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Multiple lineages with S:N481K (updated 07/25) #59

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NkRMnZr opened this issue May 15, 2023 · 12 comments
Closed
2 of 7 tasks

Multiple lineages with S:N481K (updated 07/25) #59

NkRMnZr opened this issue May 15, 2023 · 12 comments
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designated Multiple lineages
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FL.1.6 HM.1

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@NkRMnZr
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NkRMnZr commented May 15, 2023 •
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Multiple Lineages with S:N481K
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see #59 (comment) for tracking details, thanks to @FedeGueli

Branch 1: FL.1 + S:Q1208H + S:N481K

Designated as FL.1.6

Defining Mutations: FL.1 >> G25186T(S:Q1208H) >>T23005A(S:N481K)
Query: G25186T, T23005A, C23664T, -C22995G [10 seqs]
Earliest seq: 2023-04-03 (Brunei, EPI_ISL_17503927)
Most recent seq: 2023-05-03 (Shanghai, EPI_ISL_17645760)
Countries detected: South Korea (3), USA (2), Brunei (1), China (1)
Genome: EPI_ISL_17503927, EPI_ISL_17645760(C_AA014208.1), EPI_ISL_17537890, EPI_ISL_17677732, EPI_ISL_17677733, EPI_ISL_17690534, EPI_ISL_17706795

FL 1

Branch 2: FL.1.4 > S:N481K

There is another subtree that also got T23005A(S:N481K) under C22995G(S:T478R) sub-branch, which is proposed by @HynnSpylor at cov-lineages/pango-designation#1985 (which is designated FL.1.4 on 23-05-24)

Query: G25186T, T23005A, C23664T, C22995G [5 Seqs]
Countries detected: Vietnam (1), USA (2), Singapore (1), Canada (1)
Genome: EPI_ISL_17595484, EPI_ISL_17614077, EPI_ISL_17595399, EPI_ISL_17670170, EPI_ISL_17701244

Branch 3: FL.1.1 + S:N481K

Defining Mutations: FL.1.1 [A21371C(ORF1b:Q2635P)]>T23005A(S:N481K)
Query: A21371C, T23005A, C23664T, C11956T [11 Seqs]
Earliest seq: 2023-03-22 (EPI_ISL_17588026, USA)
Most recent seq: 2023-05-23 (EPI_ISL_17776857, Scotland)
Countries detected: USA (7), UK (4, Scotland)
Genome: EPI_ISL_17524181(OQ852226.1), EPI_ISL_17462785(OQ802638.1), EPI_ISL_17588012(OQ909937.1), EPI_ISL_17588026(OQ909952.1), EPI_ISL_17462476(OQ802329.1), EPI_ISL_17589492(OQ893714.1), EPI_ISL_17680758, EPI_ISL_17776849, EPI_ISL_17776854, EPI_ISL_17776856, EPI_ISL_17776857

FL 1 1

all branches above on downsample UShER Tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_411d5_200740.json?c=gt-S_481
Subtree

Branch 4: FL.11 + S:N481K

spotted by @FedeGueli

Defining Mutations: FL.11 > T23005A(S:N481K)
Query: 23005A, C9073T, T28297C [20 seqs]
Earliest seq: 2023-04-13 (EPI_ISL_17537280, Canada)
Most recent seq: 2023-05-15
Sampled Countries: Canada (8, All Ontario), USA (5, All New York), Austria (3), France (3), Denmark (1)

Genomes: EPI_ISL_17537280, EPI_ISL_17537702, EPI_ISL_17566036, EPI_ISL_17630242, EPI_ISL_17639076, EPI_ISL_17677166, EPI_ISL_17689470, EPI_ISL_17689471, EPI_ISL_17689503, EPI_ISL_17701158, EPI_ISL_17701160, EPI_ISL_17701234, EPI_ISL_17701329, EPI_ISL_17701330, EPI_ISL_17715278, EPI_ISL_17715542, EPI_ISL_17717554, EPI_ISL_17732179, EPI_ISL_17761749,

