Failure of Automatic Updates to pango-consensus-sequences_summary.json (last occurred on 6/27/25)

[brandyn-west]

Hi,

It seems like the automatic updates of certain files (such as the pango-consensus-sequences_summary.json file) have stopped. Is this intentional, or will these files be updated again in the future? I find these very useful for downstream analyses.

Thanks!
Brandyn

[bioinforME]

I have been using pango-consensus-sequences_summary.json file for some lineage Sankey plot and would much appreciate if it could be maintained.

Thanks.
Chenwei

[brandyn-west]

Hi Cornelius,

I just want to flag that the pango-consensus-sequences_summary.json file last completed an automatic update on June 27th, 2025.

thanks,
Brandyn

[corneliusroemer]

Thanks for flagging @brandyn-west! I'll have a look!

[ryhisner]

Is there any update on this? As far as I can tell, this is the only place where information on consensus sequences for designated variants is available.

[ryhisner]

@corneliusroemer, just checking in again on this. This dataset has been invaluable to me, but now it's falling out of date. If it's not possible to update this, is there another document somewhere that contains the additional new mutations of each designated variant relative to its parent?

[AngieHinrichs]

is there another document somewhere that contains the additional new mutations of each designated variant relative to its parent?

https://github.com/cov-lineages/pango-designation/blob/master/lineage_notes.txt has some (but not all) mutations noted for Omicron lineages.

It's kind of an ugly document, but https://hgwdev.gi.ucsc.edu/~angie/pango.clade-mutations.tsv is the file used by the daily update process to maintain the annotation of Pango lineages on the big tree. If you squint at the ends of the very long lines then you can see which mutations are required, in addition to the parent's mutations, for each new lineage.

For example, these are the mutations used to find the branch for XFG.3 in the big UShER tree:

XFG.3	C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A >           A23063T > T22882G,C22995A,        C23525T > C10029T,G22578A,C22674T,T22679C,C22686T,G22813T,G22992A,        A23055G,T23075C,T23599G,A27259C,C27807T > C10449A,A18163G,C23854A,G23948T,A24424T,T24469A,C25000T,C25584T,C26270T,C26577G,G26709A,A28271T,C28311T > T670G,C2790T,G4184A,C4321T,C9344T,A9424G,C9534T,       C10198T,G10447A,C12880T,C15714T,C17410T,C19955T,A20055G,C21618T,T22200G,A22688G,G22775A,A22786C,C26060T,C26858T,G27382C,A27383T,T27384C,A29510C > A23040A,A23013A > T22917G > C22295A > A22556G,A22629C > C897A,G3431T,A7842G,C8293T,G8393A,G11042T,C12789T,T13339C,T15756A,A18492G,C21622T,G21624C,C21711T,G21941T,T22032C,C22033A,A22034G,C22208T,C22353A,G22577C,G22770A,G22895C,        G22898A,A22910G,C22916T,T22942A,T23005A,G23012A,T23018C,T23019C,G23222A,C23271T,C23423T,C23604G,C24378T,C24990T,C25207T,G26529C,A26610G,C26681T,C26833T,C28958A > A6183G,C12815T > G21770N > T3565C,G11727A,C18894T,T22926C > T27810C > T22928C > G22599C > G22132T > C5239T,C7869T,G12892A,T16600C,T21653C,A22107G,        T28297C > C8818T,C22792T,A22893G > C21627A > C29409T > T4214C,T8350C, T22896G ,A23021G,C23039G,C23277T > C13608T

That's basically XFG > C13608T. Here's the line for XFG.3.1:

