Color key to Delta and Omicron variants forms

May 2022

This key was last updated May 26, 2022.

Color key view 1 PDF

In view 1, a period (.) indicates any amino acid allowed in this position, a dash (-) is a deletion, and an underscore (_) specifically requires the ancestral amino acid. Positions numbers are written vertically, and all positions required to differentiate between common circulating forms of spike are included in the mini-alignment. In some cases, for example the Delta variant, there are two very common forms at two key positions T95I/T and G142D/G. Here we enable either form to be grouped with Delta, to include these common variants in our summaries; the actual most common form includes the mutations T95I and G142D, but a virus with the ancestral state in these positions will also be included in our tracking.

In view 2, the (-) represents a deletion.

Color key view 2 PDF

View 3 shows the full mutation string for the most common sequence that matches the pattern.

Color key view 3 PDF