USA/NY-PRL-230518_81A07/2023|OR026434.1|2023-05-15

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice27_genome_3238d_d9c830.json?label=id:node_6696050 Schermata 2023-06-05 alle 12 06 27

Branch 5: XBB.1.9.1 + ORF1a:L92F + ORF1a:A3571V + S:N481K

Defining Mutations: XBB.1.9.1 > C539T(ORF1a:L92F) > C10977T(ORF1a:A3571V), T23005G(S:N481K) >
Query: C10977T, T23005G [23 seqs]
Earliest seq: 2023-03-09 (EPI_ISL_17257316, England)
Most recent seq: 2023-05-20
Sampled Countries: UK (11, England/10, Wales/1), USA (4, New Jersey/2, Virginia/2), Australia (4, NSW/3, Queensland/1), France (2), Germany (1), Isreal (1)

Genomes: EPI_ISL_17257316, EPI_ISL_17257427, EPI_ISL_17358849, EPI_ISL_17381703, EPI_ISL_17469179, EPI_ISL_17483831, EPI_ISL_17549063, EPI_ISL_17549345, EPI_ISL_17584830, EPI_ISL_17621541, EPI_ISL_17621661, EPI_ISL_17666291, EPI_ISL_17667353, EPI_ISL_17710103, EPI_ISL_17731145, EPI_ISL_17731207, EPI_ISL_17744118, EPI_ISL_17744131, EPI_ISL_17762558, EPI_ISL_17762716, EPI_ISL_17358999, EPI_ISL_17408925, EPI_ISL_17528907

UShER:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3a646_fd8580.json?c=userOrOld&f_userOrOld=uploaded%20sample

Branch 6: XBB.1.5.30 + ORF7a:V74A + ORF3a:L15F + S:N481K

Designated as HM.1 (XBB.1.5.30.1)

Defining Mutations: T27614C(ORF7a:V74A) > C24358A > C17010T, G25437T(ORF3a:L15F) > T23005A(S:N481K) >
Query: T27614C, T23005A [37 seqs]
Earliest seq: 2023-03-30 (EPI_ISL_17454852, Canada/NL)
Most recent seq: 2023-05-23
Sampled Countries: Canada (32, All NL), Australia (5, all NSW)

Genomes: EPI_ISL_17454852, EPI_ISL_17516681, EPI_ISL_17516683, EPI_ISL_17516686, EPI_ISL_17516687, EPI_ISL_17516688, EPI_ISL_17516691, EPI_ISL_17516693, EPI_ISL_17516694, EPI_ISL_17553032, EPI_ISL_17561711, EPI_ISL_17561712, EPI_ISL_17561713, EPI_ISL_17561714, EPI_ISL_17561716, EPI_ISL_17561717, EPI_ISL_17612684, EPI_ISL_17651739, EPI_ISL_17651741, EPI_ISL_17651743, EPI_ISL_17651744, EPI_ISL_17651745, EPI_ISL_17651746, EPI_ISL_17651749, EPI_ISL_17651750, EPI_ISL_17651760, EPI_ISL_17651762, EPI_ISL_17683318, EPI_ISL_17683705, EPI_ISL_17718231, EPI_ISL_17718242, EPI_ISL_17718245, EPI_ISL_17718250, EPI_ISL_17718255, EPI_ISL_17767518, EPI_ISL_17767529

EPI_ISL_17741892

UShER:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_41eec_fdc310.json?c=userOrOld&f_userOrOld=uploaded%20sample

Branch 7: XBB.1.33 + S:N481K

Defining Mutations: XBB.1.33 > C19698T > C29485T > T23005A(S:N481K)
Query: C19698T, C29485T, T23005A
Earliest seq: 2023-05-03 (EPI_ISL_17659088, Campania, Italy)
Latest seq: 2023-07-01 (EPI_ISL_18032333, Noord-Holland, Netherlands)
Sampled Countries: Italy (3), China (1, Shanghai), Spain (1), Netherlands (1)

