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Repository for suggesting new lineages that should be added to the current scheme
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FL.4.5 (XBB.1.9.1.4.5) sublineage with S:G181E (52 seqs mainly in Singapore) #2054

Open HynnSpylor opened 1 year ago

HynnSpylor commented 1 year ago

Defining mutations: FL.4>A28615G>C23635T>C28903T (ORF8:S67F, despite ORF8 has stopped before the codon)>A3948G (ORF1a: D1228G)>G22104A (S:G181E) GISAID query: Spike_G181E, C11956T, A3948G, G5720A Earliest seq: 2023-04-05 (Singapore, EPI_ISL_17496323) Most recent seq: 2023-05-27 (USA, EPI_ISL_17789896) Countries detected: Singapore (26), USA (2), China (1), Thailand (1), Netherlands (1)

Usher Tree: QQ截图20230613123404

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_bb6_7e8b30.json?c=gt-S_181 Description: A sublineage which has undergone a long evolution. S:181 site has several mutation choice (G181A, G181V, G181R, etc.), and emerged in many former lineages. This sublineage is likely originated in Singapore, and now has 5 seqs outside Singapore. S:G181E may not be the most popular choice, but we can still monitor it for a time.

Genomes: EPI_ISL_17496323, EPI_ISL_17539600, EPI_ISL_17539695, EPI_ISL_17539799, EPI_ISL_17539956, EPI_ISL_17596091, EPI_ISL_17596169, EPI_ISL_17602916, EPI_ISL_17631329, EPI_ISL_17631337, EPI_ISL_17631462, EPI_ISL_17631504, EPI_ISL_17631554, EPI_ISL_17670255, EPI_ISL_17694869, EPI_ISL_17694897, EPI_ISL_17695029, EPI_ISL_17724766, EPI_ISL_17724773, EPI_ISL_17724776-17724777, EPI_ISL_17724782, EPI_ISL_17724784, EPI_ISL_17724787, EPI_ISL_17724791, EPI_ISL_17724794, EPI_ISL_17724798, EPI_ISL_17725187, EPI_ISL_17768143, EPI_ISL_17787361, EPI_ISL_17789896,

FedeGueli commented 1 year ago

46 now and expanding in the area , in Singapore when cutting for very recent samples it represents already an 1% there.

@corneliusroemer @AngieHinrichs @InfrPopGen

HynnSpylor commented 1 year ago

Now 46 seqs and detected in Australia

there are two branches with S:S673T->S:P426S / S:D215G (recently popular in FK.1) 46582F53-553C-40C9-89A8-F362A3CBACA7

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_27ca5_816300.json

FedeGueli commented 1 year ago

My query (G22104A, C11956T, A3948G, ) finds now 49

HynnSpylor commented 1 year ago

Now its parent lineage is desingated as FL.4.5

FedeGueli commented 1 year ago

One sample only from July i think it could be closed without many doubts.

FedeGueli commented 1 year ago

ops Pango. so take this as suggestion.

DailyCovidCases commented 2 months ago

It seems that this branch has stopped growing. You should close this.