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Repository for suggesting new lineages that should be added to the current scheme
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JN.1.18 + Orf1a:N2147S (280) with three FLiRT sublineages (FLiRT1+S:K679R= 69 / FliRT2 = 46) and one FViRT sublineage(50) #2560

Closed FedeGueli closed 3 months ago

FedeGueli commented 5 months ago

There is an undesignated branch of JN.1 with Orf1a:N2147S that has further got S:R346T and then both S:F456L and S:F456V but the S:R346T sublineage is currently misplaced under JN.1.18

Query for the big Orf1a:N2147S branch: A6705G,T3565C,C897A NOW JN.1.64 Samples: 941 Tree: (correctly placed as JN.1 > A6705G )

Screenshot 2024-04-13 alle 00 37 04 Screenshot 2024-04-13 alle 00 37 24

Query for S:R346T :G22599C,A6705G,C18894T. [ correct placement JN.1 > A6705G > S:R346T (G22599C)] NOW JN.1.64.1 Samples: 280

IDs EPI_ISL_18787955, EPI_ISL_18787958, EPI_ISL_18797558, EPI_ISL_18798347, EPI_ISL_18839354, EPI_ISL_18849828, EPI_ISL_18849831, EPI_ISL_18851601, EPI_ISL_18886322, EPI_ISL_18886383, EPI_ISL_18893879, EPI_ISL_18899783, EPI_ISL_18913959, EPI_ISL_18916646, EPI_ISL_18917992, EPI_ISL_18926841, EPI_ISL_18932356, EPI_ISL_18936055, EPI_ISL_18938683, EPI_ISL_18943666, EPI_ISL_18944205, EPI_ISL_18946621, EPI_ISL_18946625, EPI_ISL_18968557, EPI_ISL_18972723-18972724, EPI_ISL_18972729-18972730, EPI_ISL_18972732, EPI_ISL_18972746, EPI_ISL_18972748, EPI_ISL_18972750, EPI_ISL_18972754-18972755, EPI_ISL_18972758-18972759, EPI_ISL_18976003, EPI_ISL_18983805, EPI_ISL_18987184, EPI_ISL_18995123, EPI_ISL_18999173, EPI_ISL_19006630, EPI_ISL_19009690, EPI_ISL_19014582, EPI_ISL_19015257, EPI_ISL_19021968, EPI_ISL_19023194, EPI_ISL_19024784, EPI_ISL_19025707, EPI_ISL_19026937, EPI_ISL_19028230, EPI_ISL_19030832, EPI_ISL_19032599, EPI_ISL_19033444, EPI_ISL_19041313, EPI_ISL_19041364, EPI_ISL_19044406, EPI_ISL_19044734,

Query for FLiRT 1 : T22930A,G22599C, A6705G,C18894T Now MD.1 [correct placement JN.1 > A6705G > S:R346T (G22599C) >S:F456L (T22930A) ] formerly tracked as Branch 71 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253 Samples: 69 ( 16 with S:N679R - edited on May 07 )

IDs EPI_ISL_19041364, EPI_ISL_19044406, EPI_ISL_19041313

Query for FLiRT 2: C10138T, T22928C, C25708T [ correct placement JN.1 > A6705G > S:R346T (G22599C) > C1060T > C9319T, C28657T > C10138T, S:F456L (T22928C), Orf3a:L106F (C25708T) NOW MD.3.1 Samples: 46 ( 1 or 2 with Orf9b:T83I (C28531T) query: C10138T, C28531T,C12049T)

IDs EPI_ISL_19026937, EPI_ISL_19051601

Query for FLiRT 3 : DEAD

C2706T, T22928C,A6705G [ correct placement JN.1 > A6705G > S:R346T (G22599C) > Orf1a:T814I (C2706T), S:F456L (T22928C) Samples: 4

