JE.1.1+S:V1122A+Orf1a:R135S(rev), N:13F (71 seqs, 15 countries, 30 with S:E554K, 1.3% Singapore)

[xz-keg]

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1116

Finds this interesting branch with interesting mutations(1 reversion Orf1a:R135S and 1 2-nuc mutation N:13 P->L->F) and good growth advantage, while also from travelers of multiple undersampled regions.

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nextcladePangoLineage=JE.1.1*&nucMutations1=670T&nextcladePangoLineage1=JE.1.1*&analysisMode=CompareToBaseline&

JE.1.1+T24927C(S:V1122A)+G670T(Orf1a:R135S rev), C28310T(N:L13F)

GISAID query: T24927C, C28310T No. of seqs: 28(Australia 5 Canada 1 Denmark 1 UK 2 France 7 Japan 1 Singapore 5(2 from Phillipines) Spain 1 USA 5(1 from Qatar 1 from Phillipines 1 from Hong Kong) Belgium 1, Taiwan 1( from Philippines) )

4 samples from Phillipine travelers sampled in different countries.

This branch is also the largest branch apart from BA.2.86* and Flip (both at ~45%) in the recent Singapore upload.

First: EPI_ISL_18278964, 2023-8-10, Singapore. Latest: EPI_ISL_18544824, 2023-11-21,Singapore

GISAID query for S:E554K branch: C28310T,T24927C,G23222A(8 seqs)

usher

[FedeGueli]

This went to 37 and 9 for the E554K sublineage: Yesterday upload : 4 France 3 Singapore 2 Usa 1 Belgium 1 South Australia all collected after Oct 30

quite impressive

Ping @corneliusroemer i suggest a rapid designation of this one.

[xz-keg]

This went to 37 and 9 for the E554K sublineage: Yesterday upload : 4 France 3 Singapore 2 Usa 1 Belgium 1 South Australia all collected after Oct 30

quite impressive

Ping @corneliusroemer i suggest a rapid designation of this one.

Yeah it went from 26 to 37 in 1 day, 4 to 9 for the S:E554K branch.

[FedeGueli]

40 now Thailand, France , Canada

[FedeGueli]

51 now. it seems one of the fastest behind JN.1 @corneliusroemer i suggest to designate it.

[xz-keg]

also new country of Curacao.

[FedeGueli]

54 one sample from Japan via Taiwan, @corneliusroemer suggesting a designation of this one one of the most different spikes with fitness circulating.

[xz-keg]

9/685 in Singapore seqs from 2023-11-29. It seems expanding despite JN.1 already dominated. All from the S:E554K branch.

[FedeGueli]

T24927C, C28310T

1% after November 25 in Singapore

@corneliusroemer this should be designated soon.

[FedeGueli]

82 now. + 4 today in the upload from Philippines it represents 7/39 related to Philippines in November:

New tree seems very intersting with further spike diveristy: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_36373_2b5620.json?c=userOrOld&label=id:node_4028655 In red recent samples related to Philippines.

@corneliusroemer i suggest a fast designation of this one.

[FedeGueli]

Thx @corneliusroemer