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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\u2014revealed by the changing composition of the mutant spectrum\u2014may facilitate finding alternative mutational pathways for HCV antiviral resistance. The possible significance of our model for other genetically variable viruses is discussed.<\/jats:p>","DOI":"10.3390\/v13040616","type":"journal-article","created":{"date-parts":[[2021,4,3]],"date-time":"2021-04-03T22:03:36Z","timestamp":1617487416000},"page":"616","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Population Disequilibrium as Promoter of Adaptive Explorations in Hepatitis C Virus"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6561-5389","authenticated-orcid":false,"given":"Carlos","family":"Garc\u00eda-Crespo","sequence":"first","affiliation":[{"name":"Centro de Biolog\u00eda Molecular \u201cSevero Ochoa\u201d (CBMSO) (CSIC-UAM), Consejo Superior de Investigaciones Cient\u00edficas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabel","family":"Gallego","sequence":"additional","affiliation":[{"name":"Centro de Biolog\u00eda Molecular \u201cSevero Ochoa\u201d (CBMSO) (CSIC-UAM), Consejo Superior de Investigaciones Cient\u00edficas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Hep\u00e1ticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda Eugenia","family":"Soria","sequence":"additional","affiliation":[{"name":"Centro de Biolog\u00eda Molecular \u201cSevero Ochoa\u201d (CBMSO) (CSIC-UAM), Consejo Superior de Investigaciones Cient\u00edficas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain"},{"name":"Department of Clinical Microbiology, Instituto de Investigaci\u00f3n Sanitaria-Fundaci\u00f3n Jim\u00e9nez D\u00edaz University Hospital, Universidad Aut\u00f3noma de Madrid (IIS-FJD, UAM), Av. Reyes Cat\u00f3licos 2, 28040 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Isabel","family":"de \u00c1vila","sequence":"additional","affiliation":[{"name":"Centro de Biolog\u00eda Molecular \u201cSevero Ochoa\u201d (CBMSO) (CSIC-UAM), Consejo Superior de Investigaciones Cient\u00edficas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4482-5181","authenticated-orcid":false,"given":"Brenda","family":"Mart\u00ednez-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, Instituto de Investigaci\u00f3n Sanitaria-Fundaci\u00f3n Jim\u00e9nez D\u00edaz University Hospital, Universidad Aut\u00f3noma de Madrid (IIS-FJD, UAM), Av. 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PLoS Genet., 15.","DOI":"10.1371\/journal.pgen.1008271"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1038\/nature12861","article-title":"Mutational and fitness landscapes of an RNA virus revealed through population se-quencing","volume":"505","author":"Acevedo","year":"2014","journal-title":"Nature"},{"key":"ref_6","first-page":"181","article-title":"Estimating Fitness of Viral Quasispecies from Next-Generation Sequencing Data","volume":"392","author":"Seifert","year":"2015","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1907","DOI":"10.1093\/bioinformatics\/bty891","article-title":"Long-term context-dependent genetic adaptation of the viral genetic cloud","volume":"35","author":"Braun","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.jviromet.2019.01.013","article-title":"Application of deep sequencing methods for inferring viral population diversity","volume":"266","author":"Huang","year":"2019","journal-title":"J. Virol. Methods"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Gregori, J., Esteban, J.I., Cubero, M., Garcia-Cehic, D., Perales, C., Casillas, R., Alvarez-Tejado, M., Rodr\u00edguez-Fr\u00edas, F., Guardia, J., and Domingo, E. (2013). Ultra-Deep Pyrosequencing (UDPS) Data Treatment to Study Amplicon HCV Minor Variants. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0083361"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.virol.2016.03.017","article-title":"Viral quasispecies complexity measures","volume":"493","author":"Gregori","year":"2016","journal-title":"Virology"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Soria, M.E., Gregori, J., Chen, Q., Garc\u00eda-Cehic, D., Llorens, M., De \u00c1vila, A.I., Beach, N.M., Domingo, E., Rodr\u00edguez-Fr\u00edas, F., and Buti, M. (2018). Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus. BMC Infect. Dis., 18.","DOI":"10.1186\/s12879-018-3356-6"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e02505","DOI":"10.1128\/JVI.02505-16","article-title":"Internal Disequilibria and Phenotypic Diversification during Replication of Hepatitis C Virus in a Noncoevolving Cellular Environment","volume":"91","author":"Moreno","year":"2017","journal-title":"J. Virol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"104694","DOI":"10.1016\/j.antiviral.2019.104694","article-title":"Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure","volume":"174","author":"Chen","year":"2020","journal-title":"Antivir. Res."