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HN.3.1 with S:P621S (13) #383

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Fearuncle opened this issue Jul 10, 2023 · 12 comments
Closed

HN.3.1 with S:P621S (13) #383

Fearuncle opened this issue Jul 10, 2023 · 12 comments
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designated S:253 S:456 S:478 s:494
Milestone
HN.3.1

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@Fearuncle
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Fearuncle commented Jul 10, 2023 •
edited by FedeGueli
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Original proposal now designated HN.3; please skip below to see its sublineage proposed

Original Proposal:
image
tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_155ee_c1cd40.json?c=gt-S_494&f_userOrOld=uploaded%20sample
EPI_ISL_17955845 EPI_ISL_17955806 EPI_ISL_17955780
first seq: 2023-06-12
most recent: 2023-06-16
gisaid query: T23042C, G20060T, C22995G (edited : @Fearuncle on Gisaid you have to use the WT as start so it is C22995 not A22995)
On https://cov-spectrum.org/collections/177 it will be the first level 6 lineage
This has been designated HN.3

New proposal:

HN.3> ORF1a:G345C (G1298T) > S:D253G (A22320G)

Gisaid query: G1298T,A22320G,T23042C

Tree:
Schermata 2023-10-17 alle 11 25 11
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_38d01_e52310.json?label=id:node_3393054

Countries : 4

Samples: 46
EPI_ISL_18104484, EPI_ISL_18162736, EPI_ISL_18165599,
EPI_ISL_18261311, EPI_ISL_18261351, EPI_ISL_18265077,
EPI_ISL_18278033, EPI_ISL_18281903, EPI_ISL_18282698,
EPI_ISL_18305109, EPI_ISL_18305602, EPI_ISL_18306310-18306311,
EPI_ISL_18308830, EPI_ISL_18309796, EPI_ISL_18316947,
EPI_ISL_18317279, EPI_ISL_18322589, EPI_ISL_18322598,
EPI_ISL_18333191, EPI_ISL_18333239, EPI_ISL_18333261,
EPI_ISL_18333595, EPI_ISL_18333602, EPI_ISL_18333649,
EPI_ISL_18339157-18339158, EPI_ISL_18340012, EPI_ISL_18340288,
EPI_ISL_18340402, EPI_ISL_18344517, EPI_ISL_18358312,
EPI_ISL_18358429, EPI_ISL_18359241, EPI_ISL_18361082,
EPI_ISL_18363844, EPI_ISL_18363959, EPI_ISL_18368449,
EPI_ISL_18368696, EPI_ISL_18369429, EPI_ISL_18369666,
EPI_ISL_18372322, EPI_ISL_18379561, EPI_ISL_18384102,
EPI_ISL_18384890, EPI_ISL_18389064
@FedeGueli FedeGueli added Rapid review needed Convergent evolution Lineages with convergent mutations labels Jul 10, 2023
@FedeGueli
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still 3

@Fearuncle
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there is a lineage of fl.1.5.1 with s:554k

@Fearuncle
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image

@FedeGueli FedeGueli changed the title FL.1.5.1 with S:494P 3 seq. in DR FL.1.5.1 with S:494P 5 seq. in DR Jul 31, 2023
@FedeGueli
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2 samples from airport surveillance with travel history from Rep.Dominicana

@NkRMnZr
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NkRMnZr commented Aug 2, 2023 •
edited
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1 more from Canada EPI_ISL_18052987 with unknown travel history

@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 5 seq. in DR FL.1.5.1 with S:494P 6 seq. in DR Aug 2, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 6 seq. in DR FL.1.5.1 with S:494P 7 seq. in DR Aug 9, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 7 seq. in DR FL.1.5.1 with S:494P 8 seq. in DR Aug 13, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 8 seq. in DR FL.1.5.1 with S:494P 9 seq. in DR Aug 14, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 9 seq. in DR FL.1.5.1 with S:494P 10 seq. in DR Aug 16, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 10 seq. in DR FL.1.5.1 with S:494P 11 seq. in DR Aug 18, 2023
@FedeGueli FedeGueli changed the title FL.1.5.1 with S:494P 11 seq. in DR FL.1.5.1 with S:494P 12 seq. in DR Aug 18, 2023
@FedeGueli
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growth tracking: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=T23042C%2CG20060T%2CC22995G&analysisMode=CompareToBaseline&

@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 12 seq. in DR FL.1.5.1 with S:494P 13 seq. in DR Aug 23, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 13 seq. in DR FL.1.5.1 with S:494P 15 seq. in DR Aug 24, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 15 seq. in DR FL.1.5.1 with S:494P 21 seq. in DR Sep 1, 2023
@Fearuncle
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new branch with s:253G
image

