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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.1.18.2 (S:F59S) FLirt lineage emerging fast in Puerto Rico - 10% prevalence (50 samples) with further S:P217S, S:N1125S (37) and a Canadian cluster with S:Q675R (8) #2654

Closed FedeGueli closed 3 months ago

FedeGueli commented 3 months ago

Now also Branch 108 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253 (edited 6/25)

Defining mutations: JN.1.18.2 > > T23377C (silent S:S605S) > Orf1a:I740V (A2483G) > N:A152T (G28727A) > S:F456L (T22930A)> S:P217S (C22211T), S:N1125S (A24936G) Query for JN.1.18.2 Plus S:F456L(T22930A): A2483G,G28727A,T3565C,-C19017T or ( T22930A, T22321C, T21738C By @aviczhl2 in # 1253) Samples: 19 (Puerto Rico, Dominica Republic,Uk, Canada) IDs: EPI_ISL_19157245, EPI_ISL_19165198, EPI_ISL_19165269, EPI_ISL_19184739, EPI_ISL_19184743, EPI_ISL_19184746, EPI_ISL_19185021, EPI_ISL_19185798, EPI_ISL_19185826, EPI_ISL_19190670, EPI_ISL_19192966, EPI_ISL_19192971-19192972, EPI_ISL_19192974, EPI_ISL_19192979, EPI_ISL_19192987, EPI_ISL_19192994, EPI_ISL_19192998, EPI_ISL_19193004,

Query for S:P217S+S:N1125S sublineage: C22211T, A24936G Samples: 13 (Puerto Rico, Dominican Republic) IDs: EPI_ISL_19184739, EPI_ISL_19184743, EPI_ISL_19184746, EPI_ISL_19190670, EPI_ISL_19192966, EPI_ISL_19192971-19192972, EPI_ISL_19192974, EPI_ISL_19192979, EPI_ISL_19192987, EPI_ISL_19192994, EPI_ISL_19192998, EPI_ISL_19193004,

Tree as of 6-26:

Screenshot 2024-06-26 alle 01 27 19

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_43cbc_b516b0.json?label=id:node_7170166

There is also a cluster in Canada with S:Q675R Query: C3583T,A23586G, G26951C Samples: 8

aviczhl2 commented 3 months ago

Pls update, 42 seqs now with query T22930A, T22321C, T21738C

FedeGueli commented 3 months ago

50 FLirt and 37 with further 217S/1125S ping @corneliusroemer

FedeGueli commented 3 months ago

Pls update, 42 seqs now with query T22930A, T22321C, T21738C

original query still finds more sequences.

aviczhl2 commented 3 months ago

Designated LZ.1 and LZ.1.1

FedeGueli commented 3 months ago

Designated LZ.1 and LZ.1.1 via https://github.com/cov-lineages/pango-designation/commit/c0e97bd72b1bcc8e0f3cd14d2f85757a078f7aff