XFG.3.1	C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A >           A23063T > T22882G,C22995A,        C23525T > C10029T,G22578A,C22674T,T22679C,C22686T,G22813T,G22992A,        A23055G,T23075C,T23599G,A27259C,C27807T > C10449A,A18163G,C23854A,G23948T,A24424T,T24469A,C25000T,C25584T,C26270T,C26577G,G26709A,A28271T,C28311T > T670G,C2790T,G4184A,C4321T,C9344T,A9424G,C9534T,       C10198T,G10447A,C12880T,C15714T,C17410T,C19955T,A20055G,C21618T,T22200G,A22688G,G22775A,A22786C,C26060T,C26858T,G27382C,A27383T,T27384C,A29510C > A23040A,A23013A > T22917G > C22295A > A22556G,A22629C > C897A,G3431T,A7842G,C8293T,G8393A,G11042T,C12789T,T13339C,T15756A,A18492G,C21622T,G21624C,C21711T,G21941T,T22032C,C22033A,A22034G,C22208T,C22353A,G22577C,G22770A,G22895C,        G22898A,A22910G,C22916T,T22942A,T23005A,G23012A,T23018C,T23019C,G23222A,C23271T,C23423T,C23604G,C24378T,C24990T,C25207T,G26529C,A26610G,C26681T,C26833T,C28958A > A6183G,C12815T > G21770N > T3565C,G11727A,C18894T,T22926C > T27810C > T22928C > G22599C > G22132T > C5239T,C7869T,G12892A,T16600C,T21653C,A22107G,        T28297C > C8818T,C22792T,A22893G > C21627A > C29409T > T4214C,T8350C, T22896G ,A23021G,C23039G,C23277T > C13608T > C6629T,A24813G > T17454N

That's XFG.3 plus C6629T,A24813G > T17454N. The N in T17454N means there may or may not be a mutation at 17454 on the path to XFG.3.1. At the time of designation, Cornelius mentioned only S:D1084G, ORF1a:L2122F in lineage_notes.txt, not the synonymous mutation at 17454. The order of mutations on the path can change as new sequences are added to the tree, so sometimes an unmentioned mutation is on the path at the time of the designation, but on some subsequent day it moves later in the path, and then we want to annotate the lineage upstream of it.

Here's the line for XFG.3.1.1:

XFG.3.1.1	C14408T > C241N > C3037T > A23403G > G28881A > G28883C > G28882A >           A23063T > T22882G,C22995A,        C23525T > C10029T,G22578A,C22674T,T22679C,C22686T,G22813T,G22992A,        A23055G,T23075C,T23599G,A27259C,C27807T > C10449A,A18163G,C23854A,G23948T,A24424T,T24469A,C25000T,C25584T,C26270T,C26577G,G26709A,A28271T,C28311T > T670G,C2790T,G4184A,C4321T,C9344T,A9424G,C9534T,       C10198T,G10447A,C12880T,C15714T,C17410T,C19955T,A20055G,C21618T,T22200G,A22688G,G22775A,A22786C,C26060T,C26858T,G27382C,A27383T,T27384C,A29510C > A23040A,A23013A > T22917G > C22295A > A22556G,A22629C > C897A,G3431T,A7842G,C8293T,G8393A,G11042T,C12789T,T13339C,T15756A,A18492G,C21622T,G21624C,C21711T,G21941T,T22032C,C22033A,A22034G,C22208T,C22353A,G22577C,G22770A,G22895C,        G22898A,A22910G,C22916T,T22942A,T23005A,G23012A,T23018C,T23019C,G23222A,C23271T,C23423T,C23604G,C24378T,C24990T,C25207T,G26529C,A26610G,C26681T,C26833T,C28958A > A6183G,C12815T > G21770N > T3565C,G11727A,C18894T,T22926C > T27810C > T22928C > G22599C > G22132T > C5239T,C7869T,G12892A,T16600C,T21653C,A22107G,        T28297C > C8818T,C22792T,A22893G > C21627A > C29409T > T4214C,T8350C, T22896G ,A23021G,C23039G,C23277T > C13608T > C6629T,A24813G > T17454C > C19979A

So it's XFG.3.1, including T17454C (which has remained on the path to XFG.3.1), plus C19979A.

[AngieHinrichs]

I should mention that pango.clade-mutations.tsv has some UShER-tree-specific warts: if a mutation from the Problematic Sites set is masked in the UShER tree then it won't appear in pango.clade-mutations.tsv, even though the sequences have that mutation. And if a reversion is masked on a specific branch of the UShER tree, then lineages that legitimately have that reversion (like recombinants) will have a mutation in pango.clade-mutations.tsv that they don't have in real life.

[ryhisner]

Thanks so much, @AngieHinrichs! I will see if I can find a way to recreate the info that used to be in pango-consensus-sequences_summary.json using that text file.

[ryhisner]

@corneliusroemer, just checking in one last time to see if there's any prospect of this JSON file being updated again. I've partially replaced it with @AngieHinrichs extremely useful Usher tree file, but there's another place where replacing it is going to take a very long time —at least a day, maybe several days, possibly a week of nonstop, grinding coding work. Hoping I can avoid that, but if this file is permanently defunct, I want to go ahead and get started on it.