Evolution of the Influenza A Virus Genome during Development of Oseltamivir ResistanceIn Vitro

Abstract

f Influenza A virus (IAV) is a major cause of morbidity and mortality throughout the world. Current antiviral therapies include oseltamivir, a neuraminidase inhibitor that prevents the release of nascent viral particles from infected cells. However, the IAV genome can evolve rapidly, and oseltamivir resistance mutations have been detected in numerous clinical samples. Using an in vitro evolution platform and whole-genome population sequencing, we investigated the population genomics of IAV during the development of oseltamivir resistance. Strain A/Brisbane/59/2007 (H1N1) was grown in Madin-Darby canine kidney cells with or without escalating concentrations of oseltamivir over serial passages. Following drug treatment, the H274Y resistance mutation fixed reproducibly within the population. The presence of the H274Y mutation in the viral population, at either a low or a high frequency, led to measurable changes in the neuraminidase inhibition assay. Surprisingly, fixation of the resistance mutation was not accompanied by alterations of viral population diversity or differentiation, and oseltamivir did not alter the selective environment. While the neighboring K248E mutation was also a target of positive selection prior to H274Y fixation, H274Y was the primary beneficial mutation in the population. In addition, once evolved, the H274Y mutation persisted after the withdrawal of the drug, even when not fixed in viral populations. We conclude that only selection of H274Y is required for oseltamivir resistance and that H274Y is not deleterious in the absence of the drug. These collective results could offer an explanation for the recent reproducible rise in oseltamivir resistance in seasonal H1N1 IAV strains in humans.

Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics

“…The distribution of effects of random mutations on folding stability has also been estimated to be universal across several classes of protein folds[28]. Stability-centric models successfully reproduced experimentally observed distributions of protein stabilities [9,24,26*,29] and distribution of fitness effects in viruses [11]. Thus, the distribution of fitness effect s (DFE) of arising random mutations is in principle the convolution of the well-established distributions of Δ G wildtype and ΔΔ G .…”

Influenza A virus preferentially snatches noncoding RNA caps

“…Our previous work used high-throughput sequencing methods and new bioinformatics and statistical tools to study the evolution of IAV (Foll et al 2014;Renzette et al 2014;Zeldovich et al 2015). Here, we apply novel strategies to demonstrate how IAV snatches caps from host RNAs, both coding and noncoding, to prime the transcription of viral RNAs.…”

Pharmacological Characterization of the Spectrum of Antiviral Activity and Genetic Barrier to Drug Resistance of M2-S31N Channel Blockers

“…In comparison with the genetic Pharmacology of M2-S31N Inhibitors barriers to drug resistance for the two classes of Food and Drug Administration-approved anti-influenza drugs, M2-S31N inhibitors outperformed amantadine and are only slightly less effective than oseltamivir. In general, complete resistance to oseltamivir was generated around passage 5 (Triana-Baltzer et al, 2011;Renzette et al, 2014). Sequencing the resulting resistant viruses revealed interesting findings.…”