IDs EPI_ISL_19143847, EPI_ISL_19143857, EPI_ISL_19143882, EPI_ISL_19143891

Query for FViRT : G22599C, T22928G,A6705G (correct placement: JN.1 > A6705G > S:R346T (G22599C) > Orf1a:T2800I (C8664T), S:F456V (T22928G)] NOW MD.2 formerly tracked as Branch 22 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253 Samples : 50

IDs EPI_ISL_18917992, EPI_ISL_18932356, EPI_ISL_18938683, EPI_ISL_19023194, EPI_ISL_19024784

Tree misplaced as JN.1.18

Screenshot 2024-04-13 alle 00 40 43
FedeGueli commented 5 months ago

N2147S now 566 346T now 65 FliRT-1 now 5 FViRT now 8

@corneliusroemer if you have time worth to look into it

FedeGueli commented 5 months ago

FViRT went to 10 today with one sample from Uk and one from Canada

FedeGueli commented 5 months ago

FLiRT 1 reached 7 with two more from Ireland (with 679R) FviRT went to 11 one from UK

FedeGueli commented 5 months ago

81 for the s:R346T 10 for FLiRT 1 and 12 for FViRT ping @corneliusroemer

FedeGueli commented 5 months ago

81 for the s:R346T 10 for FLiRT 1 and 12 for FViRT ping @corneliusroemer

Note that FLiRT 1 has S:N>K679R in 9/10 of the samples

FedeGueli commented 5 months ago

89 for 346T 11 for FLiRT1 4 for FLiRT2 14 for FViRT

cc @corneliusroemer i think designations needed here.

FliRT2 got also Orf9b:T83I (C28531T) Query: C10138T, C28531T,C12049T

Screenshot 2024-04-30 alle 11 00 31
FedeGueli commented 5 months ago

13 for FLiRT1 with samples from Us, Canada, England

FedeGueli commented 4 months ago

657 / 97 346T / 14 Flirt1 / 7 Flirt2 (2 not on gisaid, 1 with further S:D253G+S:T500N from NDL/ 16 for FViRT

cc @corneliusroemer big ping for this one.

FedeGueli commented 4 months ago

growing 106/19/7/18

FedeGueli commented 4 months ago

FliRt1 > 21 and FViRT > 20 now

FedeGueli commented 4 months ago

+1 (2 on Usher) FLiRT2 both from Sweden

FedeGueli commented 4 months ago

@corneliusroemer even if you want not to place this outside JN.1.18 for sure the Orf1a:N2147S branch with all the 456X lineages are worth to be designated

FedeGueli commented 4 months ago

@corneliusroemer even if not designating this as separate branch as it is i suggest to designate at least the two biggest FLiRT and the FviRT one.

FedeGueli commented 3 months ago

@corneliusroemer this haas slowed down, please consider to designate the FViRT sub lineage of this that seems still around. closing for now.

NkRMnZr commented 3 months ago

branch 2 seems to be boosted by recent SA batch image

FedeGueli commented 3 months ago

branch 2 seems to be boosted by recent SA batch image

thx @NkRMnZr reopening it, ping @corneliusroemer this is worth to be designated since many weeks.

FedeGueli commented 3 months ago

re closing this down, if @corneliusroemer then will designate i will tag it.

DailyCovidCases commented 3 months ago

Branch 22 and 71 might be dying off, please update this

FedeGueli commented 3 months ago

FliRT 1 likely worth to be designated.

FedeGueli commented 3 months ago

Slowing down.

aviczhl2 commented 3 months ago

Designated JN.1.64, JN.1.64.1, MD.1, MD.1.1, MD.2, MD.3 and MD.3.1

FedeGueli commented 3 months ago

Designated JN.1.64, JN.1.64.1, MD.1, MD.1.1, MD.2, MD.3 and MD.3.1

via https://github.com/cov-lineages/pango-designation/commit/c0c9b1b3e216210f1897c6a44f3983f34580e961

FedeGueli commented 3 months ago

Just designated and one singlet with S:31del popped up in Singapore (MD.1.1) query: A6705G,C18894T ,del21653,T22930A