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JN.1 + S:S60A (64, from 4 countries) with a branch with S:R346S (24) and one FLiRS singlet (1) #1462

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FedeGueli opened this issue Mar 23, 2024 · 7 comments
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JN.1 + S:S60A (64, from 4 countries) with a branch with S:R346S (24) and one FLiRS singlet (1) #1462

FedeGueli opened this issue Mar 23, 2024 · 7 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. S:60

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@FedeGueli
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FedeGueli commented Mar 23, 2024 •
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I propose this one to couple it with the sublineage carrying S:S60P proposed in #1460.
There is a clear evolutionary pressure over S:S59 and S:S60 to mutate aas we can see here (S:59 Blue/S:60 Green)
Screenshot 2024-03-23 alle 10 41 53

Defining mutations: JN.1 >S:S60A (T21740G )
Query: T21740G, t3565C,-C1762A,-C1758T,-C7113T,-G2632A,-A9922G (edited)
Samples: 37
Countries: 4 mainly US

IDs EPI_ISL_18524576, EPI_ISL_18547839, EPI_ISL_18729306, EPI_ISL_18730735, EPI_ISL_18781110, EPI_ISL_18813566, EPI_ISL_18826649, EPI_ISL_18826796, EPI_ISL_18827449, EPI_ISL_18835898, EPI_ISL_18847292, EPI_ISL_18848613, EPI_ISL_18858998, EPI_ISL_18866350, EPI_ISL_18886315, EPI_ISL_18908599, EPI_ISL_18920255, EPI_ISL_18920298, EPI_ISL_18933695, EPI_ISL_18936848, EPI_ISL_18943548, EPI_ISL_18945963, EPI_ISL_18956845, EPI_ISL_18957015, EPI_ISL_18972859, EPI_ISL_18978703, EPI_ISL_18978730, EPI_ISL_18978748, EPI_ISL_18978762, EPI_ISL_18979425, EPI_ISL_18984040, EPI_ISL_18985029, EPI_ISL_18986036, EPI_ISL_18990506, EPI_ISL_18990536, EPI_ISL_18990663, EPI_ISL_19004495

Tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_d91b_e9bf50.json?label=id:node_6955167
Screenshot 2024-03-23 alle 10 43 37

There is a subbranch of this with S:R346S that was tracked in branch 71 of #1089
JN.1 >S:S60A (T21740G )> C11020T > S:R346S (A22600T)
Query: T21740G , A22600T
Samples : 23 NY, NJ

Singlet FLiRS:
JN.1 >S:S60A (T21740G )> C11020T > S:R346S (A22600T) > Orf1a:I1159T(T3741C)>C5654T > Orf1a:P885S (C2918T),S:F456L (T22928C)
Query: T3741C, C5654T , C2918T
@FedeGueli FedeGueli added the S:60 label Mar 23, 2024
@FedeGueli FedeGueli changed the title JN.1 + S:S60A (37, 4 countries) with a sublineage with S:R346S (13 NY,NJ) JN.1 + S:S60A (42, 5 countries) with a sublineage with S:R346S (13 NY,NJ) Apr 1, 2024
@FedeGueli
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42 country added Qatar from GBW

@FedeGueli FedeGueli changed the title JN.1 + S:S60A (42, 5 countries) with a sublineage with S:R346S (13 NY,NJ) JN.1 + S:S60A (49, from 6 countries) with a sublineage with S:R346S (13 NY,NJ) Apr 17, 2024
@FedeGueli FedeGueli added the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Apr 17, 2024
@FedeGueli
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widespread in many continents but likely slow.

@FedeGueli FedeGueli changed the title JN.1 + S:S60A (49, from 6 countries) with a sublineage with S:R346S (13 NY,NJ) JN.1 + S:S60A (57, from 7 countries) with a sublineage with S:R346S (14 NY,NJ) Apr 29, 2024
@FedeGueli
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FedeGueli commented Apr 29, 2024 •
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Slow but still around, the S:r346S seems dead

@FedeGueli FedeGueli changed the title JN.1 + S:S60A (57, from 7 countries) with a sublineage with S:R346S (14 NY,NJ) JN.1 + S:S60A (57, from 7 countries) with a sublineage with S:F456L (4) Apr 29, 2024
@FedeGueli FedeGueli changed the title JN.1 + S:S60A (57, from 7 countries) with a sublineage with S:F456L (4) JN.1 + S:S60A (57, from 7 countries) Apr 29, 2024
@FedeGueli
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closing this i dont think the query finds a monophyletic branch so it collects many lineages better closing it

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Apr 29, 2024
@FedeGueli FedeGueli reopened this Apr 29, 2024
@FedeGueli
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Ok now query fixed it finds still 49 , so i let this open for a while

@FedeGueli FedeGueli changed the title JN.1 + S:S60A (57, from 7 countries) JN.1 + S:S60A (48, from 3 countries) Apr 29, 2024
@FedeGueli FedeGueli changed the title JN.1 + S:S60A (48, from 3 countries) JN.1 + S:S60A (48, from 3 countries) with a branch with S:R346S (23) and one FLiRS singlet (1) May 9, 2024
@FedeGueli FedeGueli mentioned this issue May 9, 2024
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@FedeGueli FedeGueli changed the title JN.1 + S:S60A (48, from 3 countries) with a branch with S:R346S (23) and one FLiRS singlet (1) JN.1 + S:S60A (61, from 4 countries) with a branch with S:R346S (23) and one FLiRS singlet (1) May 9, 2024
@FedeGueli
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Now it has a FLiRS singlet in the S:R346S branch

@FedeGueli FedeGueli changed the title JN.1 + S:S60A (61, from 4 countries) with a branch with S:R346S (23) and one FLiRS singlet (1) JN.1 + S:S60A (64, from 4 countries) with a branch with S:R346S (24) and one FLiRS singlet (1) May 29, 2024
@FedeGueli
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slowed down, closing it

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale May 29, 2024
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