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1.
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16 p, 586.7 KB |
Quantifying In-Host Quasispecies Evolution
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Gregori i Font, Josep (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Ibañez-Lligoña, Marta (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Quer, Josep 1963- (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
What takes decades, centuries or millennia to happen with a natural ecosystem, it takes only days, weeks or months with a replicating viral quasispecies in a host, especially when under treatment. Some methods to quantify the evolution of a quasispecies are introduced and discussed, along with simple simulated examples to help in the interpretation and understanding of the results. [...]
2023 -  10.3390/ijms24021301
International journal of molecular sciences, Vol. 24 (january 2023)
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2.
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18 p, 1.0 MB |
Hepatitis B Virus Variants with Multiple Insertions and/or Deletions in the X Open Reading Frame 3' End : Common Members of Viral Quasispecies in Chronic Hepatitis B Patients
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García-García, Selene (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Caballero, Andrea (Hospital Universitari Vall d'Hebron) ;
Tabernero, David (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas) ;
Cortese, Maria Francesca (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas) ;
Gregori i Font, Josep (Hospital Universitari Vall d'Hebron) ;
Rodriguez-Algarra, Francisco (Queen Mary University of London) ;
Quer, Josep 1963- (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Riveiro Barciela, Mar (Hospital Universitari Vall d'Hebron) ;
Homs, Maria (Institut Català de la Salut) ;
Rando-Segura, Ariadna (Hospital Universitari Vall d'Hebron) ;
Pacín Ruiz, Beatriz (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Vila, Marta (Hospital Universitari Vall d'Hebron) ;
Ferrer-Costa, Roser (Hospital Universitari Vall d'Hebron) ;
Pumarola Suñé, Tomàs (Hospital Universitari Vall d'Hebron) ;
Buti, Maria (Hospital Universitari Vall d'Hebron) ;
Rodriguez-Frias, Francisco (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Deletions in the 3' end region of the hepatitis B virus (HBV) X open reading frame (HBX) may affect the core promoter (Cp) and have been frequently associated with hepatocellular carcinoma (HCC). The aim of this study was to investigate the presence of variants with deletions and/or insertions (Indels) in this region in the quasispecies of 50 chronic hepatitis B (CHB) patients without HCC. [...]
2022 - 10.3390/biomedicines10051194
Biomedicines, Vol. 10, Issue 5 (May 2022) , art. 1194
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3.
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13 p, 1.5 MB |
Inspecting the Ribozyme Region of Hepatitis Delta Virus Genotype 1 : Conservation and Variability
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Pacín Ruiz, Beatriz (Hospital Universitari Vall d'Hebron) ;
Cortese, Maria Francesca (Hospital Universitari Vall d'Hebron) ;
Tabernero, David (Hospital Universitari Vall d'Hebron) ;
Sopena, Sara (Hospital Universitari Vall d'Hebron) ;
Gregori i Font, Josep (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
García-García, Selene (Hospital Universitari Vall d'Hebron) ;
Casillas, Rosario (Hospital Universitari Vall d'Hebron) ;
Najarro-Centeno, Adrián (Hospital Universitari Vall d'Hebron) ;
Aldama, Unai (Hospital Universitari Vall d'Hebron) ;
Palom, Adriana (Hospital Universitari Vall d'Hebron) ;
Rando-Segura, Ariadna (Hospital Universitari Vall d'Hebron) ;
Galán, Anna (Hospital Universitari Vall d'Hebron) ;
Vila, Marta (Hospital Universitari Vall d'Hebron) ;
Riveiro Barciela, Mar (Hospital Universitari Vall d'Hebron) ;
Quer, Josep 1963- (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
González-Aseguinolaza, Gloria (Univerdad de Pamplona) ;
Buti, Maria (Hospital Universitari Vall d'Hebron) ;
Rodríguez Frías, Francisco (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
The hepatitis delta virus (HDV) genome has an autocatalytic region called the ribozyme, which is essential for viral replication. The aim of this study was to use next-generation sequencing (NGS) to analyze the ribozyme quasispecies (QS) in order to study its evolution and identify highly conserved regions potentially suitable for a gene-silencing strategy. [...]
2022 - 10.3390/v14020215
Viruses, Vol. 14 (january 2022)
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4.