Genomes: EPI_ISL_17659088, EPI_ISL_17949457, EPI_ISL_17949491, EPI_ISL_17956811, EPI_ISL_17987397, EPI_ISL_18032333

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_36c93_f560.json?f_userOrOld=uploaded%20sample

view from XBB.1.33 polytomy
XBB 1 33+N481K

details
XBB 1 33+N481K_Details

K is predicted to be the most fit mutation on residue 481 of S:
481K Fitness
@FedeGueli FedeGueli added New mutations Lineage with an unusual/new/interesting mutation Multiple lineages labels May 15, 2023
@FedeGueli FedeGueli changed the title FL.1 with S:N481K (Multiple branches, 6 Seqs each, sampled in Brunei, Vietnam, USA and China) FL.1 with S:N481K (Multiple branches, 11/11/8 Seqs each, sampled in Brunei, Vietnam, USA and China) May 24, 2023
@FedeGueli
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I see 11/11/ 8 as count today.
@NkRMnZr could you check the second branch query? i modified a bit cause it ave 98 seqs at first chance.

@NkRMnZr
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NkRMnZr commented May 24, 2023

Thanks @FedeGueli , just found that FL.1>S:Q1208H>S:T478R has been designated FL.1.4, so I refined the query to distinguish the two branches, now branch 1 should have 6 and branch 2 with 5.

@NkRMnZr NkRMnZr changed the title FL.1 with S:N481K (Multiple branches, 11/11/8 Seqs each, sampled in Brunei, Vietnam, USA and China) FL.1 with S:N481K (Multiple branches, 6/5/8 Seqs each, sampled in Brunei, Singapore, Vietnam, South Korea, Canada, USA and China) May 24, 2023
@FedeGueli
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Thx i suspected that!

@FedeGueli FedeGueli changed the title FL.1 with S:N481K (Multiple branches, 6/5/8 Seqs each, sampled in Brunei, Singapore, Vietnam, South Korea, Canada, USA and China) FL.1 with S:N481K (Multiple branches, 8/5/7 Seqs each, sampled in Brunei, Singapore, Vietnam, South Korea, Canada, USA and China) May 31, 2023
@FedeGueli FedeGueli added the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label May 31, 2023
@FedeGueli
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FedeGueli commented May 31, 2023 •
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They seems slow (unsurprising cause N481K popped up multiple times without any advantage as today. Lets wait a couple more of week if they dont grow significatively we will close (better not to waste time in monitoring slow things)

edit ( Thx for proposing. My personal idea that proposing and closing is the best strategy to keep tracks of things fast and slow ones)

@NkRMnZr
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NkRMnZr commented Jun 1, 2023

2 more seqs from England on Branch 1
EPI_ISL_17736728, EPI_ISL_17736792

I'll close this issue next week if it doesn't grow any faster.

@NkRMnZr NkRMnZr changed the title FL.1 with S:N481K (Multiple branches, 8/5/7 Seqs each, sampled in Brunei, Singapore, Vietnam, South Korea, Canada, USA and China) FL.1 with S:N481K (Multiple branches, 10/5/7 Seqs each, sampled in Brunei, Singapore, Vietnam, South Korea, Canada, USA , China & UK) Jun 1, 2023
@FedeGueli
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2 more seqs from England on Branch 1 EPI_ISL_17736728, EPI_ISL_17736792

I'll close this issue next week if it doesn't grow any faster.

Agree likely just lin 1 worth to be monitored on its own. so or you re edit this one or you can open a new one just for lineage one.

@NkRMnZr NkRMnZr closed this as not planned Won't fix, can't repro, duplicate, stale Jun 5, 2023
@FedeGueli
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FedeGueli commented Jun 5, 2023 •
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FL.11 + S:N481K 22 seqs Gisaid: 23005A, C9073T, T28297C
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice27_genome_3238d_d9c830.json?label=id:node_6696050
Schermata 2023-06-05 alle 12 06 27

Maybe worth a preprosal being all quite recent?