@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 21 seq. in DR FL.1.5.1 with S:494P 21 seq. with NEW branch with S:253G (4) Sep 1, 2023
@FedeGueli FedeGueli added s:494 S:253 combo It has a couple of mutation in RBD S:456 S:478 and removed Rapid review needed Convergent evolution Lineages with convergent mutations labels Sep 2, 2023
@FedeGueli
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Tracker:https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=T23042C%2CG20060T%2CC22995G&analysisMode=CompareToBaseline&

@FedeGueli FedeGueli added the To be proposed Green light for proposal label Sep 2, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 59 seq. with NEW branch with S:253G (18) and 2 with S:P621S FL.1.5.1 with S:494P 61 seq. with NEW branch with S:253G (20) and 2 with S:P621S Oct 2, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 61 seq. with NEW branch with S:253G (20) and 2 with S:P621S FL.1.5.1 with S:494P 67 seq. with NEW branch with S:253G (26) and 3 with S:P621S Oct 4, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P 67 seq. with NEW branch with S:253G (26) and 3 with S:P621S FL.1.5.1 with S:494P with S:253G (26) and 3 with S:P621S Oct 4, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P with S:253G (26) and 3 with S:P621S FL.1.5.1 with S:494P with S:253G (32) and 3 with S:P621S Oct 5, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P with S:253G (32) and 3 with S:P621S FL.1.5.1 with S:494P with S:253G (39) and 3 with S:P621S Oct 8, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P with S:253G (39) and 3 with S:P621S FL.1.5.1 with S:494P with S:253G (40) and 3 with S:P621S Oct 10, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P with S:253G (40) and 3 with S:P621S FL.1.5.1 with S:494P with S:253G (44) and 4 with S:P621S Oct 12, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P with S:253G (44) and 4 with S:P621S FL.1.5.1 with S:494P with S:253G (47) and 4 with S:P621S Oct 13, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P with S:253G (47) and 4 with S:P621S FL.1.5.1 with S:494P with S:253G (49) and 5 with S:P621S Oct 14, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P with S:253G (49) and 5 with S:P621S FL.1.5.1 with S:494P with S:253G (51) and 6 with S:P621S Oct 15, 2023
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P with S:253G (51) and 6 with S:P621S FL.1.5.1 with S:494P with S:253G (54) and 9 with S:P621S Oct 16, 2023
Fearuncle referenced this issue in cov-lineages/pango-designation Oct 17, 2023
@corneliusroemer
Designate HN.3 (S:S494P) with 90 seqs
a5105d2
@Fearuncle Fearuncle changed the title FL.1.5.1 with S:494P with S:253G (54) and 9 with S:P621S HN.3 with S:253G (54) and 9 with S:P621S Oct 17, 2023
@FedeGueli FedeGueli mentioned this issue Oct 17, 2023
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@FedeGueli FedeGueli added this to the HN.3 milestone Oct 17, 2023
@FedeGueli FedeGueli added designated and removed To be proposed Green light for proposal labels Oct 17, 2023
@FedeGueli
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@Fearuncle when you change the title of the proposal you should update the proposal to be the same , otherwise it becomes a mess. i spotted that it is not updated and now i m editing to follow the headline.

@FedeGueli FedeGueli added Rapid review needed and removed combo It has a couple of mutation in RBD labels Oct 17, 2023
FedeGueli referenced this issue in cov-lineages/pango-designation Oct 17, 2023
@corneliusroemer
Designate HN.3.1 (S:E554D) with 50 seqs
ffa4130
@FedeGueli FedeGueli modified the milestones: HN.3, HN.3.1 Oct 17, 2023
@Fearuncle Fearuncle changed the title HN.3 with S:253G (54) and 9 with S:P621S HN.3.1 with S:P621S (9) Oct 17, 2023
@Fearuncle Fearuncle changed the title HN.3.1 with S:P621S (9) HN.3.1 with S:P621S (10) Oct 18, 2023
@Fearuncle Fearuncle changed the title HN.3.1 with S:P621S (10) HN.3.1 with S:P621S (11) Oct 19, 2023
@Fearuncle Fearuncle changed the title HN.3.1 with S:P621S (11) HN.3.1 with S:P621S (12) Oct 30, 2023
@Fearuncle Fearuncle changed the title HN.3.1 with S:P621S (12) HN.3.1 with S:P621S (13) Nov 7, 2023
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