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

项目摘要 这项提议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。我们是 为执行SARS-CoV-2整体所需的消耗品、设备和人员时间申请资金 基因组测序。我们将购买一个IndiMag48S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图书馆的核酸工作站 准备工作。我们还将购买牛津纳米孔长阅读测序平台，以 提供具有成本效益的能力来对小样本工作量进行排序，而无需对样本进行批量处理。 我们将使用ARTIC中发表的试剂来验证文库准备和测序协议 协议和商业NEBNext测序试剂盒(新英格兰生物实验室)。强大的计算能力 将购买机器以支持SARS生物信息学分析的计算需求- 冠状病毒2型测序数据。我们将开发并提供标准操作协议和分析 对兽医诊断人员进行编程，以保持对测序和数据分析的熟练程度， 在SARS-CoV-2基因组谱系测定中快速、经济高效。我们将使用这些 培训我们的员工并扩展我们的能力和能力以支持诊断活动的工具 正在进行的全球SARS-CoV-2大流行。此外，这项拟议的工作将间接改善WVDL的 对未来动物和公共卫生疾病的即时影响和反应做好准备 疫情爆发。

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.