Emergence of a Novel SARS-CoV-2 Variant in Southern California

Abstract

This research describes findings of sequencing and phylogenetic analyses of SARS-CoV-2 isolates from symptomatic patients cared for at Cedar-Sinai Medical Center in November-December 2020 during a regional surge in cases and hospitalizations.

Figure 1.. Phylogenetic Relationship of CSMC Samples to Global SARS-CoV-2 Genomes

Phylogenetic tree of 185 Cedars-Sinai Medical Center (CSMC) SARS-CoV-2 isolates and a global subsampling of 1480 isolates collected from December 2019 to January 2021 reveals a novel subcluster within 20C that share 5 mutations (ORF1a: I4205V, ORF1b: D1183Y, S: S13I; W152C; L452R), designated as CAL.20C (20C/S.452R). The phylogenetic tree shows the relationship of CAL.20C to other circulating lineages. The branch length (x-axis) reflects numbers of mutations accumulated before being discovered, and clades are designated based on Nextstrain nomenclature. The UK variant (501Y.V1), South African variant (501Y.V2), and Brazil variant (501Y.V3) are shown.

Figure 2.. Timeline for the Emergence of a Novel Southern California Variant, CAL.20C, Among All SARS-CoV-2 Circulating Variants Observed

Diagrammatic representation of circulating SARS-CoV-2 variant frequencies. A, Includes 10 431 samples from the state of California. B, Includes 4829 samples from Southern California.