1
|
Li J, Zhang Y, Luo B. The programed death-1/programed death ligand-1 axis and its potential as a therapeutic target for virus-associated tumours. Rev Med Virol 2024; 34:e2486. [PMID: 37905387 DOI: 10.1002/rmv.2486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 10/07/2023] [Accepted: 10/22/2023] [Indexed: 11/02/2023]
Abstract
As an important and serious condition impacting human health, the diagnosis, and treatment of tumours is clinically vital because tumour cell immune escape sustains tumour development. Programed death ligand-1 (PD-L1) on tumour cell surfaces binds to the programed death-1 (PD-1), inhibits T cell activation, and induces apoptosis, and incapacitates cells. This allows tumour cells to evade recognition and clearance by the immune system, thereby permitting tumour occurrence, and development and poor prognosis outcomes in patients with tumours. Currently, anti-PD-1/PD-L1 immunotherapy has become pivotal in tumour treatment. Pathogens, especially viruses, are important factors which induce many tumours. In this article, we examine associations between Epstein-Barr virus, human papilloma virus, hepatitis B virus, hepatitis C virus, and human immunodeficiency virus type 1-related tumours and PD-1/PD-L1 axis.
Collapse
Affiliation(s)
- Jing Li
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Yan Zhang
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, China
- Department of Clinical Laboratory, Zibo Central Hospital, Zibo, China
| | - Bing Luo
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, China
| |
Collapse
|
2
|
Martínez-González B, Gallego I, Gregori J, Soria ME, Somovilla P, de Ávila AI, García-Crespo C, Durán-Pastor A, Briones C, Gómez J, Quer J, Domingo E, Perales C. Fitness-Dependent, Mild Mutagenic Activity of Sofosbuvir for Hepatitis C Virus. Antimicrob Agents Chemother 2023; 67:e0039423. [PMID: 37367486 PMCID: PMC10353389 DOI: 10.1128/aac.00394-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/06/2023] [Indexed: 06/28/2023] Open
Abstract
The concept of a mild mutagen was coined to describe a minor mutagenic activity exhibited by some nucleoside analogues that potentiated their efficacy as antiretroviral agents. In the present study, we report the mild mutagen activity of sofosbuvir (SOF) for hepatitis C virus (HCV). Serial passages of HCV in human hepatoma cells, in the presence of SOF at a concentration well below its cytotoxic concentration 50 (CC50) led to pre-extinction populations whose mutant spectra exhibited a significant increase of C→U transitions, relative to populations passaged in the absence of SOF. This was reflected in an increase in several diversity indices that were used to characterize viral quasispecies. The mild mutagenic activity of SOF was largely absent when it was tested with isogenic HCV populations that displayed high replicative fitness. Thus, SOF can act as a mild mutagen for HCV, depending on HCV fitness. Possible mechanisms by which the SOF mutagenic activity may contribute to its antiviral efficacy are discussed.
Collapse
Affiliation(s)
- Brenda Martínez-González
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
| | - Isabel Gallego
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - María Eugenia Soria
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
| | - Pilar Somovilla
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Antoni Durán-Pastor
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | | | - Jordi Gómez
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
| |
Collapse
|
3
|
Atypical Mutational Spectrum of SARS-CoV-2 Replicating in the Presence of Ribavirin. Antimicrob Agents Chemother 2023; 67:e0131522. [PMID: 36602354 PMCID: PMC9872624 DOI: 10.1128/aac.01315-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We report that ribavirin exerts an inhibitory and mutagenic activity on SARS-CoV-2-infecting Vero cells, with a therapeutic index higher than 10. Deep sequencing analysis of the mutant spectrum of SARS-CoV-2 replicating in the absence or presence of ribavirin indicated an increase in the number of mutations, but not in deletions, and modification of diversity indices, expected from a mutagenic activity. Notably, the major mutation types enhanced by replication in the presence of ribavirin were A→G and U→C transitions, a pattern which is opposite to the dominance of G→A and C→U transitions previously described for most RNA viruses. Implications of the inhibitory activity of ribavirin, and the atypical mutational bias produced on SARS-CoV-2, for the search for synergistic anti-COVID-19 lethal mutagen combinations are discussed.
