, Richard Harrigan P, Dore GJ, Applegate TL, Grebely J, Howe AYM. A systematic, deep sequencing-based methodology for identification of mixed-genotype hepatitis C virus infections. INFECTION GENETICS AND EVOLUTION 2019; 69:76-84. [PMID: 30654177 DOI: 10.1016/j.meegid.2019.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/10/2019] [Accepted: 01/13/2019] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) mixed genotype infections can affect treatment outcomes and may have implications for vaccine design and disease progression. Previous studies demonstrate 0-39% of high-risk, HCV-infected individuals harbor mixed genotypes however standardized, sensitive methods of detection are lacking. This study compared PCR amplicon, random primer (RP), and probe enrichment (PE)-based deep sequencing methods coupled with a custom sequence analysis pipeline to detect multiple HCV genotypes. Mixed infection cutoff values, based on HCV read depth and coverage, were identified using receiver operating characteristic curve analysis. The methodology was validated using artificially mixed genotype samples and then applied to two clinical trials of HCV treatment in high-risk individuals (ACTIVATE, 114 samples from 90 individuals; DARE-C II, 26 samples from 18 individuals) and a cohort of HIV/HCV co-infected individuals (Canadian Coinfection Cohort (CCC), 3 samples from 2 individuals with suspected mixed genotype infections). Amplification bias of genotype (G)1b, G2, G3 and G5 was observed in artificially mixed samples using the PCR method while no genotype bias was observed using RP and PE. RP and PE sequencing of 140 ACTIVATE and DARE-C II samples identified the following primary genotypes: 15% (n = 21) G1a, 76% (n = 106) G3, and 9% (n = 13) G2. Sequencing of ACTIVATE and DARE-C II demonstrated, on average, 2% and 1% of HCV reads mapping to a second genotype using RP and PE, respectively, however none passed the mixed infection cutoff criteria and phylogenetics confirmed no mixed infections. From CCC, one mixed infection was confirmed while the other was determined to be a recombinant genotype. This study underlines the risk for false identification of mixed HCV infections and stresses the need for standardized methods to improve prevalence estimates and to understand the impact of mixed infections for management and elimination of HCV.
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Affiliation(s)
| | | | - Celia K Chui
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Winnie Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Jeffrey B Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada; Faculty of Medicine, Department of Medicine, Division of AIDS, University of British Columbia, Vancouver, BC, Canada
| | - Vera Tai
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Art F Y Poon
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Thuy Nguyen
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | | | | | - P Richard Harrigan
- Faculty of Medicine, Department of Medicine, Division of AIDS, University of British Columbia, Vancouver, BC, Canada
| | - Gregory J Dore
- UNSW Sydney, The Kirby Institute, Sydney, NSW, Australia
| | | | - Jason Grebely
- UNSW Sydney, The Kirby Institute, Sydney, NSW, Australia
| | - Anita Y M Howe
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
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24
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von Massow G, Garcia-Cehic D, Gregori J, Rodriguez-Frias F, Macià MD, Escarda A, Esteban JI, Quer J. Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype. Infect Drug Resist 2019; 12:947-955. [PMID: 31118701 PMCID: PMC6499441 DOI: 10.2147/idr.s195441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/07/2019] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus (HCV) is a highly variable infectious agent, classified into 8 genotypes and 86 subtypes. Our laboratory has implemented an in-house developed high-resolution HCV subtyping method based on next-generation sequencing (NGS) for error-free classification of the virus using phylogenetic analysis and analysis of genetic distances in sequences from patient samples compared to reference sequences. During routine diagnostic, a sample from an Equatorial Guinea patient could not be classified into any of the existing subtypes. The whole genome was analyzed to confirm that the new isolate could be classified as a new HCV subtype. In addition, naturally occurring resistance-associated substitutions (RAS) were analyzed by NGS. Whole-genome analysis based on p-distances suggests that the sample belongs to a new HCV genotype 1 subtype. Several RAS in the NS3 (S122T, D168E and I170V) and NS5A protein (Q(1b)24K, R(1b)30Q and Y93L+Y93F) were found, which could limit the use of some inhibitors for treating this subtype. RAS studies of new subtypes are of great interest for tailoring treatment, as no data on treatment efficacy are reported. In our case, the patient has not yet been treated, and the RAS report will be used to design the most effective treatment.
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Affiliation(s)
- Georg von Massow
- Liver Unit, Liver Diseases – Viral Hepatitis, Vall d’Hebron Institut of Research (VHIR) – Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Liver Diseases – Viral Hepatitis, Vall d’Hebron Institut of Research (VHIR) – Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Gregori
- Liver Unit, Liver Diseases – Viral Hepatitis, Vall d’Hebron Institut of Research (VHIR) – Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics S.L., Sant Cugat del Vallès, Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - María Dolores Macià
- Unidad de Microbiología Molecular, Servicio de Microbiología, Instituto de Investigación Sanitaria de les Illes Balears (IdISBa), Hospital Universitario Son Espases, Mallorca, Spain
| | - Ana Escarda
- Digestive Department, Hospital Universitario Son Espases, Mallorca, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Diseases – Viral Hepatitis, Vall d’Hebron Institut of Research (VHIR) – Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep Quer
- Liver Unit, Liver Diseases – Viral Hepatitis, Vall d’Hebron Institut of Research (VHIR) – Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain
- Correspondence: Josep QuerLiver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR-HUVH), Barcelona08035, SpainTel +3 493 489 4034Email
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Hepatitis C virus genotype diversity and distribution among methadone maintenance treatment patients in Jiangsu, China. Drug Alcohol Depend 2019; 194:101-106. [PMID: 30419403 DOI: 10.1016/j.drugalcdep.2018.09.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/31/2018] [Accepted: 09/10/2018] [Indexed: 12/23/2022]
Abstract
BACKGROUND Heroin users are vulnerable and represent a highly-infected reservoir for hepatitis C virus (HCV) infection. This study investigated HCV prevalence and genotypes distribution among heroin users who received methadone maintenance treatment (MMT) in Jiangsu. METHODS From June to December in 2016, a total of 534 patients among nine MMT clinics in six regions of Jiangsu were enrolled, with their demographic characteristics collected and serum samples tested for HCV antibody. 395 samples were seropositive and furthered to RNA extraction. HCV NS5B region fragments were amplified and subsequently sequenced. RESULTS Among HCV seropositive samples, 240 were characterized by NS5B partial sequences and classified into four genotypes (GPs) and eight subtypes. HCV GP3 predominated and accounted for 66.3%, followed by GP1 (27.5%), GP6 (4.2%) and GP2 (2.1%). HCV subtypes 3b (41.7%) and 3a (24.6%) were the most common subtypes. None of the demographic characteristics showed a significant difference when comparing with HCV genotypes. The geographic feature shown GPs in six regions were the same, but the frequency of subtypes exhibited regional divergence. Phylogenetic analyses demonstrated that 3b had become a local endemic in Jiangsu. CONCLUSION The distribution of HCV subtypes among heroin users in Jiangsu province was complex. The data could provide more precise estimates for HCV prevalence and genotype distribution as well as heroin users of Jiangsu province.
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Gambato M, Gregori J, Quer J, Koutsoudakis G, González P, Caro-Pérez N, García-Cehic D, García-González N, González-Candelas F, Esteban JI, Crespo G, Navasa M, Forns X, Pérez-Del-Pulgar S. Hepatitis C virus intrinsic molecular determinants may contribute to the development of cholestatic hepatitis after liver transplantation. J Gen Virol 2018; 100:63-68. [PMID: 30451649 DOI: 10.1099/jgv.0.001175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cholestatic hepatitis C (CHC) is a severe form of hepatitis C virus (HCV) infection recurrence that leads to high graft loss rates early after liver transplantation (LT). To investigate the pathogenic mechanisms of CHC, we analysed HCV quasispecies in CHC patients compared to a control group (mild hepatitis C recurrence) by deep pyrosequencing. At the time of LT, NS5B quasispecies complexity was similar between the two groups but, after LT, it decreased more sharply in CHC patients than in the control group. Interestingly, the major variant before LT propagated efficiently and remained as the dominant sequence after LT in 62 % of CHC patients versus 11 % of controls (P=0.031). Sequence analysis of the complete non-structural region in a limited number of patients revealed a potential 12 aa signature specific to the CHC group. These data suggest that intrinsic molecular determinants in the circulating HCV quasispecies may provide a fitness advantage, contributing to the development of CHC.
