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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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JN.1+S:F456L with C22858T branch (50 seqs, 8 countries) #2638

Open DailyCovidCases opened 4 weeks ago

DailyCovidCases commented 4 weeks ago

From branch 64 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253 JN.1+C22858T+S:F456L Query: C22858T,T22928C,C18894T,-7113 No. of seqs: 23 (South Korea 21 Japan 1 USA 1) First: EPI_ISL_19017513, 2024-2-27 Latest: EPI_ISL_19169455, 2024-5-9 usher Screenshot (102)

FedeGueli commented 4 weeks ago

This is interesting due the convergence with main KP.3 branch

Mydtlwn commented 4 weeks ago

@corneliusroemer

corneliusroemer commented 3 weeks ago

I'm not sure what exactly the proposal is. I see lots of KP.3. And not much else.

DailyCovidCases commented 3 weeks ago

I mean I can't find the exact query you are giving. I wonder if the query you are giving was wrong or not

corneliusroemer commented 3 weeks ago

I meant that from your Usher tree screenshot, I see mostly KP.3 and don't know which lineage you are proposing.

It's helpful to have a full 5000 sample subtree, you seem to be using a much smaller one?

DailyCovidCases commented 3 weeks ago

Yes! https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AF456L&nucMutations=C22858T&nextcladePangoLineage=JN.1& It said there were 0 seqs. I've proposed branch 86 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253 as well

DailyCovidCases commented 1 day ago

How can you find the correct query of this issue?. I used this website: nextclade It says there are 2285 sequences!

FedeGueli commented 1 day ago

How can you find the correct query of this issue?. I used this website: nextclade It says there are 2285 sequences!

You have to exclude KP.3.1 sequences: So you get the tree and then add a MINUS - for every branch not belonging to the proposed one.

About this one i would close the issue

DailyCovidCases commented 1 day ago

It says there are no sequences found: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AF456L&nucMutations=C22858T%2CT22928C%2CC18894T%2C7113-&nextcladePangoLineage=JN.1*&

FedeGueli commented 1 day ago

It says there are no sequences found: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AF456L&nucMutations=C22858T%2CT22928C%2CC18894T%2C7113-&nextcladePangoLineage=JN.1*&

that is for Gisaid . where when you search for -7113 it means all sequence with 7113 mutated well be excluded. while 71113 mean that there is. a deletion there (on covspectrum, on gisaid it would del7113)

On covspectrum to exclude one mutation you have to digit the WT nucleotide so in this case you have to digit 7113C

FedeGueli commented 1 day ago

examples of different writings deletion Covspectrum (C)7113- vs on Gisaid del7113 excluding a mutation : on Covspectrum 7113C vs on Gisaid -7113T Insertions: on covspectrrum ins_S:16:MPLF vs on gisaid Spike_ins16MPLF