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KV.2 (JN.1.4.5 + S:T572I ) with S:F456L (5,Mississippi) #2500

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FedeGueli opened this issue Feb 25, 2024 · 8 comments
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KV.2 (JN.1.4.5 + S:T572I ) with S:F456L (5,Mississippi) #2500

FedeGueli opened this issue Feb 25, 2024 · 8 comments

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@FedeGueli
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FedeGueli commented Feb 25, 2024 •
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Original KV.2 Proposal Former branch 18 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1097

Defining JN.1.4.5 [T18453C > Orf8:S103L (C28201T)]> Orf1a:P971L (C3177T), C11956T, S:T572I (C23277T)
Query: C28201T,C3177T, C11956T,
Samples: 201
Countries: 6 mostly US, but now expoerted to China,India, Portugal

Genomes EPI_ISL_18594616, EPI_ISL_18715666, EPI_ISL_18715709, EPI_ISL_18743056, EPI_ISL_18743391, EPI_ISL_18743414, EPI_ISL_18743508, EPI_ISL_18743511, EPI_ISL_18743529, EPI_ISL_18743718, EPI_ISL_18756315, EPI_ISL_18757279, EPI_ISL_18776734, EPI_ISL_18779236, EPI_ISL_18779266, EPI_ISL_18779698, EPI_ISL_18783863, EPI_ISL_18796384, EPI_ISL_18796392, EPI_ISL_18797570, EPI_ISL_18797581, EPI_ISL_18804974, EPI_ISL_18809261, EPI_ISL_18816361, EPI_ISL_18816365, EPI_ISL_18816468, EPI_ISL_18816473, EPI_ISL_18816530, EPI_ISL_18816539, EPI_ISL_18816543, EPI_ISL_18816577, EPI_ISL_18816582-18816583, EPI_ISL_18816652, EPI_ISL_18816730, EPI_ISL_18816769, EPI_ISL_18816771, EPI_ISL_18816910, EPI_ISL_18817000, EPI_ISL_18817061, EPI_ISL_18817065, EPI_ISL_18817076, EPI_ISL_18817090, EPI_ISL_18817092, EPI_ISL_18817100, EPI_ISL_18824206, EPI_ISL_18827118, EPI_ISL_18827142-18827143, EPI_ISL_18835904, EPI_ISL_18836017, EPI_ISL_18836023, EPI_ISL_18846785, EPI_ISL_18846962, EPI_ISL_18847665, EPI_ISL_18847711, EPI_ISL_18848500, EPI_ISL_18848704, EPI_ISL_18848710, EPI_ISL_18849520, EPI_ISL_18849522-18849523, EPI_ISL_18852363, EPI_ISL_18859650, EPI_ISL_18864347, EPI_ISL_18869491, EPI_ISL_18869513, EPI_ISL_18869516, EPI_ISL_18869524, EPI_ISL_18869532, EPI_ISL_18869550, EPI_ISL_18869804, EPI_ISL_18874035, EPI_ISL_18874038, EPI_ISL_18874242, EPI_ISL_18874248, EPI_ISL_18874263, EPI_ISL_18874271, EPI_ISL_18874314, EPI_ISL_18