Resistance of high fitness hepatitis C virus to lethal mutagenesis

Viral fitness quantifies the degree of virus adaptation to a given environment. How viral fitness can influence the mutant spectrum complexity of a viral quasispecies subjected to lethal mutagenesis has not been investigated. Here we document that two high fitness hepatitis C virus populations display higher resistance to the mutagenic nucleoside analogues favipiravir and ribavirin than their parental, low fitness HCV. All populations, however, exhibited a mutation transition bias indicative of active mutagenesis. Resistance to the analogues was associated with a limited expansion of mutant spectrum complexity, as evidenced by several diversity indices used to characterize mutant spectra. The results are consistent with a replicative site-drug competition mechanism that was previously proposed for HCV fitness-associated resistance to non-mutagenic inhibitors. Other alternative, non-mutually exclusive mechanisms are considered. The results introduce viral fitness as a relevant parameter to evaluate the response of viruses to lethal mutagenesis, with implications for antiviral designs.
We thank Dr. Charles M. Rice for the supply of plasmid Jc1FLAG2(p7-nsGluc2A) and helpful advice for the implement of HCV replicon in cell culture, and to Mercedes Guerrero for help with the statistics. 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 Tecnologico Industrial), Spanish Ministry of Economics and Competitiveness (MINECO), IDI-20151125. C.P. 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 Investigacion en Red de Enfermedades Hepaticas y Digestivas) is funded by Instituto de Salud Carlos III. The work in Madrid was supported by grants BFU-2011-23604, SAF2014-52400-R, SAF2017-87846-R by Spanish MINECO and S2013/ABI-2906 (PLATESA from Comunidad de Madrid/FEDER). Institutional grants from the Fundacion Ramon Areces and Banco Santander to the CBMSO are also acknowledged.