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XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(304 seqs, 24 regions) and its recombinant with KP.3.1.1(72 sequences, 10 regions) #2813

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Over-There-Is opened this issue Oct 23, 2024 · 24 comments
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XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(304 seqs, 24 regions) and its recombinant with KP.3.1.1(72 sequences, 10 regions) #2813

Over-There-Is opened this issue Oct 23, 2024 · 24 comments

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@Over-There-Is
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Over-There-Is commented Oct 23, 2024 •
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Transferred from sars-cov-2-variants/lineage-proposals#2173.

XEC> G2060A(Orf1a:A599T)> G28378T(Orf9b:R32L)

Query: G2060A, G28378T, -A11983T,-C18687T, -G25234T,-C27944T
("-"s are added to remove convergent sequences)

Earliest sequence: 08-07 Schleswig-Holstein, Germany EPI_ISL_19364163
Latest sequence: 10-11 Asturias, Spain EPI_ISL_19497008
Regions detected: Denmark 9, UK 9, Germany 8, Italy 8, Netherlands 7, Sweden 7, France 5, Spain 4, US 3(1 from Denmark, 1 pooled, 1 not on GISAID), Luxembourg 2, Belgium 1

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_7f5f_7a0d10.json?c=country&label=id:node_7267532
image

Sequences:

EPI_ISL_19364163, EPI_ISL_19378139, EPI_ISL_19383090,
EPI_ISL_19410252, EPI_ISL_19415557, EPI_ISL_19417577,
EPI_ISL_19417585, EPI_ISL_19421034, EPI_ISL_19426850,
EPI_ISL_19431751, EPI_ISL_19433943, EPI_ISL_19435638-19435640,
EPI_ISL_19436766, EPI_ISL_19436780, EPI_ISL_19443858,
EPI_ISL_19444527, EPI_ISL_19447700, EPI_ISL_19447703,
EPI_ISL_19448892, EPI_ISL_19448913, EPI_ISL_19450798,
EPI_ISL_19451326, EPI_ISL_19451444, EPI_ISL_19451506,
EPI_ISL_19451675, EPI_ISL_19456847, EPI_ISL_19456850,
EPI_ISL_19456875, EPI_ISL_19458753, EPI_ISL_19463326,
EPI_ISL_19464961, EPI_ISL_19467664, EPI_ISL_19468204,
EPI_ISL_19468795, EPI_ISL_19472522, EPI_ISL_19477073,
EPI_ISL_19477087, EPI_ISL_19477236, EPI_ISL_19477238,
EPI_ISL_19477492, EPI_ISL_19477776, EPI_ISL_19478671,
EPI_ISL_19478700, EPI_ISL_19481383, EPI_ISL_19481474,
EPI_ISL_19481484, EPI_ISL_19481515, EPI_ISL_19481533,
EPI_ISL_19484080, EPI_ISL_19485103, EPI_ISL_19485195,
EPI_ISL_19485671, EPI_ISL_19486463, EPI_ISL_19488255,
EPI_ISL_19488579, EPI_ISL_19493850, EPI_ISL_19493952,
EPI_ISL_19494033, EPI_ISL_19497008, EPI_ISL_19497087,
PQ409725.1

KP.3.1.1 / XEC

Query for recombinant: C1684A, C19716T (edited)

Mutations based on XEC:
C1684A, C7113T, C12616T / G28378T(Orf9b:R32L)
Breakpoint: 12616~13121
C1684A is likely from KP.3.1.1> C1684A, C14120T, A14226G (2 seqs, DE 1, GB 1).