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Affiliation(s)
- Martina Gambato
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain.,2Multivisceral Transplant Unit and Gastroenterology, Padova University Hospital, Padova, Italy.,†Present address: Multivisceral Transplant Unit and Gastroenterology, Padova University Hospital, Padova, Italy
| | - Josep Gregori
- 3Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain.,4Roche Diagnostics SL. Sant Cugat del Vallès, Barcelona, Spain
| | - Josep Quer
- 3Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain
| | - George Koutsoudakis
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Patricia González
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Noelia Caro-Pérez
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain.,‡Present address: Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | - Damir García-Cehic
- 3Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain
| | - Neris García-González
- 5Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain
| | - Fernando González-Candelas
- 5Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain
| | - Juan Ignacio Esteban
- 3Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain
| | - Gonzalo Crespo
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Miquel Navasa
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Xavier Forns
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Sofía Pérez-Del-Pulgar
- 1Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
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Soria ME, Gregori J, Chen Q, García-Cehic D, Llorens M, de Ávila AI, Beach NM, Domingo E, Rodríguez-Frías F, Buti M, Esteban R, Esteban JI, Quer J, Perales C. Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus. BMC Infect Dis 2018; 18:446. [PMID: 30176817 PMCID: PMC6122477 DOI: 10.1186/s12879-018-3356-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/23/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Despite the high sustained virological response rates achieved with current directly-acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 5-10% of treated patients do not respond to current antiviral therapies, and basal resistance to DAAs is increasingly detected among treatment-naïve infected individuals. Identification of amino acid substitutions (including those in minority variants) associated with treatment failure requires analytical designs that take into account the high diversification of HCV in more than 86 subtypes according to the ICTV website (June 2017). METHODS The methodology has involved five sequential steps: (i) to design 280 oligonucleotide primers (some including a maximum of three degenerate positions), and of which 120 were tested to amplify NS3, NS5A-, and NS5B-coding regions in a subtype-specific manner, (ii) to define a reference sequence for each subtype, (iii) to perform experimental controls to define a cut-off value for detection of minority amino acids, (iv) to establish bioinformatics' tools to quantify amino acid replacements, and (v) to validate the procedure with patient samples. RESULTS A robust ultra-deep sequencing procedure to analyze HCV circulating in serum samples from patients infected with virus that belongs to the ten most prevalent subtypes worldwide: 1a, 1b, 2a, 2b, 2c, 2j, 3a, 4d, 4e, 4f has been developed. Oligonucleotide primers are subtype-specific. A cut-off value of 1% mutant frequency has been established for individual mutations and haplotypes. CONCLUSION The methodological pipeline described here is adequate to characterize in-depth mutant spectra of HCV populations, and it provides a tool to understand HCV diversification and treatment failures. The pipeline can be periodically extended in the event of HCV diversification into new genotypes or subtypes, and provides a framework applicable to other RNA viral pathogens, with potential to couple detection of drug-resistant mutations with treatment planning.
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Affiliation(s)
- María Eugenia Soria
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Josep Gregori
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics, S.L, Sant Cugat del Vallés, Barcelona, Spain
| | - Qian Chen
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Damir García-Cehic
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Meritxell Llorens
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Ana I. de Ávila
- grid.465524.4Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Nathan M. Beach
- grid.465524.4Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Esteban Domingo
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- grid.465524.4Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Francisco Rodríguez-Frías
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- 0000 0001 0675 8654grid.411083.fLiver Pathology Unit, Department of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Barcelona, Spain
- grid.7080.fUniversitat Autónoma de Barcelona, Barcelona, Spain
| | - María Buti
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- grid.7080.fUniversitat Autónoma de Barcelona, Barcelona, Spain
| | - Rafael Esteban
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- grid.7080.fUniversitat Autónoma de Barcelona, Barcelona, Spain
| | - Juan Ignacio Esteban
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- grid.7080.fUniversitat Autónoma de Barcelona, Barcelona, Spain
| | - Josep Quer
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- grid.7080.fUniversitat Autónoma de Barcelona, Barcelona, Spain
| | - Celia Perales
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- grid.465524.4Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
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Sabrià A, Pintó RM, Bosch A, Quer J, Garcia-Cehic D, Gregori J, Dominguez A, Carol M, Sala-Farré MR, Guix S. Characterization of intra- and inter-host norovirus P2 genetic variability in linked individuals by amplicon sequencing. PLoS One 2018; 13:e0201850. [PMID: 30092071 PMCID: PMC6084935 DOI: 10.1371/journal.pone.0201850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/22/2018] [Indexed: 11/29/2022] Open
Abstract
Noroviruses are the main cause of epidemics of acute gastroenteritis at a global scale. Although chronically infected immunocompromised individuals are regarded as potential reservoirs for the emergence of new viral variants, viral quasispecies distribution and evolution patterns in acute symptomatic and asymptomatic infections has not been extensively studied. Amplicons of 450 nts from the P2 coding capsid domain were studied using next-generation sequencing (454/GS-Junior) platform. Inter-host diversity between symptomatic and asymptomatic acutely infected individuals linked to the same outbreak as well as their viral intra-host diversity over time were characterized. With an average of 2848 reads per sample and a cutoff frequency of 0.1%, minor variant haplotypes were detected in 5 out of 8 specimens. Transmitted variants could not be confirmed in all infected individuals in one outbreak. The observed initial intra-host viral diversity in asymptomatically infected subjects was higher than in symptomatic ones. Viral quasispecies evolution over time within individuals was host-specific, with an average of 2.8 nt changes per day (0.0062 changes per nucleotide per day) in a given symptomatic case. Nucleotide polymorphisms were detected in 28 out of 450 analyzed nucleotide positions, 32.14% of which were synonymous and 67.86% were non-synonymous. Most observed amino acid changes emerged at or near blockade epitopes A, B, D and E. Our results suggest that acutely infected individuals, even in the absence of symptoms, which go underreported and may enhance transmission, may contribute to norovirus genetic variability and evolution.
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Affiliation(s)
- Aurora Sabrià
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Institute of Nutrition and Food Safety (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Rosa M. Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Institute of Nutrition and Food Safety (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Institute of Nutrition and Food Safety (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Josep Quer
- Liver Unit, Internal Medicine, Laboratori de Malalties Hepàtiques, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron (VHIR-HUVH), Autonomous University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Internal Medicine, Laboratori de Malalties Hepàtiques, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron (VHIR-HUVH), Autonomous University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Gregori
- Liver Unit, Internal Medicine, Laboratori de Malalties Hepàtiques, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron (VHIR-HUVH), Autonomous University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics S.L., Sant Cugat del Vallès, Spain
| | - Angela Dominguez
- CIBER Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Department of Public Health, University of Barcelona, Barcelona, Spain
| | - Mónica Carol
- Public Health Agency of Catalonia, Generalitat de Catalunya, Barcelona, Spain
| | | | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Institute of Nutrition and Food Safety (INSA·UB), University of Barcelona, Barcelona, Spain
- * E-mail:
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Loggi E, Vukotic R, Conti F, Gitto S, Andreone P. Gold standard assays for the monitoring of patients with chronic hepatitis C. Future Virol 2018. [DOI: 10.2217/fvl-2018-0032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Chronic HCV infection continues to be an important concern of public health, with still a high mortality from HCV-related disease. The landscape of chronic HCV infection has been dramatically changed by the introduction of the new antiviral agents, able to cure the infection in the large majority of patients. The laboratory management of HCV infection relies on serological and molecular tests, which have undergone significant technological advancements, able to ameliorate the performance both in diagnosis of infection and in the treatment monitoring. This article describes the main laboratory tools in the chronic HCV infection, with particular emphasis on the recent changes coming along with the new therapeutic approaches.
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Affiliation(s)
- Elisabetta Loggi
- Dipartimento di Scienze Mediche e Chirurgiche, Centro di Ricerca per lo Studio delle Epatiti, Università degli Studi di Bologna, Bologna, Italy
- Current address: UOC Patologia Clinica, ASUR Area Vasta 4, Fermo (FM), Italy
| | - Ranka Vukotic
- Dipartimento di Scienze Mediche e Chirurgiche, Centro di Ricerca per lo Studio delle Epatiti, Università degli Studi di Bologna, Bologna, Italy
| | - Fabio Conti
- Dipartimento di Scienze Mediche e Chirurgiche, Centro di Ricerca per lo Studio delle Epatiti, Università degli Studi di Bologna, Bologna, Italy
| | - Stefano Gitto
- Dipartimento di Scienze Mediche e Chirurgiche, Centro di Ricerca per lo Studio delle Epatiti, Università degli Studi di Bologna, Bologna, Italy
| | - Pietro Andreone
- Dipartimento di Scienze Mediche e Chirurgiche, Centro di Ricerca per lo Studio delle Epatiti, Università degli Studi di Bologna, Bologna, Italy
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30
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Cuypers L, Pérez AB, Chueca N, Aldamiz-Echevarría T, Alados JC, Martínez-Sapiña AM, Merino D, Pineda JA, Téllez F, Espinosa N, Salméron J, Rivero-Juarez A, Vivancos MJ, Hontañón V, Vandamme AM, García F. Relapse or reinfection after failing hepatitis C direct acting antiviral treatment: Unravelled by phylogenetic analysis. PLoS One 2018; 13:e0201268. [PMID: 30044871 PMCID: PMC6059487 DOI: 10.1371/journal.pone.0201268] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/11/2018] [Indexed: 12/14/2022] Open
Abstract
Despite high response rates associated to hepatitis C virus (HCV) treatment, no protective immunity is acquired, allowing for reinfection and continued infectiousness. Distinguishing between relapse and reinfection is crucial for patient counselling and to choose the most appropriate retreatment. Here, refined phylogenetic analysis using multiple genes served to assess genotype and reinfection for 53 patients for whom the virus was sampled before start of therapy and at time of sustained virological response evaluation at week 12. At baseline, genotypes were determined as HCV1a (41.5%), HCV1b (24.5%), HCV4 (18.9%) and HCV3a (15.1%), while six cases revealed to be discordantly assigned by phylogeny and commercial assays. Overall, 60.4% was co-infected with HIV. The large majority was classified as people who inject drugs (78.6%), often co-infected with HIV. Transmission was sexual in seven cases, of which five in HIV-positive men-who-have-sex-with-men. Overall, relapse was defined for 44 patients, while no conclusion was drawn for four patients. Five patients were reinfected with a different HCV strain, of which three with a different genotype, showing that phylogeny is needed not only to determine the genotype, but also to distinguish between relapse and intra-subtype reinfection. Of note, phylogenies are more reliable when longer fragments of the viral genome are being sequenced.
