Influenza Viral Genomics and Evolution

流感病毒基因组学和进化

• 批准号: 7592347
• 负责人: Jeffery Taubenberger
• 金额: $ 98.91万
• 依托单位: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7592347
• 关键词: Age; Alaska; Alcohol consumption; Alcohols; American; Amino Acids; Animals; Area; Asians; Avian Influenza A Virus; Base Pairing; Biological Assay; Biology; Birds; Breeding; Buffers; Cessation of life; Class; Cold Chains; Complex; Detection; Diagnostic; Domestic Animals; Domestic Fowls; Ducks; Ecology; Eligibility Determination; Epidemic; Equus caballus; Ethanol; Evolution; Extramural Activities; Family suidae; Feces; Future; Genetic Variation; Genome; Genomics; Goals; Guanidines; Hemagglutinin; Hour; Human; Human Genome; Immune; Influenza; Influenza A virus; Medical Surveillance; Molecular; Morbidity - disease rate; Natural History; Neuraminidase; New York; Pattern; Phylogenetic Analysis; Play; Population; Prevalence; Procedures; Process; Protocols documentation; RNA; Rate; Readiness; Research; Research Project Grants; Reverse Transcriptase Polymerase Chain Reaction; Role; Sampling; Screening procedure; Seasons; Shapes; Site; Specimen; Stochastic Processes; Swab; Temperature; Thinking; Time; United States; United States National Institutes of Health; Vaccines; Viral; Virus; Virus Diseases; Wing; base; cold temperature; day; density; design; genetic selection; genome sequencing; guanidinium; influenza epidemic; influenzavirus; insight; migration; mortality; pandemic disease; pandemic influenza; pathogen; sample collection; sex; viral RNA; wild bird

Influenza A viruses are significant human pathogens causing yearly epidemics and occasional pandemics. Past pandemics have results in significant morbidity and mortality. The 1918 influenza pandemic was thought to have resulted in the death of at least 675,000 people in the U.S., and 40 million people worldwide. Annual influenza A virus epidemics are also very significant, resulting in approximately 30,000 deaths in the U.S. per year. Pandemic strains of influenza emerge periodically and are thought to be derived ultimately from avian influenza A viruses. The natural reservoir of influenza A viruses is thought to be wild waterfowl. Genetically and antigenically diverse influenza A viruses circulate in wild birds and viral strains from this pool can adapt to new hosts, including humans and domestic animals. Influenza A viruses are also significant pathogens for agriculturally important animals like poultry, swine, and horses. Understanding the mechanisms of host switching are very important for surveillance and pandemic preparedness. Understanding the molecular basis underlying the annual evolution of human influenza will aid in vaccine strain selection. Human influenza A virus evolution: Understanding the evolutionary dynamics of influenza A virus is central to its surveillance and control. While immune-driven antigenic drift is a key determinant of viral evolution across epidemic seasons, the evolutionary processes shaping influenza virus diversity within seasons are less clear. In this study we showed with a phylogenetic analysis of 413 complete genomes of human H3N2 influenza A viruses collected between 1997 and 2005 from New York State, United States, that genetic diversity is both abundant and largely generated through the seasonal importation of multiple divergent clades of the same subtype (1). These clades co-circulated within New York State, allowing frequent reassortment and generating genome-wide diversity. However, relatively low levels of positive selection and genetic diversity were observed at amino acid sites considered important in antigenic drift. These results indicate that adaptive evolution occurs only sporadically in influenza A virus; rather, the stochastic processes of viral migration and clade reassortment play a vital role in shaping short-term evolutionary dynamics. Thus, predicting future patterns of influenza virus evolution for vaccine strain selection is inherently complex and requires intensive surveillance, whole-genome sequencing, and phenotypic analysis. Avian influenza A virus surveillance: Surveillance for avian influenza A viruses in wild bird populations is often limited by requirements for a cold chain from time of specimen collection and availability of ultra low temperature specimen storage within a few hours or days and then laborious classical virological procedures. Successful storage of specimens in preservatives at ambient temperature and subsequent detection of RNA by RT-PCR would assist influenza surveillance efforts to become more widespread in remote areas as well as more timely and inexpensive. We evaluated the efficacy of this approach using bird feces spiked with influenza A virus preserved with guanidine and commercial buffers or alcohols at ambient temperature and analyzed by RT-PCR protocols. Virus specific RT-PCR products of at most 206 base pairs for samples were recovered when preserved with alcohols and up to 521 base pairs for samples preserved with guanidine or commercial buffers. This suggests this approach is feasible in the field and that preserved specimens may be better assayed molecularly when preserved in guanidine or commercial buffers (2). We used ethanol-fixed cloacal swabs to allow avian influenza virus surveillance in remote areas of Alaska (3). Alaska was chosen because both Asian/Pacific and North American flyways converge in central Alaska. Our extramural collaborators and NIH staff evaluated avian influenza viruses (AIV) in the Minto Flats State Game Refuge, high-density waterfowl breeding grounds in Alaska. Five hundred paired cloacal samples from dabbling ducks (Northern Pintail, Mallard, Green Wing Teal, and Widgeon) were placed into ethanol and viral transport medium. Additional ethanol-preserved samples were taken. Of the ethanol-preserved samples, 25.6% were AIV RNA-positive by real-time RT-PCR. The hemagglutinin and neuraminidase subtypes were determined for 38 of the first-passage isolates. Five influenza A virus HA-NA combinations were identified: H3N6, H3N8, H4N6, H8N4, and H12N5. Differences in the prevalence of AIV infections by sex and by age classes of Northern Pintail and Mallard ducks were detected, but the significance of these differences is undefined. In the 500 paired samples, molecular screening detected positive birds at a higher rate than viral isolation; however, 20 AIV isolates were recovered from PCR-negative ducks. Further research is warranted to compare the two screening protocols potential for estimating true prevalence in wild birds. These results indicate that the Minto Flats region of Alaska will be a valuable study site for a longitudinal research project designed to gain further insight into the natural history, evolution, and ecology of AIV in wild birds.

