Abstract
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. We have introduced a new diversity index, the rare haplotype load (RHL), to describe NS5B (polymerase) mutant spectra of hepatitis C virus (HCV) populations passaged in absence or presence of the mutagenic agents favipiravir or ribavirin. The increase in RHL is more prominent in mutant spectra whose expansions were due to nucleotide analogues than to multiple passages in absence of mutagens. Statistical tests for paired mutagenized versus non-mutagenized samples with 14 diversity indices show that RHL provides consistently the highest standardized effect of mutagenic treatment difference for ribavirin and favipiravir. The results indicate that the enrichment of viral quasispecies in very low frequency minority genomes can serve as a robust marker for lethal mutagenesis. The diagnostic value of RHL from deep sequencing data is relevant to experimental studies on enhanced mutagenesis of viruses, and to pharmacological evaluations of inhibitors suspected to have a mutagenic activity.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Amides / pharmacology
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Antiviral Agents / pharmacology*
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Cell Line
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Haplotypes
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Hepacivirus / genetics*
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Humans
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Mutation Rate
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Nucleosides / analogs & derivatives
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Pyrazines / pharmacology
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Quasispecies
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Ribavirin / pharmacology
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Serial Passage
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Synthetic Lethal Mutations*
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Viral Nonstructural Proteins / genetics*
Substances
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Amides
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Antiviral Agents
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Nucleosides
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Pyrazines
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Viral Nonstructural Proteins
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Ribavirin
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NS-5 protein, hepatitis C virus
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favipiravir
Grants and funding
Work in Barcelona was funded by Instituto de Salud Carlos III; by grants PI13/00456, PI15/00829, and PI16/00337 cofinanced by the European Regional Development Fund (ERDF); and by CDTI (Centro para el Desarrollo Tecnológico Industrial), Spanish Ministry of Economics and Competitiveness (MINECO), IDI-20151125. CP is supported by the Miguel Servet program of the Instituto de Salud Carlos III (CP14/00121) cofinanced by the European Regional Development Fund (ERDF). CIBERehd (Centro de Investigación en Red de Enfermedades Hepáticas y Digestivas) is funded by Instituto de Salud Carlos III. The work in Madrid was supported by Spanish Ministry of Economics and Competitiveness (MINECO) grants number BFU-2011-23604, SAF2014-52400-R, SAF2017-87846-R and S2013/ABI-2906 (PLATESA from Comunidad de Madrid/FEDER). Institutional grants from the Fundación Ramón Areces and Banco Santander to the CBMSO are also acknowledged.