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Affiliation(s)
- Lize Cuypers
- KU Leuven–University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ana Belén Pérez
- Clinical Microbiology Department, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. Granada, Spain
| | - Natalia Chueca
- Clinical Microbiology Department, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. Granada, Spain
| | | | | | | | - Dolores Merino
- Clinical Microbiology, Hospital Infanta Elena, Huelva, Spain
| | | | - Francisco Téllez
- UGC Enfermedades Infecciosas y Microbiología, Hospital La Línea, AGS Campo de Gibraltar, Cadiz, Spain
| | - Nuria Espinosa
- Clinical Microbiology, Hospital Virgen del Rocío, Sevilla, Spain
| | - Javier Salméron
- Hepatology Unit, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. CIBERehd, Granada, Spain
| | - Antonio Rivero-Juarez
- Infectious Diseases Unit. Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC). Hospital Universitario Reina Sofía de Córdoba. Universidad de Córdoba, Córdoba, Spain
| | | | - Víctor Hontañón
- Clinical Microbiology, University Hospital La Paz, Madrid, Spain
| | - Anne-Mieke Vandamme
- KU Leuven–University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Microbiology Unit, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Lisbon, Portugal
| | - Féderico García
- Clinical Microbiology Department, University Hospital San Cecilio Granada, Instituto de Investigación Ibs. Granada, Spain
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Karimzadeh H, Kiraithe MM, Kosinska AD, Glaser M, Fiedler M, Oberhardt V, Salimi Alizei E, Hofmann M, Mok JY, Nguyen M, van Esch WJE, Budeus B, Grabowski J, Homs M, Olivero A, Keyvani H, Rodríguez-Frías F, Tabernero D, Buti M, Heinold A, Alavian SM, Bauer T, Schulze Zur Wiesch J, Raziorrouh B, Hoffmann D, Smedile A, Rizzetto M, Wedemeyer H, Timm J, Antes I, Neumann-Haefelin C, Protzer U, Roggendorf M. Amino Acid Substitutions within HLA-B*27-Restricted T Cell Epitopes Prevent Recognition by Hepatitis Delta Virus-Specific CD8 + T Cells. J Virol 2018; 92:JVI.01891-17. [PMID: 29669837 PMCID: PMC6002722 DOI: 10.1128/jvi.01891-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/22/2018] [Indexed: 02/07/2023] Open
Abstract
Virus-specific CD8 T cell response seems to play a significant role in the outcome of hepatitis delta virus (HDV) infection. However, the HDV-specific T cell epitope repertoire and mechanisms of CD8 T cell failure in HDV infection have been poorly characterized. We therefore aimed to characterize HDV-specific CD8 T cell epitopes and the impacts of viral mutations on immune escape. In this study, we predicted peptide epitopes binding the most frequent human leukocyte antigen (HLA) types and assessed their HLA binding capacities. These epitopes were characterized in HDV-infected patients by intracellular gamma interferon (IFN-γ) staining. Sequence analysis of large hepatitis delta antigen (L-HDAg) and HLA typing were performed in 104 patients. The impacts of substitutions within epitopes on the CD8 T cell response were evaluated experimentally and by in silico studies. We identified two HLA-B*27-restricted CD8 T cell epitopes within L-HDAg. These novel epitopes are located in a relatively conserved region of L-HDAg. However, we detected molecular footprints within the epitopes in HLA-B*27-positive patients with chronic HDV infections. The variant peptides were not cross-recognized in HLA-B*27-positive patients with resolved HDV infections, indicating that the substitutions represent viral escape mutations. Molecular modeling of HLA-B*27 complexes with the L-HDAg epitope and its potential viral escape mutations indicated that the structural and electrostatic properties of the bound peptides differ considerably at the T cell receptor interface, which provides a possible molecular explanation for the escape mechanism. This viral escape from the HLA-B*27-restricted CD8 T cell response correlates with a chronic outcome of hepatitis D infection. T cell failure resulting from immune escape may contribute to the high chronicity rate in HDV infection.IMPORTANCE Hepatitis delta virus (HDV) causes severe chronic hepatitis, which affects 20 million people worldwide. Only a small number of patients are able to clear the virus, possibly mediated by a virus-specific T cell response. Here, we performed a systematic screen to define CD8 epitopes and investigated the role of CD8 T cells in the outcome of hepatitis delta and how they fail to eliminate HDV. Overall the number of epitopes identified was very low compared to other hepatotropic viruses. We identified, two HLA-B*27-restricted epitopes in patients with resolved infections. In HLA-B*27-positive patients with chronic HDV infections, however, we detected escape mutations within these identified epitopes that could lead to viral evasion of immune responses. These findings support evidence showing that HLA-B*27 is important for virus-specific CD8 T cell responses, similar to other viral infections. These results have implications for the clinical prognosis of HDV infection and for vaccine development.
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Affiliation(s)
- Hadi Karimzadeh
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Muthamia M Kiraithe
- University Hospital Freiburg, Department of Medicine II, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Anna D Kosinska
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Munich and Hannover Sites, Braunschweig, Germany
| | - Manuel Glaser
- Center for Integrated Protein Science Munich at the Department of Biosciences, Technische Universität München, Freising, Germany
| | - Melanie Fiedler
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Valerie Oberhardt
- University Hospital Freiburg, Department of Medicine II, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Elahe Salimi Alizei
- University Hospital Freiburg, Department of Medicine II, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Maike Hofmann
- University Hospital Freiburg, Department of Medicine II, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | | | | | | | - Bettina Budeus
- Department of Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Jan Grabowski
- German Center for Infection Research (DZIF), Munich and Hannover Sites, Braunschweig, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Maria Homs
- CIBERehd and Departments of Biochemistry/Microbiology and Hepatology, Vall d'Hebron Hospital, University Autònoma de Barcelona (UAB), Barcelona, Spain
| | | | - Hossein Keyvani
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran
| | - Francisco Rodríguez-Frías
- CIBERehd and Departments of Biochemistry/Microbiology and Hepatology, Vall d'Hebron Hospital, University Autònoma de Barcelona (UAB), Barcelona, Spain
| | - David Tabernero
- CIBERehd and Departments of Biochemistry/Microbiology and Hepatology, Vall d'Hebron Hospital, University Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Maria Buti
- CIBERehd and Departments of Biochemistry/Microbiology and Hepatology, Vall d'Hebron Hospital, University Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Andreas Heinold
- Institute of Transfusion Medicine, University of Duisburg-Essen, University Hospital, Essen, Germany
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Tanja Bauer
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Munich and Hannover Sites, Braunschweig, Germany
| | - Julian Schulze Zur Wiesch
- Department of Medicine, Section of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bijan Raziorrouh
- University Hospital Munich-Grosshadern, Department of Medicine II, Munich, Germany
| | - Daniel Hoffmann
- Department of Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Antonina Smedile
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Mario Rizzetto
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Heiner Wedemeyer
- German Center for Infection Research (DZIF), Munich and Hannover Sites, Braunschweig, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Jörg Timm
- Institute of Virology, Heinrich-Heine-University, University Hospital, Duesseldorf, Germany
| | - Iris Antes
- Center for Integrated Protein Science Munich at the Department of Biosciences, Technische Universität München, Freising, Germany
| | - Christoph Neumann-Haefelin
- University Hospital Freiburg, Department of Medicine II, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Munich and Hannover Sites, Braunschweig, Germany
| | - Michael Roggendorf
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- German Center for Infection Research (DZIF), Munich and Hannover Sites, Braunschweig, Germany
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Mesbahi Z, Kabbaj H, Malki H, Bouihat N, Qrafli M, Belefquih B, Marcil S, Challine D, Pawlotsky JM, Bouvier M, Seffar M. Indeterminate genotypes of hepatitis C virus by the Abbott RealTime HCV Genotype II assay in Morocco. About eight cases resolved by a sequencing method. J Med Virol 2018; 90:1352-1357. [PMID: 29663433 DOI: 10.1002/jmv.25191] [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: 07/31/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022]
Abstract
The early detection and genotyping of the hepatitis C virus (HCV) are important in the management of this infection. The genotype is the major factor influencing treatment decisions. That's why it is necessary to use fast and accurate methods in its determination. This study reports, over a period of 3 years (from May 2012 to July 2015), the percentage of indeterminate genotypes by the Abbott RealTime HCV Genotype II test and their results using a sequencing technique. Of 309 samples of 309 patients tested, 11 were indeterminate (4.4%). There were three cases of cross-reactivity (1b/4 in one case, 2/5 in two cases) and a possible co-infection 1 + 4. Among those indeterminate genotypes, cross-reactivities and co-infections, ten samples were tested by sequencing. The results were for four of them a 1d subtype, five were a 2i subtype and one was a 2l subtype. These results support the thesis of complementarity between the two methods: genotyping for the detection of mixed reactions and sequencing for resolving indeterminate cases by genotyping.
