1
|
Ibañez-Lligoña M, Colomer-Castell S, González-Sánchez A, Gregori J, Campos C, Garcia-Cehic D, Andrés C, Piñana M, Pumarola T, Rodríguez-Frias F, Antón A, Quer J. Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses. Viruses 2023; 15:v15020587. [PMID: 36851800 PMCID: PMC9965957 DOI: 10.3390/v15020587] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Epidemics and pandemics have occurred since the beginning of time, resulting in millions of deaths. Many such disease outbreaks are caused by viruses. Some viruses, particularly RNA viruses, are characterized by their high genetic variability, and this can affect certain phenotypic features: tropism, antigenicity, and susceptibility to antiviral drugs, vaccines, and the host immune response. The best strategy to face the emergence of new infectious genomes is prompt identification. However, currently available diagnostic tests are often limited for detecting new agents. High-throughput next-generation sequencing technologies based on metagenomics may be the solution to detect new infectious genomes and properly diagnose certain diseases. Metagenomic techniques enable the identification and characterization of disease-causing agents, but they require a large amount of genetic material and involve complex bioinformatic analyses. A wide variety of analytical tools can be used in the quality control and pre-processing of metagenomic data, filtering of untargeted sequences, assembly and quality control of reads, and taxonomic profiling of sequences to identify new viruses and ones that have been sequenced and uploaded to dedicated databases. Although there have been huge advances in the field of metagenomics, there is still a lack of consensus about which of the various approaches should be used for specific data analysis tasks. In this review, we provide some background on the study of viral infections, describe the contribution of metagenomics to this field, and place special emphasis on the bioinformatic tools (with their capabilities and limitations) available for use in metagenomic analyses of viral pathogens.
Collapse
Affiliation(s)
- Marta Ibañez-Lligoña
- 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
- 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
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Sergi Colomer-Castell
- 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
- 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
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Alejandra González-Sánchez
- Microbiology Department, 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
| | - 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
| | - 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, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- 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
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, 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
- 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
| | - Cristina Andrés
- Microbiology Department, 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
| | - Maria Piñana
- Microbiology Department, 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
| | - Tomàs Pumarola
- Microbiology Department, 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
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Francisco Rodríguez-Frias
- 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
- 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
- Department of Basic Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, 08195 Barcelona, Spain
| | - Andrés Antón
- Microbiology Department, 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
- Microbiology Department, 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
- 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
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence:
| |
Collapse
|
2
|
Sánchez-Montalvá A, Álvarez-Sierra D, Martínez-Gallo M, Perurena-Prieto J, Arrese-Muñoz I, Ruiz-Rodríguez JC, Espinosa-Pereiro J, Bosch-Nicolau P, Martínez-Gómez X, Antón A, Martínez-Valle F, Riveiro-Barciela M, Blanco-Grau A, Rodríguez-Frias F, Castellano-Escuder P, Poyatos-Canton E, Bas-Minguet J, Martínez-Cáceres E, Sánchez-Pla A, Zurera-Egea C, Teniente-Serra A, Hernández-González M, Pujol-Borrell R. Exposing and Overcoming Limitations of Clinical Laboratory Tests in COVID-19 by Adding Immunological Parameters; A Retrospective Cohort Analysis and Pilot Study. Front Immunol 2022; 13:902837. [PMID: 35844497 PMCID: PMC9276968 DOI: 10.3389/fimmu.2022.902837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Background Two years since the onset of the COVID-19 pandemic no predictive algorithm has been generally adopted for clinical management and in most algorithms the contribution of laboratory variables is limited. Objectives To measure the predictive performance of currently used clinical laboratory tests alone or combined with clinical variables and explore the predictive power of immunological tests adequate for clinical laboratories. Methods: Data from 2,600 COVID-19 patients of the first wave of the pandemic in the Barcelona area (exploratory cohort of 1,579, validation cohorts of 598 and 423 patients) including clinical parameters and laboratory tests were retrospectively collected. 28-day survival and maximal severity were the main outcomes considered in the multiparametric classical and machine learning statistical analysis. A pilot study was conducted in two subgroups (n=74 and n=41) measuring 17 cytokines and 27 lymphocyte phenotypes respectively. Findings 1) Despite a strong association of clinical and laboratory variables with the outcomes in classical pairwise analysis, the contribution of laboratory tests to the combined prediction power was limited by redundancy. Laboratory variables reflected only two types of processes: inflammation and organ damage but none reflected the immune response, one major determinant of prognosis. 2) Eight of the thirty variables: age, comorbidity index, oxygen saturation to fraction of inspired oxygen ratio, neutrophil-lymphocyte ratio, C-reactive protein, aspartate aminotransferase/alanine aminotransferase ratio, fibrinogen, and glomerular filtration rate captured most of the combined statistical predictive power. 3) The interpretation of clinical and laboratory variables was moderately improved by grouping them in two categories i.e., inflammation related biomarkers and organ damage related biomarkers; Age and organ damage-related biomarker tests were the best predictors of survival, and inflammatory-related ones were the best predictors of severity. 4) The pilot study identified immunological tests (CXCL10, IL-6, IL-1RA and CCL2), that performed better than most currently used laboratory tests. Conclusions Laboratory tests for clinical management of COVID 19 patients are valuable but limited predictors due to redundancy; this limitation could be overcome by adding immunological tests with independent predictive power. Understanding the limitations of tests in use would improve their interpretation and simplify clinical management but a systematic search for better immunological biomarkers is urgent and feasible.
