JN.1+S:F456L with C22858T branch (37 seqs)

[DailyCovidCases]

From branch 64 of sars-cov-2-variants/lineage-proposals#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

[FedeGueli]

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

[Mydtlwn]

@corneliusroemer

[corneliusroemer]

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

[DailyCovidCases]

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]

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]

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 sars-cov-2-variants/lineage-proposals#1253 as well

[DailyCovidCases]

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

[FedeGueli]

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]

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]

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]

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

[DailyCovidCases]

Tracked in tracker64
Is it worth to be designated? @corneliusroemer

[DailyCovidCases]

Tree now:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_5c76_8f5940.json?f_userOrOld=uploaded%20sample

[FedeGueli]

Tree now: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_5c76_8f5940.json?f_userOrOld=uploaded%20sample

not monophyletic keep this closed please

[FedeGueli]

not monophyletic close this ( u can see in your CV Spectrum tracker that sequences caught by actual query have 493E or 183H pointing immediately to an uncorrect query)