New EG.5.1.4 sublineage with S:V483I (England, 51 samples UK, as 20/10)

[FedeGueli]

thx to Dave McNally tool

i spotted a new very recent sublineage of EG.5.1.4 with a potential mutation of interest S:V483I

(EDITED)Looking at the new data coming from J.Bloom

Samples EPI_ISL_18216158, EPI_ISL_18216304, EPI_ISL_18216306, EPI_ISL_18227081, EPI_ISL_18227104, EPI_ISL_18227314, EPI_ISL_18227316, EPI_ISL_18227319-18227321, EPI_ISL_18227323-18227325, EPI_ISL_18227354, EPI_ISL_18227369, EPI_ISL_18227375, EPI_ISL_18227377-18227378

Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_11460_c8eb70.json?c=gt-S_483&label=id:node_6930888

Defining mutations: EG.5.1.4 >> Orf3a:P240L (C26111T) > T9115C > ORF1a:R1170H (G3774A), S:V483I ( G23009A)

Gisaid query: G23009A,G3774A

[aviczhl2]

It seems that this tool is based on covspectrum? So I guess it is easy to expand to global mutations?

[FedeGueli]

@aviczhl2 it is based on Climb uk database where the UK sequences are placed before they were ready (QC checks) to be uploaded to Gisaid. SO it is not reproducibile cause Gisaid doesnt allow direct unlimited access to their databases while instead releasing each 2-3-4 days an API then used by CovSpectrum or other scientists to do their analysis.
you can propose to enhance covspectrum with one more tool like this one on https://github.com/GenSpectrum/LAPIS/issues opening an issue there.

[aviczhl2]

while instead releasing each 2-3-4 days an API

How to access to such API? Maybe I can develop a tool myself(with 2-3-4 day delay).

[FedeGueli]

while instead releasing each 2-3-4 days an API

How to access to such API? Maybe I can develop a tool myself(with 2-3-4 day delay).

@corneliusroemer @tomwenseleers could you help?

[FedeGueli]

This jumped to 13 all ENgland none still on Gisaid: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_41aed_502fc0.json?c=gt-S_483&gmax=25384&gmin=21563&label=id:node_6938128

@corneliusroemer please take a look: From the new data by J.Bloom it seems quite advantageous to gain S:V4831I

There are 0 samples on Gisaid: England/CLIMB-CM7YGJSW/2023|2023-08-21 England/CLIMB-CM7YEI3F/2023|2023-08-19 England/CLIMB-CM7YJQA4/2023|2023-08-19 England/CLIMB-CM7YFWSI/2023|2023-08-21 England/CLIMB-CM7YKGGZ/2023|2023-08-24 England/CLIMB-CM7YKXEZ/2023|2023-08-24 England/CLIMB-CM7YGFKO/2023|2023-08-24 England/CLIMB-CM7YKOT9/2023|2023-08-23 England/CLIMB-CM7YENF8/2023|2023-08-23 England/CLIMB-CM7YJ9JM/2023|2023-08-23 England/CLIMB-CM7YFY64/2023|2023-08-23 England/CLIMB-CM7YF3NC/2023|2023-08-23 England/CLIMB-CM7YE4T4/2023|2023-08-23

[FedeGueli]

Sorry using Usher.dev i find already 18 of this sublineage, https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1b127_50a1d0.json?c=gt-S_483&gmax=25384&gmin=21563&label=id:node_6937949

[FedeGueli]

I ma transferring it to the main repo.

[FedeGueli]

Transferred to https://github.com/cov-lineages/pango-designation/issues/2254

[aviczhl2]

Sorry using Usher.dev i find already 18 of this sublineage, https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1b127_50a1d0.json?c=gt-S_483&gmax=25384&gmin=21563&label=id:node_6937949

What is usher.dev?

[FedeGueli]

Sorry using Usher.dev i find already 18 of this sublineage, https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1b127_50a1d0.json?c=gt-S_483&gmax=25384&gmin=21563&label=id:node_6937949

What is usher.dev?

https://genome-test.gi.ucsc.edu/cgi-bin/hgPhyloPlace

[aviczhl2]

What's the difference between usher.dev and main usher? More updated with seqs? Is the algorithm different?

[FedeGueli]

What's the difference between usher.dev and main usher? More updated with seqs? Is the algorithm different?

Usher dev shows sequences before the manual annotations the team of Usher does every evening (!!) so it precedes of just some hours Usher.bio not a big difference. but @angiehinrichs could answer better than me for sure ;)

[FedeGueli]

Refused from the main page i keep it monitored here.

The first 3 samples of the original proposal are on Gisaid now: EPI_ISL_18216158, EPI_ISL_18216304, EPI_ISL_18216306

[FedeGueli]

All the samples are now on Gisaid: EPI_ISL_18216158, EPI_ISL_18216304, EPI_ISL_18216306, EPI_ISL_18227081, EPI_ISL_18227104, EPI_ISL_18227314, EPI_ISL_18227316, EPI_ISL_18227319-18227321, EPI_ISL_18227323-18227325, EPI_ISL_18227354, EPI_ISL_18227369, EPI_ISL_18227375, EPI_ISL_18227377-18227378

[HynnSpylor]

24 seqs now and it rapidly increases in England I suggest to propose it in main page if reaches 30

[FedeGueli]

24 seqs now and it rapidly increases in England I suggest to propose it in main page if reaches 30

Thank you @HynnSpylor i already proposed it and was refused, i am waiting for samples outside Uk. Anyway i ping @corneliusroemer he could decide to review it earlier

[FedeGueli]

Still unsure if it could compete or not with Hk.3 but definetely not slow:https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=G23009A%2CG3774A&analysisMode=CompareToBaseline&

[FedeGueli]

Out competed : https://cov-spectrum.org/explore/United%20Kingdom/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=G23009A%2CG3774A&analysisMode=CompareToBaseline&