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

North Dakota State University, Fargo ND

Investigators

Abstract

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).