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Multiple FL.2.3 lineages with S:F456L (Branch 1 with further S:L455F) #526

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NkRMnZr opened this issue Aug 2, 2023 · 38 comments
Closed
4 tasks

Multiple FL.2.3 lineages with S:F456L (Branch 1 with further S:L455F) #526

NkRMnZr opened this issue Aug 2, 2023 · 38 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. S:456

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@NkRMnZr
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NkRMnZr commented Aug 2, 2023 •
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Multiple FL.2.3 lineages with S:F456L
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Branch 1

Defining Mutations: FL.2.3 > T22928C(S:F456L)
Query: C11956T, A17615G, T22928C, -G4881A, -T16977C, -C23123T
Earliest seq: 2023-06-05 (EPI_ISL_17831356, Pannes, France)
Latest seq: 2023-07-20 (EPI_ISL_18055248, Ontario, Canada )
Sampled Countries: China (4, Guangdong), Canada (2, Ontario), France (1), USA (1)

Genomes:

EPI_ISL_17831356, EPI_ISL_18022536, EPI_ISL_18034758, EPI_ISL_18034800, EPI_ISL_18036427, EPI_ISL_18036680, EPI_ISL_18055248, EPI_ISL_18055262

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_28f0a_b938b0.json?label=id:node_7021952
image

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Branch 2

Inactive

Defining Mutations: FL.2.3 > G28839T(N:R189L) > T16977C > T22928C(S:F456L)
Query: T16977C, A17615G, T22928C
Earliest seq: 2023-05-01 (EPI_ISL_17625561, Shanghai, China)
Latest seq: 2023-06-05 (EPI_ISL_17836662, Shanghai, China)
Sampled Countries: China (4, Shanghai)

Genomes:

EPI_ISL_17625561, EPI_ISL_17811306, EPI_ISL_17811318, EPI_ISL_17836662

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_28f0a_b938b0.json?f_userOrOld=uploaded%20sample&label=id:node_7022200
image

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UShER:

Trivia:

  • Note that the only sample from Branch 1 without N:R189L is France/GES-IPP15690/2023|EPI_ISL_17831356|2023-06-05, so these may be the same branch got separated by potential dropout.
  • Guangdong/GDCDC_SZHG_1719/2023|EPI_ISL_18036297|2023-06-03 seems to be a recominant of Branch 1 with XBB.2.3*, the query is using -C23123T to filter it out.

Triplets

  • South_Korea/KDCA261207/2023|EPI_ISL_18239231|2023-08-15 and South_Korea/KDCA261464/2023|EPI_ISL_18239448|2023-08-18
    FL.2.3 > G4881A(ORF1a:S1539N) > T7633C, C12754T, C17403T, T22928C(S:F456L), C26936T, C28087T(ORF8:A65V) [Query: G4881A, A17615G, T22928C, 3, 09/27]

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@NkRMnZr NkRMnZr mentioned this issue Aug 2, 2023
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@Over-There-Is
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Guangdong/GDCDC_SZHG_1719/2023|EPI_ISL_18036297|2023-06-03 FL.2.3 / XBB.2.3.7 Mutations based on FL.2.3: A4479C, T9076C, C12853T | T22317Grev, A22320G, T22928C, C23123T, C26447T, C27431T, T27915Grev, C28297Trev, C28717A, G29706T Mutations based on XBB.2.3: T4234Crev, A4479C, T4579A, G5720A, A6536Grev, T9076C, C11956T, C12789T, C12853T, T16342C, A17615G | T22928C, C26447T, C28717A

Breakpoint: 17615~22317

FL.2.3+T9076C 5 seqs (All in Nanping, Fujian, China) FL.2.3> G28980T(N:G236V)> T9076C, T28157G(Orf8:I88M)

XBB.2.3+C26447T, C28717A 14seqs (Fujian 12[Nanping 10, Sanming 2], Singapore 1, Victoria, Australia 1) XBB.2.3.7> G11042A(Orf1a:V3593I)> G1401A(Orf1a:G379E)> A3503G(Orf1a:N1080D), C8950T> C28717A> C26447T(E:S68F)

Private mutations: A4479C(Orf1a:K1405T), C12853T, T22928C(S:F456L)

Probably originates in Nanping, and exported to somewhere out of Chinese Mainland, and detected by Shenzhen Customs when entering.

#108

@Over-There-Is
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I think the French sequences is just convergent, and the branch 1 should be FL.2.3> N:R189L> S:F456L.
But I am not sure whether the branch 2 is FL.2.3> N:R189L> S:F456L> T16977C or FL.2.3> N:R189L> T16977C> S:F456L.
FL.2.3> N:R189L> T16977C have only 1 sequence in Canada, but a synonymous mutation should be less convergent than S:F456L.

