Enhancing dengue virus genomic surveillance to uncover circulating genetic diversity

加强登革热病毒基因组监测以揭示循环遗传多样性

• 批准号: 10471494
• 负责人: Nathan Dale Grubaugh
• 金额: $ 150.75万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-21 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10471494
• 关键词: 2019-nCoV; Address; Cancer Surveillance Research Program; Caribbean region; Classification; Complex; County; Dengue; Dengue Virus; Development; Disease; Disease Outbreaks; Epidemiology; Evolution; Future; Genetic Variation; Genomics; Genotype; Goals; Knowledge; Measures; Modernization; Pattern; Phylogenetic Analysis; Process; Protocols documentation; Public Health; Research; Research Personnel; Serotyping; System; Training; Travel; Variant; Virus; data tools; genome sequencing; genomic data; innovation; interest; pathogen; programs; underserved area; variants of concern; viral genomics; virus genetics; whole genome

Project Summary New solutions are desperately needed to reduce the annual global burden of dengue. As we are currently witnessing for SARS-CoV-2, virus genomics can be harnessed to directly inform public health control measures. For most other pathogens, including dengue virus, we do not have the depth of genomic information for these uses. For dengue virus, part of the issue is its complexity: it is comprised of four genetically distinct serotypes with many defined genotypes and even more undefined variants. Furthermore, our current surveillance and research programs are not set up to fully take advantage of virus genomics. In this proposal, I will address the major barriers for modernizing dengue virus genomic programs: (1) development of a universal-dengue virus whole genome sequencing approach utilizing the framework being established globally for SARS-CoV-2; (2) formation of a collaborative network in the underserved region of the Caribbean to uncover the circulating dengue virus diversity and provide local training and sequencing support; (3) utilization of travel surveillance to provide information from beyond the network to serve as a template for other genomic surveillance systems; (4) development of a new dengue virus genetic classification system to more easily identify variants of concern/interest and to better utilize the genomic data without needing complex phylogenetic analysis; (5) creation of a webtool to provide easy access to the variant classification system, detailed regional and county-level analysis, genomic data, and protocols; and (6) detailed phylogenetic analysis to uncover key epidemiological processes, like the outbreak emergence interval and patterns of spread, to aid in future disease forecasting. Completion of the goals outlined in this proposal would significantly advance our knowledge and assessment of dengue virus diversity, evolution, and epidemiology. Researchers will be able to capitalize on these data and tools to facilitate the innovation of genomics-informed control strategies.

项目概要 迫切需要新的解决方案来减少全球每年的登革热负担。正如我们目前 目睹 SARS-CoV-2，可以利用病毒基因组学直接为公共卫生控制提供信息 措施。对于大多数其他病原体，包括登革热病毒，我们没有基因组的深度 这些用途的信息。对于登革热病毒，部分问题在于其复杂性：它由四个部分组成： 遗传上不同的血清型，具有许多确定的基因型，甚至更多未确定的变体。此外， 我们目前的监测和研究计划并不是为了充分利用病毒基因组学而制定的。在 在此提案中，我将解决登革热病毒基因组计划现代化的主要障碍：(1) 利用以下框架开发通用登革热病毒全基因组测序方法 在全球范围内针对 SARS-CoV-2 建立； （2）在服务欠缺地区形成协作网络 加勒比地区发现正在传播的登革热病毒多样性并提供当地培训和测序支持； (3) 利用旅行监控提供网络以外的信息作为模板 其他基因组监测系统； (4)开发新的登革热病毒基因分类系统 更轻松地识别关注/感兴趣的变异，并更好地利用基因组数据，而无需 复杂的系统发育分析； (5) 创建一个网络工具以方便访问变体分类 系统、详细的区域和县级分析、基因组数据和协议； (6) 详细 系统发育分析以揭示关键的流行病学过程，例如爆发出现间隔和 传播模式，以帮助预测未来的疾病。完成本提案中概述的目标 将极大地增进我们对登革热病毒多样性、进化和 流行病学。研究人员将能够利用这些数据和工具来促进创新 基于基因组学的控制策略。

项目成果

Dynamics of Eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States.

2019 年美国东北部爆发期间东部马脑炎病毒的动态。

• 发表时间: 2023-03-06
• 作者: Hill, Verity;Koch, Robert T;Bialosuknia, Sean M;Ngo, Kiet;Zink, Steven D;Koetzner, Cheri A;Maffei, Joseph G;Dupuis, Alan P;Backenson, P Bryon;Oliver, JoAnne;Bransfield, Angela B;Misencik, Michael J;Petruff, Tanya A;Shepard, John J;Warren, Jo
• 通讯作者: Warren, Jo

Toward a global virus genomic surveillance network.

建立全球病毒基因组监测网络。

• 发表时间: 2023-06-14
• 影响因子: 30.3
• 作者: Hill, Verity;Githinji, George;Vogels, Chantal B F;Bento, Ana I;Chaguza, Chrispin;Carrington, Christine V F;Grubaugh, Nathan D
• 通讯作者: Grubaugh, Nathan D