EG.5.1.1 branch with orf1a:T1589I (NSP3_T771I = PLPro_T26I )that acquired then S:L455F FLip lineage - 772samples ( as Nov 21)

[FedeGueli]

This has been found once it was two and then tracked in sars-cov-2-variants/lineage-proposals#525

Defining mutations
EG.5.1.1 >> C6541T > Orf1a:T1589I (C5031T = NSP3_T771I = PLPro_T26I ) > S:L455F (G22927T)

Gisaid query: G22927T,C5031T

Samples: 15 from China (5 regions) , South Korea, Japan, Singapore
First : Liaoning (CHN) 2023-06-27
Last: Singapore 2023-08-17
IDs_
EPI_ISL_18034950, EPI_ISL_18049761, EPI_ISL_18074983,
EPI_ISL_18105346, EPI_ISL_18111106, EPI_ISL_18111145-18111146,
EPI_ISL_18111217, EPI_ISL_18138028, EPI_ISL_18138071,
EPI_ISL_18138137, EPI_ISL_18140133, EPI_ISL_18140222,
EPI_ISL_18140936, EPI_ISL_18141106

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1b7f8_d2c1d0.json?c=userOrOld&label=id:node_6937495

Here the tracker for its growth advantage vs parental lineage: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=G22927T%2CC5031T&analysisMode=CompareToBaseline&

[Memorablea]

39a35ba ？

[xz-keg]

Orf1a:T4249I is only a subbranch of this.

[FedeGueli]

Orf1a:T4249I is only a subbranch of this.

Thank you very much i got sticked to the original issue cause the query caught already the whole lineage. Thank you for noticing now updated.

[FedeGueli]

39a35ba ？

No i dont think so, L455F is just highly homoplasic in EG.5.1.1 backbone like we saw 444N/460K last year for BA.5.2

[FedeGueli]

+1 Hubei

[FedeGueli]

• 3 Yunnan.

[FedeGueli]

3 Shanghai + 1 Denmark

[xz-keg]

38 seqs now.

Seems to break into 2 sub-branches but one sub-branch(C5144T) has only 1 non-455F seq so probably the two are still the same branch.

[FedeGueli]

Impressive international spread in the last ten days from 4 country all in Asia to 9 in 3 continents.

cc @corneliusroemer i suggest to designate this one

[FedeGueli]

38 seqs now.

Seems to break into 2 sub-branches but one sub-branch(C5144T) has only 1 non-455F seq so probably the two are still the same branch.

@AngieHinrichs could you take a look? this fast lineage seems broke in two separate branches by only one sequence!

[AngieHinrichs]

@AngieHinrichs could you take a look? this fast lineage seems broke in two separate branches by only one sequence!

Yes! That is one of the few branches where I was not so sure (when looking at all the many EG.5.1 branches with G22927T for sars-cov-2-variants/lineage-proposals#537), so I will prune that one sequence (Tianjn/TJCDC0630-17/2023|EPI_ISL_17956695|2023-06-16), re-opt, re-place & see what happens in the 2023-09-07 build.

[FedeGueli]

@AngieHinrichs could you take a look? this fast lineage seems broke in two separate branches by only one sequence!

Yes! That is one of the few branches where I was not so sure (when looking at all the many EG.5.1 branches with G22927T for sars-cov-2-variants/lineage-proposals#537), so I will prune that one sequence (Tianjn/TJCDC0630-17/2023|EPI_ISL_17956695|2023-06-16), re-opt, re-place & see what happens in the 2023-09-07 build.

Thank you!

[xz-keg]

47 seqs now and today's usher re-assigns them into one branch.

[FedeGueli]

New batch from Singapore , and more from China

[xz-keg]

53 now.

[FedeGueli]

53 yunnan

[xz-keg]

There is also a HV.1+Orf1a:T1589I branch, sars-cov-2-variants/lineage-proposals#802, I guess the mutation itself has some meaning under EG.5.1 backbone, suggest to designate EG.5.1.1+Orf1a:T1589I as HK.* and the S:L455F branch as HK.*.1

[xz-keg]

BTW this one has 74 seqs now.

[FedeGueli]

Doubling slower than Hk.3 still close to 200 (196)

[FedeGueli]

it is now over 200 and starting accumulating further Spike mutations as S:14 or S:256.
it is also globally spread:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_36695_d30970.json?c=country&label=id:node_3637690
The shape of the tree suggests it have had sustained circulation in the country where it emerged.

@corneliusroemer i think it is ready to be designated.

[FedeGueli]

It now reaches 1% in Singapore and it is the third EG.5.1+FLip in Uk after HK.3 JG.3 and another hk.3 like branch

[xz-keg]

329 now.

[FedeGueli]

@corneliusroemer this is quite big, not the fastest of the bunch but stil relevant,

[FedeGueli]

411 too big to leave it undesignated @corneliusroemer

[FedeGueli]

463

[xz-keg]

613 seqs now.

[FedeGueli]

613 seqs now.

+1 Japan. @corneliusroemer i would designate this one.

[FedeGueli]

667 now

[FedeGueli]

772 as today cc @corneliusroemer despite not being fast it is big enough to be designated without regrets i think.

[xz-keg]

772 as today cc @corneliusroemer despite not being fast it is big enough to be designated without regrets i think.

Not the fastest but definitely much faster than what it is now being called. (EG.5.1.1)

[xz-keg]

875 now

[Memorablea]

Congratulations! Designated as HK.27 and HK.27.1!9c45579