title: The Mutational Robustness of Influenza A Virus.
abstract: A virus' mutational robustness is described in terms of the strength and distribution of the mutational fitness effects, or MFE. The distribution of MFE is central to many questions in evolutionary theory and is a key parameter in models of molecular evolution. Here we define the mutational fitness effects in influenza A virus by generating 128 viruses, each with a single nucleotide mutation. In contrast to mutational scanning approaches, this strategy allowed us to unambiguously assign fitness values to individual mutations. The presence of each desired mutation and the absence of additional mutations were verified by next generation sequencing of each stock. A mutation was considered lethal only after we failed to rescue virus in three independent transfections. We measured the fitness of each viable mutant relative to the wild type by quantitative RT-PCR following direct competition on A549 cells. We found that 31.6% of the mutations in the genome-wide dataset were lethal and that the lethal fraction did not differ appreciably between the HA- and NA-encoding segments and the rest of the genome. Of the viable mutants, the fitness mean and standard deviation were 0.80 and 0.22 in the genome-wide dataset and best modeled as a beta distribution. The fitness impact of mutation was marginally lower in the segments coding for HA and NA (0.88 ± 0.16) than in the other 6 segments (0.78 ± 0.24), and their respective beta distributions had slightly different shape parameters. The results for influenza A virus are remarkably similar to our own analysis of CirSeq-derived fitness values from poliovirus and previously published data from other small, single stranded DNA and RNA viruses. These data suggest that genome size, and not nucleic acid type or mode of replication, is the main determinant of viral mutational fitness effects.
authors: Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.
authors: Elisa
authors: 0000-0003-3984-4748
authors: E
authors: Visher
authors: Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America.
authors: Shawn E
authors: 0000-0002-3274-9230
authors: SE
authors: Whitefield
authors: Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America.
authors: John T
authors: JT
authors: McCrone
authors: Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.
authors: William
authors: 0000-0002-0997-1108
authors: W
authors: Fitzsimmons
authors: Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America.|Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America.
authors: Adam S
authors: AS
authors: Lauring
mesh_terms: D000072283:A549 Cells; D004279:DNA, Viral / Q000235:genetics*; D019143:Evolution, Molecular; D056084:Genetic Fitness / Q000235:genetics*; D006388:Hemagglutinins / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009980:Influenza A virus / Q000235:genetics*; D008957:Models, Genetic; D016297:Mutagenesis, Site-Directed; D009439:Neuraminidase / Q000235:genetics; D017354:Point Mutation; D060888:Real-Time Polymerase Chain Reaction; D014162:Transfection
chemical_list: D004279:DNA, Viral; D006388:Hemagglutinins; D009439:Neuraminidase