Collapse
Affiliation(s)
- Adrián Sánchez-Montalvá
- Infectious Disease Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- International Health Program Institut Català de la Salut, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Department of Medicine, Universitat Autònoma Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Barcelona, Spain
| | - Daniel Álvarez-Sierra
- Translational Immunology Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mónica Martínez-Gallo
- Translational Immunology Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Immunology Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma Barcelona, Barcelona, Spain
| | - Janire Perurena-Prieto
- Translational Immunology Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma Barcelona, Barcelona, Spain
| | - Iria Arrese-Muñoz
- Immunology Department, Hospital Universitari Vall Hebron, Barcelona, Spain
| | - Juan Carlos Ruiz-Rodríguez
- Intensive Medicine Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Organ Dysfunction and Resuscitation Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
| | - Juan Espinosa-Pereiro
- Infectious Disease Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- International Health Program Institut Català de la Salut, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Barcelona, Spain
| | - Pau Bosch-Nicolau
- Infectious Disease Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- International Health Program Institut Català de la Salut, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Barcelona, Spain
| | - Xavier Martínez-Gómez
- Epidemiology and Public Health Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Epidemiology and Public Health Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Epidemiology and Public Health, Universitat Autònoma Barcelona, Barcelona, Spain
| | - Andrés Antón
- Microbiology Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Microbiology Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Department of Genetics and Microbiology, Autonomous University of Barcelona, Barcelona, Spain
| | - Ferran Martínez-Valle
- Department of Medicine, Universitat Autònoma Barcelona, Barcelona, Spain
- Internal Medicine Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Systemic Disease Research Group, Valle Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mar Riveiro-Barciela
- Department of Medicine, Universitat Autònoma Barcelona, Barcelona, Spain
- Liver Disease Research Group, Valle Hebron Research Institute (VHIR), Barcelona, Spain
- CIBERehd - Instituto de Salud Carlos III, Barcelona, Spain
| | - Albert Blanco-Grau
- Clinical Biochemistry Department, Hospital Universitari Vall d'Hebron and Clinical Biochemistry Research Group, Valle Hebron Research Institute (VHIR), Barcelona, Spain
| | - Francisco Rodríguez-Frias
- Clinical Biochemistry Department, Hospital Universitari Vall d'Hebron and Clinical Biochemistry Research Group, Valle Hebron Research Institute (VHIR), Barcelona, Spain
| | | | - Elisabet Poyatos-Canton
- Immunology Division, Bellvitge University Hospital, Hospitalet de Llobregat, Barcelona, Spain
| | - Jordi Bas-Minguet
- Immunology Division, Bellvitge University Hospital, Hospitalet de Llobregat, Barcelona, Spain
| | - Eva Martínez-Cáceres
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma Barcelona, Barcelona, Spain
- Immunology Group, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona (Barcelona), Spain
- Immunology Department, Hospital Universitari Germans Trias Pujol, Badalona (Barcelona), Spain
| | - Alex Sánchez-Pla
- Bioinformatics and Statistics Group, University of Barcelona, Barcelona, Spain
- Statistics and Bioinformatics Unit, Vall Hebron Research Institute (VHIR), Barcelona, Spain
| | - Coral Zurera-Egea
- Immunology Department, Hospital Universitari Germans Trias Pujol, Badalona (Barcelona), Spain
| | - Aina Teniente-Serra
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma Barcelona, Barcelona, Spain
- Immunology Group, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona (Barcelona), Spain
- Immunology Department, Hospital Universitari Germans Trias Pujol, Badalona (Barcelona), Spain
| | - Manuel Hernández-González
- Translational Immunology Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Immunology Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma Barcelona, Barcelona, Spain
| | - Ricardo Pujol-Borrell
- Translational Immunology Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Immunology Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma Barcelona, Barcelona, Spain
| |
Collapse
|
3
|
Martinez-Sanchez L, Cobbaert CM, Noordam R, Brouwer N, Blanco-Grau A, Villena-Ortiz Y, Thelen M, Ferrer-Costa R, Casis E, Rodríguez-Frias F, den Elzen WPJ. Indirect determination of biochemistry reference intervals using outpatient data. PLoS One 2022; 17:e0268522. [PMID: 35588100 PMCID: PMC9119462 DOI: 10.1371/journal.pone.0268522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 05/02/2022] [Indexed: 12/22/2022] Open
Abstract
The aim of this study was to determine reference intervals in an outpatient population from Vall d'Hebron laboratory using an indirect approach previously described in a Dutch population (NUMBER project). We used anonymized test results from individuals visiting general practitioners and analysed during 2018. Analytical quality was assured by EQA performance, daily average monitoring and by assessing longitudinal accuracy between 2018 and 2020 (using trueness verifiers from Dutch EQA). Per test, outliers by biochemically related tests were excluded, data were transformed to a normal distribution (if necessary) and means and standard deviations were calculated, stratified by age and sex. In addition, the reference limit estimator method was also used to calculate reference intervals using the same dataset. Finally, for standardized tests reference intervals obtained were compared with the published NUMBER results. Reference intervals were calculated using data from 509,408 clinical requests. For biochemical tests following a normal distribution, similar reference intervals were found between Vall d'Hebron and the Dutch study. For creatinine and urea, reference intervals increased with age in both populations. The upper limits of Gamma-glutamyl transferase were markedly higher in the Dutch study compared to Vall d'Hebron results. Creatine kinase and uric acid reference intervals were higher in both populations compared to conventional reference intervals. Medical test results following a normal distribution showed comparable and consistent reference intervals between studies. Therefore a simple indirect method is a feasible and cost-efficient approach for calculating reference intervals. Yet, for generating standardized calculated reference intervals that are traceable to higher order materials and methods, efforts should also focus on test standardization and bias assessment using commutable trueness verifiers.
Collapse
Affiliation(s)
- Luisa Martinez-Sanchez
- Clinical Laboratories, Biochemistry Department, Vall d’Hebron University Hospital, Barcelona, Spain
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Centre, Leiden, The Netherlands
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Nannette Brouwer
- Diagnost-IQ, Expert Centre for Clinical Chemistry, Purmerend, The Netherlands
| | - Albert Blanco-Grau
- Clinical Laboratories, Biochemistry Department, Vall d’Hebron University Hospital, Barcelona, Spain
| | - Yolanda Villena-Ortiz
- Clinical Laboratories, Biochemistry Department, Vall d’Hebron University Hospital, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Marc Thelen
- Laboratory for Clinical Chemistry and Hematology, Amphia, Breda, The Netherlands
- Stichting Kwaliteitsbewaking Medische Laboratoriumdiagnostiek, Nijmegen, The Netherlands
- Department of Laboratory Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Roser Ferrer-Costa
- Clinical Laboratories, Biochemistry Department, Vall d’Hebron University Hospital, Barcelona, Spain
| | - Ernesto Casis
- Clinical Laboratories, Biochemistry Department, Vall d’Hebron University Hospital, Barcelona, Spain
| | - Francisco Rodríguez-Frias
- Clinical Laboratories, Biochemistry Department, Vall d’Hebron University Hospital, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Wendy P. J. den Elzen
- Clinical Laboratories, Biochemistry Department, Vall d’Hebron University Hospital, Barcelona, Spain
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Centre, Leiden, The Netherlands
- Atalmedial Diagnostics Centre, Amsterdam, The Netherlands
- Department of Clinical Chemistry, Amsterdam Public Health research institute, Amsterdam UMC, Amsterdam, The Netherlands
| |
Collapse
|
4
|
Toscano-Guerra E, Martínez-Gallo M, Arrese-Muñoz I, Giné A, Díaz-Troyano N, Gabriel-Medina P, Riveiro-Barciela M, Labrador-Horrillo M, Martinez-Valle F, Montalvá AS, Hernández-González M, Borrell RP, Rodríguez-Frias F, Ferrer R, Thomson TM, Paciucci R. Recovery of serum testosterone levels is an accurate predictor of survival from COVID-19 in male patients. BMC Med 2022; 20:129. [PMID: 35351135 PMCID: PMC8963401 DOI: 10.1186/s12916-022-02345-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 03/16/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND SARS-CoV-2 infection portends a broad range of outcomes, from a majority of asymptomatic cases to a lethal disease. Robust correlates of severe COVID-19 include old age, male sex, poverty, and co-morbidities such as obesity, diabetes, and cardiovascular disease. A precise knowledge of the molecular and biological mechanisms that may explain the association of severe disease with male sex is still lacking. Here, we analyzed the relationship of serum testosterone levels and the immune cell skewing with disease severity in male COVID-19 patients. METHODS Biochemical and hematological parameters of admission samples in 497 hospitalized male and female COVID-19 patients, analyzed for associations with outcome and sex. Longitudinal (in-hospital course) analyses of a subcohort of 114 male patients were analyzed for associations with outcome. Longitudinal analyses of immune populations by flow cytometry in 24 male patients were studied for associations with outcome. RESULTS We have found quantitative differences in biochemical predictors of disease outcome in male vs. female patients. Longitudinal analyses in a subcohort of male COVID-19 patients identified serum testosterone trajectories as the strongest predictor of survival (AUC of ROC = 92.8%, p < 0.0001) in these patients among all biochemical parameters studied, including single-point admission serum testosterone values. In lethal cases, longitudinal determinations of serum luteinizing hormone (LH) and androstenedione levels did not follow physiological feedback patterns. Failure to reinstate physiological testosterone levels was associated with evidence of impaired T helper differentiation and augmented circulating classical monocytes. CONCLUSIONS Recovery or failure to reinstate testosterone levels is strongly associated with survival or death, respectively, from COVID-19 in male patients. Our data suggest an early inhibition of the central LH-androgen biosynthesis axis in a majority of patients, followed by full recovery in survivors or a peripheral failure in lethal cases. These observations are suggestive of a significant role of testosterone status in the immune responses to COVID-19 and warrant future experimental explorations of mechanistic relationships between testosterone status and SARS-CoV-2 infection outcomes, with potential prophylactic or therapeutic implications.
