Tracking the prevalence and emergence of SARS-CoV-2 variants of concern using a regional genomic surveillance program

SARS-CoV-2 molecular testing coupled with whole-genome sequencing is instrumental for real-time genomic surveillance. Genomic surveillance is critical for monitoring the spread of variants of concern (VOCs) as well as discovery of novel variants. Since the beginning of the pandemic, millions of SARS-CoV-2 genomes have been deposited into public sequence databases. This is the result of effortsof both national and regional diagnostic laboratories. In this study, we describe the results of SARS-CoV-2 genomic surveillance from February 2021 to June 2022 at a metropolitan hospital in the United States. We demonstrate that consistent daily sampling is sufficientto track the regional prevalence and emergence of VOCs and recapitulate national trends. Similar sampling effortsshould be considered a viable option for local SARS-CoV-2 genomic surveillance at other regional laboratories.