09-02~10-01, Bayern, Germany 3
Date unavailable, Ohio, US 1
Sequences:
EPI_ISL_19424919, EPI_ISL_19477344, EPI_ISL_19488853,
EPI_ISL_19497066

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_29260_7a80e0.json?c=country&label=id:node_7268393
image
@Over-There-Is Over-There-Is mentioned this issue Oct 23, 2024
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@FedeGueli
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I suggest to use this query: T3565C, G28378T, G2060A,-C18687T,-C27944T, -G25234T,-A11983T it finds 66

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(63 seqs, 11 countries) and its recombinant with KP.3.1.1(4 sequences, DE 3, US 1) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(68 seqs, 11 countries) and its recombinant with KP.3.1.1(4 sequences, DE 3, US 1) Oct 26, 2024
@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(68 seqs, 11 countries) and its recombinant with KP.3.1.1(4 sequences, DE 3, US 1) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(69 seqs, 11 countries) and its recombinant with KP.3.1.1(4 sequences, DE 3, US 1) Oct 26, 2024
@Over-There-Is
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I suggest to use this query: T3565C, G28378T, G2060A,-C18687T,-C27944T, -G25234T,-A11983T it finds 66

G2060A, G28378T, -A11983T,-C18687T, -G25234T,-C27944T is used now.

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(69 seqs, 11 countries) and its recombinant with KP.3.1.1(4 sequences, DE 3, US 1) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(86 seqs, 12 countries) and its recombinant with KP.3.1.1(4 sequences, DE 3, US 1) Oct 30, 2024
@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(86 seqs, 12 countries) and its recombinant with KP.3.1.1(4 sequences, DE 3, US 1) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(86 seqs, 13 countries) and its recombinant with KP.3.1.1(4 sequences, DE 3, US 1) Oct 30, 2024
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Ireland, Canada

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(86 seqs, 13 countries) and its recombinant with KP.3.1.1(4 sequences, DE 3, US 1) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(95 seqs, 14 countries) and its recombinant with KP.3.1.1(4 sequences, DE 3, US 1) Nov 3, 2024
@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(95 seqs, 14 countries) and its recombinant with KP.3.1.1(4 sequences, DE 3, US 1) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(95 seqs, 14 countries) and its recombinant with KP.3.1.1(5 sequences, 3 countries) Nov 3, 2024
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Portugal via US, Austria, and recombinant +1(Denmark)

@FedeGueli
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FedeGueli commented Nov 7, 2024 •
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109/7

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(95 seqs, 14 countries) and its recombinant with KP.3.1.1(5 sequences, 3 countries) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(118 seqs, 14 countries) and its recombinant with KP.3.1.1(7 sequences, 3 countries) Nov 10, 2024
@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(118 seqs, 14 countries) and its recombinant with KP.3.1.1(7 sequences, 3 countries) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(129 seqs, 14 countries) and its recombinant with KP.3.1.1(10 sequences, 4 countries) Nov 13, 2024
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Rec: Sweden

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(129 seqs, 14 countries) and its recombinant with KP.3.1.1(10 sequences, 4 countries) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(164 seqs, 15 countries) and its recombinant with KP.3.1.1(14 sequences, 5 countries) Nov 21, 2024
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Australia, rec:Italy

@xz-keg
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xz-keg commented Nov 25, 2024

@corneliusroemer also suggest to designate this and the recombinant here.

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(164 seqs, 15 countries) and its recombinant with KP.3.1.1(14 sequences, 5 countries) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(177 seqs, 16 countries) and its recombinant with KP.3.1.1(18 sequences, 6 countries) Nov 26, 2024
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Israel, rec:Netherlands

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Japan, rec:United Kingdom

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(177 seqs, 16 countries) and its recombinant with KP.3.1.1(18 sequences, 6 countries) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(201 seqs, 17 countries) and its recombinant with KP.3.1.1(25 sequences, 7 countries) Dec 3, 2024
@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(201 seqs, 17 countries) and its recombinant with KP.3.1.1(25 sequences, 7 countries) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(205 seqs, 17 countries) and its recombinant with KP.3.1.1(25 sequences, 7 countries) Dec 6, 2024
@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(205 seqs, 17 countries) and its recombinant with KP.3.1.1(25 sequences, 7 countries) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(212 seqs, 17 countries) and its recombinant with KP.3.1.1(30 sequences, 7 countries) Dec 8, 2024
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Recombinant query edited: C1684A, C19716T

@FedeGueli
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C1684A, C19716T

thx it doesnt seem slow at all

@xz-keg
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xz-keg commented Dec 12, 2024

223/ 40 now.

