Update lineage_notes.txt

[NkRMnZr]

FL*/EG* corrections; replace further mutations like T478R or K478R to unified/most common 478R

[AngieHinrichs]

Thanks for the corrections. Is there consensus from the group about removing the "from" allele (like T or K in T478R or K478R) and keeping only the "to" allele (R)? I guess missing information can't be incorrect, but sometimes it is interesting to keep track of multiple successive changes. @corneliusroemer @FedeGueli @aviczhl2 @ciscorucinski @Over-There-Is @HynnSpylor @Memorablea ?

[FedeGueli]

Thanks for the corrections. Is there consensus from the group about removing the "from" allele (like T or K in T478R or K478R) and keeping only the "to" allele (R)? I guess missing information can't be incorrect, but sometimes it is interesting to keep track of multiple successive changes. @corneliusroemer @FedeGueli @aviczhl2 @ciscorucinski @Over-There-Is @HynnSpylor @Memorablea ?

I prefer always wild type to actual mutation as S:G339 S:V445A it leaves without doubt. I spoke with Ryan many months ago but we didnt end with a way or another.

[NkRMnZr]

I think this should be related/addition to the Lineage Notes Standardization PR #2283 to keep multi-step mutations well informed and in a unified manner.

There are a few options:

• Keep it strict to Lineage B/wildtype reference, eg. S:T478R (✔️fits most places with a query ❌ does not show the mutation history)
• Keep it to nearest phylogenetic ancestor as reference, eg. S:K478R (✔️ shows part of the mutation history ❌ does not fit query on certain places like GISAID; causing confusions especially multi-step mutations)
• Using what is most common in lineage_notes, which omitted the original aa, eg. S:478R (✔️ most clear without any confusions ❌ does not fit query; does not show the mutation history)
• Or, any other way that can satisfy both criteria: showing the AA changes/transitions while CTRL+F searchable (ie. if writing it as S:T478K>R which shows the 2-step mutations from WT to Omicron then to certain XBB lineages, however it does not seem to be search-friendly to 478R)

I had a chat with @HynnSpylor on this topic on another PR before ( #2139 , obsoleted so retracted) and I have no problem with it then, but now we are having lineages like sars-cov-2-variants/lineage-proposals#961 and potentially even more with multi-step mutations in the future, so maybe it's time to regulate it to a proper format.

[Memorablea]

I think this should be related/addition to the Lineage Notes Standardization PR #2283 to keep multi-step mutations well informed and in a unified manner.

There are a few options:

• Keep it strict to reference, eg. (✔️fits most places with a query ❌ does not show the mutation history)Lineage B/wildtype``S:T478R
• Keep it to nearest phylogenetic ancestor as reference, eg. (✔️ shows part of the mutation history ❌ does not fit query on certain places like GISAID; causing confusions especially multi-step mutations)S:K478R
• Using what is most common in lineage_notes, which omitted the original aa, eg. (✔️ most clear without any confusions ❌ does not fit query; does not show the mutation history)S:478R
• Or, any other way that can satisfy both criteria: showing the AA changes/transitions while searchable (ie. if writing it as which shows the 2-step mutations from WT to Omicron then to certain XBB lineages, however it does not seem to be search-friendly to CTRL+F``S:T478K>R``478R)

I had a chat with @HynnSpylor on this topic on another PR before ( #2139 , obsoleted so retracted) and I have no problem with it then, but now we are having lineages like sars-cov-2-variants/lineage-proposals#961 and potentially even more with multi-step mutations in the future, so maybe it's time to regulate it to a proper format.

agree

[HynnSpylor]

Sorry for a late reply!
Now I support the WT-latest mutation (e.g. S:T478R for XBB.1.16*, E484K for BA.2.86*) for the formal usage (used in the defining of a lineage). The "intermediate" mutation (like S:K478R) can be used for preliminary discussion, or some detail description (with the previous mutations or the whole pathway)