Building next generation sequencing capacity at Wisconsin Veterinary Diagnostic Laboratory for diagnosis of COVID-19 (SARS-CoV-2 infection) in animals

威斯康星州兽医诊断实验室建设下一代测序能力，用于诊断动物中的 COVID-19（SARS-CoV-2 感染）

• 批准号: 10610665
• 负责人: Ailam Lee Lim
• 金额: $ 4.78万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-01 至 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10610665
• 关键词: Building; next; generation; sequencing; capacity

Project Abstract The goal of this proposal is to build viral whole genome sequencing capacity at the Wisconsin Veterinary Diagnostic Laboratory (WVDL) for sequencing of SARS‐CoV‐2 from animal samples. We are requesting funding for consumables, equipment, and personnel time to perform SARS‐CoV‐2 whole genome sequencing. We will purchase an IndiMag48S nucleic acids extraction platform, which is critical equipment for high‐quality samples preparation, and a nucleic acid workstation to use for library preparation. We will also purchase an Oxford Nanopore Flongle long read sequencing platform to provide cost effective capacity to sequence small sample caseloads without the need to batch samples. We will validate library preparation and sequencing protocols using published reagents in ARTIC protocol and a commercial NEBNext sequencing kit (New England BioLabs). A high computing power machine will be purchased to support the computation demand in bioinformatics analysis of the SARS‐ CoV‐2 sequencing data. We will develop and provide standard operating protocols and analysis programing to veterinary diagnostic personnel to maintain proficiency in sequencing and data analysis, and fast and economically efficient in SARS‐CoV‐2 genomic lineages determination. We will use these tools to train our staff and expand our capacity and capability to support diagnostic activities for the ongoing global SARS‐CoV‐2 pandemic. Additionally, this proposed work will indirectly improve WVDL's readiness for immediate impact and response during future animal and public health disease outbreaks.

项目摘要 该提案的目标是在威斯康星州建立病毒全基因组测序能力 兽医诊断实验室（WVDL）对动物样本中的SARS-CoV-2进行测序。我们 要求为消耗品、设备和人员时间提供资金，以执行SARS-CoV-2整体 基因组测序我们将购买一个IndiMag 48 S核酸提取平台，这是至关重要的 用于高质量样品制备的设备和用于文库的核酸工作站 准备.我们还将购买Oxford Nanopore Flongle长读测序平台， 提供具有成本效益的能力来对少量样品进行测序，而无需批量样品。 我们将使用ARTIC中已发表的试剂验证文库制备和测序方案 方案和商业NEBNext测序试剂盒（新英格兰BioLabs）。高计算能力 我们会购置计算机，以支援SARS的生物信息学分析的计算需求。 CoV-2测序数据。我们将开发和提供标准的操作协议和分析 为兽医诊断人员编程，以保持测序和数据分析的熟练程度， 并且在SARS-CoV-2基因组谱系测定中快速且经济有效。我们将会用这些 工具，以培训我们的工作人员，并扩大我们的能力和能力，以支持诊断活动， 全球SARS-CoV-2大流行此外，这项拟议的工作将间接改善WVDL的 在未来动物和公共卫生疾病期间，准备好立即影响和响应 爆发