Implementation of a liquid handler that can increase capacity of SARS-CoV-2 sequencing in animals with COVID-19.

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SUMMARY The overall goal of this project is to purchase equipment that will increase capacity and speed up the library prep workflow and whole genome sequencing of the SARS-CoV-2 virus in companion animals by implementing an automated library prep process (NEBNext® ARTIC SARS-CoV-2 Companion Kit with ARTIC primers) and adding higher computing capabilities. Automating the library prep process with an affordable and versatile Opentron OT-2 liquid handling robot, in a one-way sequencing workflow, will benefit the laboratory by increasing throughput; improving sample consistency; minimizing contamination; freeing up hands-on time; reducing technician strain and fatigue; and minimize tech errors. Installation of a high-end computer workstation dedicated to sequencing and bioinformatics will significantly speed up the basecalling process and SARS-CoV-2 strain identification. This equipment proposal has three specific aims. 1) Purchase and install an Opentron OT-2 liquid handling robot in the new NDSU-VDL Sequencing Laboratory Section to maintain a one-way next-generation sequencing (NGS) workflow that will minimize contamination. The NDSU-VDL is familiar with the operation of OT-2 robots and hands-on library preparation. 2) Write a custom protocol in Python script for the OT-2 robot to automate the library prep steps for the NEBNext ARTIC SARS-CoV-2 Companion Kit for Oxford Nanopore Technologies (MinION) sequencers. The script will be made freely available to OT-2 users through protocol.io and/or github. 3) Purchase and install a high-end computer workstation to run MinION sequencers, complete basecalling, and for downstream bioinformatic analyses on SARS-CoV-2 companion animal samples (i.e. feline and canine respiratory swabs).