An Update on SARS-CoV-2 Diversity in the United States National Capital Region: Evolution of Novel and Variants of Concern.

Background SARS-CoV-2 Variants concerning for enhanced transmission, evasion of immune responses, or associated with severe disease have motivated the global increase in genomic surveillance. In this study, large scale whole genome sequencing was performed between November 2020 and end of March 2021 to provide a phylodynamic analysis of circulating variants over-time. In addition, we compared the viral genomic features of March 2020 and March 2021. Methods A total of 1,600 complete SARS-CoV-2 genomes were analyzed. Genomic analysis was associated with laboratory diagnostic volumes and positivity rates in addition to an analysis of the association of selected variants of concern/ interest with disease severity and outcomes. Our real-time surveillance features a cohort of specimens from patients who tested positive after the completion of vaccination. Results Our data showed genomic diversity over-time that was not limited to the Spike sequence. A significant increase in the B.1.1.7 lineage (alpha variant) in March 2021 as well as a transient circulation of regional variants that carried both the concerning S: E484K and S: P681H substitutions were noted. Lineage B.1.243 was significantly associated with ICU admission and mortality. Genomes recovered from fully-vaccinated individuals represented the predominant lineages circulating at specimen collection time, and those infections recovered with no hospitalizations. Conclusions Our results emphasize the importance of genomic surveillance coupled with laboratory, clinical, and metadata analysis for a better understanding of the dynamics of viral spread and evolution.