Collapse
|
4
|
Zoghi S, Masoudi MS, Taheri R. The Evolving Role of Next Generation Sequencing in Pediatric Neurosurgery: a Call for Action for Research, Clinical Practice, and Optimization of Care. World Neurosurg 2022; 168:232-242. [PMID: 36122859 DOI: 10.1016/j.wneu.2022.09.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
Abstract
NGS (Next-Generation Sequencing) is one of the most promising technologies that have truly revolutionized many aspects of clinical practice in recent years. It has been and is increasingly applied in many disciplines of medicine; however, it appears that pediatric neurosurgery despite its great potential has not truly embraced this new technology and is hesitant to employ it in its routine practice and guidelines. In this review, we briefly summarized the developments that lead to the establishment of NGS technology, reviewed the current applications and potentials of NGS in the disorders treated by pediatric neurosurgeons, and lastly discuss the steps we need to take to better harness NGS in pediatric neurosurgery.
Collapse
Affiliation(s)
- Sina Zoghi
- Department of Neurosurgery, Shiraz University of Medical Sciences, Shiraz, Iran; Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Reza Taheri
- Department of Neurosurgery, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
5
|
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: 9] [Impact Index Per Article: 4.5] [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.
Collapse
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;
| |
Collapse
|
6
|
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: 16] [Impact Index Per Article: 8.0] [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.
Collapse
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
| |
Collapse
|
7
|
Pacin-Ruiz B, Cortese MF, Tabernero D, Sopena S, Gregori J, García-García S, Casillas R, Najarro A, Aldama U, Palom A, Rando-Segura A, Galán A, Vila M, Riveiro-Barciela M, Quer J, González-Aseguinolaza G, Buti M, Rodríguez-Frías F. Inspecting the Ribozyme Region of Hepatitis Delta Virus Genotype 1: Conservation and Variability. Viruses 2022; 14:v14020215. [PMID: 35215809 PMCID: PMC8877431 DOI: 10.3390/v14020215] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/07/2023] Open
Abstract
The hepatitis delta virus (HDV) genome has an autocatalytic region called the ribozyme, which is essential for viral replication. The aim of this study was to use next-generation sequencing (NGS) to analyze the ribozyme quasispecies (QS) in order to study its evolution and identify highly conserved regions potentially suitable for a gene-silencing strategy. HDV RNA was extracted from 2 longitudinal samples of chronic HDV patients and the ribozyme (nucleotide, nt 688-771) was analyzed using NGS. QS conservation, variability and genetic distance were analyzed. Mutations were identified by aligning sequences with their specific genotype consensus. The main relevant mutations were tested in vitro. The ribozyme was conserved overall, with a hyper-conserved region between nt 715-745. No difference in QS was observed over time. The most variable region was between nt 739-769. Thirteen mutations were observed, with three showing a higher frequency: T23C, T69C and C64 deletion. This last strongly reduced HDV replication by more than 1 log in vitro. HDV Ribozyme QS was generally highly conserved and was maintained during follow-up. The most conserved portion may be a valuable target for a gene-silencing strategy. The presence of the C64 deletion may strongly impair viral replication, as it is a potential mechanism of viral persistence.
Collapse
Affiliation(s)
- Beatriz Pacin-Ruiz
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
| | - María Francesca Cortese
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Correspondence: (M.F.C.); (D.T.)
| | - David Tabernero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Correspondence: (M.F.C.); (D.T.)
| | - Sara Sopena
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Josep Gregori
- Liver Unit, Liver Disease, Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.G.); (J.Q.)
| | - Selene García-García
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
| | - Rosario Casillas
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Adrián Najarro
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Unai Aldama
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Adriana Palom
- Liver Unit, Department of Internal Medicine, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Ariadna Rando-Segura
- Department of Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Anna Galán
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Marta Vila
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Liver Unit, Department of Internal Medicine, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Josep Quer
- Liver Unit, Liver Disease, Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.G.); (J.Q.)