@NkRMnZr
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NkRMnZr commented Jun 6, 2023 •
edited by FedeGueli
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MULTIPLE LINEAGES - Updated 26/06 Fede

How about turn this proposal into N481K diversity tracker? Since K has the highest fitness on that residue.
481K Fitness

There are several branches with original proposal:

******** NOW FL.1.6

  • FL.1 > G25186T(S:Q1208H) > T23005A(S:N481K)
  • Query: G25186T, T23005A, C23664T, -C22995G
  • Sequences: 23 (+4) it doesnt seem slow at all.
  • FL.1.4 > T23005A(S:N481K)
  • Query:G25186T, T23005A, C23664T, C22995G]
  • 7 sequences (change 0)
  • FL.1.1 > T23005A(S:N481K
  • Query: A21371C, T23005A, C23664T, C11956T
  • 14 seqs (change 0)
  • FL.11 > T23005A(S:N481K)
  • [Query: 23005A, C9073T, T28297C]
  • 27 Sequences (Change: +1)
  • XBB.1.9.1 > C539T(ORF1a:L92F) > C10977T(ORF1a:A3571V), T23005G(S:N481K)
  • Gisaid: C10977T, T23005G
  • Seqs: 25 (+3)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_242e7_ea23d0.json?f_userOrOld=uploaded%20sample&label=id:node_6696186

  • XBB.1.5.30: G22604A(S:A348T) > T27614C(ORF7a:V74A) > C24358A > C17010T, G25437T(ORF3a:L15F) > T23005A(S:N481K) > [34 seqs]
  • Gisaid : 27614C, C24358A , C17010T, G25437T, T23005A
  • Sequences: 42 (change: +4)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_242e7_ea23d0.json?f_userOrOld=uploaded%20sample

@FedeGueli FedeGueli changed the title FL.1 with S:N481K (Multiple branches, 10/5/7 Seqs each, sampled in Brunei, Singapore, Vietnam, South Korea, Canada, USA , China & UK) S:N481K Carrying lineages Jun 6, 2023
@FedeGueli FedeGueli changed the title S:N481K Carrying lineages Multiple lineages with S:N481K Jun 6, 2023
@FedeGueli FedeGueli removed New mutations Lineage with an unusual/new/interesting mutation Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. labels Jun 6, 2023
@FedeGueli FedeGueli reopened this Jun 6, 2023
@FedeGueli
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Edited : @NkRMnZr now i will update your last post, i ve slight edited to make it more readable

NkRMnZr referenced this issue in cov-lineages/pango-designation Jun 13, 2023
@corneliusroemer
Designate FL.1.6 (S:N481K, S:Q1208H) with 12 seqs
13ec39a
@FedeGueli FedeGueli changed the title Multiple lineages with S:N481K Multiple lineages with S:N481K (updated 26/06) Jun 26, 2023
@FedeGueli FedeGueli changed the title Multiple lineages with S:N481K (updated 26/06) Multiple lineages with S:N481K (updated 09/07) Jul 9, 2023
@FedeGueli
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@NkRMnZr very little new sequences i am tempted to close this one, but if you will find some of these growing please ping me.

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Jul 9, 2023
@HynnSpylor
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Branch 6 has been designated as HM.1 (XBB.1.5.30.1)

FedeGueli referenced this issue in cov-lineages/pango-designation Jul 24, 2023
@corneliusroemer
Designate HM.1 (XBB.1.5.30.1, S:N481K, Canada/Australia) with 50 seqs
84c9030
@FedeGueli FedeGueli modified the milestones: XM.1, HM.1 Jul 24, 2023
@NkRMnZr NkRMnZr changed the title Multiple lineages with S:N481K (updated 09/07) Multiple lineages with S:N481K (updated 07/25) Jul 25, 2023
@Over-There-Is
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@FedeGueli I think FL.1.6 should also be added to the milestone.

@FedeGueli FedeGueli modified the milestones: HM.1, FL.1.6 HM.1 Sep 9, 2023
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