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

EG.5.1.15 sublineage with Orf9b:S50L (242 Seqs) with a sublineage of interest S:V341I sampled in California, Brazil and India (8 seqs) #798

Closed
FedeGueli opened this issue Sep 12, 2023 · 2 comments
Closed

EG.5.1.15 sublineage with Orf9b:S50L (242 Seqs) with a sublineage of interest S:V341I sampled in California, Brazil and India (8 seqs) #798

FedeGueli opened this issue Sep 12, 2023 · 2 comments
Labels
ORF9b S:52 S:456

Comments

@FedeGueli
Copy link

FedeGueli commented Sep 12, 2023 •
edited
Loading

Tree:
Schermata 2023-09-12 alle 15 12 12
Schermata 2023-09-12 alle 15 12 38
Schermata 2023-09-12 alle 15 13 38
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice16_genome_test_4ed07_f93300.json?c=gt-S_341&label=id:node_6945001

Defining mutations: EG.5.1.15 (Orf1a:T753I (C2523T = NSP2_T573I)) > Orf9b:S50L (C28432T) > ORF1a :Y2262H (T7049C=NSP3_Y1444H) > C19017T, S:V341I (G22583A) ,C25294T

Query for Orf9b:S50L parental lineage: C2523T ,C28432T,C29625T

Samples: 57 First : US 2023-05-14 Last > US 2023-09-09

IDs EPI_ISL_17653547, EPI_ISL_17768398, EPI_ISL_17965982, EPI_ISL_17988613, EPI_ISL_17995577, EPI_ISL_18049133, EPI_ISL_18075175, EPI_ISL_18095695, EPI_ISL_18104352, EPI_ISL_18106510, EPI_ISL_18106736, EPI_ISL_18108430, EPI_ISL_18111295, EPI_ISL_18112534, EPI_ISL_18112554, EPI_ISL_18112712, EPI_ISL_18112755, EPI_ISL_18112761, EPI_ISL_18112781, EPI_ISL_18114695, EPI_ISL_18121262, EPI_ISL_18130055, EPI_ISL_18130480, EPI_ISL_18133586, EPI_ISL_18137066, EPI_ISL_18143749, EPI_ISL_18144049, EPI_ISL_18144052, EPI_ISL_18144090, EPI_ISL_18144934, EPI_ISL_18151527, EPI_ISL_18157714, EPI_ISL_18158417, EPI_ISL_18158965, EPI_ISL_18159708, EPI_ISL_18159968, EPI_ISL_18161809, EPI_ISL_18168318, EPI_ISL_18209636, EPI_ISL_18209972, EPI_ISL_18215053, EPI_ISL_18218424, EPI_ISL_18220859, EPI_ISL_18220995, EPI_ISL_18221450, EPI_ISL_18223082, EPI_ISL_18225024, EPI_ISL_18228287, EPI_ISL_18238006, EPI_ISL_18241323, EPI_ISL_18244328, EPI_ISL_18245543, EPI_ISL_18245572, EPI_ISL_18245580, EPI_ISL_18245583, EPI_ISL_18245590, EPI_ISL_18245648,

Query for S:V341I sublineage : G22583A,C25294T

Samples : 3 (Us,2 India,1)
@FedeGueli FedeGueli changed the title EG.5.1 sublineage with Orf9b:S50L (57Seqs), and a sublineage of interest S:V341I sampled in California and India (3 seqs) EG.5.1 sublineage with Orf9b:S50L (57 Seqs) with a sublineage of interest S:V341I sampled in California and India (3 seqs) Sep 12, 2023
@FedeGueli FedeGueli changed the title EG.5.1 sublineage with Orf9b:S50L (57 Seqs) with a sublineage of interest S:V341I sampled in California and India (3 seqs) EG.5.1 sublineage with Orf9b:S50L (68 Seqs) with a sublineage of interest S:V341I sampled in California, Brazil and India (4 seqs) Sep 15, 2023
@FedeGueli FedeGueli changed the title EG.5.1 sublineage with Orf9b:S50L (68 Seqs) with a sublineage of interest S:V341I sampled in California, Brazil and India (4 seqs) EG.5.1 sublineage with Orf9b:S50L (94 Seqs) with a sublineage of interest S:V341I sampled in California, Brazil and India (4 seqs) Sep 24, 2023
@FedeGueli
Copy link
Author

it cannot compete.
https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=C2523T%2CC28432T%2CC29625T&analysisMode=CompareToBaseline&

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Sep 24, 2023
@FedeGueli FedeGueli changed the title EG.5.1 sublineage with Orf9b:S50L (94 Seqs) with a sublineage of interest S:V341I sampled in California, Brazil and India (4 seqs) EG.5.1.15 sublineage with Orf9b:S50L (94 Seqs) with a sublineage of interest S:V341I sampled in California, Brazil and India (4 seqs) Nov 28, 2023
@FedeGueli FedeGueli changed the title EG.5.1.15 sublineage with Orf9b:S50L (94 Seqs) with a sublineage of interest S:V341I sampled in California, Brazil and India (4 seqs) EG.5.1.15 sublineage with Orf9b:S50L (242 Seqs) with a sublineage of interest S:V341I sampled in California, Brazil and India (8 seqs) Nov 28, 2023
@FedeGueli
Copy link
Author

parental lineage is now EG.5.1.15 ,
This is now 242 and managed to enter some long term care homes in Canada, circualting in France and Sweden too.

FedeGueli referenced this issue in cov-lineages/pango-designation Nov 28, 2023
@corneliusroemer
Designate EG.5.1.14 (C16017T, C19524T) and EG.5.1.15 (ORF1a:T753I)
9266cca
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
ORF9b S:52 S:456
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@FedeGueli