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Affiliation(s)
- Zineb Mesbahi
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
| | - Hakima Kabbaj
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
| | - Houcine Malki
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
| | - Najat Bouihat
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
| | - Mounia Qrafli
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
| | - Bouchra Belefquih
- Laboratory of Virology, Cheikh Khalifa Hospital, Casablanca, Morocco
| | - Sarrah Marcil
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
| | - Dominique Challine
- National Reference Center for Viral Hepatitis B, C and delta, Henry Mondor Hospital, University of Paris-Est, Créteil, France
| | - Jean-Michel Pawlotsky
- National Reference Center for Viral Hepatitis B, C and delta, Henry Mondor Hospital, University of Paris-Est, Créteil, France
| | - Magali Bouvier
- National Reference Center for Viral Hepatitis B, C and delta, Henry Mondor Hospital, University of Paris-Est, Créteil, France
| | - Myriam Seffar
- Mohamed V University, Ibn Sina University Hospital Center, Faculty of Medecine and Pharmacy of Rabat, Central Laboratory of Virology, Rabat, Morocco
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Rodriguez C, Soulier A, Demontant V, Poiteau L, Mercier-Darty M, Bouvier-Alias M, Pawlotsky JM, Chevaliez S. A novel standardized deep sequencing-based assay for hepatitis C virus genotype determination. Sci Rep 2018; 8:4180. [PMID: 29520035 PMCID: PMC5843601 DOI: 10.1038/s41598-018-22614-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/26/2018] [Indexed: 01/06/2023] Open
Abstract
Hepatitis C virus (HCV) genotype and subtype (1a/1b) identification is needed to tailor anti-HCV therapy. Currently available methods accurately identify the genotype and differentiate subtypes 1a from 1b. However, these assays have not been designed to identify other HCV subtypes, nor to recognize mixed genotype/subtype infections, emphasizing the need for a high-resolution system based on phylogenetic analysis of reads obtained by deep sequencing of a relevant genome region. The aim of this study was to evaluate the performance of the Sentosa SQ HCV Genotyping Assay, a novel deep sequencing-based assay targeting the HCV nonstructural 5B (NS5B) region, in clinical samples from patients with an indication for anti-HCV therapy. A high concordance rate with Sanger sequencing of the NS5B region, the reference method, was found for genotype 1 to 6 determination, 1a/1b subtype identification, and genotype 4, 5 and 6 subtyping. Discrepancies were seen essentially for HCV genotype 2 subtyping. Overall, the performance of the deep sequencing-based assay in generating the genotypes/subtype information needed to tailor anti-HCV treatment was adequate in this study. Further improvements, such as a longer NS5B fragment analyzed and enriching the database of reference prototype strains used for subtype assignment would make it a method of choice for HCV genotyping and subtyping for future clinical practice and research.
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Affiliation(s)
- Christophe Rodriguez
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Alexandre Soulier
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Vanessa Demontant
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Lila Poiteau
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Mélanie Mercier-Darty
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Magali Bouvier-Alias
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Jean-Michel Pawlotsky
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Stéphane Chevaliez
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.
- INSERM, U955, Créteil, France.
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Ordeig L, Garcia-Cehic D, Gregori J, Soria ME, Nieto-Aponte L, Perales C, Llorens M, Chen Q, Riveiro-Barciela M, Buti M, Esteban R, Esteban JI, Rodriguez-Frias F, Quer J. New hepatitis C virus genotype 1 subtype naturally harbouring resistance-associated mutations to NS5A inhibitors. J Gen Virol 2018; 99:97-102. [PMID: 29239718 DOI: 10.1099/jgv.0.000996] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus (HCV) is a highly divergent virus currently classified into seven major genotypes and 86 subtypes (ICTV, June 2017), which can have differing responses to therapy. Accurate genotyping/subtyping using high-resolution HCV subtyping enables confident subtype identification, identifies mixed infections and allows detection of new subtypes. During routine genotyping/subtyping, one sample from an Equatorial Guinea patient could not be classified into any of the subtypes. The complete genomic sequence was compared to reference sequences by phylogenetic and sliding window analysis. Resistance-associated substitutions (RASs) were assessed by deep sequencing. The unclassified HCV genome did not belong to any of the existing genotype 1 (G1) subtypes. Sliding window analysis along the complete genome ruled out recombination phenomena suggesting that it belongs to a new HCV G1 subtype. Two NS5A RASs (L31V+Y93H) were found to be naturally combined in the genome which could limit treatment possibilities in patients infected with this subtype.
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Affiliation(s)
- Laura Ordeig
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Josep Gregori
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
- Roche Diagnostics SL, Sant Cugat del Vallès, 08174, Barcelona, Spain
| | - Maria Eugenia Soria
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
| | - Leonardo Nieto-Aponte
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
- Liver Pathology Unit, Department of Biochemistry and Microbiology, HUVH, 08035, Barcelona, Spain
| | - Celia Perales
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Meritxell Llorens
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
| | - Qian Chen
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
| | - Mar Riveiro-Barciela
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Maria Buti
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Rafael Esteban
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
- Liver Pathology Unit, Department of Biochemistry and Microbiology, HUVH, 08035, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Josep Quer
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
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Perales C, Chen Q, Soria ME, Gregori J, Garcia-Cehic D, Nieto-Aponte L, Castells L, Imaz A, Llorens-Revull M, Domingo E, Buti M, Esteban JI, Rodriguez-Frias F, Quer J. Baseline hepatitis C virus resistance-associated substitutions present at frequencies lower than 15% may be clinically significant. Infect Drug Resist 2018; 11:2207-2210. [PMID: 30519058 PMCID: PMC6233951 DOI: 10.2147/idr.s172226] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Controversy is ongoing about whether a minority mutant present at frequencies below 15% may be clinically relevant and should be considered to guide treatment. METHODS Resistance-associated substitution (RAS) studies were performed in patients before and at failure of antiviral treatments using Next-generation hepatitis C virus (HCV) sequencing (NGS). RESULTS We have found two patients with genotype 1a infection having RAS in 3.5%-7.1% of the viral population at baseline that were selected during ledipasvir + sofosbuvir treatment. Co-selection of RAS located in a region not directly affected by the antiviral treatment also occurred. This observation calls into question, the recommendations to guide RAS-based direct-acting antiviral (DAA) treatment only when RAS are present in >15% of the sequences generated. CONCLUSION Our results suggests that RAS study should include all three HCV DAA target proteins and minority mutants should be considered as clinically relevant.
