Rapid Lineage Assignment of SARS-CoV-2 Cases Through Automated Library Preparation, Sequencing and Bioinformatic Analysis.

The COVID-19 pandemic has provided a stage to illustrate that there is considerable value in obtaining rapid, whole genomic information about pathogens. Herein we describe the utility of a commercially available, automated SARS-CoV-2 library preparation, genomic sequencing and a bioinformatic analysis pipeline to provide rapid, near- "real-time" SARS-CoV-2 variant description. We evaluated the turnaround time, accuracy and other quality parameters obtained from Clear Labs Dx automated sequencing instrumentation from analysis of continuous clinical samples from January 1, 2021 to October 6, 2021. This includes a base-by-base assessment of sequencing accuracy at every position in the SARS-CoV-2 chromosome for both Illumina and Oxford Nanopore-based methods. Turnaround time from reception of specimen for SARS-CoV-2 testing, to result, with lineage assignment was less than 3 days. Accuracy of sequencing by the Clear Labs Dx was found to be 100%, though certain sites in the genome were found repeatedly to be sequenced with varying degrees of read error rate.