Collapse
Affiliation(s)
- Emily Toscano-Guerra
- Biochemistry Service, Vall d'Hebron Hospital, Autonomous University of Barcelona (UAB), Barcelona, Spain
- Cell Signaling and Cancer Progression Laboratory, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain
- Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mónica Martínez-Gallo
- Immunology Division, Vall d'Hebron Hospital, Barcelona, Spain.
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.
- Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Barcelona, Spain.
| | - Iria Arrese-Muñoz
- Immunology Division, Vall d'Hebron Hospital, Barcelona, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - Anna Giné
- Biochemistry Service, Vall d'Hebron Hospital, Autonomous University of Barcelona (UAB), Barcelona, Spain
- Cell Signaling and Cancer Progression Laboratory, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain
| | - Noelia Díaz-Troyano
- Biochemistry Service, Vall d'Hebron Hospital, Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - Pablo Gabriel-Medina
- Biochemistry Service, Vall d'Hebron Hospital, Autonomous University of Barcelona (UAB), Barcelona, Spain
| | | | | | | | - Adrián Sánchez Montalvá
- Infectious Diseases Department, International Health and Tuberculosis Unit National Referral Centre for Tropical Diseases, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain
| | - Manuel Hernández-González
- Immunology Division, Vall d'Hebron Hospital, Barcelona, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - Ricardo Pujol Borrell
- Immunology Division, Vall d'Hebron Hospital, Barcelona, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - Francisco Rodríguez-Frias
- Biochemistry Service, Vall d'Hebron Hospital, Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - Roser Ferrer
- Biochemistry Service, Vall d'Hebron Hospital, Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - Timothy M Thomson
- Universidad Peruana Cayetano Heredia, Lima, Perú.
- Barcelona Institute for Molecular Biology, National Science Council (IBMB-CSIC), Barcelona, Spain.
- Networked Center for Hepatic and Digestive Diseases (CIBER-EHD), Instituto Nacional de la Salud Carlos III, Madrid, Spain.
- Plataforma Temática Interdisciplinar Salud Global (PTI-Global Health) CSIC, Madrid, Spain.
| | - Rosanna Paciucci
- Biochemistry Service, Vall d'Hebron Hospital, Autonomous University of Barcelona (UAB), Barcelona, Spain.
- Cell Signaling and Cancer Progression Laboratory, Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.
| |
Collapse
|
5
|
Villena-Ortiz Y, Giralt M, Castellote-Bellés L, Lopez-Martínez RM, Martinez-Sanchez L, García-Fernández AE, Ferrer-Costa R, Rodríguez-Frias F, Casis E. A descriptive and validation study of a predictive model of severity of SARS-COV-2 infection. Adv Lab Med 2021; 2:390-408. [PMID: 37362407 PMCID: PMC10197269 DOI: 10.1515/almed-2021-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/16/2021] [Indexed: 06/28/2023]
Abstract
Objectives The strain the SARS-COV-2 pandemic is putting on hospitals requires that predictive values are identified for a rapid triage and management of patients at a higher risk of developing severe COVID-19. We developed and validated a prognostic model of COVID-19 severity. Methods A descriptive, comparative study of patients with positive vs. negative PCR-RT for SARS-COV-2 and of patients who developed moderate vs. severe COVID-19 was conducted. The model was built based on analytical and demographic data and comorbidities of patients seen in an Emergency Department with symptoms consistent with COVID-19. A logistic regression model was designed from data of the COVID-19-positive cohort. Results The sample was composed of 410 COVID-positive patients (303 with moderate disease and 107 with severe disease) and 81 COVID-negative patients. The predictive variables identified included lactate dehydrogenase, C-reactive protein, total proteins, urea, and platelets. Internal calibration showed an area under the ROC curve (AUC) of 0.88 (CI 95%: 0.85-0.92), with a rate of correct classifications of 85.2% for a cut-off value of 0.5. External validation (100 patients) yielded an AUC of 0.79 (95% CI: 0.71-0.89), with a rate of correct classifications of 73%. Conclusions The predictive model identifies patients at a higher risk of developing severe COVID-19 at Emergency Department, with a first blood test and common parameters used in a clinical laboratory. This model may be a valuable tool for clinical planning and decision-making.
