emmahodcroft
commented
1 year ago Hi Amanda @a-qvecell - I'm so sorry about this confusion! You're right, this isn't very clear. In general, I always list mutations relative to ancestral (Wuhan). However, sometimes I try to convey more information (for better or worse). For example, here in 22E this is a reversion from the S:Q493R that happened in ancestor 21L.
What made this doubly confusing is that usually I try to ensure on the variant page anything like this is explained a bit, but for 22E this is completely missing. I'll add to the text so that this is explained for those who look for it, but I recognise that it's still a bit confusing. I'm not sure the best way to handle this going forward - I'll try to have a think about whether there's a better way to convey this information!
Thanks for alerting us that it's not clarified anywhere, though - at least I can try to make it more clear on the variant page!
Best, Emma
a-qvecell
Hello :) Thank you for a really useful page! I am a little confused as to how to interpret the mutations on spike position 493 as they are listed here: https://covariants.org/shared-mutations Here, we see both S:Q493R, S:Q493Q and S:R493Q. My intuition regarding the table is that the first amino acid mentioned for each mutation would be Wuhan-hu-1, here Q, changed to R in e.g. Omicron BA.1. When I then read S:Q493Q, I imagine that this mutation must have reverted but in another position in the codon. But when I then see S:R493Q, I start thinking if all initial positions are relative to the variant that the clade in question arises from.
I hope you can help me understand the table - thank you in advance :) Best, Amanda