Figure 1. Prevalence of E484K-harboring SARS-CoV-2 and B.1.526.

(a) Detection of viruses with key signature mutations in spike over time. The earliest detected E484K-harboring variant was collected in mid-November 2020. The prevalence of E484K (samples with E484K/total PCR-genotyped samples) subsequently increased over time, from 4.8% in early December 2020 up to 24.3% in early March 2021. Throughout late 2020 and early 2021, we identified fewer N501Y-than E484K-harboring isolates, with a maximum of 5.9% of N501Y during mid-February 2021. (b) Distribution of different viral lineages identified by whole genome sequencing. Within our genomic collection (n=1,507), the B.1.526 lineage rose rapidly in early 2021, replacing the majority of other lineages (shown as the white blank space) present during this timeframe. This was followed by a steady rise in B.1.1.7 by mid-2021. The marking below the X axis denotes the time-period used to calculate the growth advantage of B.1.526 over other earlier viruses. (c) Phylogenetic tree of SARS-CoV-2 variants identified by sequencing and alignment of key spike mutations. Unique patterns of spike protein mutations present in genomes sequenced from our hospital center with at least one mutation of interest or concern (E484K, N501Y, S477N, or L452R; n=64) are shown. Residues at which at least one sample harbored a mutation are displayed above the S-protein schematic.