Collapse
Affiliation(s)
- Yolanda Villena-Ortiz
- Department of Clinical Biochemistry, Laboratoris Clínics, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Marina Giralt
- Department of Clinical Biochemistry, Laboratoris Clínics, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Laura Castellote-Bellés
- Department of Clinical Biochemistry, Laboratoris Clínics, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Rosa M. Lopez-Martínez
- Department of Clinical Biochemistry, Laboratoris Clínics, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Luisa Martinez-Sanchez
- Department of Clinical Biochemistry, Laboratoris Clínics, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | | | - Roser Ferrer-Costa
- Department of Clinical Biochemistry, Laboratoris Clínics, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Francisco Rodríguez-Frias
- Department of Clinical Biochemistry, Laboratoris Clínics, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Ernesto Casis
- Department of Clinical Biochemistry, Laboratoris Clínics, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| |
Collapse
|
6
|
Aguilera A, Trastoy R, Rodríguez-Frias F, Muñoz-Bellido JL, Melón S, Suárez A, Orduña A, Viciana I, Bernal S, García-Bujalance S, Montiel N, Molina JM, Basaras M, Fernández-Cuenca F, García-Arata I, Reina G, Ocete MD, Fuentes A, Navarro-de la Cruz D, Nieto L, Blazquez de Castro A, Buti M, Álvarez M, García F. GEHEP 010 study: Prevalence and distribution of hepatitis B virus genotypes in Spain (2000-2016). J Infect 2020; 81:600-606. [PMID: 32711039 DOI: 10.1016/j.jinf.2020.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 06/29/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To study the prevalence and distribution of HBV genotypes in Spain for the period 2000-2016. METHODS Retrospective study recruiting 2559 patients from 17 hospitals. Distribution of HBV genotypes, as well as sex, age, geographical origin, mode of transmission, HDV-, HIV- and/or HCV-coinfection, and treatment were recorded. RESULTS 1924 chronically HBV native Spanish patients have been recruited. Median age was 54 years (IQR: 41-62), 69.6% male, 6.3% HIV-coinfected, 3.1% were HCV-coinfected, 1.7% HDV-co/superinfected. Genotype distribution was: 55.9% D, 33.5% A, 5.6% F, 0.8% G, and 1.9% other genotypes (E, B, H and C). HBV genotype A was closely associated with male sex, sexual transmission, and HIV-coinfection. In contrast, HBV genotype D was associated with female sex and vertical transmission. Different patterns of genotype distribution and diversity were found between different geographical regions. In addition, HBV epidemiological patterns are evolving in Spain, mainly because of immigration. Finally, similar overall rates of treatment success across all HBV genotypes were found. CONCLUSIONS We present here the most recent data on molecular epidemiology of HBV in Spain (GEHEP010 Study). This study confirms that the HBV genotype distribution in Spain varies based on age, sex, origin, HIV-coinfection, geographical regions and epidemiological groups.
Collapse
Affiliation(s)
- Antonio Aguilera
- Complexo Hospitalario Universitario de Santiago, Santiago de Compostela, Instituto de Investigación Sanitaria de Santiago IDIS, Spain
| | - Rocío Trastoy
- Hospital Universitario Vall d'Hebrón, Barcelona, Spain
| | | | | | - Santiago Melón
- Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Avelina Suárez
- Hospital Clínico Universitario San Carlos, Madrid, Spain
| | - Antonio Orduña
- Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Isabel Viciana
- Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - Samuel Bernal
- Hospital Universitario Virgen de Valme, Sevilla, Spain
| | | | | | | | | | | | | | | | | | - Ana Fuentes
- Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Av. de la Innovación S/N, 18016 Granada, Spain
| | | | | | | | - María Buti
- Hospital Universitario Vall d'Hebrón, Barcelona, Spain
| | - Marta Álvarez
- Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Av. de la Innovación S/N, 18016 Granada, Spain
| | - Federico García
- Hospital Universitario San Cecilio, Instituto de Investigación Biosanitaria Ibs, Av. de la Innovación S/N, 18016 Granada, Spain.
| |
Collapse
|
7
|
Greulich T, Rodríguez-Frias F, Belmonte I, Klemmer A, Vogelmeier CF, Miravitlles M. Real world evaluation of a novel lateral flow assay (AlphaKit® QuickScreen) for the detection of alpha-1-antitrypsin deficiency. Respir Res 2018; 19:151. [PMID: 30103740 PMCID: PMC6090649 DOI: 10.1186/s12931-018-0826-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/08/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Alpha-1-Antitrypsin (AAT) deficiency (AATD) is a hereditary disorder that manifests primarily as pulmonary emphysema and liver cirrhosis. The clinically most relevant mutation causing AATD is a single nucleotide polymorphism Glu342Lys (Z-mutation). Despite the recommendation to test every COPD patient, the condition remains severely underdiagnosed with a delay of several years between first symptoms and diagnosis. The Grifols' AlphaKit® QuickScreen is a novel qualitative point-of-care (POC) in vitro screening test developed for the detection of the Z AAT protein in capillary whole blood. The objective of this prospective, international, multi-center, diagnostic, interventional real-world study was to assess the performance of this device for the detection of AATD in test-naïve COPD patients. METHODS 1044 test-naïve COPD patients were recruited from 9 centers in Spain and 10 centers in Germany, ranging from primary to tertiary care. To evaluate the performance of the test, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated compared with the gold standard (genotyping). RESULTS Genotyping and phenotyping of all 1019 evaluable samples revealed 4.12% of patients as carriers of at least one Z-allele, while 0.29% carried the homozygous genotype Pi*ZZ. The evaluation of the test's ability to detect the PiZ protein yielded the following results: specificity 97.8%, sensitivity 73.8%, negative predictive value 98.9%, and positive predictive value 58.5%. All false negatives (n = 11) were heterozygote Pi*MZ samples. CONCLUSIONS The tested device can be used as an appropriate tool to exclude AATD in primary care and in the overall COPD population, except in patients with a high a-priori- probability of AATD.
Collapse
Affiliation(s)
- Timm Greulich
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Centre Giessen and Marburg, Philipps-University, Marburg, Germany.
- German Centre for Lung Research (DZL), Marburg, Germany.
- Respiratory Medicine, University Hospital of Gießen and Marburg, 35043, Marburg, Germany.
