Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

KR.1 got S:186-189del resulting in S:R190W ( S:F186W plus S:187-190del for Gisaid) (14 seqs, 5 states, 3 continents) #1703

Closed
FedeGueli opened this issue Jul 6, 2024 · 3 comments
Closed

KR.1 got S:186-189del resulting in S:R190W ( S:F186W plus S:187-190del for Gisaid) (14 seqs, 5 states, 3 continents) #1703

FedeGueli opened this issue Jul 6, 2024 · 3 comments
Labels
Deletions between S:180-190 it is an umbrella that collects lineages with mutations in the S:180-190 area of the NTD Deletions/Truncations/Frameshifted Lineage showing any deletions or stop codons or TRS changes. FLiRT FLiRT is an Acronym for S:R346T + S:F456L S:186 S:190

Comments

@FedeGueli
Copy link

This lineage has been sampled multiple times in multiple distant countries around the world in the few last days.
Usher doesn't put all together missing the node that likely corresponds to the deletion only.

Defining mutations:
KR.1 > S:186-189del, S:R190W (del22118_22129)
Query: del22118_22129,C1762A
Samples: 11
Countries: Canada (3 states), Japan (GBW), Philippines, Singapore , Ethiopia (GBW)

Tree:
Screenshot 2024-07-06 alle 16 03 50
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_41b42_94c5d0.json?f_userOrOld=uploaded%20sample&label=id:node_7075016

IDs:
EPI_ISL_19152980, EPI_ISL_19165450, EPI_ISL_19190970,
EPI_ISL_19199111, EPI_ISL_19201548, EPI_ISL_19211107,
EPI_ISL_19222244, EPI_ISL_19228327, EPI_ISL_19238330,
EPI_ISL_19239264, EPI_ISL_19240958
@FedeGueli FedeGueli added Deletions/Truncations/Frameshifted Lineage showing any deletions or stop codons or TRS changes. S:190 S:186 FLiRT FLiRT is an Acronym for S:R346T + S:F456L labels Jul 8, 2024
@FedeGueli FedeGueli changed the title KR.1 got S:186-189del resulting in S:R190W ( S:F186W plu S:187-190del for Gisaid) (11 seqs, 5 states, 3 continents) KR.1 got S:186-189del resulting in S:R190W ( S:F186W plu S:187-190del for Gisaid) (12 seqs, 5 states, 3 continents) Jul 11, 2024
@FedeGueli
Copy link
Author

+1 Canada

@FedeGueli FedeGueli changed the title KR.1 got S:186-189del resulting in S:R190W ( S:F186W plu S:187-190del for Gisaid) (12 seqs, 5 states, 3 continents) KR.1 got S:186-189del resulting in S:R190W ( S:F186W plu S:187-190del for Gisaid) (14 seqs, 5 states, 3 continents) Jul 17, 2024
@FedeGueli
Copy link
Author

+2 Singapore (one only caught by the query

@FedeGueli FedeGueli changed the title KR.1 got S:186-189del resulting in S:R190W ( S:F186W plu S:187-190del for Gisaid) (14 seqs, 5 states, 3 continents) KR.1 got S:186-189del resulting in S:R190W ( S:F186W plus S:187-190del for Gisaid) (14 seqs, 5 states, 3 continents) Jul 24, 2024
@FedeGueli FedeGueli mentioned this issue Jul 30, 2024
Closed
@FedeGueli FedeGueli added the Deletions between S:180-190 it is an umbrella that collects lineages with mutations in the S:180-190 area of the NTD label Aug 4, 2024
@FedeGueli
Copy link
Author

no new seqs

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Aug 10, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
Deletions between S:180-190 it is an umbrella that collects lineages with mutations in the S:180-190 area of the NTD Deletions/Truncations/Frameshifted Lineage showing any deletions or stop codons or TRS changes. FLiRT FLiRT is an Acronym for S:R346T + S:F456L S:186 S:190
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@FedeGueli