| | | | - María Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Liver Unit, Department of Internal Medicine, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Francisco Rodríguez-Frías
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Plaça Cívica, 08193 Bellaterra, Spain
| |
Collapse
|
8
|
Garcia-Garcia S, Cortese MF, Tabernero D, Gregori J, Vila M, Pacín B, Quer J, Casillas R, Castillo-Ribelles L, Ferrer-Costa R, Rando-Segura A, Trejo-Zahínos J, Pumarola T, Casis E, Esteban R, Riveiro-Barciela M, Buti M, Rodríguez-Frías F. Cross-sectional evaluation of circulating hepatitis B virus RNA and DNA: Different quasispecies? World J Gastroenterol 2021; 27:7144-7158. [PMID: 34887634 PMCID: PMC8613647 DOI: 10.3748/wjg.v27.i41.7144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/20/2021] [Accepted: 10/18/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Different forms of pregenomic and other hepatitis B virus (HBV) RNA have been detected in patients’ sera. These circulating HBV-RNAs may be useful for monitoring covalently closed circular DNA activity, and predicting hepatitis B e-antigen seroconversion or viral rebound after nucleos(t)ide analog cessation. Data on serum HBV-RNA quasispecies, however, is scarce. It is therefore important to develop methodologies to thoroughly analyze this quasispecies, ensuring the elimination of any residual HBV-DNA. Studying circulating HBV-RNA quasispecies may facilitate achieving functional cure of HBV infection.
AIM To establish a next-generation sequencing (NGS) methodology for analyzing serum HBV-RNA and comparing it with DNA quasispecies.
METHODS Thirteen untreated chronic hepatitis B patients, showing different HBV-genotypes and degrees of severity of liver disease were enrolled in the study and a serum sample with HBV-DNA > 5 Log10 IU/mL and HBV-RNA > 4 Log10 copies/mL was taken from each patient. HBV-RNA was treated with DNAse I to remove any residual DNA, and the region between nucleotides (nt) 1255-1611 was amplified using a 3-nested polymerase chain reaction protocol, and analyzed with NGS. Variability/conservation and complexity was compared between HBV-DNA and RNA quasispecies.
RESULTS No HBV-DNA contamination was detected in cDNA samples from HBV-RNA quasispecies. HBV quasispecies complexity showed heterogeneous behavior among patients. The Rare Haplotype Load at 1% was greater in DNA than in RNA quasispecies, with no statistically significant differences (P = 0.1641). Regarding conservation, information content was equal in RNA and DNA quasispecies in most nt positions [218/357 (61.06%)]. In 102 of the remaining 139 (73.38%), HBV-RNA showed slightly higher variability. Sliding window analysis identified 4 hyper-conserved sequence fragments in each quasispecies, 3 of them coincided between the 2 quasispecies: nts 1258-1286, 1545-1573 and 1575-1604. The 2 hyper-variable sequence fragments also coincided: nts 1311-1344 and 1461-1485. Sequences between nts 1519-1543 and 1559-1587 were only hyper-conserved in HBV-DNA and RNA, respectively.
CONCLUSION Our methodology allowed analyzing HBV-RNA quasispecies complexity and conservation without interference from HBV-DNA. Thanks to this, we have been able to compare both quasispecies in the present study.
Collapse
Affiliation(s)
- Selene Garcia-Garcia
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Maria Francesca Cortese
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Josep Gregori
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
| | - Marta Vila
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Beatriz Pacín
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
| | - Rosario Casillas
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Laura Castillo-Ribelles
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Roser Ferrer-Costa
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Ariadna Rando-Segura
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Department of Microbiology, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
| | - Jesús Trejo-Zahínos
- Department of Microbiology, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
| | - Tomas Pumarola
- Department of Microbiology, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
| | - Ernesto Casis
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Rafael Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Universitat Autónoma de Barcelona, Barcelona 08035, Spain
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Universitat Autónoma de Barcelona, Barcelona 08035, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Universitat Autónoma de Barcelona, Barcelona 08035, Spain
| | - Francisco Rodríguez-Frías
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| |
Collapse
|
9
|
Feng X, Bao J, Song C, Xie L, Tan X, Li J, Jia H, Tian M, Qi J, Qin C, Bian H. Functional role of miR‑155 in physiological and pathological processes of liver injury (Review). Mol Med Rep 2021; 24:714. [PMID: 34396452 DOI: 10.3892/mmr.2021.12353] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/09/2021] [Indexed: 11/05/2022] Open
Abstract
There are several types of liver injury, including alcohol‑induced liver injury, drug‑induced liver injury, infectious liver injury, cirrhosis, liver ischemia/reperfusion injury and liver failure. In recent years, accumulated data have demonstrated that microRNAs (miRNAs/miRs) may be involved in the occurrence and development of a variety of systemic diseases, such as immune diseases, tumors and nervous system diseases. miR‑155 is a key miRNA, which has been studied extensively and has been shown to target different genes. In the present review, the potential effects and mechanisms of miR‑155 on the physiological and pathological processes of liver injury were reviewed from the perspective of cell stress, inflammation and activation of fibrosis. In addition, the potential benefits of miR‑155 as a therapeutic target and predictor of liver injury were summarized.
