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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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Multiple EG.5.1.1+S:Q14R branches (x - 81-45-29, total=904） #601

Closed xz-keg closed 10 months ago

xz-keg commented 1 year ago

I don't think a proper query can be made to exclude everything else, given the fact that new separate lineages are popping up from time to time.

image Proposal (edited by mod)

Branch 1 ( Proposed in https://github.com/cov-lineages/pango-designation/issues/2252) CLOSED EG.5.1.1+S:Q14R, X(about 500) seqs, A21603G,C25572T,T23018C,-29386

Branch 2 proposed in https://github.com/cov-lineages/pango-designation/issues/2387 Designated HK.3.13 HK.3+C14889T+S:Q14R , 61 Seqs A21603G,C6541T,T23018C, C14889T,, China,Singapore, USA image

Branch 3 proposed in https://github.com/cov-lineages/pango-designation/issues/2436 HK.13.1+S:Q14R, 81 seqs , 12/29 A21603G,C6541T,T23018C, A24604G, Hong Kong, Singapore, Hubei

Branch 4 HK.12+S:Q14R Orf1b:K2085E, 45 seqs , 12/29 A21603G,C6541T,T23018C, A22629C, China, Singapore, Australia

Branch 5 dead EG.5.1.1+Orf1a:T1589I+S:L455F+N:T24I+S:Q14R A21603G,C6541T,T23018C, C5031T, G22927T, 20 seqs, Canada

image

Branch 6 Designated HK.32 EG.5.1.1+Orf1a:S2193F+S:Q14R, 28 seqs, 12/03 A21603G,C6541T,T23018C, C6843T, China, Australia,Canada image

Other Branches

EG.5.1.1+Orf1a:V2116L+V121I,N:G19R,S:Q14R, 11 seqs A21603G,C6541T,T23018C, G6611T, China, Singapore, Ireland

EG.5.1.1+S:P1263L+Orf1a:E2070D,Q14R, 17 seqs A21603G,C6541T,T23018C, C25350T,Hubei

HK.13.2+S:Q14R, 38 seqs A21603G,C6541T,T23018C, T23953A, Hubei, Sichuan

EG.5.1.1+C21742T+S:Q14R, 13 seqs A21603G,C6541T,T23018C,C21742T, France, Australia, Peru， Belgium, UK

EG.5.1.1+A8443G+S:Q14R, 7 seqs A21603G,C6541T,T23018C, A8443G, Shanghai, Xinjiang

EG.5.1.1+Orf1b:I1539T+S:Q14R, 7 seqs A21603G,C6541T,T23018C, T18083C, Sichuan, Canada

An EG.5.1.1/BA.5 recombinant, 3 seqs A21603G,C6541T,T23018C, G1886C, Shanghai (this one has 405A so likely recomb with BA.5* on 5'-side)

xz-keg commented 1 year ago

+1 South Korea

FedeGueli commented 1 year ago

All the samples are very recent please propose it.

xz-keg commented 1 year ago

All the samples are very recent please propose it.

Sorry My bad. It seems that this one is quite convergent like S:L455F and has become various different lineages since my proposal. I'll change my title.

FedeGueli commented 1 year ago

Thank you @aviczhl2 very weird such a convergence! cc @ryhisner did u know anything on S:14 ?? Asking you cause i know you went deep on 9-13-16 mutations

xz-keg commented 1 year ago

Thank you @aviczhl2 very weird such a convergence! cc @ryhisner did u know anything on S:14 ?? Asking you cause i know you went deep on 9-13-16 mutations

Maybe due to the high population of China. If sth. appears at say 1/10^8 rate, it will happen 14 times in China but only 1 time in Japan.

ryhisner commented 1 year ago

Thank you @aviczhl2 very weird such a convergence! cc @ryhisner did u know anything on S:14 ?? Asking you cause i know you went deep on 9-13-16 mutations

I don't know what's going on with S:Q14. There have also been a ton of S:Q14H and S:Q14K mutations, so it seems to want to go to a positive charge there. No idea why that would be.