流感病毒是重要的人类病原体，导致年度流行病和偶尔出现。过去的大流行物具有显着的发病率和死亡率。人们认为，1918年的流感大流行导致了美国至少有67.5万人死亡，全世界有4000万人死亡。年度流感病毒流行病也非常重要，每年在美国大约30,000人死亡。流感的大流行菌株定期出现，被认为最终来自禽流感病毒。流感的天然水库被认为是野生水禽。从遗传和抗原上多样化的流感病毒在野生鸟类中循环，该池的病毒菌株可以适应新宿主，包括人类和家畜。流感病毒也是农业重要动物（如家禽，猪和马）的重要病原体。了解宿主切换的机制对于监视和大流行准备非常重要。了解人类流感的年度演变的分子基础将有助于疫苗菌株的选择。 人类流感的一种病毒进化： 了解流感病毒的进化动力学对于其监测和控制是核心。尽管免疫驱动的抗原漂移是整个流行病季节病毒进化的关键决定因素，但塑造季节中流感病毒多样性的进化过程尚不清楚。在这项研究中，我们通过系统发育分析对1997年至2005年2005年从美国纽约州收集的413个人类H3N2流感病毒的完整基因组进行了分析，遗传多样性是丰富的，并且很大程度上是通过季节性进口相同亚型的多个发散成枝的季节性进口（1）。这些进化枝在纽约州内共存，允许频繁地放置并产生全基因组的多样性。但是，在被认为在抗原漂移中很重要的氨基酸位点观察到了相对较低的阳性选择和遗传多样性。这些结果表明，自适应进化仅在流感病毒中偶发地发生。相反，病毒迁移和进化枝的随机过程在塑造短期进化动力学方面起着至关重要的作用。因此，预测用于疫苗菌株选择的流感病毒演化的未来模式本质上是复杂的，需要密集的监视，全基因组测序和表型分析。 禽流感病毒监测： 野生鸟类种群中禽流感病毒的监测通常受到从标本收集时间到冷链的要求，并在几个小时或几天内可用的超低温度标本存储，然后是费力的经典病毒学程序。在环境温度和随后通过RT-PCR检测RNA在防腐剂中成功存储标本将有助于流感监视的努力，以在偏远地区以及更及时，更便宜的情况下变得更加普遍。我们使用在环境温度下用鸟嘌呤和商业缓冲液或酒精保存的鸟类粪便评估了这种方法的功效，并通过RT-PCR方案进行了分析。当醇保存时，回收了最多206个碱基对的病毒特异性RT-PCR产物，并最多可用于521个碱基对，用于保存的鸟嘌呤或商业缓冲液的样品。这表明这种方法在田间是可行的，并且在保存在鸟嘌呤或商业缓冲液中时，保留的标本可以更好地测定分子（2）。 我们使用乙醇固定的泄殖腔拭子允许阿拉斯加偏远地区的鸟类流感病毒监测（3）。之所以选择阿拉斯加，是因为亚洲/太平洋和北美飞行道汇聚在阿拉斯加中部。我们的壁外合作者和NIH员工评估了阿拉斯加的Minto Flats州游戏避难所，高密度水禽繁殖地的禽流感病毒（AIV）。将少量鸭子（北匹尾，野鸭，绿翼蓝绿色和维木）配对的五百个配对的泄殖腔样品放入乙醇和病毒运输培养基中。采集其他保留乙醇的样品。在保留乙醇的样品中，通过实时RT-PCR为AIV RNA阳性25.6％。针对38个第一个小分离株测定了血凝素和神经氨酸酶亚型。鉴定了五种流感病毒HA-NA组合：H3N6，H3N8，H4N6，H8N4和H12N5。发现了性别感染AIV感染的差异，以及北长尾和野鸭的年龄类别的差异，但是这些差异的重要性是不确定的。在500个配对样品中，分子筛选以比病毒分离更高的速率检测到阳性鸟类。但是，从PCR阴性鸭子中回收了20个AIV分离株。有必要进行进一步的研究，以比较估计野生鸟类真正患病率的两种筛选方案。这些结果表明，阿拉斯加的Minto Flats地区将是一个纵向研究项目的宝贵研究地点，旨在进一步了解野生鸟类AIV的自然历史，进化和生态学。