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KP.2.2.1 (S:T22N) NH.1 =S:K97E/478T (12) / NY cluster with S:244-247 (15)/NH.3 = 475V sublineage (9) with further S:ins678THKLL-S:K679E (4) #2748

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FedeGueli opened this issue Aug 24, 2024 · 21 comments
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KP.2.2.1 (S:T22N) NH.1 =S:K97E/478T (12) / NY cluster with S:244-247 (15)/NH.3 = 475V sublineage (9) with further S:ins678THKLL-S:K679E (4) #2748

FedeGueli opened this issue Aug 24, 2024 · 21 comments

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@FedeGueli
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FedeGueli commented Aug 24, 2024 •
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From sars-cov-2-variants/lineage-proposals#1662

S:T22N seems currently as fast as S:S31del globally. This derives by many different combinations so i think it is prudent to say S:T22N is at least not slow for sure in the current landscape.
For sure XEC with the slighty different 22N+59S combo (here we have 22N +59L) is going up rapidly.
We were tracking Kp.2.2 + 22N since some weeks in the secondary repo but now i think it is worth to be proposed here:

Proposal updated as of 10/02

KP.2.2.1 [ = T24364C > S:T22N (C21627A) >> Orf1b:K2660R ( A21446G)] >> ORF1a:T1794I (C5646T = PLPro_T231I) > C4276T > S:K97E (A21851G), S:K478T (A22995C REV)
KP.2.2.1 QUERY: T24364C ,C21627A,-C7594A
Samples: 165
First sampled on 2024-05-13 in NJ and few days after that in Nepal.
Places : >15 including Nepal and Bhutan

With a S:K97E/S:K478T (rev) branch: Now designated NH.1 via 4744b7a
Query for S:K478T S:K97E branch: C4276T,C5646T,A21851G
Samples: 6 (All GBW)
Places : Netherlands and India

With a 478Q branch now designated NH.2 via via 4744b7a
KP.2.2 > T24364C > S:T22N (C21627A) >>Orf1b:K2660R (A21446G) then Orf1a:T1794I (C5646T)>>S:T478Q (A22994C), C24904T
Query for 478Q: T24364C ,A22994C, C24904T
Samples: 2 (Canada)

With a branch with S:A475V Now designated NH.3
Query for 475V: C22986T,G2591T,T3565C finds 9 samples from India, Australia, Singapore
On october 9 @ryhisner spotted first four recent samples from Singapore belonging to this lineage with a large insertion in the FCS :
S:ins678THKLL + S:N679E resulting in a FCS 673SYQTQTTHKLLESRRRARSVASQS691
Screenshot 2024-10-10 alle 13 29 53
Query for Ins678: C5842T, T26146G or ins23596ACACACAAGCTTCTA, finds 3 (but there are 4) from Singapore
tree for S:ins678:
Screenshot 2024-10-10 alle 13 39 33
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1c4b7_7b91e0.json?c=userOrOld&label=id:node_11694906

And an undesignated cluster with S:244-247 (spotted by @Over-There-Is) with a large deletion at S:244-247:
Query: G11243A,C1190T
Samples: 14
Places : NY only

dead sublineages WIth two sibling branches after: KP.2.2 > T24364C > S:T22N (C21627A) >>**Orf1b:K2660R** (A21446G) then Orf1a:T1794I (C5646T) =PLPro_T201I then or **KP.2.2 > T24364C > S:T22N (C21627A) >>**Orf1b:K2660R** (A21446G) then Orf1a:T1794I (C5646T)>>** C4276T >T6971C, T17400C, S:K97E (A21851G), **S:K478T** (A22995C) rev, T23119C or

Query for 478T : C5646T,C4276T,T6971C
Samples: 3 (GBW Netherlands)

there is a single patient with S:A475V & S:G181E , that has been sampled by GBW arriving from India
Query for S:A475V: C1911T, T6082C,G22104A,
Samples:2 (GBW India)

and there is an interesting lineage on a different branch with S:K478E and Orf3a:T24N
KP.2.2 > T24364C > S:T22N (C21627A) >> Orf1b:K2660R (A21446G) >> S:K478E (A22994G), Orf3a:T24N (C25463A)
Query: T24364C ,A22994G, C25463A
Samples: 3 India (GBW)with further S:L461P , Italy with further S:A794T, NZL