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Affiliation(s)
- Celia Perales
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut of Research (VHIR)-Vall d'Hebron University Hospital(HUVH), 08035, Barcelona, Spain, ;
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain, ; , ;
| | - Qian Chen
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut of Research (VHIR)-Vall d'Hebron University Hospital(HUVH), 08035, Barcelona, Spain, ;
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain, ; , ;
| | - Maria Eugenia Soria
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut of Research (VHIR)-Vall d'Hebron University Hospital(HUVH), 08035, Barcelona, Spain, ;
| | - Josep Gregori
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut of Research (VHIR)-Vall d'Hebron University Hospital(HUVH), 08035, Barcelona, Spain, ;
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain, ; , ;
- Roche Diagnostics SL, Sant Cugat del Vallès, 08174, Barcelona, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut of Research (VHIR)-Vall d'Hebron University Hospital(HUVH), 08035, Barcelona, Spain, ;
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain, ; , ;
| | - Leonardo Nieto-Aponte
- Liver Pathology Unit, Department of Biochemistry and Microbiology, HUVH, 08035, Barcelona, Spain, ;
| | - Lluis Castells
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut of Research (VHIR)-Vall d'Hebron University Hospital(HUVH), 08035, Barcelona, Spain, ;
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain, ; , ;
| | - Arkaitz Imaz
- HIV and STD Unit, Infectious Diseases Department, Bellvitge University Hospital-Bellvitge Biomedical Research Institut (IDIBELL), Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Meritxell Llorens-Revull
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut of Research (VHIR)-Vall d'Hebron University Hospital(HUVH), 08035, Barcelona, Spain, ;
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain, ; , ;
- Virology and Microbiology Department, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain
| | - Maria Buti
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut of Research (VHIR)-Vall d'Hebron University Hospital(HUVH), 08035, Barcelona, Spain, ;
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain, ; , ;
- Medicine Department. Autonomous University of Barcelona, Bellaterra, 08193, Barcelona, Spain, ; , ;
| | - Juan Ignacio Esteban
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut of Research (VHIR)-Vall d'Hebron University Hospital(HUVH), 08035, Barcelona, Spain, ;
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain, ; , ;
- Medicine Department. Autonomous University of Barcelona, Bellaterra, 08193, Barcelona, Spain, ; , ;
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain, ; , ;
- Liver Pathology Unit, Department of Biochemistry and Microbiology, HUVH, 08035, Barcelona, Spain, ;
- Medicine Department. Autonomous University of Barcelona, Bellaterra, 08193, Barcelona, Spain, ; , ;
| | - Josep Quer
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut of Research (VHIR)-Vall d'Hebron University Hospital(HUVH), 08035, Barcelona, Spain, ;
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain, ; , ;
- Medicine Department. Autonomous University of Barcelona, Bellaterra, 08193, Barcelona, Spain, ; , ;
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Del Campo JA, Parra-Sánchez M, Figueruela B, García-Rey S, Quer J, Gregori J, Bernal S, Grande L, Palomares JC, Romero-Gómez M. Hepatitis C virus deep sequencing for sub-genotype identification in mixed infections: A real-life experience. Int J Infect Dis 2017; 67:114-117. [PMID: 29253705 PMCID: PMC5812776 DOI: 10.1016/j.ijid.2017.12.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/05/2017] [Accepted: 12/07/2017] [Indexed: 12/26/2022] Open
Abstract
Routine strategies for hepatitis C virus (HCV) genotyping have several limitations. Deep sequencing methods can solve this problem. Accurate determination of viral genotypes and subtypes would allow optimal patient management and the most effective therapy. Mixed infections may represent a key factor for efficient therapy. Patients infected with more than one HCV genotype (mixed infection) can be detected only by deep sequencing methods. These patients can fail treatment with direct-acting antiviral agents, hence next-generation sequencing methods are highly recommended in clinical practice.
Background The effectiveness of the new generation of hepatitis C treatments named direct-acting antiviral agents (DAAs) depends on the genotype, subtype, and resistance-associated substitutions present in individual patients. The aim of this study was to evaluate a massive sequencing platform for the analysis of genotypes and subtypes of hepatitis C virus (HCV) in order to optimize therapy. Methods A total of 84 patients with hepatitis C were analyzed. The routine genotyping methodology for HCV used at the study institution (Versant HCV Assay, LiPA) was compared with a deep sequencing platform (454/GS-Junior and Illumina MiSeq). Results The mean viral load in these HCV patients was 6.89 × 106 ± 7.02 × 105. Viral genotypes analyzed by LiPA were distributed as follows: 26% genotype 1a (22/84), 55% genotype 1b (46/84), 1% genotype 1 (1/84), 2.5% genotype 3 (2/84), 6% genotype 3a (5/84), 6% genotype 4a/c/d (5/84). When analyzed by deep sequencing, the samples were distributed as follows: 27% genotype 1a (23/84), 56% genotype 1b (47/84), 8% genotype 3a (7/84), 5% genotype 4d (4/84), 2.5% genotype 4f (2/84). Six of the 84 patients (7%) were infected with more than one subtype. Among these, 33% (2/6) failed DAA-based triple therapy. Conclusions The detection of mixed infection could explain some treatment failures. Accurate determination of viral genotypes and subtypes would allow optimal patient management and improve the effectiveness of DAA therapy.
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Affiliation(s)
- José A Del Campo
- UCM Digestive Diseases, Valme University Hospital, Seville, Spain; Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain.
| | - Manuel Parra-Sánchez
- UCM Infectious Diseases and Microbiology, Valme University Hospital, Seville, Spain
| | | | - Silvia García-Rey
- UCM Infectious Diseases and Microbiology, Valme University Hospital, Seville, Spain
| | - Josep Quer
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Liver Disease Laboratory - Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR-HUVH), Universitat Autonoma Barcelona, Barcelona, Spain
| | - Josep Gregori
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Liver Disease Laboratory - Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR-HUVH), Universitat Autonoma Barcelona, Barcelona, Spain; Roche Diagnostics SL, Sant Cugat del Vallès, Barcelona, Spain
| | - Samuel Bernal
- UCM Infectious Diseases and Microbiology, Valme University Hospital, Seville, Spain
| | - Lourdes Grande
- UCM Digestive Diseases, Valme University Hospital, Seville, Spain
| | - José C Palomares
- UCM Infectious Diseases and Microbiology, Valme University Hospital, Seville, 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 del Rocío, Instituto de Investigación Biomédica de Sevilla (IBiS), Seville, Spain
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Cabezas J, Llerena S, Puente Á, Fábrega E, Crespo J. Causes of treatment failure for hepatitis C in the era of direct-acting antiviral therapy. REVISTA ESPANOLA DE ENFERMEDADES DIGESTIVAS 2017; 108:421-30. [PMID: 26666379 DOI: 10.17235/reed.2015.3894/2015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hepatitis C therapy in the era of the newer direct-acting antiviral agents has radically changed our treatment schemes by achieving very high rates of sustained virological response. However, treatment with direct antiviral agents fails in a subgroup of patients. This group of so-called difficult-to-treat individuals is the subject of this paper, which reviews the causes of virological failure, their clinical implications, and some final recommendations.
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Affiliation(s)
- Joaquín Cabezas
- Aparato Digestivo/Unidad de Hepatología, Hospital Universitario Marqués de Valdecilla, España
| | - Susana Llerena
- Aparato Digestivo/ Unidad de Hepatologia, Hospital Universitario Marqués de Valdecilla, España
| | - Ángela Puente
- Aparato Digestivo/Unidad de Hepatología, Hospital Universitario Marqués de Valdecilla, España
| | | | - Javier Crespo
- Servicio Aparato Digestivo, Hospital Universitario Marqués de Valdecilla, 39002
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38
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Dirani G, Paesini E, Mascetra E, Farabegoli P, Dalmo B, Bartolini B, Garbuglia AR, Capobianchi MR, Sambri V. A novel next generation sequencing assay as an alternative to currently available methods for hepatitis C virus genotyping. J Virol Methods 2017; 251:88-91. [PMID: 29045810 DOI: 10.1016/j.jviromet.2017.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/17/2017] [Accepted: 10/05/2017] [Indexed: 12/31/2022]
Abstract
Chronic HCV infection is one of the leading causes of liver-related death and in many countries it is a primary reason for having a liver transplant. HCV genotype identification has long been used in the clinical practice, since different genotypes have different response rates and required different doses and durations of IFN/RBV treatment; moreover both the frequency and the pattern of resistance to different Direct-Acting Antivirals (DAAs) classes are subtype specific. Hence the necessity to make an accurate HCV subtyping becomes a fundamental tool to optimize current and future clinical management of HCV infected subjects. In the present study the performance of a next generation sequencing (NGS: based on the Ion Torrent Platform-Vela Sentosa SQ 301 sequencer) HCV genotyping assay has been evaluated. The current method targets a region of the NS5B gene and it is the unique NGS based market CE-IVD assay. As a comparative method a commercial method based on the detection via reverse hybridization of 5'UTR and core regions (Versant HCV Genotype 2.0 Assay, LiPA, Siemens) was selected. A total 207 plasma samples from HCV infected individuals were used. No selection was made for these samples that were submitted for routine HCV genotyping. The results show Vela NGS assay assigns major number of HCV subtypes with respect LiPA. Concerning genotype 1 and 3, the discrepancy of assigned subtypes for LiPA with respect to Vela NGS assay is not relevant (1.8% and 2%, respectively); in contrast, the difference of assigned subtypes for genotypes 2 and 4 is very high (96.6% and 100%, respectively). The resistance mutations data, except for 1a and 1b subtypes, remain scarce; the future relevant challenge will be to identify subtypes-specific drug resistance mutations, which are essential to create highly personalized therapeutic pathways.
