Sequencing of MA viruses. (A) Amino acid changes and deletions (∆) in MA1, MA2, MA3, MA4, and MA5 (full dataset in Supplementary Dataset 1). Amino acid changes that only appear in one MA virus are in red, with other colors used to show amino acid changes common between at least two MA viruses. (B) Amino acids changes and deletions in any of the MA viruses as shown on the structure of SARS-CoV-2QLD02 spike bound to hACE2 (PDB: 7DF4). Underlining indicates the non-conservative amino changes. (C) Spike changes in the MA viruses. *—amino acid changes located within the RBD. Underlining indicates the non-conservative amino acid changes. GISAID n—number of GISAID submissions that contain this change; GISAID %—percentage of all GISAID submissions with this change. Alpha, Beta, Gamma, Delta, and Omicron: black text—hallmark changes in variants of concern; gray text—not a hallmark change in variants of concern. Match of amino acid changes in MA viruses with hallmark changes in variants of concern (green—exact match, blue—conservative, and brown—non-conservative change).