Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity

Abstract

RNA viruses exist as genetically diverse populations. This standing genetic diversity gives them the potential to adapt rapidly, evolve resistance to antiviral therapeutics, and evade immune responses. Viral mutants with altered mutation rates or mutational tolerance have provided insights into how genetic diversity arises and how it affects the behavior of RNA viruses. To this end, we identified variants within the polymerase complex of influenza virus that are able tolerate drug-mediated increases in viral mutation rates. We find that drug resistance is highly dependent on interactions among mutations in the polymerase complex. In contrast to other viruses, influenza virus counters the effect of higher mutation rates primarily by maintaining high levels of genome replication. These findings suggest the importance of maintaining large population sizes for viruses with high mutation rates and show that multiple proteins can affect both mutation rate and genome synthesis.

Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy

“…Of the latter ( Arias et al. 2008 ; Pauly et al 2017 ; Van Slyke et al. 2015 ), three low-fidelity mutants have been identified that are resistant to the nucleoside analog used for passaging, but are sensitive to other nucleoside analogs.…”

“…2010 ; Graham et al. 2012 ; Graepel et al 2017 ), influenza virus ( Cheung et al 2014 ; Pauly et al 2017 ), Norovirus ( Arias et al 2016 ) and Coxsackie B virus ( Gnädig et al. 2012 ; Levi et al.…”

Mutation and Epistasis in Influenza Virus Evolution

“…Experimental assays for measuring the fitness effects of single mutations can also be used to determine the sign (positive or negative) and magnitude of epistasis between two or more mutations. Previous studies have employed site-directed mutagenesis to study interactions among small numbers of mutations, usually those implicated in adaptation to immune pressure or antiviral drugs [ 53 , 54 , 55 ]. As above, the advantage of site-directed mutagenesis is that one can precisely quantify the epistatic interactions between chosen mutations.…”

“…Contingency has been identified in M2 and NP phylogenies and immune escape mutations in NP [ 54 , 65 ]. We have found that mutations in PA and PB1 interact epistatically to mediate high-level resistance to mutagenic drugs in vitro [ 55 ]. Epistatic interactions in M2 may also mediate increased resistance to amantadine and/or increase virulence in amantadine-resistant strains [ 98 , 99 , 100 ].…”

The mechanism of resistance to favipiravir in influenza

“…One study reported a small change in susceptibility to favipiravir in an H3N2 viral mutant selected for resistance to the nucleoside analog ribavirin ( 31 ). However, the effect of the resistance mutation was not reproducible in an H1N1 influenza virus strain ( 32 ), and this, together with the small change in favipiravir susceptibility, makes the clinical significance of the observed mutation debatable. So far, significant resistance in other RNA viruses to favipiravir has only been reported from experimental evolution studies in chikungunya virus (CV) ( 33 ) and enterovirus 71 (EV-71) ( 34 ).…”