874334, EPI_ISL_18874339, EPI_ISL_18874407, EPI_ISL_18874410, EPI_ISL_18874412, EPI_ISL_18874419, EPI_ISL_18874456, EPI_ISL_18874515, EPI_ISL_18874519, EPI_ISL_18874558, EPI_ISL_18874567, EPI_ISL_18874588, EPI_ISL_18874591, EPI_ISL_18874658, EPI_ISL_18874728, EPI_ISL_18874744, EPI_ISL_18874757, EPI_ISL_18874771, EPI_ISL_18874833, EPI_ISL_18874966, EPI_ISL_18874979, EPI_ISL_18880134, EPI_ISL_18882451, EPI_ISL_18882949, EPI_ISL_18887092, EPI_ISL_18887270, EPI_ISL_18887524, EPI_ISL_18887575, EPI_ISL_18892319, EPI_ISL_18895049, EPI_ISL_18895338, EPI_ISL_18895462, EPI_ISL_18899522, EPI_ISL_18902909, EPI_ISL_18911402, EPI_ISL_18911973, EPI_ISL_18914459, EPI_ISL_18914722, EPI_ISL_18915345, EPI_ISL_18916903, EPI_ISL_18917125, EPI_ISL_18917145, EPI_ISL_18917164, EPI_ISL_18917611, EPI_ISL_18917636, EPI_ISL_18917773, EPI_ISL_18917779, EPI_ISL_18918021, EPI_ISL_18918033, EPI_ISL_18920044, EPI_ISL_18920115, EPI_ISL_18920177, EPI_ISL_18920180, EPI_ISL_18920195, EPI_ISL_18920209, EPI_ISL_18920410, EPI_ISL_18921082, EPI_ISL_18921273, EPI_ISL_18922106, EPI_ISL_18922425, EPI_ISL_18923193, EPI_ISL_18923211, EPI_ISL_18923217, EPI_ISL_18923226, EPI_ISL_18923230, EPI_ISL_18927428, EPI_ISL_18927432, EPI_ISL_18927437, EPI_ISL_18927480, EPI_ISL_18927517, EPI_ISL_18927524, EPI_ISL_18927534, EPI_ISL_18927540, EPI_ISL_18927554, EPI_ISL_18927598, EPI_ISL_18927630, EPI_ISL_18927646, EPI_ISL_18927648, EPI_ISL_18927696-18927697, EPI_ISL_18927700, EPI_ISL_18927724, EPI_ISL_18927736, EPI_ISL_18927747, EPI_ISL_18927768, EPI_ISL_18927778, EPI_ISL_18927780, EPI_ISL_18927805, EPI_ISL_18927807, EPI_ISL_18927819-18927820, EPI_ISL_18927830, EPI_ISL_18927865, EPI_ISL_18927877, EPI_ISL_18927900, EPI_ISL_18927915, EPI_ISL_18927929, EPI_ISL_18927962, EPI_ISL_18927986, EPI_ISL_18928020, EPI_ISL_18928042, EPI_ISL_18928080, EPI_ISL_18928134, EPI_ISL_18928138, EPI_ISL_18928154, EPI_ISL_18928173, EPI_ISL_18928176, EPI_ISL_18928261, EPI_ISL_18928301, EPI_ISL_18928323, EPI_ISL_18928339, EPI_ISL_18928632, EPI_ISL_18928712-18928713, EPI_ISL_18928715, EPI_ISL_18930631, EPI_ISL_18930703, EPI_ISL_18930749, EPI_ISL_18931261, EPI_ISL_18931263, EPI_ISL_18931339, EPI_ISL_18931388,
Tree: Screenshot 2024-02-25 alle 08 34 42 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5917c_aed620.json?f_userOrOld=uploaded%20sample&label=id:node_6964174

