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XBB.1.5 Sublineages (3) with S:K304Q, mostly in USA (191/105/51 seq, May 8) #1798

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ryhisner opened this issue Mar 24, 2023 · 12 comments
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XBB.1.5 Sublineages (3) with S:K304Q, mostly in USA (191/105/51 seq, May 8) #1798

ryhisner opened this issue Mar 24, 2023 · 12 comments
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monitor currently too small, watch for future developments XBB.1.5 Sublineage of XBB.1.5

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@ryhisner
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ryhisner commented Mar 24, 2023 •
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Full credit to @FedeGueli for tracking this mutation (and hundreds of others!) in the XBB.1.5 spike diversity issue, #1510. Fede had documented this long before I noticed the trend.

Description for Lineage 1 — XBB.1.5 + S:K304Q
Sub-lineage of: XBB.1.5
Earliest sequence: 2023-1-18, USA, Texas — EPI_ISL_17120697
Most recent sequence: 2023-3-11, USA, Pennsylvania — EPI_ISL_17279077
Countries circulating: USA
Number of Sequences: 58
GISAID AA Query: Spike_K304Q, NSP13_S36P, -Spike_F486S, -N_I131R, -N_Q260L, -NSP1_L149R
GISAID Nucleotide Query: T16342C, A22472C, -T711G, -T10204C, -A29052T, -T28665G
CovSpectrum Query: Nextcladepangolineage:XBB.1.5* & A22472C & !T711G & !T10204C & !A29052T & !T28665G
Substitutions on top of XBB.1.5:
Spike: K304Q
Nucleotide: A22472C

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.5_K304Q_Lineage_1_subtreeAuspice1_genome_38b97_dd0fe0.json
image

Evidence
S:K305Q is a mutation that, before XBB.1.5, had only occurred about 20 times throughout the entire pandemic. Now there appear to be at least three substantial sublineages of XBB.1.5 that have acquired it independently, and all seem to be growing fairly quickly, though sample sizes are too small at this point to draw any conclusions about their growth potential. This seems to me a strong indication that something about XBB.1.5 permits S:K304Q where all previous lineages did not. Whether or not this mutation is advantageous or not remains to be seen.

Genomes

Genomes EPI_ISL_16916659, EPI_ISL_16919295, EPI_ISL_16919734, EPI_ISL_16919737, EPI_ISL_16957540, EPI_ISL_16962358, EPI_ISL_16992526, EPI_ISL_16992992, EPI_ISL_17009307, EPI_ISL_17023378, EPI_ISL_17027198, EPI_ISL_17035090, EPI_ISL_17035242, EPI_ISL_17037387, EPI_ISL_17037430, EPI_ISL_17084701, EPI_ISL_17084948, EPI_ISL_17085120, EPI_ISL_17085161, EPI_ISL_17099098, EPI_ISL_17120697, EPI_ISL_17139282, EPI_ISL_17139821, EPI_ISL_17140243, EPI_ISL_17147035, EPI_ISL_17147482, EPI_ISL_17170014, EPI_ISL_17170022, EPI_ISL_17170040, EPI_ISL_17170342, EPI_ISL_17170360, EPI_ISL_17170361, EPI_ISL_17170389, EPI_ISL_17180109, EPI_ISL_17181363, EPI_ISL_17181379, EPI_ISL_17181861, EPI_ISL_17191626, EPI_ISL_17193231, EPI_ISL_17193497, EPI_ISL_17193717, EPI_ISL_17197256, EPI_ISL_17224080, EPI_ISL_17237229, EPI_ISL_17238375, EPI_ISL_17238663, EPI_ISL_17248802, EPI_ISL_17249727, EPI_ISL_17250474, EPI_ISL_17251207, EPI_ISL_17251260, EPI_ISL_17259478, EPI_ISL_17279077, EPI_ISL_17280091, EPI_ISL_17280202, EPI_ISL_17286996, EPI_ISL_17287145, EPI_ISL_17287166,

