Epistasis Within and Between Genomic Segments in Influenza Virus

流感病毒基因组片段内部和之间的上位性

• 批准号: 9608579
• 负责人: Daniel Lyons
• 金额: $ 3.62万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-01 至 2020-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9608579
• 关键词: Affect; Biological Assay; Biology; Buffers; Clinical Medicine; Communication; Complex; Data; Data Analyses; Drug resistance; Economic Burden; Event; Evolution; Genes; Genetic; Genetic Engineering; Genetic Epistasis; Genetic Variation; Genome; Genomic Segment; Goals; Growth; Health; Hemagglutinin; Human; Immune system; Immunity; Individual; Infection; Influenza; Influenza A virus; Libraries; Measurement; Membrane Proteins; Mentorship; Methods; Mission; Modeling; Molecular Evolution; Mutation; Outcome; Pattern; Pharmaceutical Preparations; Phylogenetic Analysis; Physicians; Point Mutation; Polymerase; Population Genetics; Process; Proteins; Public Health; Research Project Grants; Scientist; Site; System; Testing; Time; Training; United States National Institutes of Health; Vaccines; Variant; Viral; Virus; Work; base; design; fitness; gene interaction; genome-wide; improved; influenzavirus; innovation; mutant; novel; pandemic disease; protein folding; response; theories; trait

Project Summary/Abstract Influenza A virus (IAV) evolves rapidly in response to vaccines and drugs, causing significant public health and economic burdens. Interactions between mutations, or epistasis, determine how IAV will evolve. Different types of epistasis, including positive and negative, have different evolutionary consequences. However, little is known about the types of epistasis in IAV, limiting our ability to predict and control the virus. The long-term goal is to elucidate how basic evolutionary processes affect public health. The objectives of this project are to characterize pairwise epistasis between all 8 genomic segments of IAV and within the HA gene encoding the antigenic hemagglutinin protein. A tractable genetic system will allow the creation of thousands of double mutants using an existing genome-wide library of influenza viruses with defined point mutations. Using a novel, sensitive, and high-throughput fitness assay for viral growth, the fitness of each single and double mutant will be determined, and the magnitude and sign of epistasis will be quantified. Preliminary data indicate that this fitness assay has very low measurement error, enabling precise measurement of epistasis in thousands of mutants. The first aim is to characterize pairwise epistasis between all pairs of IAV segments. Based on theoretical predictions related to viral evolutionary constraints, the hypothesis is that epistasis in IAV is negative on average. Distinct epistatic patterns between segments may reveal previously unknown functional interactions between IAV segments. To complete this aim, the fitness of thousands of double and single mutants in all pairs of segments will be compared. The second aim is to characterize pairwise epistasis within HA. Based on previous work on protein- folding constraints, the hypothesis is that epistasis within HA is negative on average. To test this hypothesis, the fitness of hundreds of double and single mutants within HA will be compared. This project is innovative because, to our knowledge, it will be the only study of epistasis between random point mutations in different genes of IAV and almost a hundred times larger than the largest such study in a virus. This innovation is enabled by creative use of the IAV genetic engineering system and a novel fitness assay. This project is significant because characterizing the types of epistasis in IAV will improve predictions of the evolution of seasonal and pandemic strains and aid in the design of effective vaccines. Through completion of the proposed research project, mentorship, and other activities, the applicant will achieve his training goals in the fields of molecular evolution and population genetics, high-throughput methods and data analysis, effective scientific communication, and clinical medicine. This will enable the applicant to achieve his ultimate goal of becoming a physician-scientist who answers fundamental questions in evolutionary biology with practical implications for human health.

项目概要/摘要 甲型流感病毒 (IAV) 在疫苗和药物的作用下迅速进化，对公众健康和健康造成重大影响。 经济负担。突变之间的相互作用或上位性决定了 IAV 将如何进化。不同类型 上位性，包括积极的和消极的，具有不同的进化后果。然而，鲜为人知 关于 IAV 的上位性类型，限制了我们预测和控制病毒的能力。长期目标是 阐明基本进化过程如何影响公共健康。该项目的目标是表征 IAV 的所有 8 个基因组片段之间以及编码抗原的 HA 基因内成对上位 血凝素蛋白。一个易于处理的遗传系统将允许使用 现有的具有明确点突变的流感病毒全基因组文库。使用新颖、敏感、 病毒生长的高通量适合度测定，将确定每个单突变体和双突变体的适合度， 并且上位性的大小和符号将被量化。初步数据表明，该适应性测定具有 非常低的测量误差，能够精确测量数千个突变体的上位性。第一个目标 是为了表征所有 IAV 片段对之间的成对上位性。基于相关理论预测 由于病毒进化的限制，假设 IAV 的上位性平均为负。明显上位 片段之间的模式可能揭示 IAV 片段之间以前未知的功能相互作用。到 完成这一目标，所有片段对中数千个双突变体和单突变体的适应度将是 比较的。第二个目标是描述 HA 内成对上位性的特征。基于之前对蛋白质的研究—— 折叠约束，假设 HA 内的上位性平均为负。为了检验这个假设， 将比较 HA 内数百个双突变体和单突变体的适应性。这个项目之所以具有创新性是因为， 据我们所知，这将是唯一一项关于 IAV 不同基因随机点突变之间上位性的研究 比最大的此类病毒研究规模几乎一百倍。这项创新是通过创意来实现的 使用 IAV 基因工程系统和新颖的适应性测定。这个项目意义重大，因为 表征 IAV 的上位性类型将改善对季节性和流行病演变的预测 菌株并有助于设计有效的疫苗。通过完成拟议的研究项目， 指导和其他活动，申请人将实现其在分子进化领域的培训目标 和群体遗传学、高通量方法和数据分析、有效的科学交流，以及 临床医学。这将使申请人能够实现成为一名医师科学家的最终目标 他回答了进化生物学中对人类健康具有实际影响的基本问题。