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Affiliation(s)
- G Dirani
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy.
| | - E Paesini
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy
| | - E Mascetra
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy
| | - P Farabegoli
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy
| | - B Dalmo
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy
| | - B Bartolini
- Virology Laboratory, National Institute for Infectious Diseases "L.Spallanzani", Rome, Italy
| | - A R Garbuglia
- Virology Laboratory, National Institute for Infectious Diseases "L.Spallanzani", Rome, Italy
| | - M R Capobianchi
- Virology Laboratory, National Institute for Infectious Diseases "L.Spallanzani", Rome, Italy
| | - V Sambri
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Cesena, Italy; DIMES, University of Bologna, Bologna, Italy
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High HCV subtype heterogeneity in a chronically infected general population revealed by high-resolution hepatitis C virus subtyping. Clin Microbiol Infect 2017; 23:775.e1-775.e6. [DOI: 10.1016/j.cmi.2017.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 01/17/2023]
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40
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Manee N, Thongbaiphet N, Pasomsub E, Chantratita W. Clinical evaluation of a newly developed automated massively parallel sequencing assay for hepatitis C virus genotyping and detection of resistance-association variants. Comparison with a line probe assay. J Virol Methods 2017; 249:31-37. [PMID: 28851606 DOI: 10.1016/j.jviromet.2017.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 07/13/2017] [Accepted: 08/21/2017] [Indexed: 02/08/2023]
Abstract
Hepatitis C virus (HCV) infection is a leading cause of chronic liver disease, cirrhosis and hepatocellular carcinoma. Recently, HCV was classified into 6 major genotypes (GTs) and 67 subtypes (STs). Efficient genotyping has become an essential tool for prognosis and indicating suitable treatment, prior to starting therapy in all HCV-infected individuals. The widely used genotyping assays have limitation with regard to genotype accuracy. This study was a comparative evaluation of exact HCV genotyping in a newly developed automated-massively parallel sequencing (MPS) system, versus the established Line probe assay 2.0 (LiPA), substantiated by Sanger sequencing, using 120 previously identified-HCV RNA positive specimens. LiPA gave identical genotypes in the majority of samples tested with MPS. However, as much as 25% of LiPA did not identify subtypes, whereas MPS did, and 0.83% of results were incompatible. Interestingly, only MPS could identify mixed infections in the remaining cases (1.67%). In addition, MPS could detect Resistance-Associated Variants (RAVs) simultaneously in GT1 in 56.82% of the specimens, which were known to affect drug resistance in the HCV NS3/NS4A and NS5A genomic regions. MPS can thus be deemed beneficial for guiding decisions on HCV therapy and saving costs in the long term when compared to traditional methods.
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Affiliation(s)
- Narathon Manee
- Department of Clinical Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Nipa Thongbaiphet
- Virology Laboratory and Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Ekawat Pasomsub
- Department of Clinical Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; Virology Laboratory and Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Wasun Chantratita
- Department of Clinical Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; Virology Laboratory and Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand.
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Characterization of Naturally Occurring NS5A and NS5B Polymorphisms in Patients Infected with HCV Genotype 3a Treated with Direct-Acting Antiviral Agents. Viruses 2017; 9:v9080212. [PMID: 28783119 PMCID: PMC5580469 DOI: 10.3390/v9080212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/27/2017] [Accepted: 07/31/2017] [Indexed: 12/20/2022] Open
Abstract
Hepatitis C virus (HCV) genotype (GT)3 is associated with increased risk of steatosis, development of cirrhosis and hepatocellular carcinoma. Limited data are available regarding genetic variability and use of direct-acting antiviral agents in these patients. non-structural protein 5A (NS5A) and non-structural protein 5B (NS5B) sequencing was performed on 45 HCV GT3-infected Italian patients subsequently treated with sofosbuvir ± daclatasvir (SOF ± DCV). Novel GT3a polymorphisms were observed by Sanger sequencing in three NS5A (T79S, T107K, and T107S) and three NS5B (G166R, Q180K, and C274W) baseline sequences in patients who achieved sustained virological response (SVR). Baseline NS5A resistance-associated substitutions (RASs) A30K and Y93H were detected in 9.5% of patients; one patient with A30K did not achieve SVR. Phylogenetic analyses of sequences showed no distinct clustering. Genetic heterogeneity of NS5A and NS5B was evaluated using ultra-deep pyrosequencing (UDPS) in samples longitudinally collected in patients not achieving SVR. Some novel NS5A and NS5B polymorphisms detected at baseline may not impact treatment outcome, as they were not enriched in post-failure samples. In contrast, the clinically novel GT3 NS5A-L31F RAS emerged in one treatment failure, and I184T, G188D and N310S, located on the same NS5B haplotype, became predominant after failure. These findings suggest a potential impact of these novel substitutions on the treatment outcome; however, their significance requires further investigation.
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Neukam K, Martínez AP, Culasso ACA, Ridruejo E, García G, Di Lello FA. NS3 genomic sequencing and phylogenetic analysis as alternative to a commercially available assay to reliably determine hepatitis C virus subtypes 1a and 1b. PLoS One 2017; 12:e0182193. [PMID: 28753662 PMCID: PMC5533332 DOI: 10.1371/journal.pone.0182193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/13/2017] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVE To evaluate the use of hepatitis C virus (HCV) NS3 sequencing as alternative to the comercially available Versant HCV 2.0 reverse hybridization line-probe assay (LiPA 2.0) to determine HCV genotype 1 (HCV-1) subtypes. PATIENTS AND METHODS A cohort of 104 patients infected by HCV-1 according to LiPA 2.0 was analyzed in a cross-sectional study conducted in patients seen from January 2012 to June 2016 at an outpatient clinic in Buenos Aires, Argentina. RESULTS The samples were included within well supported subtype clades: 64 with HCV-1b and 39 with HCV-1a infection. Twenty of the HCV-1a infected patientes were included in a supported sub-clade "1" and 19 individuals were among the basal sub-clade "2". LiPA 2.0 failed to subtype HCV-1 in 20 (19.2%) individuals. Subtype classification determined by NS3 direct sequencing showed that 2/18 (11.1%) of the HCV-1a-infected patients as determined by LiPA 2.0 were in fact infected by HCV-1b. Of the HCV-1b-infected according to LiPA 2.0, 10/66 (15.2%) patients showed HCV-1a infection according to NS3 sequencing. Overall misclassification was 14.3% (κ-index for the concordance with NS3 sequencing = 0.635). One (1%) patient was erroneously genotyped as HCV-1 and was revealed as HCV genotype 4 infection. CONCLUSIONS Genomic sequencing of the HCV NS3 region represents an adequate alternative since it provides reliable genetic information. It even distinguishes between HCV-1a clades related to resistance-associated substitutions to HCV protease inhibitors, it provides reliable genetic information for genotyping/subgenotyping and simultaneously allows to determine the presence of resistance-associated substitutions to currently recommended DAAs.
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Affiliation(s)
- Karin Neukam
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Virología, Buenos Aires, Argentina
- Instituto de Biomedicina de Sevilla / Hospital Universitario Virgen del Rocío / CSIC / Universidad de Sevilla, Unit of Infectious Diseases, Microbiology and Preventive Medicine, Seville, Spain
- Hospital Universitario de Valme, Unit of Infectious Diseases and Mirobiology, Seville, Spain
| | - Alfredo P. Martínez
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno "CEMIC", Virology Section, Buenos Aires, Argentina
| | - Andrés C. A. Culasso
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Virología, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ezequiel Ridruejo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno "CEMIC", Hepatology Section, Department of Medicine, Buenos Aires, Argentina
| | - Gabriel García
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Virología, Buenos Aires, Argentina
| | - Federico A. Di Lello
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Virología, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Quer J, Rodríguez-Frias F, Gregori J, Tabernero D, Soria ME, García-Cehic D, Homs M, Bosch A, Pintó RM, Esteban JI, Domingo E, Perales C. Deep sequencing in the management of hepatitis virus infections. Virus Res 2017; 239:115-125. [PMID: 28040474 DOI: 10.1016/j.virusres.2016.12.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/10/2016] [Accepted: 12/22/2016] [Indexed: 02/07/2023]
Abstract
The hepatitis viruses represent a major public health problem worldwide. Procedures for characterization of the genomic composition of their populations, accurate diagnosis, identification of multiple infections, and information on inhibitor-escape mutants for treatment decisions are needed. Deep sequencing methodologies are extremely useful for these viruses since they replicate as complex and dynamic quasispecies swarms whose complexity and mutant composition are biologically relevant traits. Population complexity is a major challenge for disease prevention and control, but also an opportunity to distinguish among related but phenotypically distinct variants that might anticipate disease progression and treatment outcome. Detailed characterization of mutant spectra should permit choosing better treatment options, given the increasing number of new antiviral inhibitors available. In the present review we briefly summarize our experience on the use of deep sequencing for the management of hepatitis virus infections, particularly for hepatitis B and C viruses, and outline some possible new applications of deep sequencing for these important human pathogens.