Description for Lineage 2 — XBB.1.5.3 (S:A411S) + S:K304Q, N:I131R
Sub-lineage of: XBB.1.5.3 (S:A411S)
Earliest sequence: 2023-1-18, USA, Nevada — EPI_ISL_16859435
Most recent sequence: 2023-3-13, USA, California — EPI_ISL_17279134
Countries circulating: USA
Number of Sequences: 38
GISAID AA Query: Spike_K304Q, NSP13_S36P, N_I131R
GISAID Nucleotide Query: T16342C, A22472C, T28665G
CovSpectrum Query: Nextcladepangolineage:
Substitutions on top of XBB.1.5.3:
Spike: K304Q
N: I131R
Nucleotide: A22472C, G22793T, T28665G

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.5.3_K304Q_Lineage_2_subtreeAuspice2_genome_38b97_dd0fe0.json
image

Evidence
See comments on Lineage 1 above.

Genomes

Genomes EPI_ISL_16859435, EPI_ISL_16991536, EPI_ISL_16991537, EPI_ISL_17001566, EPI_ISL_17073180, EPI_ISL_17084827, EPI_ISL_17084952, EPI_ISL_17102474, EPI_ISL_17146251, EPI_ISL_17146707, EPI_ISL_17169365, EPI_ISL_17179782, EPI_ISL_17179979, EPI_ISL_17180086, EPI_ISL_17180099, EPI_ISL_17182039, EPI_ISL_17183338, EPI_ISL_17183340, EPI_ISL_17183343, EPI_ISL_17183345, EPI_ISL_17194646, EPI_ISL_17197035, EPI_ISL_17204095, EPI_ISL_17205263, EPI_ISL_17205266, EPI_ISL_17224677, EPI_ISL_17224851, EPI_ISL_17224852, EPI_ISL_17250682, EPI_ISL_17261170, EPI_ISL_17264663, EPI_ISL_17271707, EPI_ISL_17278484, EPI_ISL_17278531, EPI_ISL_17278596, EPI_ISL_17279134, EPI_ISL_17279748, EPI_ISL_17286477

Description for Lineage 3 — XBB.1.5 + S:G261V, S:K304Q, N:Q260L
Sub-lineage of: XBB.1.5
Earliest sequence: 2023-1-25, USA, Iowa — EPI_ISL_16853962
Most recent sequence: 2023-3-10, USA, Florida — EPI_ISL_17287229
Countries circulating: USA (13), Mexico (11), Denmark (7), South Korea (1)
Number of Sequences: 32
GISAID AA Query: Spike_K304Q, NSP13_S36P, N_Q260L
GISAID Nucleotide Query: T16342C, A22472C, A29052T
CovSpectrum Query: Nextcladepangolineage:XBB.1.5 & A22472C & A29052T
Substitutions on top of XB.1.5:
Spike: G261V, K304Q
N: Q260L
Nucleotide: G22344T, A22472C, A29052T

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.5_K304Q_Lineage_3_subtreeAuspice3_genome_38b97_dd0fe0.json

image

Evidence
(See comments for lineage 1 above.) This lineage is likely most prevalent in Mexico or Central America and likely is the most globally widespread of the three XBB.1.5 + S:K304Q lineages described here.

Genomes

Genomes EPI_ISL_16853962, EPI_ISL_16991186, EPI_ISL_16991332, EPI_ISL_17007616, EPI_ISL_17026377, EPI_ISL_17048537, EPI_ISL_17048801, EPI_ISL_17066276, EPI_ISL_17167717, EPI_ISL_17170127, EPI_ISL_17170170, EPI_ISL_17170222, EPI_ISL_17170233, EPI_ISL_17170262, EPI_ISL_17170273, EPI_ISL_17172014, EPI_ISL_17196744, EPI_ISL_17196752, EPI_ISL_17210284, EPI_ISL_17210289, EPI_ISL_17210319, EPI_ISL_17223535, EPI_ISL_17268872, EPI_ISL_17270146, EPI_ISL_17270151, EPI_ISL_17270155, EPI_ISL_17270158, EPI_ISL_17272393, EPI_ISL_17272466, EPI_ISL_17273319, EPI_ISL_17286216, EPI_ISL_17287229
@oobb45729
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K304Q? That's intriguing. I was wondering about what S50L would do yesterday. S50L is a known chronic infection marker but it is relatively rare (for a C to U mutation) otherwise. S50 is very close to K304.