Tree (updated on October 2):

Screenshot 2024-10-03 alle 00 42 40 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice19_genome_test_7b41_d11a50.json?c=gt-S_97,478&gmax=25384&gmin=21563&label=id:node_7317231
IDs EPI_ISL_19175957, EPI_ISL_19195789, EPI_ISL_19195940, EPI_ISL_19196466, EPI_ISL_19196469, EPI_ISL_19196472, EPI_ISL_19215569, EPI_ISL_19215579, EPI_ISL_19215584, EPI_ISL_19221625, EPI_ISL_19227119, EPI_ISL_19227848, EPI_ISL_19262919, EPI_ISL_19263096, EPI_ISL_19266639, EPI_ISL_19268121, EPI_ISL_19273639, EPI_ISL_19273650, EPI_ISL_19273754, EPI_ISL_19279853, EPI_ISL_19280236, EPI_ISL_19281309, EPI_ISL_19284847, EPI_ISL_19286287, EPI_ISL_19288317, EPI_ISL_19288321, EPI_ISL_19289660, EPI_ISL_19289751, EPI_ISL_19298481, EPI_ISL_19298698, EPI_ISL_19300171, EPI_ISL_19306360, EPI_ISL_19308849, EPI_ISL_19309114, EPI_ISL_19311662, EPI_ISL_19311737, EPI_ISL_19311762, EPI_ISL_19315274, EPI_ISL_19317137, EPI_ISL_19318636, EPI_ISL_19318656, EPI_ISL_19323618, EPI_ISL_19328302, EPI_ISL_19328305, EPI_ISL_19328481, EPI_ISL_19328538, EPI_ISL_19329420, EPI_ISL_19329974, EPI_ISL_19333104, EPI_ISL_19338989, EPI_ISL_19339143, EPI_ISL_19339618, EPI_ISL_19340061, EPI_ISL_19340255, EPI_ISL_19341177, EPI_ISL_19341265-19341266, EPI_ISL_19346691, EPI_ISL_19346811, EPI_ISL_19346825, EPI_ISL_19346919, EPI_ISL_19347330, EPI_ISL_19349917, EPI_ISL_19350183, EPI_ISL_19350328, EPI_ISL_19350667, EPI_ISL_19351728, EPI_ISL_19351751, EPI_ISL_19353646, EPI_ISL_19361224, EPI_ISL_19362045, EPI_ISL_19369828, EPI_ISL_19369853, EPI_ISL_19369946, EPI_ISL_19369990, EPI_ISL_19372150, EPI_ISL_19373024, EPI_ISL_19373028, EPI_ISL_19376200, EPI_ISL_19377834, EPI_ISL_19377854, EPI_ISL_19378943, EPI_ISL_19379273, EPI_ISL_19379565, EPI_ISL_19379731, EPI_ISL_19380400, EPI_ISL_19381041, EPI_ISL_19383565, EPI_ISL_19384523, EPI_ISL_19384542, EPI_ISL_19386041, EPI_ISL_19386108, EPI_ISL_19386115, EPI_ISL_19387400, EPI_ISL_19388724, EPI_ISL_19390397
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (71, 13 countries likely emerged in Nepal) mostly with ORF1b:K2660R (60) KP.2.2 + S:T22N (76, 15 countries likely emerged in Nepal) mostly with ORF1b:K2660R (60) Aug 30, 2024
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76 South Korea, Singapore.

@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (76, 15 countries likely emerged in Nepal) mostly with ORF1b:K2660R (60) KP.2.2 + S:T22N (80, 15 countries likely emerged in Nepal) mostly with ORF1b:K2660R (60) Aug 30, 2024
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FedeGueli commented Aug 30, 2024 •
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80 now with two more aptient caught by GBW from India and Hong Kong. ping @corneliusroemer

@FedeGueli FedeGueli mentioned this issue Aug 30, 2024
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@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (80, 15 countries likely emerged in Nepal) mostly with ORF1b:K2660R (60) KP.2.2 + S:T22N (75, 15 countries likely emerged in Nepal) mostly with ORF1b:K2660R (60) Aug 30, 2024
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75 after editing the query to exclude sars-cov-2-variants/lineage-proposals#1963