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20 p, 4.3 MB |
Population Disequilibrium as Promoter of Adaptive Explorations in Hepatitis C Virus
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García-Crespo, Carlos (Centro de Biología Molecular Severo Ochoa) ;
Gallego, Isabel (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas) ;
Soria, María Eugenia (Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz) ;
de Ávila, Ana Isabel (Centro de Biología Molecular Severo Ochoa) ;
Martínez-González, Brenda (Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz) ;
Vázquez-Sirvent, Lucía (Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz) ;
Lobo-Vega, Rebeca (Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz) ;
Moreno del Olmo, Elena (Centro de Biología Molecular Severo Ochoa) ;
Gómez, Jordi (Instituto de Parasitología y Biomedicina "López-Neyra") ;
Briones, Carlos (Centro de Astrobiología (CAB, CSIC-INTA), Torrejón de Ardoz, 28850 Madrid, Spain) ;
Gregori i Font, Josep (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Quer, Josep 1963- (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Domingo, Esteban (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas) ;
Perales Viejo, Celia (Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz) ;
Universitat Autònoma de Barcelona
Replication of RNA viruses is characterized by exploration of sequence space which facilitates their adaptation to changing environments. It is generally accepted that such exploration takes place mainly in response to positive selection, and that further diversification is boosted by modifications of virus population size, particularly bottleneck events. [...]
2021 - 10.3390/v13040616
Viruses, Vol. 13 (april 2021)
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5.
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13 p, 974.8 KB |
Clinical Application of Estimating Hepatitis B Virus Quasispecies Complexity by Massive Sequencing : Correlation between Natural Evolution and On-Treatment Evolution
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Homs, Maria (Hospital Universitari Vall d'Hebron) ;
Caballero, Andrea (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Gregori i Font, Josep (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Tabernero, David (Hospital Universitari Vall d'Hebron) ;
Quer, Josep 1963- (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Nieto, Leonardo (Hospital Universitari Vall d'Hebron) ;
Esteban, Rafael (Esteban Mur) (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Buti, Maria (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Rodríguez Frías, Francisco (Hospital Universitari Vall d'Hebron) ;
Universitat Autònoma de Barcelona
To evaluate HBV quasispecies (QA) complexity in the preCore/Core regions in relation to HBeAg status, and explore QA changes under natural evolution and nucleoside analogue (NUC) treatment. Ultra-deep pyrosequencing of HBV preCore/Core regions in 30 sequential samples (baseline [diagnosis], treatment-free, and treatment-nonresponse) from 10 retrospectively selected patients grouped according to HBeAg status over time: HBeAg+ (N = 4), HBeAg- (N = 2), and fluctuating HBeAg (transient seroreversion/seroconversion pattern) (N = 4). [...]
2014 - 10.1371/journal.pone.0112306
PloS one, Vol. 9 (november 2014)
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6.
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13 p, 470.0 KB |
Ultra-Deep Pyrosequencing (UDPS) Data Treatment to Study Amplicon HCV Minor Variants
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Gregori i Font, Josep (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Esteban Mur, Juan Ignacio (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Cubero, María Dolores (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Garcia-Cehic, D. (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Perales Viejo, Celia (Centro de Biología Molecular Severo Ochoa) ;
Casillas, Rosario (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Alvarez-Tejado, Miguel (Roche Diagnostics, Sant Cugat del Vallès) ;
Rodríguez Frías, Francisco (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Guardia Massó, Jaume (Universitat Autònoma de Barcelona) ;
Domingo, Esteban (Centro de Biología Molecular Severo Ochoa) ;
Quer, Josep 1963- (Universitat Autònoma de Barcelona)
We have investigated the reliability and reproducibility of HCV viral quasispecies quantification by ultra-deep pyrosequencing (UDPS) methods. Our study has been divided in two parts. First of all, by UDPS sequencing of clone mixes samples we have established the global noise level of UDPS and fine tuned a data treatment workflow previously optimized for HBV sequence analysis. [...]
2013 - 10.1371/journal.pone.0083361
PloS one, Vol. 8 (december 2013)
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7.
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19 p, 2.2 MB |
Lethal Mutagenesis of Hepatitis C Virus Induced by Favipiravir
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de Ávila, Ana Isabel (Consejo Superior de Investigaciones Científicas) ;
Gallego, Isabel (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas) ;
Soria, Maria Eugenia (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Gregori i Font, Josep (Roche Diagnostics (Sant Cugat)) ;
Quer, Josep 1963- (Universitat Autònoma de Barcelona) ;
Esteban Mur, Juan Ignacio (Universitat Autònoma de Barcelona) ;
Rice, Charles M. (The Rockefeller University) ;
Domingo, Esteban (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas) ;
Perales Viejo, Celia (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Lethal mutagenesis is an antiviral approach that consists in extinguishing a virus by an excess of mutations acquired during replication in the presence of a mutagen. Here we show that favipiravir (T-705) is a potent mutagenic agent for hepatitis C virus (HCV) during its replication in human hepatoma cells. [...]
