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

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.