| | - Francisco Rodríguez-Frias
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto Nacional de Salud Carlos III, Madrid, Spain
| | - Irene Belmonte
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Andreas Klemmer
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Centre Giessen and Marburg, Philipps-University, Marburg, Germany
- German Centre for Lung Research (DZL), Marburg, Germany
| | - Claus F Vogelmeier
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Centre Giessen and Marburg, Philipps-University, Marburg, Germany
- German Centre for Lung Research (DZL), Marburg, Germany
| | - Marc Miravitlles
- Pneumology Department, Hospital Universitari Vall d'Hebron, CIBER de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
| |
Collapse
|
8
|
Suárez-Amarán L, Usai C, Di Scala M, Godoy C, Ni Y, Hommel M, Palomo L, Segura V, Olagüe C, Vales A, Ruiz-Ripa A, Buti M, Salido E, Prieto J, Urban S, Rodríguez-Frias F, Aldabe R, González-Aseguinolaza G. Erratum to "A new HDV mouse model identifies mitochondrial antiviral signaling protein (MAVS) as a key player in IFN-β induction" [J Hepatol 67 (2017) 669-679]. J Hepatol 2018; 69:262-264. [PMID: 29776712 DOI: 10.1016/j.jhep.2018.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lester Suárez-Amarán
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Carla Usai
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Marianna Di Scala
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Cristina Godoy
- Centro de Investigación Biomédica en red: Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain; Virology Unit, Department of Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Yi Ni
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mirja Hommel
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Laura Palomo
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Víctor Segura
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain; Bioinformatics Unit, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Cristina Olagüe
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Africa Vales
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Alicia Ruiz-Ripa
- Centro de Investigación Biomédica en red: Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain; Virology Unit, Department of Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en red: Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain; Virology Unit, Department of Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Eduardo Salido
- Department of Pathology, Centre for Biomedical Research on Rare Diseases (CIBERER), La Laguna, S/C Tenerife, Spain
| | - Jesús Prieto
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain; Centro de Investigación Biomédica en red: Enfermedades Hepáticas y Digestivas ( CIBERehd), Instituto de Salud Carlos III, Pamplona, Spain
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Francisco Rodríguez-Frias
- Centro de Investigación Biomédica en red: Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain; Virology Unit, Department of Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rafael Aldabe
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Gloria González-Aseguinolaza
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain.
| |
Collapse
|
9
|
Suárez-Amarán L, Usai C, Di Scala M, Godoy C, Ni Y, Hommel M, Palomo L, Segura V, Olagüe C, Vales A, Ruiz-Ripa A, Buti M, Salido E, Prieto J, Urban S, Rodríguez-Frias F, Aldabe R, González-Aseguinolaza G. A new HDV mouse model identifies mitochondrial antiviral signaling protein (MAVS) as a key player in IFN-β induction. J Hepatol 2017; 67:669-679. [PMID: 28527664 DOI: 10.1016/j.jhep.2017.05.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/28/2017] [Accepted: 05/06/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Studying hepatitis delta virus (HDV) and developing new treatments is hampered by the limited availability of small animal models. Herein, a description of a robust mouse model of HDV infection that mimics several important characteristics of the human disease is presented. METHODS HDV and hepatitis B virus (HBV) replication competent genomes were delivered to the mouse liver using adeno-associated viruses (AAV; AAV-HDV and AAV-HBV). Viral load, antigen expression and genomes were quantified at different time points after AAV injection. Furthermore, liver pathology, genome editing, and the activation of the innate immune response were evaluated. RESULTS AAV-HDV infection initiated HDV replication in mouse hepatocytes. Genome editing was confirmed by the presence of small and large HDV antigens and sequencing. Viral replication was detected for 45days, even after the AAV-HDV vector had almost disappeared. In the presence of HBV, HDV infectious particles were detected in serum. Furthermore, as observed in patients, co-infection was associated with the reduction of HBV antigen expression and the onset of liver damage that included the alteration of genes involved in the development of liver pathologies. HDV replication induced a sustained type I interferon response, which was significantly reduced in immunodeficient mice and almost absent in mitochondrial antiviral signaling protein (MAVS)-deficient mice. CONCLUSION The animal model described here reproduces important characteristics of human HDV infection and provides a valuable tool for characterizing the viral infection and for developing new treatments. Furthermore, MAVS was identified as a main player in HDV detection and adaptive immunity was found to be involved in the amplification of the innate immune response. Lay summary: Co-infection with hepatitis B and D virus (HBV and HDV, respectively) often causes a more severe disease condition than HBV alone. Gaining more insight into HDV and developing new treatments is hampered by limited availability of adequate immune competent small animal models and new ones are needed. Here, a mouse model of HDV infection is described, which mimics several important characteristics of the human disease, such as the initiation and maintenance of replication in murine hepatocytes, genome editing and, in the presence of HBV, generation of infectious particles. Lastly, the involvement of an adaptive immunity and the intracellular signaling molecule MAVS in mounting a strong and lasting innate response was shown. Thus, our model serves as a useful tool for the investigation of HDV biology and new treatments.
Collapse
MESH Headings
- Adaptive Immunity
- Adaptor Proteins, Signal Transducing/deficiency
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/immunology
- Animals
- Cell Line
- Coinfection/immunology
- Coinfection/pathology
- Coinfection/virology
- Dependovirus/genetics
- Disease Models, Animal
- Genome, Viral
- Hepatitis B/complications
- Hepatitis B/immunology
- Hepatitis B/virology
- Hepatitis B Antigens/metabolism
- Hepatitis B virus/genetics
- Hepatitis B virus/immunology
- Hepatitis D/complications
- Hepatitis D/immunology
- Hepatitis D/virology
- Hepatitis Delta Virus/genetics
- Hepatitis Delta Virus/immunology
- Hepatitis Delta Virus/physiology
- Hepatitis delta Antigens/metabolism
- Humans
- Immunity, Innate
- Interferon-beta/biosynthesis
- Liver/pathology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Models, Immunological
- Signal Transduction/immunology
- Virus Replication
Collapse
Affiliation(s)
- Lester Suárez-Amarán
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Carla Usai
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Marianna Di Scala
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Cristina Godoy
- Centro de Investigación Biomédica en red: Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain; Virology Unit, Department of Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Yi Ni
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mirja Hommel
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Laura Palomo
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Víctor Segura
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain; Bioinformatics Unit, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Cristina Olagüe
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Africa Vales
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Alicia Ruiz-Ripa
- Centro de Investigación Biomédica en red: Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain; Virology Unit, Department of Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en red: Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain; Virology Unit, Department of Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Eduardo Salido
- Department of Pathology, Centre for Biomedical Research on Rare Diseases (CIBERER), La Laguna, S/C Tenerife, Spain
| | - Jesús Prieto
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain; Centro de Investigación Biomédica en red: Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Pamplona, Spain
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Francisco Rodríguez-Frias
- Centro de Investigación Biomédica en red: Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Barcelona, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain; Virology Unit, Department of Microbiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rafael Aldabe
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain
| | - Gloria González-Aseguinolaza
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), Pamplona, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Calle Irunlarrea 3, Pamplona 31008, Spain.
