CoV spike glycoprotein trimer
Spike glycoprotein variation occurring 100 times or less
Spike glycoprotein variation occurring greater than 100 times
lineage defining muts: aa changes found in >=10% of sequences in the lineage
Spike glycoprotein variation near host receptor, or other functional annotation
Insertion/deletion
Spike glycoprotein variation altering potential N-glycosylation sites
lineage emerging muts: aa changes found in <10% of sequences in the lineage that are also found in top 50 emerging constellations by Spread and top 20 emerging constellations by Acceleration (See emerging variant analysis for details)
GISAID automatically updates this site daily. The updates include spike protein changes in sequences submitted to GISAID with collection date within the past 60 days, displayed in structures organized by the fastest spreading lineages and color-coded for the change type including changes of the receptor binding interface.
Receptor binding interface changes are of particular interest because they could alter the virus’ receptor binding affinity and viral fitness. However, most receptor binding interface changes do not have such an effect and these changes may not be associated with increased clinical severity.
Because receptor binding interfaces are also common epitopes, receptor binding interface changes could also affect binding of some antibodies to the virus and, in rare cases, have the potential to affect vaccine response. Any claims of such an effect must be demonstrated experimentally.
In addition to the occurrences of changes listed in the main text, all emerging Spike amino acid changes found in the top 4 fast spreading lineages are reported in the table titled: "List of all emerging changes".
Strains with a specific Spike change can be retrieved from EpiCoV™ by typing the amino acid change in the “Variants” drop-down menu or by selecting one already displayed in the menu. For example, you may type "Spike_F486V" in the AA substitution menu to display strains with this change. Individual sequences can be analyzed with the CoVsurver at this link or by selecting them from the EpiCoV™ analysis interface.