@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (75, 15 countries likely emerged in Nepal) mostly with ORF1b:K2660R (60) KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) mostly with ORF1b:K2660R (60) Sep 9, 2024
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96 it goes one growing

@FedeGueli
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Now two sublineages of this got 478T and 478Q, i m updating the proposal

@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) mostly with ORF1b:K2660R (60) KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with a S:K97E,S:K478T and a S:K478Q sublineages after ORF1b:K2660R Sep 9, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with a S:K97E,S:K478T and a S:K478Q sublineages after ORF1b:K2660R KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with two sibling sub lineages with S:K97E,S:K478T and S:K478Q after ORF1b:K2660R Sep 9, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with two sibling sub lineages with S:K97E,S:K478T and S:K478Q after ORF1b:K2660R KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with two sibling sub lineages with S:K97E,S:K478T and S:K478Q on the ORF1b:K2660R branch Sep 9, 2024
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@corneliusroemer ping similar to XEC it has 59L +22N but also further mutations have been acquired

@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with two sibling sub lineages with S:K97E,S:K478T and S:K478Q on the ORF1b:K2660R branch KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with two sibling sub lineages with S:K97E,S:K478T (3) and S:K478Q (2) on a ORF1b:K2660R branch Sep 9, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with two sibling sub lineages with S:K97E,S:K478T (3) and S:K478Q (2) on a ORF1b:K2660R branch KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with two sibling sub lineages with S:K97E,S:K478T (3) and S:K478Q (2) on a ORF1b:K2660R + Orf1a:T1794I (=PLPRO_T201I) branch Sep 9, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with two sibling sub lineages with S:K97E,S:K478T (3) and S:K478Q (2) on a ORF1b:K2660R + Orf1a:T1794I (=PLPRO_T201I) branch KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with three sibling sub lineages with S:K97E,S:K478T (3) and S:K478Q (2) and S:A475V (2) on a ORF1b:K2660R + Orf1a:T1794I (=PLPRO_T201I) branch Sep 9, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with three sibling sub lineages with S:K97E,S:K478T (3) and S:K478Q (2) and S:A475V (2) on a ORF1b:K2660R + Orf1a:T1794I (=PLPRO_T201I) branch KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with three sibling sub lineages with S:K97E,S:K478T (3) and S:K478Q (2) and S:A475V,S:G181E (2) on a ORF1b:K2660R + Orf1a:T1794I (=PLPRO_T201I) branch Sep 9, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (96, 15 countries likely emerged in Nepal) with three sibling sub lineages with S:K97E,S:K478T (3) and S:K478Q (2) and S:A475V,S:G181E (2) on a ORF1b:K2660R + Orf1a:T1794I (=PLPRO_T201I) branch KP.2.2 + S:T22N (101, 15 countries likely emerged in Nepal) with three sibling sub lineages with S:K97E,S:K478T (3) and S:K478Q (2) and S:A475V,S:G181E (2) on a ORF1b:K2660R + Orf1a:T1794I (=PLPRO_T201I) branch Sep 11, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (101, 15 countries likely emerged in Nepal) with three sibling sub lineages with S:K97E,S:K478T (3) and S:K478Q (2) and S:A475V,S:G181E (2) on a ORF1b:K2660R + Orf1a:T1794I (=PLPRO_T201I) branch KP.2.2 + S:T22N (106, 16 countries likely emerged in Nepal) with three sibling sub lineages with S:K97E,S:K478T (3) and S:K478Q (2) and S:A475V,S:G181E (2) on a ORF1b:K2660R + Orf1a:T1794I (=PLPRO_T201I) branch and a S:K478E+Orf3a:t24N branch from India and Italy Sep 13, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (106, 16 countries likely emerged in Nepal) with three sibling sub lineages with S:K97E,S:K478T (3) and S:K478Q (2) and S:A475V,S:G181E (2) on a ORF1b:K2660R + Orf1a:T1794I (=PLPRO_T201I) branch and a S:K478E+Orf3a:t24N branch from India and Italy KP.2.2 + S:T22N (106, 16 countries likely emerged in Nepal) with mulitple sublineages with S:K478T/E/Q/I and one with S:A475V Sep 13, 2024
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106 new country South Korea
there are two more branches with 478X :
478E+Orf3a:T24N from Italy and India
478I recent singlet from Singapore

@corneliusroemer i suggest to designate the 22N branch so we will track eaasily the further 478X branches that looks interesting

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a cluster in new york gets S:244-247 deleted.