2016 - 10.1371/journal.pone.0164691
PloS one, Vol. 11 (october 2016)
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8.
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14 p, 618.6 KB |
Evidence of an Exponential Decay Pattern of the Hepatitis Delta Virus Evolution Rate and Fluctuations in Quasispecies Complexity in Long-Term Studies of Chronic Delta Infection
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Homs, Maria (Hospital Universitari Vall d'Hebron) ;
Rodríguez Frías, Francisco (Hospital Universitari Vall d'Hebron) ;
Gregori i Font, Josep (Roche Diagnostics SL (Sant Cugat del Vallès, Barcelona)) ;
Ruiz, Alicia (Hospital Universitari Vall d'Hebron) ;
Reimundo, Pilar (Hospital Universitari Vall d'Hebron) ;
Casillas, Rosario (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Tabernero, David (Hospital Universitari Vall d'Hebron) ;
Godoy, Cristina (Hospital Universitari Vall d'Hebron) ;
Barakat, Salma (National Centre for Gastrointestinal and Liver disease, Khartoum, Sudan) ;
Quer, Josep 1963- (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Riveiro Barciela, Mar (Hospital Universitari Vall d'Hebron) ;
Roggendorf, Michael (Technische Universität München/Helmholtz Zentrum München) ;
Esteban, Rafael (Esteban Mur) (Hospital Universitari Vall d'Hebron) ;
Buti, Maria (Hospital Universitari Vall d'Hebron) ;
Universitat Autònoma de Barcelona
Chronic HDV infection can cause a severe form of viral hepatitis for which there is no specific treatment. Characterization of the hepatitis B or C viral quasispecies has provided insight into treatment failure and disease recurrence following liver transplantation, has proven useful to understand hepatitis B e antigen seroconversion, and has helped to predict whether hepatitis C infection will resolve or become chronic. [...]
2016 - 10.1371/journal.pone.0158557
PloS one, Vol. 11 (june 2016)
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9.
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17 p, 3.0 MB |
Rare haplotype load as marker for lethal mutagenesis
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Gregori i Font, Josep (Roche Diagnostics) ;
Soria, María Eugenia (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Gallego, Isabel (Centro de Biología Molecular Severo Ochoa) ;
Guerrero-Murillo, Mercedes (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Esteban Mur, Juan Ignacio (Universitat Autònoma de Barcelona) ;
Quer, Josep 1963- (Universitat Autònoma de Barcelona) ;
Perales Viejo, Celia (Centro de Biología Molecular Severo Ochoa) ;
Domingo, Esteban (Centro de Biología Molecular Severo Ochoa)
RNA viruses replicate with a template-copying fidelity, which lies close to an extinction threshold. Increases of mutation rate by nucleotide analogues can drive viruses towards extinction. This transition is the basis of an antiviral strategy termed lethal mutagenesis. [...]
2018 - 10.1371/journal.pone.0204877
PloS one, Vol. 13 (october 2018)
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10.
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15 p, 3.3 MB |
Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus
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Soria, María Eugenia (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Gregori i Font, Josep (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Chen, Qian (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Garcia-Cehic, D. (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Llorens, Meritxell (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
de Ávila, Ana Isabel (Centro de Biología Molecular Severo Ochoa) ;
Beach, Nathan M. (Centro de Biología Molecular Severo Ochoa) ;
Domingo, Esteban (Centro de Biología Molecular Severo Ochoa) ;
Rodríguez Frías, Francisco (Universitat Autònoma de Barcelona) ;
Buti, Maria (Universitat Autònoma de Barcelona) ;
Esteban, Rafael (Esteban Mur) (Universitat Autònoma de Barcelona) ;
Esteban Mur, Juan Ignacio (Universitat Autònoma de Barcelona) ;
Quer, Josep 1963- (Universitat Autònoma de Barcelona) ;
Perales Viejo, Celia (Centro de Biología Molecular Severo Ochoa)
Despite the high sustained virological response rates achieved with current directly-acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 5-10% of treated patients do not respond to current antiviral therapies, and basal resistance to DAAs is increasingly detected among treatment-naïve infected individuals. [...]
2018 - 10.1186/s12879-018-3356-6
BMC Infectious diseases, Vol. 18 (september 2018)
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