@thomasppeacock thomasppeacock added XBB proposed sublineage of XBB XBB.1.5 Sublineage of XBB.1.5 and removed XBB proposed sublineage of XBB labels Mar 24, 2023
@FedeGueli
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Thx Ryan! it was the american par of S:I410V in Europe, they popped up quite at the same time and grew fast since. Happy you finally proposed them!

@ryhisner
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It looks like 304 is also very close to 275-278 and somewhat close to 957 and 960, at least based on this tool made by @OliasDave, which is the only way I know of figuring out the proximity of different spike sites.
https://ukcovid.xyz/proximity.php?targetposition=304

@corneliusroemer corneliusroemer added the monitor currently too small, watch for future developments label Mar 27, 2023
@ryhisner ryhisner changed the title XBB.1.5 Sublineages (3) with S:K304Q, mostly in USA XBB.1.5 Sublineages (3) with S:K304Q, mostly in USA (108 seq, Apr 16) Apr 16, 2023
@ryhisner ryhisner changed the title XBB.1.5 Sublineages (3) with S:K304Q, mostly in USA (108 seq, Apr 16) XBB.1.5 Sublineages (3) with S:K304Q, mostly in USA (191/105/51 seq, May 8) May 8, 2023
@xz-keg
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xz-keg commented Jul 4, 2023

363/143/61 now.

@FedeGueli
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363/143/61 now.

Lineage 1 doubled in two months, not super fast but probably worth a designation. @aviczhl2 did any of them acquired some further mutations?

@xz-keg
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xz-keg commented Jul 4, 2023 •
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T16342C, A22472C, -T711G, -T10204C, -A29052T, -T28665G

53 of them have the convergent Orf1a:T4175I (XBB.1.9/XBB.1.42/XBB.1.23/XCC/BF.30/BA.2.1/BF.35/BN.1.4.1)

FedeGueli referenced this issue Sep 1, 2023
@corneliusroemer
Designate XBB.1.5.104 (S:K304Q, USA) with 380 seqs
9e08418
@FedeGueli
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Branch 1 designated XBB.1.5.104 via 9e08418

MIlestone missing

FedeGueli referenced this issue Sep 1, 2023
@corneliusroemer
Designate JH.1 (XBB.1.5.3.1, S:K304Q, USA) with 200 seqs
f9cd663 
Note for @AngieHinrichs: the lineage is broken into two on the Usher tree
most likely due to a few artefactual reversions of S:K304Q
@FedeGueli
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FedeGueli commented Sep 1, 2023 •
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Branch 2 designated JK.1 via f9cd663

(Lineages note corrected from JH.1 to JK.1 , annotation for readers)

Milestone missing.

@HynnSpylor
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Yeah the partially alias of BQ.1.2.2 and XBB.1.5.3 are conflict.
@corneliusroemer

@corneliusroemer
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Oh damn, I'll fix it, sorry for the confusion

@DailyCovidCases
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Please close this issue

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@DailyCovidCases
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Please close this issue

@DailyCovidCases DailyCovidCases mentioned this issue Aug 12, 2024
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@ryhisner ryhisner closed this as not planned Won't fix, can't repro, duplicate, stale Aug 16, 2024
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@xz-keg @corneliusroemer @ryhisner @thomasppeacock @FedeGueli @DailyCovidCases @oobb45729 @HynnSpylor