@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (106, 16 countries likely emerged in Nepal) with mulitple sublineages with S:K478T/E/Q/I and one with S:A475V KP.2.2 + S:T22N (106, 16 countries likely emerged in Nepal) with multiple sublineages with S:K478T/E/Q/I and one with S:A475V Sep 19, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (106, 16 countries likely emerged in Nepal) with multiple sublineages with S:K478T/E/Q/I and one with S:A475V KP.2.2 + S:T22N (120, 16 countries likely emerged in Nepal) with multiple sublineages with S:K478T/E/Q/I and one with S:A475V and one with a large deletion S:244-47del Sep 19, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (120, 16 countries likely emerged in Nepal) with multiple sublineages with S:K478T/E/Q/I and one with S:A475V and one with a large deletion S:244-47del KP.2.2 + S:T22N (120, 16 countries likely emerged in Nepal) with multiple sublineages with S:K478T/E/Q/I and one with S:A475V and one with a large deletion S:244-47del (4) Sep 19, 2024
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@corneliusroemer i would designate this one also to track better its several sublineages with Spike muts/dels

@FedeGueli FedeGueli mentioned this issue Sep 21, 2024
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Another KP.2.2 popped up with sars-cov-2-variants/lineage-proposals#2072

@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (120, 16 countries likely emerged in Nepal) with multiple sublineages with S:K478T/E/Q/I and one with S:A475V and one with a large deletion S:244-47del (4) KP.2.2 + S:T22N (130, 17 countries likely emerged in Nepal) with multiple sublineages with S:K478T/E/Q/I and one with S:A475V and one with a large deletion S:244-47del (4) Sep 23, 2024
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130, Russia

@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (130, 17 countries likely emerged in Nepal) with multiple sublineages with S:K478T/E/Q/I and one with S:A475V and one with a large deletion S:244-47del (4) KP.2.2 + S:T22N (133, 17 countries likely emerged in Nepal) with multiple sublineages with S:K478T/E/Q/I or S:A475V Sep 25, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (133, 17 countries likely emerged in Nepal) with multiple sublineages with S:K478T/E/Q/I or S:A475V KP.2.2 + S:T22N (133, 17 countries likely emerged in Nepal) Sep 25, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (133, 17 countries likely emerged in Nepal) KP.2.2 + S:T22N (138, 17 countries likely emerged in Nepal) Sep 26, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (138, 17 countries likely emerged in Nepal) KP.2.2 + S:T22N (165, sampled in >25 places , likely emerged in Nepal) Oct 2, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (165, sampled in >25 places , likely emerged in Nepal) KP.2.2 + S:T22N (165, sampled in >25 places , likely emerged in Nepal) with a S:K97E/478T sublineage (6) and a S:K478E sublineage (3) Oct 2, 2024
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This is growing and likely very prevalent in the Indian Peninsula.

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172

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a cluster in new york gets S:244-247 deleted.

Still growing

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a cluster in new york gets S:244-247 deleted.

Still growing

yeah in NY

@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (165, sampled in >25 places , likely emerged in Nepal) with a S:K97E/478T sublineage (6) and a S:K478E sublineage (3) KP.2.2 + S:T22N (179, sampled in >25 places , likely emerged in Nepal) with a S:K97E/478T sublineage (8) and a S:K478E sublineage (3) and a NY cluster with S:244-247 (15) Oct 9, 2024
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179 , and 8 for the 478T+97E sublineage with two from Ireland