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Gallego, I., Soria, M.E., Garc\u00eda-Crespo, C., Chen, Q., Mart\u00ednez-Barrag\u00e1n, P., Khalfaoui, S., Mart\u00ednez-Gonz\u00e1lez, B., Sanchez-Martin, I., Palacios-Blanco, I., and De \u00c1vila, A.I. (2020). Broad and Dynamic Diversification of Infectious Hepatitis C Virus in a Cell Culture Environment. J. Virol., 94.","DOI":"10.1128\/JVI.01856-19"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1985","DOI":"10.1128\/JCM.01985-20","article-title":"Amino Acid Substitutions Associated with Treatment Failure for Hepatitis C Virus Infection","volume":"58","author":"Soria","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Garc\u00eda-Crespo, C., Soria, M.E., Gallego, I., De \u00c1vila, A.I., Mart\u00ednez-Gonz\u00e1lez, B., V\u00e1zquez-Sirvent, L., G\u00f3mez, J., Briones, C., Gregori, J., and Quer, J. (2020). Dissimilar Conservation Pattern in Hepatitis C Virus Mutant Spectra, Consensus Sequences and Data Banks. J. Clin. Med., 9.","DOI":"10.1101\/2020.07.03.186171"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"7593","DOI":"10.1128\/JVI.02824-12","article-title":"Response of Hepatitis C Virus to Long-Term Passage in the Presence of Alpha Interferon: Multiple Mutations and a Common Phenotype","volume":"87","author":"Perales","year":"2013","journal-title":"J. Virol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"12098","DOI":"10.1128\/JVI.01860-14","article-title":"Increased Replicative Fitness Can Lead to Decreased Drug Sensitivity of Hepatitis C Virus","volume":"88","author":"Sheldon","year":"2014","journal-title":"J. Virol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1016\/j.virol.2018.07.030","article-title":"Resistance of high fitness hepatitis C virus to lethal mutagenesis","volume":"523","author":"Gallego","year":"2018","journal-title":"Virology"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Heiny, A.T., Miotto, O., Srinivasan, K.N., Khan, A.M., Zhang, G.L., Brusic, V., Tan, T.W., and August, J.T. (2007). Evolutionarily Conserved Protein Sequences of Influenza A Viruses, Avian and Human, as Vaccine Targets. PLoS ONE, 2.","DOI":"10.1371\/journal.pone.0001190"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e02133","DOI":"10.1128\/JVI.02133-17","article-title":"Induction of Genotype Cross-Reactive, Hepatitis C Virus-Specific, Cell-Mediated Immunity in DNA-Vaccinated Mice","volume":"92","author":"Wijesundara","year":"2018","journal-title":"J. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"016004","DOI":"10.1088\/1478-3975\/aaeec0","article-title":"Computational design of hepatitis C virus immunogens from host-pathogen dynamics over empirical viral fitness landscapes","volume":"16","author":"Hart","year":"2018","journal-title":"Phys. Biol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.2146\/ajhp60632","article-title":"Sofosbuvir\u2013velpatasvir: A single-tablet treatment for hepatitis C infection of all genotypes","volume":"74","author":"Miller","year":"2017","journal-title":"Am. J. Health Pharm."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1080\/21645515.2019.1661207","article-title":"Vaccine strategies to induce broadly protective immunity to rhinoviruses","volume":"16","author":"McLean","year":"2020","journal-title":"Hum. Vaccines Immunother."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"135","DOI":"10.3389\/fmicb.2020.00135","article-title":"Broadly Protective Strategies Against Influenza Viruses: Universal Vaccines and Therapeutics","volume":"11","author":"Vogel","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1080\/14760584.2018.1541408","article-title":"Universal influenza vaccines: From viruses to nanoparticles","volume":"17","author":"Wang","year":"2018","journal-title":"Expert Rev. Vaccines"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12985-017-0918-y","article-title":"Towards a universal influenza vaccine: Different approaches for one goal","volume":"15","author":"Sautto","year":"2018","journal-title":"Virol. J."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Qiu, X., Duvvuri, V.R., and Bahl, J. (2019). Computational Approaches and Challenges to Developing Universal Influenza Vaccines. Vaccines, 7.","DOI":"10.3390\/vaccines7020045"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"103749","DOI":"10.1016\/j.compbiomed.2020.103749","article-title":"COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achille\u2019s heel conserved region to minimize probability of escape mutations and drug re-sistance","volume":"121","author":"Robson","year":"2020","journal-title":"Comput. Biol. Med."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1843","DOI":"10.1002\/hep.22550","article-title":"Cell culture-produced hepatitis C virus does not infect peripheral blood mononuclear cells","volume":"48","author":"Marukian","year":"2008","journal-title":"Hepatology"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1093\/oxfordjournals.aje.a118408","article-title":"A simple method of estimating fifty per cent endpoints","volume":"27","author":"Reed","year":"1938","journal-title":"Am. J. Epidemiol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Ortega-Prieto, A.M., Sheldon, J., Grande-Perez, A., Tejero, H., Gregori, J., Quer, J., Esteban, J.I., Domingo, E., and Perales, C. (2013). Ex-tinction of hepatitis C virus by ribavirin in hepatoma cells involves lethal mutagenesis. