Fig 1. RBD amplification.

A. Schematic of regions targeted by the RBD and S1 primer sets (see Methods for primer sequences). Overview of the SARS-COV-2 Spike RBD lineages identified in B. the MO33 sewershed and C. the MO45 sewershed. Each row represents a unique lineage and each column is an amino acid position in the Spike protein (left). Amino acid changes similar to (green boxes) or identical to (orange boxes) changes in Omicron (BA.1, BA.2 or BA.5) are indicated. Synonymous changes (syn) are indicated in gray. The major US VOCs (Alpha, Beta, Gamma, BA.1, BA.2, and BA.5) are indicated. The heatmap (right) illustrates lineage (row) detection by date (column), colored by the log₁₀ percent relative abundance of that lineage. Uncondensed output in S1 and S2 Data.