Collapse
Affiliation(s)
- Xiao Feng
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Jiaying Bao
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Chunxia Song
- Department of Emergency Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Ling Xie
- Department of Obstetrics and Gynecology, Jinan Zhangqiu District Maternal and Child Health Hospital, Jinan, Shandong 250200, P.R. China
| | - Xu Tan
- Department of Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Jiaqi Li
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Huimin Jia
- Department of Emergency Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Miaomiao Tian
- Department of Immunology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Jianni Qi
- Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Chengyong Qin
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Hongjun Bian
- Department of Emergency Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| |
Collapse
|
10
|
Fuhrmann L, Jablonski KP, Beerenwinkel N. Quantitative measures of within-host viral genetic diversity. Curr Opin Virol 2021; 49:157-163. [PMID: 34153841 DOI: 10.1016/j.coviro.2021.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 12/22/2022]
Abstract
The genetic diversity of virus populations within their hosts is known to influence disease progression, treatment outcome, drug resistance, cell tropism, and transmission risk, and the study of dynamic changes of genetic heterogeneity can provide insights into the evolution of viruses. Several measures to quantify within-host genetic diversity capturing different aspects of diversity patterns in a sample or population are used, based on incidence, relative frequencies, pairwise distances, or phylogenetic trees. Here, we review and compare several of these measures.
Collapse
Affiliation(s)
- Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland
| | - Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland.
| |
Collapse
|
11
|
Minosse C, Gruber CEM, Rueca M, Taibi C, Zaccarelli M, Grilli E, Montalbano M, Capobianchi MR, Antinori A, D’Offizi G, McPhee F, Garbuglia AR. Late Relapse and Reinfection in HCV Patients Treated with Direct-Acting Antiviral (DAA) Drugs. Viruses 2021; 13:v13061151. [PMID: 34208646 PMCID: PMC8235384 DOI: 10.3390/v13061151] [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: 04/19/2021] [Revised: 06/09/2021] [Accepted: 06/14/2021] [Indexed: 12/02/2022] Open
Abstract
The risk of hepatitis C virus (HCV) recurrence after direct-acting antiviral (DAA) treatment is <0.5%. However, the distinction between HCV RNA late relapse and reinfection still represents a challenge in virological diagnostics. The aim of this study was to employ next-generation sequencing (NGS) to investigate HCV RNA recurrence in patients achieving a sustained virologic response (SVR) at least six months post-treatment. NGS was performed on plasma samples from six HCV-positive patients (Pt1–6) treated with DAA. NGS of HCV NS5B was analyzed before treatment (T0), after HCV RNA rebound (T1), and, for Pt3, after a second rebound (T2). Reinfection was confirmed for Pt5, and for the first rebound observed in Pt3. Conversely, viral relapse was observed when comparing T0 and T1 for Pt6 and T1 and T2 for Pt3. Z-scores were calculated and used to predict whether HCV-positive patient samples at different time points belonged to the same quasispecies population. A low Z-score of <2.58 confirmed that viral quasispecies detected at T0 and T1 were closely related for both Pt1 and Pt2, while the Z-score for Pt4 was suggestive of possible reinfection. NGS data analyses indicate that the Z-score may be a useful parameter for distinguishing late relapse from reinfection.