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Affiliation(s)
- Josep Quer
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Francisco Rodríguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Josep Gregori
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Roche Diagnostics, S.L., Sant Cugat del Vallés, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Maria Eugenia Soria
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain
| | - Damir García-Cehic
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Maria Homs
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Albert Bosch
- Department of Microbiology, Enteric Virus Laboratory, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Rosa María Pintó
- Department of Microbiology, Enteric Virus Laboratory, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Celia Perales
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Research-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autonoma de Barcelona, 08035, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
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Llerena S, Cabezas J, Iruzubieta P, Crespo J. Resistance to hepatitis C virus. Implications and therapeutic options. GASTROENTEROLOGIA Y HEPATOLOGIA 2017. [PMID: 28647053 DOI: 10.1016/j.gastrohep.2017.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We are currently living in an unprecedented era of hepatitis C treatment with the availability of highly effective drugs yielding minimal side effects. The problem we currently face is the retreatment of patients refractory to these drugs. Although several factors can influence treatment failure, this review focuses on antiviral resistance. Resistance-associated substitutions may be identified at baseline or be treatment-emergent. The latter seem to be more clinically relevant and must be studied in the event of treatment failure (no virological response). In this article, we present the latest data from clinical trials and studies in real-life clinical practice. Finally, based on this current evidence, we propose some recommendations for the management and retreatment of these patients.
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Affiliation(s)
- Susana Llerena
- Servicio de Gastroenterología y Hepatología, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, España; Instituto de Investigación Valdecilla (IDIVAL), Santander, Cantabria, España
| | - Joaquín Cabezas
- Servicio de Gastroenterología y Hepatología, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, España; Instituto de Investigación Valdecilla (IDIVAL), Santander, Cantabria, España
| | - Paula Iruzubieta
- Servicio de Gastroenterología y Hepatología, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, España; Instituto de Investigación Valdecilla (IDIVAL), Santander, Cantabria, España
| | - Javier Crespo
- Servicio de Gastroenterología y Hepatología, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, España; Instituto de Investigación Valdecilla (IDIVAL), Santander, Cantabria, España.
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Caro-Pérez N, Martínez-Rebollar M, Gregori J, Quer J, González P, Gambato M, García-González N, González-Candelas F, Costa J, Esteban JI, Mallolas J, Forns X, Laguno M, Pérez-Del-Pulgar S. Phylogenetic analysis of an epidemic outbreak of acute hepatitis C in HIV-infected patients by ultra-deep pyrosequencing. J Clin Virol 2017; 92:42-47. [PMID: 28521213 DOI: 10.1016/j.jcv.2017.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/29/2017] [Accepted: 05/06/2017] [Indexed: 01/18/2023]
Abstract
BACKGROUND The incidence of acute hepatitis C (AHC) among HIV-infected men who have sex with men (MSM) has increased significantly in the last 10 years. Several studies point to a social and sexual network of HIV-positive MSM that extends internationally. OBJECTIVES The aim of our study was to investigate the dynamics of HCV transmission in an outbreak of AHC in HIV-infected MSM in Barcelona by ultra-deep pyrosequencing. STUDY DESIGN Between 2008 and 2013, 113 cases of AHC in HIV-infected MSM were diagnosed in the Infectious Diseases Unit, Hospital Clínic, Barcelona. Massive sequencing was performed using the Roche 454 GS Junior platform. To define possible transmission networks, maximum likelihood phylogenetic trees were constructed, and levels of genetic diversity within and among patients were compared. RESULTS Among the 70 cases analyzed, we have identified 16 potential clusters of transmission: 8 for genotype 1a (23 cases involved), 1 for genotype 1b (3 cases) and 7 for genotype 4d (27 cases). Although the initial phylogenetic reconstruction suggested a local transmission cluster of HCV gt4d, our approach based on low genetic differentiation did not corroborate it. Indeed, gt4d strains formed 4 independent groups related to patients from other countries. CONCLUSIONS Frequent clustering of HIV-positive MSM shows that HCV infection has spread through a local network in Barcelona. This outbreak is related to a large international HCV transmission network among MSM. Public health efforts are needed to reduce HCV transmission among this high-risk group.
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Affiliation(s)
- Noelia Caro-Pérez
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | | | - Josep Gregori
- Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain; Roche Diagnostics SL, Sant Cugat del Vallès, Barcelona, Spain.
| | - Josep Quer
- Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain.
| | - Patricia González
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | - Martina Gambato
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | - Neris García-González
- Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain.
| | - Fernando González-Candelas
- Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain.
| | - Josep Costa
- Microbiology Department, Centre Diagnòstic Biomèdic, Hospital Clínic, CIBERehd, Barcelona, Spain.
| | - Juan Ignacio Esteban
- Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain.
| | - Josep Mallolas
- Infectious Diseases Unit, Hospital Clínic, IDIBAPS, Barcelona, Spain.
| | - Xavier Forns
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | - Montse Laguno
- Infectious Diseases Unit, Hospital Clínic, IDIBAPS, Barcelona, Spain.
| | - Sofía Pérez-Del-Pulgar
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
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Daniel HD, David J, Raghuraman S, Gnanamony M, Chandy GM, Sridharan G, Abraham P. Comparison of Three Different Hepatitis C Virus Genotyping Methods: 5'NCR PCR-RFLP, Core Type-Specific PCR, and NS5b Sequencing in a Tertiary Care Hospital in South India. J Clin Lab Anal 2017; 31:e22045. [PMID: 27580956 PMCID: PMC6816979 DOI: 10.1002/jcla.22045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/28/2016] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Based on genetic heterogeneity, hepatitis C virus (HCV) is classified into seven major genotypes and 64 subtypes. In spite of the sequence heterogeneity, all genotypes share an identical complement of colinear genes within the large open reading frame. The genetic interrelationships between these genes are consistent among genotypes. Due to this property, complete sequencing of the HCV genome is not required. HCV genotypes along with subtypes are critical for planning antiviral therapy. Certain genotypes are also associated with higher progression to liver cirrhosis. METHODS In this study, 100 blood samples were collected from individuals who came for routine HCV genotype identification. These samples were used for the comparison of two different genotyping methods (5'NCR PCR-RFLP and HCV core type-specific PCR) with NS5b sequencing. RESULTS Of the 100 samples genotyped using 5'NCR PCR-RFLP and HCV core type-specific PCR, 90% (κ = 0.913, P < 0.00) and 96% (κ = 0.794, P < 0.00) correlated with NS5b sequencing, respectively. Sixty percent and 75% of discordant samples by 5'NCR PCR-RFLP and HCV core type-specific PCR, respectively, belonged to genotype 6. All the HCV genotype 1 subtypes were classified accurately by both the methods. CONCLUSION This study shows that the 5'NCR-based PCR-RFLP and the HCV core type-specific PCR-based assays correctly identified HCV genotypes except genotype 6 from this region. Direct sequencing of the HCV core region was able to identify all the genotype 6 from this region and serves as an alternative to NS5b sequencing.
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Affiliation(s)
| | - Joel David
- Department of Clinical VirologyChristian Medical CollegeVelloreIndia
| | | | - Manu Gnanamony
- Department of Clinical VirologyChristian Medical CollegeVelloreIndia
| | - George M. Chandy
- Department of Gastrointestinal SciencesChristian Medical CollegeVelloreIndia
| | - Gopalan Sridharan
- Department of Clinical VirologyChristian Medical CollegeVelloreIndia
| | - Priya Abraham
- Department of Clinical VirologyChristian Medical CollegeVelloreIndia
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Uddin R, Downard KM. Subtyping of hepatitis C virus with high resolution mass spectrometry. CLINICAL MASS SPECTROMETRY 2017. [DOI: 10.1016/j.clinms.2017.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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48
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Nieto-Aponte L, Quer J, Ruiz-Ripa A, Tabernero D, Gonzalez C, Gregori J, Vila M, Asensio M, Garcia-Cehic D, Ruiz G, Chen Q, Ordeig L, Llorens M, Saez M, Esteban JI, Esteban R, Buti M, Pumarola T, Rodriguez-Frias F. Assessment of a Novel Automatic Real-Time PCR Assay on the Cobas 4800 Analyzer as a Screening Platform for Hepatitis C Virus Genotyping in Clinical Practice: Comparison with Massive Sequencing. J Clin Microbiol 2017; 55:504-509. [PMID: 27927921 PMCID: PMC5277520 DOI: 10.1128/jcm.01960-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/14/2016] [Indexed: 02/06/2023] Open
Abstract
The unequivocal identification of hepatitis C virus (HCV) subtypes 1a/1b and genotypes 2 to 6 is required for optimizing the effectiveness of interferon-free, direct-acting antiviral therapies. We compared the performance of a new real-time HCV genotyping assay used on the Cobas 4800 system (C4800) with that of high-resolution HCV subtyping (HRCS). In total, 502 samples were used, including 184 samples from chronic HCV patients (from routine laboratory activity during April 2016), 5 stored samples with double HCV genotype infections for testing the limitations of the method, and 313 samples from a screening protocol implemented in our hospital (from May to August 2016) based on the new method to further determine its genotyping accuracy. A total of 282 samples, including 171 from April 2016 (the 13 remaining had too low of a viral load for HRCS), 5 selected with double infections, and 106 from screening, were analyzed by both methods, and 220 were analyzed only by the C4800. The C4800 correctly subtyped 125 of 126 1a/1b samples, and the 1 remaining sample was reported as genotype 1. The C4800 correctly genotyped 38 of 45 non-1a/1b samples (classified by HRCS), and it reported the remaining 7 samples as indeterminate. One hundred two of 106 non-1a/1b genotype samples that were identified using the C4800 for screening were confirmed by HRCS. In the 4 remaining samples, 3 were correctly reported as genotype 1 (without defining the subtype) and 1 was reported as indeterminate. None of the samples were misgenotyped. Four of 7 samples with double HCV infections were correctly genotyped by the C4800. Excluding the 5 selected double-infected samples, the C4800 showed 95.7% concordant results for genotyping HCVs 2 to 6 and 1a/1b subtyping, and 99.2% concordance for subtyping 1a/1b single infections in clinical samples. To improve laboratory workflow, we propose using the C4800 as a first-line test for HCV genotyping and 1a/1b classification, followed by transferring non-1a/1b samples to a center where HRCS is available, if further characterization is needed.
