Correct defining mutations for 21K/B.1.1529/omicron

[Jeppingr]

according to this link: https://github.com/cov-lineages/pango-designation/issues/343 the following corrections should be made: G142D instead of G142- Y145- instead of Y145D L212I missing

I did not check original sequences, im only referring to the data available from that link!

[emmahodcroft]

Dear @Jeppingr - thanks so much for looking into this! The 142-145 deletion & mutation can be shifted back and forth, so that it's either ---D or D--- - depending on how you align the mutations. I follow the convention of Nextstrain & Nextclade to ensure that what visitors see on the page is the same as if they view the builds.

However, you're right that I was missing the L212I! Thank you so much - I'm putting this in now!

[Jeppingr]

Welcome!

You are right of corse, on the amino acid level it does not matter if the D is before or after the deletion, however on the nucleotide level it does. Where did the mutation take place, at the former G142 codon (typically a one nucleotide shift A->G) or in the former Y145 codon (a 2-3 nucleotide mutation)? The G142D seems to make more sense to me. That is also reflected here: https://outbreak.info/compare-lineages?pango=B.1.1.529&gene=S&threshold=0.2; https://outbreak.info/situation-reports?pango=B.1.1.529

By the way, thank you so much for your maintaining the COVariants web page, a great resource.

Kind regards, Jörg Eppinger

On 2. Dec 2021, at 14:46, Emma Hodcroft @.**@.>> wrote:

Dear @Jeppingrhttps://urldefense.com/v3/__https://github.com/Jeppingr__;!!Nmw4Hv0!iAn_NVWHQTTmLJPBGMphldU1X5hs5XPwWt9H29QKlo7tol1DVBZb75Q7ILXfPer60V--w3w$ - thanks so much for looking into this! The 142-145 deletion & mutation can be shifted back and forth, so that it's either ---D or D--- - depending on how you align the mutations. I follow the convention of Nextstrain & Nextclade to ensure that what visitors see on the page is the same as if they view the builds.

However, you're right that I was missing the L212I! Thank you so much - I'm putting this in now!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/hodcroftlab/covariants/issues/227*issuecomment-984641623__;Iw!!Nmw4Hv0!iAn_NVWHQTTmLJPBGMphldU1X5hs5XPwWt9H29QKlo7tol1DVBZb75Q7ILXfPer66pxrHJU$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AWVSIVMO2GJR652ZJU4XKQDUO52CNANCNFSM5I3HTP4A__;!!Nmw4Hv0!iAn_NVWHQTTmLJPBGMphldU1X5hs5XPwWt9H29QKlo7tol1DVBZb75Q7ILXfPer6YvEf4gE$. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.com/v3/__https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675__;!!Nmw4Hv0!iAn_NVWHQTTmLJPBGMphldU1X5hs5XPwWt9H29QKlo7tol1DVBZb75Q7ILXfPer6HNOE6UA$ or Androidhttps://urldefense.com/v3/__https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign*3Dnotification-email*26utm_medium*3Demail*26utm_source*3Dgithub__;JSUlJSU!!Nmw4Hv0!iAn_NVWHQTTmLJPBGMphldU1X5hs5XPwWt9H29QKlo7tol1DVBZb75Q7ILXfPer6H_oY5Bg$.

[emmahodcroft]

Hi @Jeppingr - you're right, it is of some interest on a nucleotide level, but mostly we don't particularly know this, and how the deletions get aligned is a matter of what convention is being followed. At CoVariants I follow the alignment conventions of Nextclade/Nextstrain - so that if one clicks to a focal build and looks for the sites there, you'd use the same numbering and get the same results - but others follow other conventions. I'm glad to add a note to clarify this though, as it's definitely a point of confusion, and I've had a few emails about it! Do you have a twitter I can tag to credit you? Best, Emma

[Jeppingr]

Hi Emma,

thanks, too kind. My twitter is @Jeppinger - never use it. Again, I am really grateful for the work that you put into the NextStrain project, has helped me a lot to stay on top of developments. I am supporting two vaccine developers with their decision on target sequences, and while I cross-check what I find on NestStrain, it safes me a lot of work. I guess, omicron is the first variant to mandate a new vaccine, but time will tell.

Best, Jörg

On 2. Dec 2021, at 15:12, Emma Hodcroft @.**@.>> wrote:

Hi @Jeppingrhttps://urldefense.com/v3/__https://github.com/Jeppingr__;!!Nmw4Hv0!jUip2dhMGC3GaMotFLtKM-xNX-mz1mGk-mBr2JXTw7W7NP-KDBt735n8x9Pn6-88NI2vBuU$ - you're right, it is of some interest on a nucleotide level, but mostly we don't particularly know this, and how the deletions get aligned is a matter of what convention is being followed. At CoVariants I follow the alignment conventions of Nextclade/Nextstrain - so that if one clicks to a focal build and looks for the sites there, you'd use the same numbering and get the same results - but others follow other conventions. I'm glad to add a note to clarify this though, as it's definitely a point of confusion, and I've had a few emails about it! Do you have a twitter I can tag to credit you? Best, Emma

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