Collapse
Affiliation(s)
- Claudia Minosse
- Virology Unit, National Institute for Infectious Diseases, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (C.M.); (C.E.M.G.); (M.R.); (M.R.C.); (A.R.G.)
| | - Cesare E. M. Gruber
- Virology Unit, National Institute for Infectious Diseases, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (C.M.); (C.E.M.G.); (M.R.); (M.R.C.); (A.R.G.)
| | - Martina Rueca
- Virology Unit, National Institute for Infectious Diseases, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (C.M.); (C.E.M.G.); (M.R.); (M.R.C.); (A.R.G.)
| | - Chiara Taibi
- Infectious Disease—Clinical Department, National Institute for Infectious Diseases, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (M.Z.); (E.G.); (M.M.); (A.A.); (G.D.)
- Correspondence:
| | - Mauro Zaccarelli
- Infectious Disease—Clinical Department, National Institute for Infectious Diseases, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (M.Z.); (E.G.); (M.M.); (A.A.); (G.D.)
| | - Elisabetta Grilli
- Infectious Disease—Clinical Department, National Institute for Infectious Diseases, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (M.Z.); (E.G.); (M.M.); (A.A.); (G.D.)
| | - Marzia Montalbano
- Infectious Disease—Clinical Department, National Institute for Infectious Diseases, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (M.Z.); (E.G.); (M.M.); (A.A.); (G.D.)
| | - Maria R. Capobianchi
- Virology Unit, National Institute for Infectious Diseases, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (C.M.); (C.E.M.G.); (M.R.); (M.R.C.); (A.R.G.)
| | - Andrea Antinori
- Infectious Disease—Clinical Department, National Institute for Infectious Diseases, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (M.Z.); (E.G.); (M.M.); (A.A.); (G.D.)
| | - Gianpiero D’Offizi
- Infectious Disease—Clinical Department, National Institute for Infectious Diseases, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (M.Z.); (E.G.); (M.M.); (A.A.); (G.D.)
| | - Fiona McPhee
- Bristol-Myers Squibb Research and Development, Cambridge, MA 02142, USA;
| | - Anna Rosa Garbuglia
- Virology Unit, National Institute for Infectious Diseases, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy; (C.M.); (C.E.M.G.); (M.R.); (M.R.C.); (A.R.G.)
| |
Collapse
|
12
|
Jeong HW, Kim MK, Yi HJ, Kim DM, Jeon SJ, Lee HK, Oh YH, Hwang YO. Hepatitis A virus strains identified in jogaejeot associated with outbreaks in Seoul, South Korea. Lett Appl Microbiol 2021; 73:107-112. [PMID: 33797771 DOI: 10.1111/lam.13482] [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: 12/14/2020] [Revised: 02/23/2021] [Accepted: 03/25/2021] [Indexed: 12/15/2022]
Abstract
Jogaejeot, seasoned Venerupis philippinarum, is a traditional Korean fermented food, and hepatitis A virus (HAV) can be transmitted through contaminated food, especially bivalve shellfish, causing acute gastroenteritis worldwide. Here, we carried out a phylogenetic analysis to identify and characterize HAV strains in jogaejeot samples associated with hepatitis A (HA) outbreaks in Seoul, South Korea, in 2019. The HAV strains were identified using blast and molecular analysis of the amplified HAV VP1-P2B genome region. The HAV strains identified in the five jogaejeot samples shared at least 99% sequence identity, were all classified as genotype IA and were most closely related to strains that are widespread in East Asia. These results support a link between the consumption of jogaejeot and the HA outbreaks observed in 2019 in Seoul. In addition, they indicate a need for more stringent enforcement of food safety regulations for the shellfish industry, especially against HAV, and the value of widespread vaccination.