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Affiliation(s)
- Leonardo Nieto-Aponte
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Viral Hepatitis Laboratory, Liver Unit-Internal Medicine, Vall d'Hebron Research Institute (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Alicia Ruiz-Ripa
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - David Tabernero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Carolina Gonzalez
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Josep Gregori
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Viral Hepatitis Laboratory, Liver Unit-Internal Medicine, Vall d'Hebron Research Institute (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
- Roche Diagnostics SL, Sant Cugat del Vallès, Spain
| | - Marta Vila
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Miriam Asensio
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Damir Garcia-Cehic
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Viral Hepatitis Laboratory, Liver Unit-Internal Medicine, Vall d'Hebron Research Institute (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Gerardo Ruiz
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Qian Chen
- Viral Hepatitis Laboratory, Liver Unit-Internal Medicine, Vall d'Hebron Research Institute (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Laura Ordeig
- Viral Hepatitis Laboratory, Liver Unit-Internal Medicine, Vall d'Hebron Research Institute (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Meritxell Llorens
- Viral Hepatitis Laboratory, Liver Unit-Internal Medicine, Vall d'Hebron Research Institute (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Montserrat Saez
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Juan I Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Hospital Universitari Vall d'Hebron (HUVH), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Rafael Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Hospital Universitari Vall d'Hebron (HUVH), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Hospital Universitari Vall d'Hebron (HUVH), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Tomas Pumarola
- Microbiology Department, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron (HUVH), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Viral Hepatitis Laboratory, Liver Unit-Internal Medicine, Vall d'Hebron Research Institute (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
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49
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Garvey MI, Bradley CW, Holden KL, Hewins P, Ngui SL, Tedder R, Jumaa P, Smit E. Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting. J Hosp Infect 2017; 96:157-162. [PMID: 28196726 DOI: 10.1016/j.jhin.2017.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/09/2017] [Indexed: 01/24/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) infection is a major health burden worldwide. A patient with no history of HCV infection while on a renal unit was found to seroconvert to HCV. AIM To report the use of sequencing to postulate how transmission of HCV occurred in a healthcare setting, and how this guided our outbreak investigation. FINDINGS Based on infection control inspections the transmission event was surmised to be due to ward environmental contamination with blood and subsequent inoculation from intravenous interventions on the patient acquiring HCV. We discuss the interventions put in place in response to the outbreak investigation findings. CONCLUSION Sequencing of healthcare-acquired HCV infections should be undertaken as routine practice in outbreak investigations.
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Affiliation(s)
- M I Garvey
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Edgbaston, Birmingham, UK.
| | - C W Bradley
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Edgbaston, Birmingham, UK
| | - K L Holden
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Edgbaston, Birmingham, UK
| | - P Hewins
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Edgbaston, Birmingham, UK
| | - S-L Ngui
- Blood Borne Virus Unit, Microbiology Service Colindale, Public Health England, London, UK
| | - R Tedder
- Blood Borne Virus Unit, Microbiology Service Colindale, Public Health England, London, UK
| | - P Jumaa
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Edgbaston, Birmingham, UK
| | - E Smit
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Edgbaston, Birmingham, UK; Public Health England Birmingham Laboratory, Birmingham Heartlands Hospital, Birmingham, UK
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50
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Gozlan Y, Ben-Ari Z, Moscona R, Shirazi R, Rakovsky A, Kabat A, Veizman E, Berdichevski T, Weiss P, Cohen-Ezra O, Lurie Y, Gafanovich I, Braun M, Cohen-Naftaly M, Shlomai A, Shibolet O, Zigmond E, Zuckerman E, Carmiel-Haggai M, Nimer A, Hazzan R, Maor Y, Kitay-Cohen Y, Shemer-Avni Y, Kra-Oz Z, Schreiber L, Peleg O, Sierra S, Harrigan PR, Mendelson E, Mor O. HCV genotype-1 subtypes and resistance-associated substitutions in drug-naive and in direct-acting antiviral treatment failure patients. Antivir Ther 2017; 22:431-441. [PMID: 28067632 DOI: 10.3851/imp3123] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Direct-acting antiviral (DAA) treatment regimens and response rates of patients with HCV genotype-1 (GT1) are currently considered subtype-dependent. Identification of clinically relevant resistance-associated substitutions (RASs) in the NS3 and NS5A proteins at baseline and in DAA failures, may also impact clinical decisions. METHODS In a multicentre cohort study (n=308), NS3 or NS5B sequencing (n=248) was used to discriminate between GT1 subtypes. The correlation between baseline NS3 and NS5A RASs on the 12-week sustained virological response (SVR12) rates of 160 of the patients treated with second-generation DAAs was also assessed. Post-treatment resistance analysis was performed on samples from 58 patients exhibiting DAA virological failure. RESULTS GT1a, GT1b and GT1d subtypes were identified in 23.0%, 75.4% and 1.2% of tested samples. GT1b was most prevalent (97.7%, 128/131) among patients born in the former Soviet Union. The Q80K NS3 RAS was identified in 17.5% (10/57) of the GT1a carriers, most of whom were Israeli-born. NS3 and NS5A baseline RASs showed a negligible correlation with SVR12 rates. Treatment-emergent RASs were observed among 8.9% (4/45) and 76.9% (10/13) of first- and second-generation DAA failures, respectively, with D168V/E (NS3), Y93H and L31M (NS5A) being the most prevalent mutations. CONCLUSIONS NS3 sequencing analysis can successfully discriminate between GT1 subtypes and identify NS3 amino acid substitutions. While pre-treatment NS3 and NS5A RASs marginally affect second-generation DAA SVR12 rates, post-treatment resistance analysis should be considered prior to re-therapy.
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Affiliation(s)
- Yael Gozlan
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Ziv Ben-Ari
- Liver Disease Center, Sheba Medical Center, Ramat-Gan, Israel.,The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Roy Moscona
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Rachel Shirazi
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Aviya Rakovsky
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Arij Kabat
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Ella Veizman
- Liver Disease Center, Sheba Medical Center, Ramat-Gan, Israel
| | | | - Peretz Weiss
- Liver Disease Center, Sheba Medical Center, Ramat-Gan, Israel
| | | | - Yoav Lurie
- Liver Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Marius Braun
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Liver Institute, Rabin Medical Center, Petah-Tikva, Israel
| | - Michal Cohen-Naftaly
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Liver Institute, Rabin Medical Center, Petah-Tikva, Israel
| | - Amir Shlomai
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Liver Institute, Rabin Medical Center, Petah-Tikva, Israel
| | - Oren Shibolet
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Gastroenterology, Tel-Aviv Medical Center, Tel Aviv, Israel
| | - Ehud Zigmond
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Gastroenterology, Tel-Aviv Medical Center, Tel Aviv, Israel
| | | | - Michal Carmiel-Haggai
- Liver Unit, Galilee Medical Center, Naharya, Israel.,Faculty of Medicine in the Galilee, Bar-Ilan University, Ramat-Gan, Israel
| | - Assy Nimer
- Faculty of Medicine in the Galilee, Bar-Ilan University, Ramat-Gan, Israel.,Internal Medicine Department, Galilee Medical Center, Naharya, Israel
| | - Rawi Hazzan
- Liver Unit, Haemek Medical Center, Afula, Israel
| | - Yaakov Maor
- Division of Gastroenterology, Kaplan Health Sciences Centre, Department of Medicine, Faculty of Medicine, Hebrew University, Rehovot, Israel
| | - Yona Kitay-Cohen
- Gastroenterology and Hepatology Institute, Meir Medical Center, Kfar Saba, Israel
| | | | - Zipi Kra-Oz
- Virology Laboratory, Rambam Medical Center, Haifa, Israel
| | | | | | - Saleta Sierra
- Institute of Virology, University of Cologne, Cologne, Germany
| | | | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel.,School of Public Health, Tel Aviv University, Tel Aviv, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
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