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)

[FedeGueli]

Now also Branch 108 of sars-cov-2-variants/lineage-proposals#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:

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

[xz-keg]

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

[FedeGueli]

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

[FedeGueli]

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

original query still finds more sequences.

[xz-keg]

Designated LZ.1 and LZ.1.1

[FedeGueli]

Designated LZ.1 and LZ.1.1 via c0e97bd