| |
Collapse
|
10
|
Aguilera A, Navarro D, Rodríguez-Frias F, Viciana I, Martínez-Sapiña AM, Rodríguez MJ, Martró E, Lozano MC, Coletta E, Cardeñoso L, Suárez A, Trigo M, Rodríguez-Granjer J, Montiel N, de la Iglesia A, Alados JC, Vegas C, Bernal S, Fernández-Cuenca F, Pena MJ, Reina G, García-Bujalance S, Echevarria MJ, Benítez L, Pérez-Castro S, Ocete D, García-Arata I, Guerrero C, Rodríguez-Iglesias M, Casas P, García F. Prevalence and distribution of hepatitis C virus genotypes in Spain during the 2000-2015 period (the GEHEP 005 study). J Viral Hepat 2017; 24:725-732. [PMID: 28248445 DOI: 10.1111/jvh.12700] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/09/2017] [Indexed: 12/11/2022]
Abstract
We report the largest study on the prevalence and distribution of HCV genotypes in Spain (2000-2015), and we relate them with clinical, epidemiological and virological factors. Patients from 29 hospitals in 10 autonomous communities (Andalusia, Aragon, Castilla-Leon, Catalonia, Galicia, Canary Islands, Madrid Community, Valencian Community, Murcia Region and Basque Country) have been studied. Annual distribution of HCV genotypes and subtypes, as well as gender, age, transmission route, HIV and/or HBV coinfection, and treatment details were recorded. We included 48595 chronically HCV-infected patients with the following characteristics: median age 51 years (IQR, 44-58), 67.9% male, 19.1% HIV-coinfected, 23.5% HBV-coinfected. Parenteral transmission route was the most frequent (58.7%). Genotype distribution was 66.9% GT1 (24.9% subtype 1a and 37.9% subtype 1b), 2.8% GT2, 17.3% GT3, 11.4% GT4 and 0.1% GT5 and 0.02% GT6. LiPA was the most widely HCV genotyping test used (52.4%). HCV subtype 1a and genotypes 3 and 4 were closely associated with male gender, parenteral route of infection and HIV and HBV coinfection; in contrast, subtype 1b and genotype 2 were associated with female gender, nonparenteral route and mono-infection. Age was related to genotype distribution, and different patterns of distribution and biodiversity index were observed between different geographical areas. Finally, we describe how treatment and changes in transmission routes may have affected HCV genotype prevalence and distribution patterns. We present the most recent data on molecular epidemiology of hepatitis C virus in Spain. This study confirms that genotype distributions vary with age, sex, HIV and HBV coinfection and within geographical areas and epidemiological groups.
Collapse
Affiliation(s)
- A Aguilera
- Complexo Hospitalario Universitario de Santiago de Compostela, A Coruña, Spain
| | - D Navarro
- Complexo Hospitalario Universitario de Santiago de Compostela, A Coruña, Spain
| | | | - I Viciana
- Hospital Clínico Universitario Virgen de la Victoria, Malaga, Spain
| | | | | | - E Martró
- Hospital Universitari Germans Trías i Pujol, Badalona, CIBER en Epidemiología y Salud Pública, Barcelona, Spain
| | - M C Lozano
- Hospital Universitario Virgen del Rocio, Sevilla, Spain
| | - E Coletta
- Hospital Clínico Universitario Valladolid, Valladolid, Spain
| | - L Cardeñoso
- Hospital Universitario de la Princesa, Madrid, Spain
| | - A Suárez
- Hospital Clínico San Carlos, Madrid, Spain
| | - M Trigo
- Complexo Hospitalario de Pontevedra, Pontevedra, Spain
| | | | - N Montiel
- Hospital Costa del Sol, Marbella, Spain
| | - A de la Iglesia
- Complejo Hospitalario Universitario de Huelva, Huelva, Spain
| | - J C Alados
- Hospital del SAS de Jerez de la Frontera, Sevilla, Spain
| | - C Vegas
- Fundación Jiménez Díaz, Madrid, Spain
| | - S Bernal
- Hospital Universitario Virgen de Valme, Sevilla, Spain
| | | | - M J Pena
- Hospital Doctor Negrín, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - G Reina
- Clínica Universitaria de Navarra, Pamplona, Spain
| | | | | | - L Benítez
- Hospital Universitario Puerta de Hierro, Majadahonda, Spain
| | | | - D Ocete
- Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - I García-Arata
- Hospital Universitario de Fuenlabrada, Fuenlabrada, Spain
| | - C Guerrero
- Hospital General Universitario Morales Meseguer, Murcia, Spain
| | | | - P Casas
- Hospital Universitario San Cecilio, Instituto de Investigación Ibs-Granada, Granada, Spain
| | - F García
- Hospital Universitario San Cecilio, Instituto de Investigación Ibs-Granada, Granada, Spain
| |
Collapse
|
11
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
12
|
Quer J, Gregori J, Rodríguez-Frias F, Buti M, Madejon A, Perez-Del-Pulgar S, Garcia-Cehic D, Casillas R, Blasi M, Homs M, Tabernero D, Alvarez-Tejado M, Muñoz JM, Cubero M, Caballero A, delCampo JA, Domingo E, Belmonte I, Nieto L, Lens S, Muñoz-de-Rueda P, Sanz-Cameno P, Sauleda S, Bes M, Gomez J, Briones C, Perales C, Sheldon J, Castells L, Viladomiu L, Salmeron J, Ruiz-Extremera A, Quiles-Pérez R, Moreno-Otero R, López-Rodríguez R, Allende H, Romero-Gómez M, Guardia J, Esteban R, Garcia-Samaniego J, Forns X, Esteban JI. Correction for Quer at al., High-Resolution Hepatitis C Virus Subtyping Using NS5B Deep Sequencing and Phylogeny, an Alternative to Current Methods. J Clin Microbiol 2016; 54:1933. [PMID: 27343299 PMCID: PMC4922086 DOI: 10.1128/jcm.01007-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Josep Quer
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep Gregori
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics SL, Barcelona, Spain
| | - Francisco Rodríguez-Frias
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Biochemistry Unit, Virology Unit/Microbiology Department, HUVH, Barcelona, Spain
| | - Maria Buti
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Antonio Madejon
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Hospital La Paz-Carlos III, Madrid, Spain
| | - Sofia Perez-Del-Pulgar
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Rosario Casillas
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry Unit, Virology Unit/Microbiology Department, HUVH, Barcelona, Spain
| | - Maria Blasi
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry Unit, Virology Unit/Microbiology Department, HUVH, Barcelona, Spain
| | - Maria Homs
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry Unit, Virology Unit/Microbiology Department, HUVH, Barcelona, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry Unit, Virology Unit/Microbiology Department, HUVH, Barcelona, Spain
| | | | | | - Maria Cubero
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Andrea Caballero
- Biochemistry Unit, Virology Unit/Microbiology Department, HUVH, Barcelona, Spain
| | - Jose Antonio delCampo
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Hospital Universitario Virgen de Valme, Seville, Spain
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Irene Belmonte
- Biochemistry Unit, Virology Unit/Microbiology Department, HUVH, Barcelona, Spain
| | - Leonardo Nieto
- Biochemistry Unit, Virology Unit/Microbiology Department, HUVH, Barcelona, Spain
| | - Sabela Lens
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Paloma Muñoz-de-Rueda
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Hospital San Cecilio, Granada, Spain
| | - Paloma Sanz-Cameno
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Hospital de la Princesa, Madrid, Spain
| | - Silvia Sauleda
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Banc de Sang i de Teixits, Institut Català de la Salut, Barcelona, Spain
| | - Marta Bes
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Banc de Sang i de Teixits, Institut Català de la Salut, Barcelona, Spain
| | - Jordi Gomez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- CSIC, Instituto de Parasitología y Biomedicina López Neyra, Granada, Spain
| | - Carlos Briones
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Celia Perales
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Julie Sheldon
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Lluis Castells
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Lluis Viladomiu
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Salmeron
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Hospital San Cecilio, Granada, Spain
| | - Angela Ruiz-Extremera
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Hospital San Cecilio, Granada, Spain
| | - Rosa Quiles-Pérez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Hospital San Cecilio, Granada, Spain
