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Multiple XBB.1.22.1 lineages with S:R408X #410

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NkRMnZr opened this issue Jul 14, 2023 · 9 comments
Closed
7 tasks

Multiple XBB.1.22.1 lineages with S:R408X #410

NkRMnZr opened this issue Jul 14, 2023 · 9 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. It can not compete It means it has growth disadvantage versus dominant lineages but worth tracking Multiple lineages New mutations Lineage with an unusual/new/interesting mutation

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@NkRMnZr
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NkRMnZr commented Jul 14, 2023 •
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Multiple XBB.1.22.1 lineages with S:R408N or S:R408G
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Branch 1: FY.1.1 with S:R408N

Slow

Defining Mutations: FY.1.1 > G22785A(S:R408N over existing R408S/A22786C)
Query: G22785A, G21809T, G18811A
Earliest seq: 2023-03-15 (EPI_ISL_17487887, Zhejiang, China)
Latest seq: 2023-06-12 (EPI_ISL_17815912, Singapore)
Sampled Countries: Malaysia (8), China (5, Guangdong/3, Yunnan/1, Zhejiang/1), Singapore (3), Australia (2), South Korea (2), Thailand (1)

Genomes: EPI_ISL_17388568, EPI_ISL_17487887, EPI_ISL_17502933, EPI_ISL_17502951, EPI_ISL_17563694, EPI_ISL_17604181, EPI_ISL_17640397, EPI_ISL_17671127, EPI_ISL_17691828, EPI_ISL_17698150, EPI_ISL_17698227, EPI_ISL_17698239, EPI_ISL_17698981, EPI_ISL_17709531, EPI_ISL_17715941, EPI_ISL_17778659, EPI_ISL_17790422, EPI_ISL_17807880, EPI_ISL_17815912, EPI_ISL_17823700-17823701

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_2653e_c639b0.json?c=gt-S_408&label=id:node_6907676
image

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Branch 2: XBB.1.22.1 with S:Q675K mini-saltation then S:R408N, sub-lineage of cov-lineages/pango-designation#2053

Slowly grows in SEA region

Defining Mutations: XBB.1.22.1 > C925A(ORF1a:D220E), G2265A(ORF1a:C667Y), C23585A(S:Q675K) > G22785A(S:R408N over existing R408S/A22786C)
Query: G2265A, C23585A, G22785A
Earliest seq: 2023-03-28 (EPI_ISL_17503882, Brunei)
Latest seq: 2023-06-19 (EPI_ISL_17837743, Singapore)
Sampled Countries: Malaysia (4), Brunei (2), Belgium (1), China (1, Shanghai), Singapore (1)

Genomes: EPI_ISL_17503882, EPI_ISL_17503885, EPI_ISL_17712546, EPI_ISL_17786621, EPI_ISL_17836615, EPI_ISL_17837743, EPI_ISL_17859155, EPI_ISL_17884247, EPI_ISL_17950413,

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2653e_c639b0.json?label=id:node_6909142
image

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Branch 3, XBB.1.22.1 2-step mini-saltation with S:Q675K then S:R408G, another sub-lineage of cov-lineages/pango-designation#2053

Slowly grows in NA region

Defining Mutations: XBB.1.22.1 > C925A(ORF1a:D220E), G2265A(ORF1a:C667Y), C23585A(S:Q675K) > A8072G(ORF1a:N2603D), C13115T, C18744T, A22784G(S:R408G over existing R408S/A22786C), G25423A(ORF3a:G11R), C27427A(ORF7a:L12I)
Query: A22784G, G25423A, C27427A
Earliest seq: 2023-06-06 (EPI_ISL_17951461, Hawaii)
Latest seq: 2023-06-23 (EPI_ISL_17979140, California)
Sampled Countries: USA (5, Arizona/2, California/1, Hawaii/1, Tennessee/1)

Genomes: EPI_ISL_17856656, EPI_ISL_17951461, EPI_ISL_17976413, EPI_ISL_17976435, EPI_ISL_17979140

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2653e_c639b0.json?label=id:node_6909186
image

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Branch 4: FY.5 with S:R408G

Inactive

Defining Mutations: FY.5 > A6019G > G28300A(ORF9b:S6N) > C22088T(S:L176F) > C10408T, A22784G(S:R408G)
Query: A6019G, C22088T, A22784G
Earliest seq: 2023-05-30 (EPI_ISL_17835856, Jakarta, Indonesia)
Latest seq: 2023-08-15 (EPI_ISL_18161750, Iowa, USA)
Sampled Countries: South Korea (2), USA (1), Indonesia (1)

Genomes:

EPI_ISL_17835856, EPI_ISL_18031163, EPI_ISL_18046949, EPI_ISL_18161750

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice4_genome_2653e_c639c0.json?c=gt-S_408&gmax=25384&gmin=21563
image

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Branch 5: XBB.1.22.1 with S:R408N, S:T716I, S:D1153Y

Defining Mutations: XBB.1.22.1 > G2246A(ORF1a:G661S), G26888A > G25019T(S:D1153Y) > C23709T(S:T716I), C24023T > T13890C, G22785A(S:R408N), A28168G(ORF8:E92G)
Query: G2246A, G22785A, G25019T
Earliest seq: 2023-06-29 (EPI_ISL_18076051, Colmar, France)
Latest seq: 2023-08-20 (EPI_ISL_18221560, Mulhouse, France)
Sampled Countries: France (2), Lebanon (1), USA (1)

Genomes:

EPI_ISL_18012789, EPI_ISL_18076051, EPI_ISL_18216522, EPI_ISL_18221560

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice5_genome_2653e_c639c0.json?c=gt-S_408&gmax=25384&gmin=21563&label=id:node_6915951
image

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Branch 6: FY.3 with S:R408N

Defining Mutations: FY.3 > C23191T > T10810C > T1216C, G22785A(S:R408N)
Query: T10810C, G22785A, C23191T
Earliest seq: 2023-07-26 (EPI_ISL_18096933, Nagasaki, Japan)
Latest seq: 2023-08-23 (EPI_ISL_18257739, Hiroshima, Japan)
Sampled Countries: Japan (4)

Genomes:

EPI_ISL_18096933, EPI_ISL_18139672, EPI_ISL_18165254, EPI_ISL_18257739

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice6_genome_2653e_c639c0.json?f_userOrOld=uploaded%20sample&label=id:node_6913141
image

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Trivia:

  • S:R408S/A22786C introduced by BA.2 now seems to have many alterations all of a sudden, especially on XBB.1.22* backbone. Instead of S:R408G and S:R408N, there's also a singlet with triple nuc mutations like S:R408D(A22784G, G22785A, A22786C), Spain/AN-PMC-35778/2023|EPI_ISL_17948484|2023-05-27
    triple
@FedeGueli
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Thx for keeping track of these ones, i have noticed this 408 thing on xbb.1.22.1 backbone in the issue you.mentioned: cov-lineages/pango-designation#2053 (comment)

@FedeGueli FedeGueli added Multiple lineages New mutations Lineage with an unusual/new/interesting mutation labels Jul 14, 2023
@NkRMnZr
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NkRMnZr commented Jul 18, 2023 •
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Tracking updates:

23-07-18: 1 sequence from California, USA on Branch 3: EPI_ISL_17986352
23-07-28: adding sequences on Branch 2/3/4

@NkRMnZr
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NkRMnZr commented Jul 28, 2023

23-07-28

Branch 2: 3 seqs from Malaysia: EPI_ISL_18040854, EPI_ISL_18040876-18040877

Branch 3: 2 seqs from California: EPI_ISL_18045913, EPI_ISL_18046174

Branch 4: 2 seqs from South Korea: EPI_ISL_18031163, EPI_ISL_18046949

@FedeGueli FedeGueli added the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Aug 6, 2023
@FedeGueli
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@NkRMnZr thanks for tracking them. they seem to me all slow. Closing them all now.

@FedeGueli FedeGueli added the It can not compete It means it has growth disadvantage versus dominant lineages but worth tracking label Aug 6, 2023
@NkRMnZr NkRMnZr mentioned this issue Aug 6, 2023
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@NkRMnZr NkRMnZr mentioned this issue Sep 2, 2023
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@NkRMnZr
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NkRMnZr commented Sep 21, 2023

Made an update, was courious which one surges after a long hiatus, and it was #296 @FedeGueli

@FedeGueli
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Made an update, was courious which one surges after a long hiatus, and it was #296 @FedeGueli

Thank you. I ve reopened it

@FedeGueli FedeGueli reopened this Sep 26, 2023
@NkRMnZr
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NkRMnZr commented Sep 26, 2023

Branch 1 now got K356T and T478Q, follows:
Branch 1 > C5884T > G393A(ORF1a:R43H) > A1072G, A3744G(ORF1a:H1160R), C17012T(ORF1b:S1182L), A22629C(S:K356T), A22994C(S:T478Q)

@NkRMnZr
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NkRMnZr commented Oct 15, 2023

seems slowed again

@NkRMnZr NkRMnZr closed this as not planned Won't fix, can't repro, duplicate, stale Oct 15, 2023
@FedeGueli
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Thx for tracking them

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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. It can not compete It means it has growth disadvantage versus dominant lineages but worth tracking Multiple lineages New mutations Lineage with an unusual/new/interesting mutation
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