Collapse
Affiliation(s)
- H W Jeong
- Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Korea
| | - M K Kim
- Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Korea
| | - H J Yi
- Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Korea
| | - D M Kim
- Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Korea
| | - S J Jeon
- Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Korea
| | - H K Lee
- Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Korea
| | - Y H Oh
- Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Korea
| | - Y O Hwang
- Seoul Metropolitan Government Research Institute of Public Health and Environment, Gyeonggi-do, Korea
| |
Collapse
|
13
|
Broad and Dynamic Diversification of Infectious Hepatitis C Virus in a Cell Culture Environment. J Virol 2020; 94:JVI.01856-19. [PMID: 31852791 DOI: 10.1128/jvi.01856-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Previous studies documented that long-term hepatitis C virus (HCV) replication in human hepatoma Huh-7.5 cells resulted in viral fitness gain, expansion of the mutant spectrum, and several phenotypic alterations. In the present work, we show that mutational waves (changes in frequency of individual mutations) occurred continuously and became more prominent as the virus gained fitness. They were accompanied by an increasing proportion of heterogeneous genomic sites that affected 1 position in the initial HCV population and 19 and 69 positions at passages 100 and 200, respectively. Analysis of biological clones of HCV showed that these dynamic events affected infectious genomes, since part of the fluctuating mutations became incorporated into viable genomes. While 17 mutations were scored in 3 biological clones isolated from the initial population, the number reached 72 in 3 biological clones from the population at passage 200. Biological clones differed in their responses to antiviral inhibitors, indicating a phenotypic impact of viral dynamics. Thus, HCV adaptation to a specific constant environment (cell culture without external influences) broadens the mutant repertoire and does not focus the population toward a limited number of dominant genomes. A retrospective examination of mutant spectra of foot-and-mouth disease virus passaged in cell cultures suggests a parallel behavior here described for HCV. We propose that virus diversification in a constant environment has its basis in the availability of multiple alternative mutational pathways for fitness gain. This mechanism of broad diversification should also apply to other replicative systems characterized by high mutation rates and large population sizes.IMPORTANCE The study shows that extensive replication of an RNA virus in a constant biological environment does not limit exploration of sequence space and adaptive options. There was no convergence toward a restricted set of adapted genomes. Mutational waves and mutant spectrum broadening affected infectious genomes. Therefore, profound modifications of mutant spectrum composition and consensus sequence diversification are not exclusively dependent on environmental alterations or the intervention of population bottlenecks.
Collapse
|
14
|
Machine-learning based patient classification using Hepatitis B virus full-length genome quasispecies from Asian and European cohorts. Sci Rep 2019; 9:18892. [PMID: 31827222 PMCID: PMC6906359 DOI: 10.1038/s41598-019-55445-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/27/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic infection with Hepatitis B virus (HBV) is a major risk factor for the development of advanced liver disease including fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). The relative contribution of virological factors to disease progression has not been fully defined and tools aiding the deconvolution of complex patient virus profiles is an unmet clinical need. Variable viral mutant signatures develop within individual patients due to the low-fidelity replication of the viral polymerase creating 'quasispecies' populations. Here we present the first comprehensive survey of the diversity of HBV quasispecies through ultra-deep sequencing of the complete HBV genome across two distinct European and Asian patient populations. Seroconversion to the HBV e antigen (HBeAg) represents a critical clinical waymark in infected individuals. Using a machine learning approach, a model was developed to determine the viral variants that accurately classify HBeAg status. Serial surveys of patient quasispecies populations and advanced analytics will facilitate clinical decision support for chronic HBV infection and direct therapeutic strategies through improved patient stratification.
Collapse
|
15
|
Synergistic lethal mutagenesis of hepatitis C virus. Antimicrob Agents Chemother 2019:AAC.01653-19. [PMID: 31570400 DOI: 10.1128/aac.01653-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Lethal mutagenesis is an antiviral approach that consists in extinguishing a virus by an excess of mutations acquired during replication in the presence of a mutagenic agent, often a nucleotide analogue. One of its advantages is its broad spectrum nature that renders the strategy potentially effective against emergent RNA viral infections. Here we describe synergistic lethal mutagenesis of hepatitis C virus (HCV) by a combination of favipiravir (T-705) and ribavirin. Synergy has been documented over a broad range of analogue concentrations using the Chou-Talalay method as implemented in the CompuSyn graphics, with average dose reduction index (DRI) above 1 (68.02±101.6 for favipiravir, and 5.83±6.07 for ribavirin), and average combination indices (CI) below 1 (0.52±0.28). Furthermore, analogue concentrations that individually did not extinguish high fitness HCV in ten serial infections, when used in combination they extinguished high fitness HCV in one to two passages. Although both analogues display a preference for G→A and C→U transitions, deep sequencing analysis of mutant spectra indicated a different preference of the two analogues for the mutation sites, thus unveiling a new possible synergy mechanism in lethal mutagenesis. Prospects of synergy among mutagenic nucleotides as a strategy to confront emerging viral infections are discussed.