| | - Ricardo Moreno-Otero
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Hospital de la Princesa, Madrid, Spain
| | - Rosario López-Rodríguez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Hospital de la Princesa, Madrid, Spain
| | - Helena Allende
- Pathological Anatomy Department, VHIR-HUVH, Barcelona, Spain
| | - Manuel Romero-Gómez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Hospital Universitario Virgen de Valme, Seville, Spain
| | - Jaume Guardia
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rafael Esteban
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Javier Garcia-Samaniego
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Hospital La Paz-Carlos III, Madrid, Spain
| | - Xavier Forns
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| |
Collapse
|
13
|
Quer J, Gregori J, Rodríguez-Frias F, Buti M, Madejon A, Perez-del-Pulgar S, Garcia-Cehic D, Casillas R, Blasi M, Homs M, Tabernero D, Alvarez-Tejado M, Muñoz JM, Cubero M, Caballero A, del Campo JA, Domingo E, Belmonte I, Nieto L, Lens S, Muñoz-de-Rueda P, Sanz-Cameno P, Sauleda S, Bes M, Gomez J, Briones C, Perales C, Sheldon J, Castells L, Viladomiu L, Salmeron J, Ruiz-Extremera A, Quiles-Pérez R, Moreno-Otero R, López-Rodríguez R, Allende H, Romero-Gómez M, Guardia J, Esteban R, Garcia-Samaniego J, Forns X, Esteban JI. High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods. J Clin Microbiol 2015; 53:219-26. [PMID: 25378574 PMCID: PMC4290919 DOI: 10.1128/jcm.02093-14] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) is classified into seven major genotypes and 67 subtypes. Recent studies have shown that in HCV genotype 1-infected patients, response rates to regimens containing direct-acting antivirals (DAAs) are subtype dependent. Currently available genotyping methods have limited subtyping accuracy. We have evaluated the performance of a deep-sequencing-based HCV subtyping assay, developed for the 454/GS-Junior platform, in comparison with those of two commercial assays (Versant HCV genotype 2.0 and Abbott Real-time HCV Genotype II) and using direct NS5B sequencing as a gold standard (direct sequencing), in 114 clinical specimens previously tested by first-generation hybridization assay (82 genotype 1 and 32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 calling by population Sanger sequencing (69% 1b, 31% 1a) in 81 specimens and identified a mixed-subtype infection (1b/3a/1a) in one sample. Similarly, among the 32 previously indeterminate specimens, identical genotype and subtype results were obtained by direct and deep sequencing in all but four samples with dual infection. In contrast, both Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II failed subtype 1 calling in 13 (16%) samples each and were unable to identify the HCV genotype and/or subtype in more than half of the non-genotype 1 samples. We concluded that deep sequencing is more efficient for HCV subtyping than currently available methods and allows qualitative identification of mixed infections and may be more helpful with respect to informing treatment strategies with new DAA-containing regimens across all HCV subtypes.
Collapse
Affiliation(s)
- Josep Quer
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep Gregori
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Roche Diagnostics SL, Barcelona, Spain
| | - Francisco Rodríguez-Frias
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - Maria Buti
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Antonio Madejon
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital La Paz-Carlos III, Madrid, Spain
| | - Sofia Perez-del-Pulgar
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Rosario Casillas
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - Maria Blasi
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - Maria Homs
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | | | | | - Maria Cubero
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Andrea Caballero
- Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - Jose Antonio del Campo
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital Universitario Virgen de Valme, Seville, Spain
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Irene Belmonte
- Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - Leonardo Nieto
- Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain
| | - Sabela Lens
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Paloma Muñoz-de-Rueda
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital San Cecilio, Granada, Spain
| | - Paloma Sanz-Cameno
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital de la Princesa, Madrid, Spain
| | - Silvia Sauleda
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Banc de Sang i de Teixits, Institut Català de la Salut, Barcelona, Spain
| | - Marta Bes
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Banc de Sang i de Teixits, Institut Català de la Salut, Barcelona, Spain
| | - Jordi Gomez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain CSIC, Instituto de Parasitología y Biomedicina López Neyra, Granada, Spain
| | - Carlos Briones
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Celia Perales
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Julie Sheldon
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Lluis Castells
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Lluis Viladomiu
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Salmeron
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital San Cecilio, Granada, Spain
| | - Angela Ruiz-Extremera
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital San Cecilio, Granada, Spain
| | - Rosa Quiles-Pérez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital San Cecilio, Granada, Spain
| | - Ricardo Moreno-Otero
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital de la Princesa, Madrid, Spain
| | - Rosario López-Rodríguez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital de la Princesa, Madrid, Spain
| | - Helena Allende
- Pathological Anatomy Department, VHIR-HUVH, Barcelona, Spain
| | - Manuel Romero-Gómez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Hospital Universitario Virgen de Valme, Seville, Spain
| | - Jaume Guardia
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rafael Esteban
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Javier Garcia-Samaniego
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital La Paz-Carlos III, Madrid, Spain
| | - Xavier Forns
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain Universitat Autònoma de Barcelona, Barcelona, Spain
| |
Collapse
|
14
|
Rodríguez-Frias F, Jardi R, Buti M. [Hepatitis E: molecular virology, epidemiology and pathogenesis]. Enferm Infecc Microbiol Clin 2012; 30:624-34. [PMID: 22386306 DOI: 10.1016/j.eimc.2012.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 01/11/2012] [Accepted: 01/18/2012] [Indexed: 02/07/2023]
Abstract
Hepatitis E represents a significant proportion of enteric transmitted liver diseases and poses a major public health problem, mainly associated with epidemics due to contamination of water supplies, especially in developing countries. Hepatitis E virus (HEV) is responsible for self-limiting acute liver oral-faecal infections. In industrialised countries, acute hepatitis E is sporadic, detected in travellers from endemic areas but also in sporadic cases with no risk factors. HEV is a non-enveloped virus with a single-stranded RNA genome classified into 4 genotypes and a single serotype. Genotypes 1 and 2 only infect humans, and are predominant in the developing countries, while 3 and 4 are predominant in industrialised countries, and also infect other species of mammals, especially pigs, and multiple evidence classifies HEV as a zoonotic agent. Some HEV chronic infections have recently been reported in kidney and liver transplant patients. The mortality rate of HEV infection is greater than hepatitis A. In addition to faecal-oral transmission, parenteral transmission of HEV has also been reported. Several vaccines are currently in development. The severity of this infection in some groups of patients, especially pregnant women, and the occurrence of chronic hepatitis, even with progression to cirrhosis, have raised interest in the application of interferon and/or ribavirin therapy.