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(212 seqs, 17 countries) and its recombinant with KP.3.1.1(30 sequences, 7 countries) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(225 seqs, 18 countries) and its recombinant with KP.3.1.1(40 sequences, 8 countries) Dec 12, 2024
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Chile, rec:UK

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(225 seqs, 18 countries) and its recombinant with KP.3.1.1(40 sequences, 8 countries) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(241 seqs, 18 countries) and its recombinant with KP.3.1.1(42 sequences, 8 countries) Dec 14, 2024
@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(241 seqs, 18 countries) and its recombinant with KP.3.1.1(42 sequences, 8 countries) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(253 seqs, 20 regions) and its recombinant with KP.3.1.1(43 sequences, 8 regions) Dec 16, 2024
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Over-There-Is commented Dec 16, 2024 •
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Finland, Canary Islands(Spanish)

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(253 seqs, 20 regions) and its recombinant with KP.3.1.1(43 sequences, 8 regions) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(258 seqs, 20 regions) and its recombinant with KP.3.1.1(51 sequences, 9 regions) Dec 17, 2024
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Rec:France

@Over-There-Is
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Mutations based on XEC:
C1684A, C7113T, C12616T / G28378T(Orf9b:R32L)
Breakpoint: 12616~13121
C1684A is likely from KP.3.1.1> C1684A, C14120T, A14226G (2 seqs, DE 1, GB 1).

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(258 seqs, 20 regions) and its recombinant with KP.3.1.1(51 sequences, 9 regions) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(261 seqs, 20 regions) and its recombinant with KP.3.1.1(53 sequences, 9 regions) Dec 18, 2024
@Over-There-Is
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https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=G2060A%2CG28378T%2CA11983A%2CC18687C%2CG25234G%2CC27944C
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=C1684A%2CC19716T
XEC+Orf9b:R32L is 25% faster than average and as fast as XEC*.
The recombinant is 48% faster than average and 28% faster than XEC*.

@FedeGueli
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https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=G2060A%2CG28378T%2CA11983A%2CC18687C%2CG25234G%2CC27944C https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=C1684A%2CC19716T XEC+Orf9b:R32L is 25% faster than average and as fast as XEC*. The recombinant is 48% faster than average and 28% faster than XEC*.

yes it is fast. a bit less than that but still i dont see cluster effect so it may be real.

@FedeGueli
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ping @corneliusroemer

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(261 seqs, 20 regions) and its recombinant with KP.3.1.1(53 sequences, 9 regions) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(269 seqs, 23 regions) and its recombinant with KP.3.1.1(55 sequences, 9 regions) Dec 21, 2024
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New Zealand, Norway, Malaysia

@FedeGueli
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Ping @corneliusroemer this should be designated this non spike mutation is apparently beneficial

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(269 seqs, 23 regions) and its recombinant with KP.3.1.1(55 sequences, 9 regions) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(280 seqs, 23 regions) and its recombinant with KP.3.1.1(60 sequences, 10 regions) Dec 24, 2024
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rec:Canada

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(280 seqs, 23 regions) and its recombinant with KP.3.1.1(60 sequences, 10 regions) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(293 seqs, 23 regions) and its recombinant with KP.3.1.1(61 sequences, 10 regions) Dec 27, 2024
@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(293 seqs, 23 regions) and its recombinant with KP.3.1.1(61 sequences, 10 regions) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(302 seqs, 24 regions) and its recombinant with KP.3.1.1(71 sequences, 10 regions) Jan 1, 2025
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Singapore

@Over-There-Is Over-There-Is changed the title XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(302 seqs, 24 regions) and its recombinant with KP.3.1.1(71 sequences, 10 regions) XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(304 seqs, 24 regions) and its recombinant with KP.3.1.1(72 sequences, 10 regions) Jan 2, 2025
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