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Population Disequilibrium as Promoter of Adaptive Explorations in Hepatitis C Virus

AuthorsGarcía-Crespo, Carlos; Gallego, Isabel CSIC ORCID; Soria, María Eugenia; Ávila, Ana Isabel de; Martínez-González, Brenda; Vázquez-Sirvent, Lucía; Lobo-Vega, Rebeca; Moreno, Elena CSIC; Gómez, Jordi; Briones, Carlos CSIC ORCID; Gregori, Josep; Quer, Josep; Domingo, Esteban CSIC ORCID; Perales, Celia CSIC ORCID
Keywordsviral quasispecies
hepatitis C virus
mutational waves
residue conservation
sequence space
Antiviral drug resistance
universal vaccines
Issue Date2021
PublisherMultidisciplinary Digital Publishing Institute
CitationVIRUSES 13 (2021)
AbstractReplication 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. Our recent results with hepatitis C virus (HCV) have shown that the expansion in sequence space of a viral clone continues despite prolonged replication in a stable cell culture environment. Diagnosis of the expansion was based on the quantification of diversity indices, the occurrence of intra-population mutational waves (variations in mutant frequencies), and greater individual residue variations in mutant spectra than those anticipated from sequence alignments in data banks. In the present report, we review our previous results, and show additionally that mutational waves in amplicons from the NS5A-NS5B-coding region are equally prominent during HCV passage in the absence or presence of the mutagenic nucleotide analogues favipiravir or ribavirin. In addition, by extending our previous analysis to amplicons of the NS3- and NS5A-coding region, we provide further evidence of the incongruence between amino acid conservation scores in mutant spectra from infected patients and in the Los Alamos National Laboratory HCV data banks. We hypothesize that these observations have as a common origin a permanent state of HCV population disequilibrium even upon extensive viral replication in the absence of external selective constraints or changes in population size. Such a persistent disequilibrium¿revealed by the changing composition of the mutant spectrum¿may facilitate finding alternative mutational pathways for HCV antiviral resistance. The possible significance of our model for other genetically variable viruses is discussed.
Publisher version (URL)
Identifiersdoi: 10.3390/v13040616
issn: 1999-4915
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(CAB) Artículos

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