Collapse
Affiliation(s)
- Francisco Rodríguez-Frias
- Unidad de Proteínas Hepatitis, Servicio de Bioquímica, Hospital Universitario Vall d'Hebron, Barcelona, España.
| | | | | |
Collapse
|
15
|
Alegre C, Barceló M, Jardí R, Rodríguez-Frias F, Camprubí S. α1-Antitrypsin in fibromyalgia: results of a randomized, placebo-controlled, double-blind and crossover pilot trial. Musculoskeletal Care 2012; 10:178-83. [PMID: 22190533 DOI: 10.1002/msc.1000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To assess clinical effect of a human plasma-derived alpha-1 antitrypsin (AAT) concentrate in reducing pain severity of patients with fibromyalgia (FM). METHODS Thirteen subjects with FM completed a randomized, double-blind, placebo-controlled, crossover study which consisted of 9 weeks trial of AAT or placebo with a washout period of 6 weeks. Primary efficacy endpoint was change on pain severity score, assessed by a daily visual analogue scale (VAS) for pain. Other outcome measures included a tender point score, the Fibromyalgia Impact Questionnaire, (FIQ), the Medical Outcomes Study Short Form 36 (SF-36), the Health Assessment Questionnaire Disability Index (HAQ-DI), the Hospital Anxiety and Depression Scale (HADS) and tiredness score evaluated by VAS. RESULTS No statistically significant differences were observed in either pain severity or other secondary outcome measures in either of the treatment groups, or between treatment groups in either of the treatment periods. No carryover or order of intervention effect was observed from one treatment to the other. Both investigational interventions were generally well tolerated, and vital signs during the drug infusions were within the respective normal ranges. CONCLUSION Treatment with a human plasma-derived AAT concentrate did not demonstrate significant improvement over placebo on reducing pain severity and other symptoms of FM. Further research should examine other FM subpopulations and drug doses.
Collapse
Affiliation(s)
- Cayetano Alegre
- Department of Rheumatology, Hospital Universitari Vall d'Hebron, Barcelona, Spain.
| | | | | | | | | |
Collapse
|
16
|
Van den Eynde E, Crespo M, Esteban JI, Jardi R, Ribera E, Carbonell J, Rodríguez-Frias F, Falco V, Curran A, Imaz A, Villar del Saz S, Ocaña I, Esteban R, Pahissa A. Response-guided therapy for chronic hepatitis C virus infection in patients coinfected with HIV: a pilot trial. Clin Infect Dis 2009; 48:1152-9. [PMID: 19275492 DOI: 10.1086/597470] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND To study the feasibility of a response-guided therapy for chronic hepatitis C virus (HCV) infection in patients coinfected with human immunodeficiency virus (HIV) in a tertiary care hospital. METHODS Treatment duration was individualized on the basis of week 4 and week 12 virologic response. Sixty patients were enrolled and received pegylated interferon alfa-2b (1.5 microg/kg per week) plus weight-based ribavirin (800-1400 mg/day). Patients who achieved a rapid virologic response, defined as viral load <50 IU/mL at treatment week 4, completed 24 weeks of therapy. Patients who did not achieve a rapid virologic response were reassessed at treatment week 12. Patients with a complete early virologic response, defined as an HCV RNA level <600 IU/mL, were treated for 48 weeks. Patients with a partial response, defined as a decrease in the viral load > or = 2 log10 and an HCV RNA level > or = 600 IU/mL, who attained an undetectable viral load at week 24 were treated for 60 weeks. The primary efficacy end point was sustained virologic response, defined as HCV RNA <50 IU/mL, 24 weeks after the end of treatment. RESULTS Overall, 33 (55%) of 60 patients achieved a sustained virologic response: 11 (44%) of 25 patients with HCV genotype 1, 3 (27%) of 11 patients with genotype 4, and 19 (79%) of 24 patients with genotype 3. One-third of patients showed a rapid virologic response. Of patients with genotype 1, there was a rapid virologic response in 4 (16%) of 25; with genotype 4, in 1 (9%) of 11; and with genotype 3, in 14 (58%) of 24. Of the 19 patients with a rapid virologic response, 17 (89.5%) eradicated the virus after 24 weeks of therapy. The rate of sustained virologic response was significantly higher among patients with genotype 3 and low pretreatment HCV RNA levels. A high relapse rate (46%) after 48 weeks of therapy occurred among patients infected with genotypes 1 or 4 who first achieved undetectable viral load at treatment week 12. CONCLUSION A response-guide therapy is feasible and may be useful to optimize the individual outcome of HCV treatment in patients coinfected with HIV.
Collapse
Affiliation(s)
- Eva Van den Eynde
- Infectious Diseases Department, Vall d'Hebron Hospital, Autonomous University of Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
The hepatitis B virus (HBV) belongs to the hepadnavirus family. The genome of the virus, formed by a small DNA molecule with 3,200 base pairs, has 4 strongly overlapping protein coding regions: ORF preS/S, corresponding to the envelope proteins that constitute the HBV surface antigen (HBsAg); ORF preC/C, which encodes the viral capsid component (core antigen or HBcAg) and a non-structural protein that, after postranslation modification, is secreted and constitutes the "e" antigen (HBeAg); ORF P, which encodes the viral polymerase (polyprotein with DNA polymerase activity, reverse transcriptase and RNAase), and ORF X, which encodes a protein that acts as a multifunctional regulator for both the viral and cell cycles. HBV has a mutation rate of 1.4-3.2 x 105 substitutions/nucleotide/year. As a result of this variability, the virus circulates as a complex mixture of genetic variants, constituting a semi-species, that evolves throughout the infection depending on the evolutionary pressure of factors such as the immune response and antiviral treatments. Based on this variability, HBV has been classified into 8 genotypes (A-H) defined by a difference of more than 8% in the sequences of the complete viral genome. This variability is also responsible for HBV resistance to antiviral treatments with nucleotide and nucleoside analogs. Diagnosis of HBV infection includes determination of virological markers: viral antigens (HBsAg, HBeAg), specific antibodies (anti-HBc, anti-HBe, anti-HBs) and study of HBV-DNA for its detection and quantification and determination of genotypes and viral variants.
Collapse
|