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0071039"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"De \u00c1vila, A.I., Gallego, I., Soria, M.E., Gregori, J., Quer, J., Esteban, J.I., Rice, C.M., Domingo, E., and Perales, C. (2016). Lethal Mutagenesis of Hepatitis C Virus Induced by Favipiravir. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0164691"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"e01653-19","DOI":"10.1128\/AAC.01653-19","article-title":"Synergistic Lethal Mutagenesis of Hepatitis C Virus","volume":"63","author":"Gallego","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1093\/bioinformatics\/btt768","article-title":"Inference with viral quasispecies diversity indices: Clonal and NGS approaches","volume":"30","author":"Gregori","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1016\/j.jhep.2005.05.032","article-title":"Mutagenic effects of ribavirin and response to interferon\/ribavirin combination therapy in chronic hepatitis C","volume":"43","author":"Asahina","year":"2005","journal-title":"J. Hepatol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"6172","DOI":"10.1128\/JVI.02778-12","article-title":"Deep Sequencing Reveals Mutagenic Effects of Ribavirin during Monotherapy of Hepatitis C Virus Genotype 1-Infected Patients","volume":"87","author":"Dietz","year":"2013","journal-title":"J. Virol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.4155\/fmc-2018-0457","article-title":"The increasing impact of lethal mutagenesis of viruses","volume":"11","author":"Perales","year":"2019","journal-title":"Future Med. Chem."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3741","DOI":"10.1128\/JVI.02346-12","article-title":"T-705 (Favipiravir) Induces Lethal Mutagenesis in Influenza A H1N1 Viruses In Vitro","volume":"87","author":"Baranovich","year":"2013","journal-title":"J. Virol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e03679","DOI":"10.7554\/eLife.03679","article-title":"Favipiravir elicits antiviral mutagenesis during virus replication in vivo","volume":"3","author":"Arias","year":"2014","journal-title":"Elife"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"4682","DOI":"10.1038\/s41467-020-18463-z","article-title":"Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis","volume":"11","author":"Shannon","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"104278","DOI":"10.1016\/j.meegid.2020.104278","article-title":"A new implication of quasispecies dynamics: Broad virus diversification in absence of external perturbations","volume":"82","author":"Domingo","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"3786","DOI":"10.1128\/AAC.00581-16","article-title":"Barrier-Independent, Fitness-Associated Differences in Sofosbuvir Efficacy against Hepatitis C Virus","volume":"60","author":"Gallego","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Domingo, E. (2006). Quasispecies: Concepts and Implications for Virology. Current Topics in Microbiology and Immunology, Springer. Available online: https:\/\/www.springer.com\/gp\/book\/9783540263951.","DOI":"10.1007\/b137531"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1128\/MMBR.05023-11","article-title":"Viral Quasispecies Evolution","volume":"76","author":"Domingo","year":"2012","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Domingo, E., and Perales, C. (2021). The time for COVID-19 vaccination. J. Virol.","DOI":"10.1128\/JVI.02437-20"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"281","DOI":"10.3851\/IMP3317","article-title":"Pre-treatment antiviral resistance in Australians with chronic hepatitis C: Prevalence of NS3 and NS5A resistance data in the state of New South Wales","volume":"24","author":"Ong","year":"2019","journal-title":"Antivir. Ther."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1970","DOI":"10.1002\/jmv.25536","article-title":"Hepatitis C virus genotype 1 infection: Prevalence of NS5A and NS5B resistance-associated substitutions in na\u00efve patients from Argentina","volume":"91","author":"Ridruejo","year":"2019","journal-title":"J. Med. Virol."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Martinez, M.A., and Franco, S. (2020). Therapy Implications of Hepatitis C Virus Genetic Diversity. Viruses, 13.","DOI":"10.3390\/v13010041"},{"key":"ref_50","unstructured":"European Association for the Study of the Liver, Clinical Practice Guidelines Panel: Chair, and EASL Governing Board Representative (2020). EASL recommendations on treatment of hepatitis C: Final update of the series. J. Hepatol., 73, 1170\u20131218."},{"key":"ref_51","unstructured":"Domingo, E. (2020). Virus as Populations, Elsevier. [2nd ed.]."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1111\/liv.13327","article-title":"Multiclass HCV resistance to direct-acting antiviral failure in real-life patients advocates for tailored second-line therapies","volume":"37","author":"Cento","year":"2017","journal-title":"Liver Int."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1053\/j.gastro.2017.11.007","article-title":"Patterns of Resistance-Associated Substitutions in Patients with Chronic HCV Infection Following Treatment with Direct-Acting Antivirals","volume":"154","author":"Dietz","year":"2018","journal-title":"Gastroenterology"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"221","DOI":"10.3851\/IMP3301","article-title":"High frequency of multiclass HCV resistance-associated mutations in patients failing direct-acting antivirals: Real-life data","volume":"24","author":"Gozlan","year":"2019","journal-title":"Antivir. Ther."