The S:14 mutation trend is driven almost entirely by China, so I feel pretty certain that the very different infection history has created a population immunity environment that strongly favors S:Q14 mutations.

image
FedeGueli commented 1 year ago

Thx @ryhisner

xz-keg commented 1 year ago

We get 9 more seqs in 2 days, 17+4+2*3+1*7 now.

FedeGueli commented 1 year ago

ok lets start to propose them once they reach 20. ok?

xz-keg commented 1 year ago

ok lets start to propose them once they reach 20. ok?

Is it better to give up the main branch and only treat those with at least one additional mutation other than S:Q14R as a separate lineage?

However I think the main branch at least needs a designation like HK.2 or HK.3.

FedeGueli commented 1 year ago

@aviczhl2 propose each of them separately when they reach 20 . so lets start with the main one.

xz-keg commented 1 year ago

It seems that branch 1 already reaches 25, but there may be more separate branches.

xz-keg commented 1 year ago

@FedeGueli EG.5.1.1 baseline: 22480T,19720A

There is a weird branch that cannot be queried by any GISAID queries.

We have 3 seqs of S:Q14R on a branch, with

22480C+19720A 22480C+19720G 22480T+19720G

image

FedeGueli commented 1 year ago

@FedeGueli EG.5.1.1 baseline: 22480T,19720A

There is a weird branch that cannot be queried by any GISAID queries.

We have 3 seqs of S:Q14R on a branch, with

22480C+19720A 22480C+19720G 22480T+19720G

image

Crazy! maybe @corneliusroemer @angiehinrichs could help?

xz-keg commented 1 year ago

Total of the whole is 44 now. I'm trying to clear up current branches.

ryhisner commented 1 year ago

@FedeGueli EG.5.1.1 baseline: 22480T,19720A

There is a weird branch that cannot be queried by any GISAID queries.

We have 3 seqs of S:Q14R on a branch, with

22480C+19720A 22480C+19720G 22480T+19720G

image

This is a branch with an alleged reversion at 22480 (T22480C). The Washington, USA, sequence has no coverage at 22480, so it almost certainly doesn't belong in this branch. Most likely, the entire T22480C "reversion" branch is an artifact. As usual with these sort of branches, it's full of C22480T "unreversions."

image

The Shanghai sequence and Hubei sequence clearly are related, but they probably have no connection whatsoever to any of the other sequences in this branch.

xz-keg commented 1 year ago

Thanks! So this shall be part of the main branch, so the main branch actually has 24 confirmed seqs.

xz-keg commented 1 year ago

Total 50 now. Will review this when total=100.

xz-keg commented 1 year ago

Total 65 now.

xz-keg commented 1 year ago

Total 79 now

xz-keg commented 1 year ago

Total=107 now. Shall start a second investigation on this.

xz-keg commented 1 year ago

@FedeGueli Total 25 branches now, the main branch 63 seqs with 55 on main branch and some others misplaced on other branches with artefact/flip-flop reversions.

FedeGueli commented 1 year ago

Crazy thank you for your work

xz-keg commented 1 year ago

Total=164 now

xz-keg commented 1 year ago

Total=185 now

xz-keg commented 1 year ago

Total=227 now

xz-keg commented 1 year ago

Analyse it again, the main branch has 113 seqs and there are a lot of new branches including an EG.5.1.1/BA.5 recomb now.

Total 41 branches.

current usher

FedeGueli commented 1 year ago

EG.5.1.1+S:L455F(G22927C)+C13378T,A24604G,S:Q14R, 4 seqs A21603G,C6541T,T23018C, A24604G, Hong Kong, Singapore, Hubei

this one is a subbranch of HK.13.1

FedeGueli commented 1 year ago

EG.5.1.1+S:L455F(G22927C)+S:F797L,D1153H,Q14R, 4 seqs A21603G,C6541T,T23018C, T23953A, Hubei, Sichuan

This is a subbranch of HK.13.2

FedeGueli commented 1 year ago

Betond the main branches they other doesnt seem growing especially fast.

