ef3bfc5ac3e67e91a86172602c2fcb23 pmc_33916702.pdf e54a9689198d9372ae17a2eb5c3c3b591ef9a51b pmc_33916702.pdf df2d4cad3158bc20e3511d2c4ea91daa09fc4fb29485c6b773591b233745f9d7 pmc_33916702.pdf Title: Population Disequilibrium as Promoter of Adaptive Explorations in Hepatitis C Virus Subject: 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. 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. Keywords: viral quasispecies; hepatitis C virus; mutational waves; residue conservation; sequence space; antiviral drug resistance; universal vaccines; COVID-19 Author: Carlos García-Crespo, Isabel Gallego, María Eugenia Soria, Ana Isabel de Ávila, Brenda Martínez-González, Lucía Vázquez-Sirvent, Rebeca Lobo-Vega, Elena Moreno, Jordi Gómez, Carlos Briones, Josep Gregori, Josep Quer, Esteban Domingo and Celia Perales Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Sat Apr 3 09:29:15 2021 CEST ModDate: Fri Apr 9 05:47:46 2021 CEST Custom Metadata: no Metadata Stream: no Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 20 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 4515916 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- WOPBRX+URWPalladioL-Ital Type 1 Custom yes yes no 10 0 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Sequencing of Cell Culture Populations Destination: subsection.2.2 Item: Title: RNA Extraction, Viral RNA Amplification, and Ultra-Deep Sequencing of HCV from Infected Patients Destination: subsection.2.3 Item: Title: Controls in the Ultra-Deep Sequencing Analyses Destination: subsection.2.4 Item: Title: Amino Acid Conservation in Infected Patients versus Los Alamos Database (LANL) Destination: subsection.2.5 Item: Title: Statistics Destination: subsection.2.6 Item: Title: HCV Mutational Waves in the Presence of Mutagenic Nucleotide Analogues Destination: section.3 Item: Title: Amino Acid Conservation in HCV Quasispecies from Infected Patients Destination: section.4 Item: Title: Antiviral Resistance Mechanisms during Hepatitis C Virus Infections Destination: section.5 Item: Title: A Unifying Disequilibrium Model for Expanded Adaptive Potential Destination: section.6 Item: Title: Concluding Remarks: Remembering John Holland in COVID-19 Times Destination: section.7 Item: Title: References Destination: section.7 Info: Title: Population Disequilibrium as Promoter of Adaptive Explorations in Hepatitis C Virus Author: Carlos García-Crespo, Isabel Gallego, María Eugenia Soria, Ana Isabel de Ávila, Brenda Martínez-González, Lucía Vázquez-Sirvent, Rebeca Lobo-Vega, Elena Moreno, Jordi Gómez, Carlos Briones, Josep Gregori, Josep Quer, Esteban Domingo and Celia Perales Subject: 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. 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. Keywords: viral quasispecies; hepatitis C virus; mutational waves; residue conservation; sequence space; antiviral drug resistance; universal vaccines; COVID-19 Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Sat Apr 03 09:29:15 CEST 2021 ModDate: Fri Apr 09 05:47:46 CEST 2021 ID: 0xa1b598070c9516e4bb4210ca01906587, 0xa1b598070c9516e4bb4210ca01906587 Filters: FilterPipeline: FlateDecode Fonts: Type1: Font: BaseFont: RFPHKI+CMSY10 FontSubset: true FirstChar: 0 LastChar: 15 FontDescriptor: FontName: RFPHKI+CMSY10 Flags: Symbolic FontBBox: -29, -960, 1116, 775 FontFile: true Font: BaseFont: XODQRZ+URWPalladioL-Roma FontSubset: true FirstChar: 2 LastChar: 252 FontDescriptor: FontName: XODQRZ+URWPalladioL-Roma Flags: Symbolic FontBBox: -166, -283, 1021, 943 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: WIPXQR+VnURWPalladioL-Bold FontSubset: true FirstChar: 129 LastChar: 226 FontDescriptor: FontName: WIPXQR+VnURWPalladioL-Bold Flags: Symbolic 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