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DV.7.1.5 sublineage with ORF1a:V3782F and ORF1a:T4175I (>190 seq) #2238

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oobb45729 opened this issue Sep 1, 2023 · 4 comments
Open

DV.7.1.5 sublineage with ORF1a:V3782F and ORF1a:T4175I (>190 seq) #2238

oobb45729 opened this issue Sep 1, 2023 · 4 comments

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@oobb45729
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Transferred from sars-cov-2-variants/lineage-proposals#729. (Thanks @FedeGueli for completing the proposal.)
1
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b28d_10d2e0.json?label=id:node_7682428
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3ADV.7*%26N%3AT135A&

Query for the bigger lineage: A28676G, G22927T, T22928C, >> 67 samples
Query for the sublineage with Orf1a:T4175I : A28676G, G11609T, C12789T >> 22 samples

Growth advantage versus EG.5.1.1 lineage of the small sub-sublineage:
https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=A28676G%2CG11609T%2CC12789T&analysisMode=CompareToBaseline&

Growth advantage versus parental DV.7.1 lineage:
https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=DV.7.1*&nucMutations1=A28676G%2CG11609T%2CC12789T&analysisMode=CompareToBaseline&

Defining mutations:
DV.7.1 > N:T135A >> second level sublineage > Orf1a:V3782F (G11609T), Orf1a:T4175I (C12789T)

Samples id:
Parental lineage:
EPI_ISL_17837117, EPI_ISL_17949275, EPI_ISL_17949297,
EPI_ISL_17953149, EPI_ISL_17953158-17953159, EPI_ISL_17971963,
EPI_ISL_17971972, EPI_ISL_17985278-17985279, EPI_ISL_17989177,
EPI_ISL_18010894, EPI_ISL_18010897, EPI_ISL_18010901,
EPI_ISL_18010903-18010904, EPI_ISL_18010908, EPI_ISL_18057943,
EPI_ISL_18075734, EPI_ISL_18097326, EPI_ISL_18097347,
EPI_ISL_18103765, EPI_ISL_18112352, EPI_ISL_18112364,
EPI_ISL_18112385, EPI_ISL_18112397, EPI_ISL_18112401,
EPI_ISL_18112405, EPI_ISL_18112539, EPI_ISL_18113410,
EPI_ISL_18118203, EPI_ISL_18118364, EPI_ISL_18119341,
EPI_ISL_18123915, EPI_ISL_18134027, EPI_ISL_18135335,
EPI_ISL_18163434, EPI_ISL_18163667, EPI_ISL_18163683,
EPI_ISL_18167715, EPI_ISL_18168253, EPI_ISL_18168438,
EPI_ISL_18168440, EPI_ISL_18168442, EPI_ISL_18168444,

Descendant lineage:
EPI_ISL_18118562, EPI_ISL_18118659, EPI_ISL_18123913-18123914,
EPI_ISL_18136334, EPI_ISL_18137922, EPI_ISL_18142266,
EPI_ISL_18142481, EPI_ISL_18142547, EPI_ISL_18142948,
EPI_ISL_18142950, EPI_ISL_18142952, EPI_ISL_18142956-18142959,
EPI_ISL_18142966-18142968, EPI_ISL_18167452, EPI_ISL_18167962,
EPI_ISL_18168130
@oobb45729 oobb45729 mentioned this issue Sep 1, 2023
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@oobb45729 oobb45729 changed the title DV.7.1 sublineage with N:T135A (>60 seq) and a further sublineage with ORF1a:V3782F and ORF1a:T4175I (>20 seq. Mainly Ireland) DV.7.1 sublineage with N:T135A (>80 seq) and a further sublineage with ORF1a:V3782F and ORF1a:T4175I (>30 seq. Mainly Ireland) Sep 4, 2023
@FedeGueli
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FedeGueli commented Sep 7, 2023 •
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98 seqs / 33 seqs respectively. slowed down a bit.:

https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=A28676G%2CG22927T%2CT22928C&analysisMode=CompareToBaseline&

still the subliineage seems very fast.
https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=A28676G%2CG11609T%2CC12789T&analysisMode=CompareToBaseline&

@FedeGueli FedeGueli mentioned this issue Sep 8, 2023
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@oobb45729 oobb45729 changed the title DV.7.1 sublineage with N:T135A (>80 seq) and a further sublineage with ORF1a:V3782F and ORF1a:T4175I (>30 seq. Mainly Ireland) DV.7.1 sublineage with N:T135A (>100 seq) and a further sublineage with ORF1a:V3782F and ORF1a:T4175I (>40 seq. Mainly Ireland) Sep 9, 2023
@FedeGueli
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179 for the parental lineage and 68 for its sublineage , it appears to be fast. ping @corneliusroemer doubling (subm.) under 10days

@FedeGueli
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258 the parental lineage
101 for the 4175 sublineage.

@corneliusroemer i have it as the fastest branch of DV.7.1 could you take a look?
interestingly ther is a N:T135 branch in BA.2.86 too with a different AA

@oobb45729 oobb45729 changed the title DV.7.1 sublineage with N:T135A (>100 seq) and a further sublineage with ORF1a:V3782F and ORF1a:T4175I (>40 seq. Mainly Ireland) DV.7.1 sublineage with N:T135A (>300 seq) and a further sublineage with ORF1a:V3782F and ORF1a:T4175I (>100 seq) Oct 7, 2023
@Over-There-Is
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DV.7.1.5

Over-There-Is referenced this issue Oct 15, 2023
@corneliusroemer
Designate DV.7.1.5 (N:T135I, Spain) with 500 seqs
c57b914
@oobb45729 oobb45729 changed the title DV.7.1 sublineage with N:T135A (>300 seq) and a further sublineage with ORF1a:V3782F and ORF1a:T4175I (>100 seq) DV.7.1.5 sublineage with ORF1a:V3782F and ORF1a:T4175I (>120 seq) Oct 16, 2023
@oobb45729 oobb45729 changed the title DV.7.1.5 sublineage with ORF1a:V3782F and ORF1a:T4175I (>120 seq) DV.7.1.5 sublineage with ORF1a:V3782F and ORF1a:T4175I (>190 seq) Oct 31, 2023
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@Over-There-Is @FedeGueli @oobb45729