FedeGueli commented 1 year ago

Closing it as completed.

FedeGueli commented 1 year ago

If any of this will get Flip or other mutations to restore their fitness please ping me i will reopen it.

Over-There-Is commented 11 months ago

HK.3>C14889T>S:Q14R C6541T, C14889T, A21603G is 57 now.

FedeGueli commented 11 months ago

A21603G,C6541T,T23018C, C14889T

éPlease propose it @aviczhl2

FedeGueli commented 11 months ago

These 3 lineages are the ones to watch and propose once 50 So i will shuffle the proposal putting them on the top. the rest is near dead, almost.

HK.13.1+S:Q14R, 42 seqs A21603G,C6541T,T23018C, A24604G, Hong Kong, Singapore, Hubei

EG.5.1.1+S:Q14R,K356T, Orf1b:K2085E, 36 seqs A21603G,C6541T,T23018C, A22629C, China, Singapore, Australia

HK.3+C14889T+S:Q14R A21603G,C6541T,T23018C, C14889T, 56 seqs, China,Singapore, USA

FedeGueli commented 11 months ago

I have updated and reorganized the issue to track it at the est for a while more. reopening.

FedeGueli commented 11 months ago

Branch 2 has a 15/20%prevalence in Henan China in November worth proposing it.

FedeGueli commented 11 months ago

Branch 2 has a 15/20%prevalence in Henan China in November worth proposing it.

already proposed : https://github.com/cov-lineages/pango-designation/issues/2387

xz-keg commented 11 months ago

Branch 6 designated HK.32.
Why start from branch 6?

xz-keg commented 11 months ago

Branch 2 designated HK.3.13

FedeGueli commented 11 months ago

HK.3.13 via https://github.com/cov-lineages/pango-designation/commit/b1f5bb0f8ac43fbf64a98b2af357bfe23d134614

FedeGueli commented 11 months ago

HK.32 via https://github.com/cov-lineages/pango-designation/commit/fde1fd9c60a1c3070815c89476c3af4cc9efc2f8

xz-keg commented 11 months ago

Branch 3 reaches 52.

FedeGueli commented 11 months ago

Branch 3 reaches 52.

let s see if some more recent samples will come , only 4 in November.

xz-keg commented 10 months ago

Branch 3 is 81 now.

ryhisner commented 10 months ago

A unique HK.3 popped up today in Henan, China with S:Q14R, S:C15R, and S:P479R. EPI_ISL_18700325 The S:S375F that appears in the Usher Tree is actually a synonymous mutation in the third nucleotide of S:V367 (C22663T). For reasons I've never quite understood, almost any mutation that occurs between ~365-377 is registered by Usher as an S:S375F reversion. @AngieHinrichs, do you know why this is?

image
FedeGueli commented 10 months ago

Branch 3 is 81 now.

Propose it please.

ryhisner commented 10 months ago

A second HK.3 sequence with S:Q14R, S:C15R, and S:P479R showed up today. Both collected on December 15 from Henan, China, but from different cities—Zhoukou and Xuchang. EPI_ISL_18700325, EPI_ISL_18703895

FedeGueli commented 10 months ago

A second HK.3 sequence with S:Q14R, S:C15R, and S:P479R showed up today. Both collected on December 15 from Henan, China, but from different cities—Zhoukou and Xuchang. EPI_ISL_18700325, EPI_ISL_18703895

better to propose it in a separate issue

FedeGueli commented 10 months ago

Thx for proposing Branch 3. I m closing this one. i suggest @aviczhl2 to monitor these two : HK.13.2+S:Q14R, 29 seqs A21603G,C6541T,T23018C, T23953A, Hubei, Sichuan

EG.5.1.1+C21742T+S:Q14R, 13 seqs A21603G,C6541T,T23018C,C21742T, France, Australia, Peru， Belgium, UK

Pleas ping if they keep on circulating.

@ryhisner i would monitor your S:C15R sublineage.