Examinando por Autor "Chen, Qian"

Mostrando 1 - 2 de 2

Restringido
Amino acid substitutions associated with treatment failure for Hepatitis C virus infection
(American Society for Microbiology, 2020-12) Soria, María Eugenia; García Crespo, Carlos; Martínez González, Brenda; Vázquez Sirvent, L.; Lobo Vega, Rebeca; De Ávila, Ana Isabel; Gallego, Isabel; Chen, Qian; García Cehic, Damir; Llorens Revull, Meritxell; Briones, C.; Gómez, Jordi; Ferrer Orta, Cristina; Verdaguer, Nuria; Gregori, Josep; Rodríguez Frías, Francisco; Buti, María; Ignacio Esteban, Juan; Domingo, Esteban; Quer, Josep; Perales, Celia; Ministerio de Economía y Competitividad (MINECO); Agencia Estatal de Investigación (AEI); Instituto de Salud Carlos III (ISCIII); Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas, España; Centro para el Desarrollo Tecnológico Industrial (CDTI); Fundación Ramón Areces; Banco de Santander; CSIC-INTA - Centro de Astrobiología, CAB; Unidad de Excelencia Científica María de Maeztu Centro de Astrobiología del Instituto Nacional de Técnica Aeroespacial y CSIC, MDM-2017-0737
Despite the high virological response rates achieved with current directly acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 2% to 5% of treated patients do not achieve a sustained viral response. The identification of amino acid substitutions associated with treatment failure requires analytical designs, such as subtype-specific ultradeep sequencing (UDS) methods, for HCV characterization and patient management. Using this procedure, we have identified six highly represented amino acid substitutions (HRSs) in NS5A and NS5B of HCV, which are not bona fide resistance-associated substitutions (RAS), from 220 patients who failed therapy. They were present frequently in basal and posttreatment virus of patients who failed different DAA-based therapies. Contrary to several RAS, HRSs belong to the acceptable subset of substitutions according to the PAM250 replacement matrix. Their mutant frequency, measured by the number of deep sequencing reads within the HCV quasispecies that encode the relevant substitutions, ranged between 90% and 100% in most cases. They also have limited predicted disruptive effects on the three-dimensional structures of the proteins harboring them. Possible mechanisms of HRS origin and dominance, as well as their potential predictive value for treatment response, are discussed.
Restringido
Broad and dynamic diversification of infectious hepatitis c virus in a cell culture environment
(American Society for Microbiology, 2020-02-28) Gallego, Isabel; Eugenia Soria, M.; García Crespo, Carlos; Chen, Qian; Martínez Barragán, P.; Khalfaoui, S.; Martínez González, Brenda; Sánchez Martín, I.; Palacios Blanco, I.; Isabel de Ávila, A.; García Cehic, Damir; Ignacio Esteban, Juan; Gómez, Jordi; Briones, C.; Gregori, Josep; Quer, Josep; Perales, Celia; Domingo, Esteban; Instituto de Salud Carlos III (ISCIII); Comunidad de Madrid; Ministerio de Economia y Competitividad (MINECO); Fundación Ramón Areces; Banco Santander; Agencia Estatal de Investigación (AEI); Eugenia Soria, M. [0000-0003-1755-6382]; García Crespo, C. [0000-0001-6561-5389]; García Cehic, D. [0000-0002-0009-038X]; Briones, C. [0000-0003-2213-8353]; Domingo, E. [0000-0002-0573-1676]; Martínez González, B. [0000-0002-4482-5181]; Perales Viejo, C. B. [0000-0003-1618-1937]; García Crespo, C. [0000-0001-6561-5389]; Gregori Font, J. [0000-0002-4253-8015]; Gómez, J. [0000-0002-7806-1503]; Quer, J. [0000-0003-0014-084X]
Previous studies documented that long-term hepatitis C virus (HCV) replication in human hepatoma Huh-7.5 cells resulted in viral fitness gain, expansion of the mutant spectrum, and several phenotypic alterations. In the present work, we show that mutational waves (changes in frequency of individual mutations) occurred continuously and became more prominent as the virus gained fitness. They were accompanied by an increasing proportion of heterogeneous genomic sites that affected 1 position in the initial HCV population and 19 and 69 positions at passages 100 and 200, respectively. Analysis of biological clones of HCV showed that these dynamic events affected infectious genomes, since part of the fluctuating mutations became incorporated into viable genomes. While 17 mutations were scored in 3 biological clones isolated from the initial population, the number reached 72 in 3 biological clones from the population at passage 200. Biological clones differed in their responses to antiviral inhibitors, indicating a phenotypic impact of viral dynamics. Thus, HCV adaptation to a specific constant environment (cell culture without external influences) broadens the mutant repertoire and does not focus the population toward a limited number of dominant genomes. A retrospective examination of mutant spectra of foot-and-mouth disease virus passaged in cell cultures suggests a parallel behavior here described for HCV. We propose that virus diversification in a constant environment has its basis in the availability of multiple alternative mutational pathways for fitness gain. This mechanism of broad diversification should also apply to other replicative systems characterized by high mutation rates and large population sizes. IMPORTANCE The study shows that extensive replication of an RNA virus in a constant biological environment does not limit exploration of sequence space and adaptive options. There was no convergence toward a restricted set of adapted genomes. Mutational waves and mutant spectrum broadening affected infectious genomes. Therefore, profound modifications of mutant spectrum composition and consensus sequence diversification are not exclusively dependent on environmental alterations or the intervention of population bottlenecks.