Collapse
|
16
|
Godoy C, Tabernero D, Sopena S, Gregori J, Cortese MF, González C, Casillas R, Yll M, Rando A, López-Martínez R, Quer J, González-Aseguinolaza G, Esteban R, Riveiro-Barciela M, Buti M, Rodríguez-Frías F. Characterization of hepatitis B virus X gene quasispecies complexity in mono-infection and hepatitis delta virus superinfection. World J Gastroenterol 2019; 25:1566-1579. [PMID: 30983817 PMCID: PMC6452231 DOI: 10.3748/wjg.v25.i13.1566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/25/2019] [Accepted: 03/02/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatitis delta virus (HDV) seems to strongly suppress hepatitis B virus (HBV) replication, although little is known about the mechanism of this interaction. Both these viruses show a dynamic distribution of mutants, resulting in viral quasispecies. Next-generation sequencing is a viable approach for analyzing the composition of these mutant spectra. As the regulatory hepatitis B X protein (HBx) is essential for HBV replication, determination of HBV X gene (HBX) quasispecies complexity in HBV/HDV infection compared to HBV mono-infection may provide information on the interactions between these two viruses.
AIM To compare HBV quasispecies complexity in the HBX 5’ region between chronic hepatitis delta (CHD) and chronic HBV mono-infected patients.
METHODS Twenty-four untreated patients were included: 7/24 (29.2%) with HBeAg-negative chronic HBV infection (CI, previously termed inactive carriers), 8/24 (33.3%) with HBeAg-negative chronic hepatitis B (CHB) and 9/24 (37.5%) with CHD. A serum sample from each patient was first tested for HBV DNA levels. The HBX 5’ region [nucleotides (nt) 1255-1611] was then PCR-amplified for subsequent next-generation sequencing (MiSeq, Illumina, United States). HBV quasispecies complexity in the region analyzed was evaluated using incidence-based indices (number of haplotypes and number of mutations), abundance-based indices (Hill numbers of order 1 and 2), and functional indices (mutation frequency and nucleotide diversity). We also evaluated the pattern of nucleotide changes to investigate which of them could be the cause of the quasispecies complexity.
RESULTS CHB patients showed higher median HBV-DNA levels [5.4 logIU/mL, interquartile range (IQR) 3.5-7.9] than CHD (3.4 logIU/mL, IQR 3-7.6) (P = n.s.) or CI (3.2 logIU/mL, IQR 2.3-3.5) (P < 0.01) patients. The incidence and abundance indices indicated that HBV quasispecies complexity was significantly greater in CI than CHB. A similar trend was observed in CHD patients, although only Hill numbers of order 2 showed statistically significant differences (CHB 2.81, IQR 1.11-4.57 vs CHD 8.87, 6.56-11.18, P = 0.038). There were no significant differences in the functional indices, but CI and CHD patients also showed a trend towards greater complexity than CHB. No differences were found for any HBV quasispecies complexity indices between CHD and CI patients. G-to-A and C-to-T nucleotide changes, characteristic of APOBEC3G, were higher in CHD and CI than in CHB in genotype A haplotypes, but not in genotype D. The proportion of nt G-to-A vs A-to-G changes and C-to-T vs T-to-C changes in genotype A and D haplotypes in CHD patients showed no significant differences. In CHB and CI the results of these comparisons were dependent on HBV genotype.
CONCLUSION The lower-replication CHD and CI groups show a trend to higher quasispecies complexity than the higher-replication CHB group. The mechanisms associated with this greater complexity require elucidation.
