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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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GN.1 (XBB.1.5.73.1) with ORF1a:A2345V (nsp3_A1527V) and S:L455W (23 seqs, Spain, Peru) #1021

Closed NkRMnZr closed 9 months ago

NkRMnZr commented 1 year ago

Defining Mutations: GN.1 > C7299T(ORF1a:A2345V) > T682C > T22926G(S:L455W) Query: T682C, C7299T, T22926G Earliest seq: 2023-09-20 (EPI_ISL_18437542, Lima, Peru) Latest seq: 2023-09-27 (EPI_ISL_18392020, Badajoz, Spain) Sampled Countries: Peru (1), Spain (1)

Genomes: `EPI_ISL_18392020, EPI_ISL_18437542`

UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_4f700_b45380.json?label=id:node_3574499 image

ryhisner commented 1 year ago

I think there are actually 16 sequences in this lineage with S:L455W. Ten of them also have S:H49L.

image

EPI_ISL_18392020, EPI_ISL_18437542, EPI_ISL_18440190, EPI_ISL_18440194, EPI_ISL_18440201, EPI_ISL_18440206, EPI_ISL_18440212, EPI_ISL_18440215, EPI_ISL_18440218, EPI_ISL_18440220-18440223, EPI_ISL_18440226, EPI_ISL_18440248,

NkRMnZr commented 1 year ago

Wow I'm pretty sure when I started this proposal there were only 2 sequences. Thanks for the update @ryhisner

FedeGueli commented 1 year ago

Wow I'm pretty sure when I started this proposal there were only 2 sequences. Thanks for the update @ryhisner

Yes it was two, do your query catches all of them?

@ryhisner xbb.1.5.73 /GN.1 was quite fast and it is the lineage with A28271C (edited sorry i ve wrongoed the nuc before) different from everything since Delta.

FedeGueli commented 1 year ago

The query catches 15

ryhisner commented 1 year ago

The query catches 15

Yes, 15 is correct. I didn't catch that there was one duplicate on the Usher tree.

NkRMnZr commented 1 year ago

Tracking updates

11-07, +1 Peru EPI_ISL_18474457 12-01, +2 Peru 01-05, +3 Peru 01-23, +2 Peru

NkRMnZr commented 11 months ago

12-01, +2 Peru EPI_ISL_18572524, EPI_ISL_18572526

FedeGueli commented 11 months ago

around 1% in Peru recently

NkRMnZr commented 11 months ago

There should be another one from New Jersey that cannot be caught by query USA/NJ-CDC-LC1071458/2023|EPI_ISL_18601797|2023-11-18, after a GBW sequence (without L455W) USA/NJ-GBW-H20-334-0496/2023|EPI_ISL_18252015|2023-09-02 with travel history to Peru

FedeGueli commented 10 months ago

lets wait the next upload from Peru before closing it.

NkRMnZr commented 10 months ago

01-05, +3 Peru: EPI_ISL_18723283, EPI_ISL_18723725, EPI_ISL_18723729

NkRMnZr commented 10 months ago

01-23, +2 Peru EPI_ISL_18743901, EPI_ISL_18814837

FedeGueli commented 10 months ago

Likley circualting at low levels there. @corneliusroemer pls take a look at this.

FedeGueli commented 9 months ago

No recent sample pls let me know if something changes.