Barriers have existed to having sequence and phylogenetic information concurrent to the investigational process: Sequencing itself is a laboratory process of significant complexity that can require extensive hands-on time, followed by lengthy sequencing processes. In epidemiology-based investigations, discrepancies at the level of single-nucleotide polymorphisms can provide powerful intelligence in the determination of the relatedness (phylogenetics) of cases. Genome sequencing of infectious agents provides data that describe organisms at the single-nucleotide polymorphic matrix, the highest level of discriminatory capability. 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. 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. 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. ![]() ![]() ![]() 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 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. 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.
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