Rapid Lineage Assignment of Severe Acute Respiratory Syndrome coronavirus 2 Cases through Automated Library Preparation, Sequencing, and Bioinformatic Analysis

Andrew Gorzalski et al. February 6, 2023

The Journal of Molecular Diagnostics

Gorzalski A.J., Kerwin H., Verma S., Hess D.C., Sevinsky J., Libuit K., Vlasova-St. Louis I., Siao D., Siao L., Buñuel D., Van Hooser S. & Pandori M.W.


The coronavirus disease 2019 (COVID-19) pandemic has provided a stage to illustrate that there is considerable value in obtaining rapid, whole-genome–based information about pathogens. This article describes the utility of a commercially available, automated severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) library preparation, genome sequencing, and a bioinformatics analysis pipeline to provide rapid, near–real-time SARS-CoV-2 variant description. This study evaluated the turnaround time, accuracy, and other quality-related parameters obtained from commercially available automated sequencing instrumentation, from analysis of continuous clinical samples obtained from January 1, 2021, to October 6, 2021. This analysis included a base-by-base assessment of sequencing accuracy at every position in the SARS-CoV-2 chromosome using two commercially available methods. Mean turnaround time, from the receipt of a specimen for SARS-CoV-2 testing to the availability of the results, with lineage assignment, was <3 days. Accuracy of sequencing by one method was 100%, although certain sites on the genome were found repeatedly to have been sequenced with varying degrees of read error rate.

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