@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (179, sampled in >25 places , likely emerged in Nepal) with a S:K97E/478T sublineage (8) and a S:K478E sublineage (3) and a NY cluster with S:244-247 (15) KP.2.2 + S:T22N (184, sampled in >25 places , likely emerged in Nepal) with a S:K97E/478T sublineage (8) and a S:K478E sublineage (3) and a NY cluster with S:244-247 (15) Oct 10, 2024
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FedeGueli commented Oct 10, 2024 •
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As noted by @ryhisner first , four recent samples from Singapore have a large insertion in the FCS :
Screenshot 2024-10-10 alle 13 29 53
S:ins678THKLL + S:N679E resulting in a FCS 673SYQTQTTHKLLESRRRARSVASQS691
notably they belong to a branch with S:A475V different from the one formerly tracked (singlet dead)
Query for 475V: C22986T,G2591T,T3565C finds 9 samples from India, Australia, Singapore
Query for Ins678: ins23596ACACACAAGCTTCTA, finds 3 (but there are 4) from Singapore
tree for S:ins678:
Screenshot 2024-10-10 alle 13 39 33
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1c4b7_7b91e0.json?c=userOrOld&label=id:node_11694906

cc @corneliusroemer it looks like relevant

@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (184, sampled in >25 places , likely emerged in Nepal) with a S:K97E/478T sublineage (8) and a S:K478E sublineage (3) and a NY cluster with S:244-247 (15) KP.2.2 + S:T22N (184, sampled in >25 places , likely emerged in Nepal) with several sublineages of interest: S:K97E/478T (8) / S:K478E (3) / NY cluster with S:244-247 (15)/ 475V sublineage (9) with further S:ins678THKLL-S:K679E (4) Oct 10, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (184, sampled in >25 places , likely emerged in Nepal) with several sublineages of interest: S:K97E/478T (8) / S:K478E (3) / NY cluster with S:244-247 (15)/ 475V sublineage (9) with further S:ins678THKLL-S:K679E (4) KP.2.2 + S:T22N (192, sampled in >25 places , likely emerged in Nepal) with several sublineages of interest: S:K97E/478T (9) / S:K478E (3) / NY cluster with S:244-247 (15)/ 475V sublineage (9) with further S:ins678THKLL-S:K679E (4) Oct 14, 2024
@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (192, sampled in >25 places , likely emerged in Nepal) with several sublineages of interest: S:K97E/478T (9) / S:K478E (3) / NY cluster with S:244-247 (15)/ 475V sublineage (9) with further S:ins678THKLL-S:K679E (4) KP.2.2 + S:T22N (204, sampled in >25 places , likely emerged in Nepal) with several sublineages of interest: S:K97E/478T (12) / NY cluster with S:244-247 (15)/ 475V sublineage (9) with further S:ins678THKLL-S:K679E (4) Oct 18, 2024
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Put to sleep the tracking for the 478E branch. the main branch goes to 204 with the 478T/97E branch rising to 12 with samples from Slovenia too.

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Main proposal designated KP.2.2.1 via efe8e07

@FedeGueli FedeGueli changed the title KP.2.2 + S:T22N (204, sampled in >25 places , likely emerged in Nepal) with several sublineages of interest: S:K97E/478T (12) / NY cluster with S:244-247 (15)/ 475V sublineage (9) with further S:ins678THKLL-S:K679E (4) KP.2.2.1 (S:T22N) S:K97E/478T (12) / NY cluster with S:244-247 (15)/ 475V sublineage (9) with further S:ins678THKLL-S:K679E (4) Oct 20, 2024
FedeGueli referenced this issue Oct 20, 2024
@corneliusroemer
Designate MC.10.1 (435S) and KP.2.2.1 (T22N)
efe8e07
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Descendants of Kp.2.2.1 tracked here have been designated via 4744b7a#diff-ead4244ff49c81bc758e9f068f5ef42156bd985b9c86de8fa4d6fcd7f2829090R1177
NH.1 is 97E+478T
NH.2 is 478Q
NH.3 is 475V + orf1a:ORF1a:A776S

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FedeGueli commented Oct 24, 2024 •
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cc @Over-There-Is if you want to open an issue on the secondary repo for the sublineage with the 244-247 deletion it would be welcomed please.

Same for @ryhisner if you would like to propose the insertion branch of NH.3 it will be great!

@FedeGueli FedeGueli changed the title KP.2.2.1 (S:T22N) S:K97E/478T (12) / NY cluster with S:244-247 (15)/ 475V sublineage (9) with further S:ins678THKLL-S:K679E (4) KP.2.2.1 (S:T22N) NH.1 =S:K97E/478T (12) / NY cluster with S:244-247 (15)/NH.3 = 475V sublineage (9) with further S:ins678THKLL-S:K679E (4) Oct 24, 2024
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