title: Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA.
abstract: The innate-immune restriction factor MxA inhibits influenza replication by targeting the viral nucleoprotein (NP). Human influenza virus is more resistant than avian influenza virus to inhibition by human MxA, and prior work has compared human and avian viral strains to identify amino-acid differences in NP that affect sensitivity to MxA. However, this strategy is limited to identifying sites in NP where mutations that affect MxA sensitivity have fixed during the small number of documented zoonotic transmissions of influenza to humans. Here we use an unbiased deep mutational scanning approach to quantify how all single amino-acid mutations to NP affect MxA sensitivity in the context of replication-competent virus. We both identify new sites in NP where mutations affect MxA resistance and re-identify mutations known to have increased MxA resistance during historical adaptations of influenza to humans. Most of the sites where mutations have the greatest effect are almost completely conserved across all influenza A viruses, and the amino acids at these sites confer relatively high resistance to MxA. These sites cluster in regions of NP that appear to be important for its recognition by MxA. Overall, our work systematically identifies the sites in influenza nucleoprotein where mutations affect sensitivity to MxA. We also demonstrate a powerful new strategy for identifying regions of viral proteins that affect inhibition by host factors.
authors.affiliation: Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
authors.forename: Orr
authors.initials: O
authors.lastname: Ashenberg
authors.affiliation: Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
authors.forename: Jai
authors.initials: J
authors.lastname: Padmakumar
authors.affiliation: Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.|Department of Genome Sciences, University of Washington, Seattle, WA, USA.|Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA, USA.
authors.forename: Michael B
authors.identifier: 0000-0002-8172-6342
authors.initials: MB
authors.lastname: Doud
authors.affiliation: Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.|Department of Genome Sciences, University of Washington, Seattle, WA, USA.
authors.forename: Jesse D
authors.identifier: 0000-0003-1267-3408
authors.initials: JD
authors.lastname: Bloom
mesh_terms: D004252:DNA Mutational Analysis; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics* / Q000276:immunology*; D009154:Mutation; D064547:Myxovirus Resistance Proteins / Q000276:immunology*; D009698:Nucleoproteins / Q000235:genetics* / Q000276:immunology*; D016133:Polymerase Chain Reaction
chemical_list: C579071:MX1 protein, human; D064547:Myxovirus Resistance Proteins; D009698:Nucleoproteins