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"105562","DOI":"10.1016\/j.ijantimicag.2018.10.005","article-title":"Quasispecies dynamics and clinical significance of hepatitis C virus (HCV) antiviral resistance","volume":"56","author":"Perales","year":"2020","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"8818","DOI":"10.1038\/s41598-018-27291-7","article-title":"Significance of NS5B Substitutions in Genotype 1b Hepatitis C Virus Evaluated by Bioinformatics Analysis","volume":"8","author":"Uchida","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Bellocchi, M.C., Aragri, M., Carioti, L., Fabeni, L., Pipitone, R.M., Brancaccio, G., Sorbo, M.C., Barbaliscia, S., Di Maio, V.C., and Bronte, F. (2019). NS5A Gene Analysis by Next Generation Sequencing in HCV Nosocomial Transmission Clusters of HCV Genotype 1b Infected Patients. Cells, 8.","DOI":"10.3390\/cells8070666"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"2902","DOI":"10.3748\/wjg.v20.i11.2902","article-title":"Hepatitis C virus NS5A inhibitors and drug resistance mutations","volume":"20","author":"Nakamoto","year":"2014","journal-title":"World J. Gastroenterol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Kim, D.-W., Lee, S.-A., Kim, H., Won, Y.-S., and Kim, B.-J. (2014). Naturally Occurring Mutations in the Nonstructural Region 5B of Hepatitis C Virus (HCV) from Treatment-Na\u00efve Korean Patients Chronically Infected with HCV Genotype 1b. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0087773"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"5456","DOI":"10.1128\/AAC.03052-14","article-title":"Genotypic and Phenotypic Analyses of Hepatitis C Virus Variants Observed in Clinical Studies of VX-222, a Nonnucleoside NS5B Polymerase Inhibitor","volume":"58","author":"Jiang","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"8316","DOI":"10.1128\/JVI.74.18.8316-8323.2000","article-title":"Response of Foot-and-Mouth Disease Virus to Increased Mutagenesis: Influence of Viral Load and Fitness in Loss of Infectivity","volume":"74","author":"Sierra","year":"2000","journal-title":"J. Virol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"9723","DOI":"10.1128\/JVI.75.20.9723-9730.2001","article-title":"Efficient virus extinction by combinations of a mutagen and antiviral inhibitors","volume":"75","author":"Pariente","year":"2001","journal-title":"J. Virol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.virol.2005.05.008","article-title":"Combination of a mutagenic agent with a reverse transcriptase inhibitor results in systematic inhibition of HIV-1 infection","volume":"338","author":"Tapia","year":"2005","journal-title":"Virology"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"2054","DOI":"10.1128\/AAC.02494-12","article-title":"Persistence of resistant variants in hepatitis C virus-infected patients treated with the NS5A replication complex inhibitor daclatasvir","volume":"57","author":"Wang","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_65","first-page":"23","article-title":"The Nucleation of Semantic Information in Prebiotic Matter","volume":"392","year":"2015","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/978-3-0348-9146-2_5","article-title":"RNA virus evolution and the control of viral disease","volume":"33","author":"Domingo","year":"1989","journal-title":"Prog. Drug Res."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/j.tim.2012.08.010","article-title":"The impact of quasispecies dynamics on the use of therapeutics","volume":"20","author":"Perales","year":"2012","journal-title":"Trends Microbiol."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Trypsteen, W., Van Cleemput, J., Snippenberg, W.V., Gerlo, S., and Vandekerckhove, L. (2020). On the whereabouts of SARS-CoV-2 in the human body: A systematic review. PLoS Pathog., 16.","DOI":"10.1371\/journal.ppat.1009037"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41579-020-00468-6","article-title":"Coronavirus biology and replication: Implications for SARS-CoV-2","volume":"19","author":"Kratzel","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_70","first-page":"1","article-title":"RNA Virus Populations as Quasispecies","volume":"176","author":"Holland","year":"1992","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Rosenberg, C.E. (1992). Explaining Epidemics and Other Studies in the History of Medicine, Cambridge University Press.","DOI":"10.1017\/CBO9780511666865"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/4\/616\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T13:58:16Z","timestamp":1760363896000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/4\/616"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,4,3]]},"references-count":71,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2021,4]]}},"alternative-id":["v13040616"],"URL":"https:\/\/doi.org\/10.3390\/v13040616","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,4,3]]}}}