EDITED

Just identified a branch of this proposed lineage with S:F456L
JN.1.4 >> T18453C > Orf8:S103L (C28201T) Orf1a:P971L (C3177T)> C11956T, S:T572I (C23277T) > C2005T > C1188T , 7981G, Orf1b:P2313T (C20404A), S:F456L (T22928C)
Query: C2005T ,C1188T , 7981G
Samples: 2
@FedeGueli FedeGueli changed the title JN.1.4 plus S:T572I emerge in Texas (201 sequences, 4 countries) JN.1.4 plus S:T572I emerged in Texas (201 sequences, 4 countries) Feb 25, 2024
@FedeGueli FedeGueli mentioned this issue Feb 25, 2024
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@FedeGueli FedeGueli changed the title JN.1.4 plus S:T572I emerged in Texas (201 sequences, 4 countries) JN.1.4 plus S:T572I emerged in Texas (202 sequences, 4 countries) Feb 26, 2024
@FedeGueli FedeGueli mentioned this issue Feb 29, 2024
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@FedeGueli FedeGueli changed the title JN.1.4 plus S:T572I emerged in Texas (202 sequences, 4 countries) JN.1.4 plus S:T572I emerged in Texas (202 sequences, 4 countries) with a cluster with S:F456L (2) Feb 29, 2024
@FedeGueli FedeGueli changed the title JN.1.4 plus S:T572I emerged in Texas (202 sequences, 4 countries) with a cluster with S:F456L (2) JN.1.4 plus S:T572I emerged in Texas (229 sequences, 4 countries) with a cluster with S:F456L (2) Feb 29, 2024
@FedeGueli FedeGueli changed the title JN.1.4 plus S:T572I emerged in Texas (229 sequences, 4 countries) with a cluster with S:F456L (2) JN.1.4 plus S:T572I emerged in Texas (234 sequences, 4 countries) with a cluster with S:F456L (2) Feb 29, 2024
@FedeGueli FedeGueli changed the title JN.1.4 plus S:T572I emerged in Texas (234 sequences, 4 countries) with a cluster with S:F456L (2) JN.1.4 plus S:T572I emerged in Texas (250 sequences, 4 countries) with a cluster with S:F456L (4,Mississippi) Mar 4, 2024
@FedeGueli
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250 total the 456L sublinegae doubled to 4 all from Mississippi

@FedeGueli FedeGueli changed the title JN.1.4 plus S:T572I emerged in Texas (250 sequences, 4 countries) with a cluster with S:F456L (4,Mississippi) JN.1.4 plus S:T572I emerged in Texas (285 sequences, 6 countries) with a cluster with S:F456L (4,Mississippi) Mar 7, 2024
@FedeGueli FedeGueli changed the title JN.1.4 plus S:T572I emerged in Texas (285 sequences, 6 countries) with a cluster with S:F456L (4,Mississippi) JN.1.4.5 plus S:T572I emerged in Texas (285 sequences, 6 countries) with a cluster with S:F456L (4,Mississippi) Mar 14, 2024
@FedeGueli FedeGueli changed the title JN.1.4.5 plus S:T572I emerged in Texas (285 sequences, 6 countries) with a cluster with S:F456L (4,Mississippi) JN.1.4.5 plus S:T572I emerged in Texas (387 sequences, 7 countries) with a cluster with S:F456L (4,Mississippi) Mar 17, 2024
@FedeGueli
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387

@FedeGueli FedeGueli changed the title JN.1.4.5 plus S:T572I emerged in Texas (387 sequences, 7 countries) with a cluster with S:F456L (4,Mississippi) JN.1.4.5 plus S:T572I emerged in Texas (467 sequences, 10 countries) with a cluster with S:F456L (5,Mississippi) Mar 28, 2024
@FedeGueli
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467 now, while 456L sublin. went to 5

@xz-keg
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xz-keg commented Apr 1, 2024

479 now @corneliusroemer

@Memorablea
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@corneliusroemer

@FedeGueli FedeGueli changed the title JN.1.4.5 plus S:T572I emerged in Texas (467 sequences, 10 countries) with a cluster with S:F456L (5,Mississippi) JN.1.4.5 plus S:T572I emerged in Texas (479 sequences, 10 countries) with a cluster with S:F456L (5,Mississippi) Apr 1, 2024
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xz-keg commented Apr 2, 2024

Designated KV.2

@FedeGueli
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Designated KV.2 via 4a1ca73

@FedeGueli FedeGueli reopened this Apr 2, 2024
@FedeGueli FedeGueli changed the title JN.1.4.5 plus S:T572I emerged in Texas (479 sequences, 10 countries) with a cluster with S:F456L (5,Mississippi) KV.2 (JN.1.4.5 + S:T572I ) with S:F456L (5,Mississippi) Apr 2, 2024
FedeGueli referenced this issue Apr 2, 2024
@corneliusroemer
Designate KV.2 (JN.1.4.5.2, S:T572I, ORF1a:P971L, C11956T, USA)
4a1ca73
@FedeGueli
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i think i can close this one

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@xz-keg @FedeGueli @Memorablea