Collapse
Affiliation(s)
- Cristina Godoy
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - David Tabernero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Sara Sopena
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Josep Gregori
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Roche Diagnostics SL, Sant Cugat del Vallès 08174, Spain
| | - Maria Francesca Cortese
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Carolina González
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Rosario Casillas
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Marçal Yll
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Ariadna Rando
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Rosa López-Martínez
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | | | - Rafael Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona 08035, Spain
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona 08035, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona 08035, Spain
| | - Francisco Rodríguez-Frías
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
| |
Collapse
|
17
|
Petronella N, Ronholm J, Suresh M, Harlow J, Mykytczuk O, Corneau N, Bidawid S, Nasheri N. Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique. BMC Infect Dis 2018; 18:521. [PMID: 30333011 PMCID: PMC6191920 DOI: 10.1186/s12879-018-3419-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/27/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Human norovirus is the leading cause of viral gastroenteritis globally, and the GII.4 has been the most predominant genotype for decades. This genotype has numerous variants that have caused repeated epidemics worldwide. However, the molecular evolutionary signatures among the GII.4 variants have not been elucidated throughout the viral genome. METHOD A metagenomic, next-generation sequencing method, based on Illumina RNA-Seq, was applied to determine norovirus sequences from clinical samples. RESULTS Herein, the obtained deep-sequencing data was employed to analyze full-genomic sequences from GII.4 variants prevailing in Canada from 2012 to 2016. Phylogenetic analysis demonstrated that the majority of these sequences belong to New Orleans 2009 and Sydney 2012 strains, and a recombinant sequence was also identified. Genome-wide similarity analyses implied that while the capsid gene is highly diverse among the isolates, the viral protease and polymerase genes remain relatively conserved. Numerous amino acid substitutions were observed at each putative antigenic epitope of the VP1 protein, whereas few amino acid changes were identified in the polymerase protein. Co-infection with other enteric RNA viruses was investigated and the astrovirus genome was identified in one of the samples. CONCLUSIONS Overall this study demonstrated the application of whole genome sequencing as an important tool in molecular characterization of noroviruses.
Collapse
Affiliation(s)
- Nicholas Petronella
- Biostatistics and Modeling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada Ottawa, Ottawa, ON, Canada
| | - Jennifer Ronholm
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, QC, Canada.,Department of Animal Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, QC, Canada
| | - Menka Suresh
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Jennifer Harlow
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Oksana Mykytczuk
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Nathalie Corneau
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Sabah Bidawid
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Neda Nasheri
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| |
Collapse
|
18
|
Perales C. Quasispecies dynamics and clinical significance of hepatitis C virus (HCV) antiviral resistance. Int J Antimicrob Agents 2018; 56:105562. [PMID: 30315919 DOI: 10.1016/j.ijantimicag.2018.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/01/2018] [Accepted: 10/06/2018] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) follows quasispecies dynamics in infected hosts and this influences its biology, how the virus diversifies into several genotypes and many subtypes, and how viral populations respond to antiviral therapies. Despite current antiviral combinations being able to cure a great percentage of HCV-infected patients, the presence of resistance-associated substitutions (RASs) diminishes the success of antiviral therapies, which is a main concern in the re-treatment of patients treated with direct-acting antiviral agents. Current methodologies such as ultra deep sequencing are ideal tools to obtain a detailed representation of the mutant spectrum composition circulating in infected patients. Such knowledge should allow optimisation of rescue treatments. A new mechanism of antiviral resistance not based on the selection of RASs but on high viral fitness is discussed.
Collapse
Affiliation(s)
- Celia Perales
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain.
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Resistance of high fitness hepatitis C virus to lethal mutagenesis. Virology 2018; 523:100-109. [PMID: 30107298 DOI: 10.1016/j.virol.2018.07.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/30/2018] [Accepted: 07/30/2018] [Indexed: 01/07/2023]
Abstract
Viral fitness quantifies the degree of virus adaptation to a given environment. How viral fitness can influence the mutant spectrum complexity of a viral quasispecies subjected to lethal mutagenesis has not been investigated. Here we document that two high fitness hepatitis C virus populations display higher resistance to the mutagenic nucleoside analogues favipiravir and ribavirin than their parental, low fitness HCV. All populations, however, exhibited a mutation transition bias indicative of active mutagenesis. Resistance to the analogues was associated with a limited expansion of mutant spectrum complexity, as evidenced by several diversity indices used to characterize mutant spectra. The results are consistent with a replicative site-drug competition mechanism that was previously proposed for HCV fitness-associated resistance to non-mutagenic inhibitors. Other alternative, non-mutually exclusive mechanisms are considered. The results introduce viral fitness as a relevant parameter to evaluate the response of viruses to lethal mutagenesis, with implications for antiviral designs.
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|