@FedeGueli
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FedeGueli commented Aug 8, 2023 •
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One more sequence fro Branch 2 collected in July in Shanghai

@NkRMnZr
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NkRMnZr commented Aug 9, 2023 •
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Tracking updates:

08-08, Branch 1, +1 (Québec, Canada): EPI_ISL_18073999; Branch 2 +1 (Shanghai, China): EPI_ISL_18074552

08-18, Branch 1: 2 seqs from China

08-26, Branch 1, +1 (USA)

09-01, Branch 1, +3 (Canada)

09-08, Branch 1, +2 (USA), one saltation branch with further S:L455F EPI_ISL_18225798, EPI_ISL_18239091

@NkRMnZr NkRMnZr changed the title Multiple FL.2.3 lineages with S:F456L (8/4) Multiple FL.2.3 lineages with S:F456L (9/5) Aug 9, 2023
@Over-There-Is
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Branch 1 +1(Shanghai)
and a sequence from Henan under T14961C branch gains F456L convergently.

@FedeGueli FedeGueli changed the title Multiple FL.2.3 lineages with S:F456L (9/5) Multiple FL.2.3 lineages with S:F456L (10/5) Aug 17, 2023
@FedeGueli FedeGueli changed the title Multiple FL.2.3 lineages with S:F456L (10/5) Multiple FL.2.3 lineages with S:F456L (9/5) Aug 17, 2023
@Over-There-Is
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@FedeGueli 2 Canadian sequences are 4579 dropped-out, and 1 Chinese sequence is convergent, so it's actually 10 seqs.

@FedeGueli FedeGueli changed the title Multiple FL.2.3 lineages with S:F456L (9/5) Multiple FL.2.3 lineages with S:F456L (10/5) Aug 18, 2023
@NkRMnZr
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NkRMnZr commented Aug 19, 2023

08-18, Branch 1: 2 seqs from China

1 from Henan: EPI_ISL_18105470
1 from Shanghai: EPI_ISL_18108609

@NkRMnZr NkRMnZr changed the title Multiple FL.2.3 lineages with S:F456L (10/5) Multiple FL.2.3 lineages with S:F456L (11/5) Aug 19, 2023
@NkRMnZr NkRMnZr changed the title Multiple FL.2.3 lineages with S:F456L (11/5) Multiple FL.2.3 lineages with S:F456L (12/5) Aug 26, 2023
@NkRMnZr
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NkRMnZr commented Aug 26, 2023

08-26, Branch 1, +1 (USA): EPI_ISL_18126784

@FedeGueli
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why i got 10 with T4579A, A17615G, T22928C, -T16977C, -C23123T??

@NkRMnZr
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NkRMnZr commented Aug 28, 2023

why i got 10 with T4579A, A17615G, T22928C, -T16977C, -C23123T??

Ah I forgot to copy the updated one on tasklist header, again, try this C11956T, A17615G, T22928C, -T16977C, -C23123T, it can find 12
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e9e4_c6cbb0.json?f_userOrOld=uploaded%20sample

@FedeGueli
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Thank you!

@Over-There-Is
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But I don't think EPI_ISL_18105470 belongs to Branch 1.

@NkRMnZr NkRMnZr changed the title Multiple FL.2.3 lineages with S:F456L (12/5) Multiple FL.2.3 lineages with S:F456L (15/5) Sep 1, 2023
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NkRMnZr commented Sep 1, 2023

09-01, Branch 1, +3 (Canada)

Branch 1, 3 seqs from Québec and New Brunswick: EPI_ISL_18157427-18157428, EPI_ISL_18168488
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_41181_1c6b30.json?f_userOrOld=uploaded%20sample
Branch1

@FedeGueli
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I want to see how they will behave with the newcoming dominant lineages.

@Over-There-Is
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Over-There-Is commented Sep 6, 2023 •
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NY+1, on the Orf8:Q18* branch

@Over-There-Is
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USA/WA-GBW-H10-016-4168/2023|EPI_ISL_18239091|2023-08-31 FL.2.3>N:R189L>S:F456L>Saltated and gained L455F.

@Over-There-Is
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2 South Korean sequences under FL.2.3> G4881A(Orf1a:S1539N) gained F456L.

@Over-There-Is
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2023-09-09 (9)
2023-09-09 (10)
2023-09-09 (11)
2023-09-09 (5)
2023-09-09 (6)

@Over-There-Is
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Since F456L is homoplastic enough, and N:R189L is the largest branch of FL.2.3, EPI_ISL_17831356 and N:R189L>S:F456L are doubtless unrelated. But I'm not sure whether Canada/NS-NSH-632615/2023|EPI_ISL_17799177|2023-06-05 a sequence with S:F456L dropout, and whether branch 2 a subbranch of N:R189L>S:F456L.

@FedeGueli
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We could add them as branches if you agee just give me the queries and the defining mutations for each branch.

@NkRMnZr NkRMnZr changed the title Multiple FL.2.3 lineages with S:F456L (15/5) Multiple FL.2.3 lineages with S:F456L (17/5) Sep 8, 2023
@Over-There-Is
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Branch A: G28839T, T22928C, -T16977C
15 seq, CA 6, CN 5, US 4. 06-10~08-31.
Still growing, 1 sequence gained L455F recently.
FL.2.3> G28839T(N:R189L)> T22928C(S:F456L)

Branch B: G28839T, T22928C, T16977C
5 seq, Shanghai, China. 05-01~07-05.
FL.2.3> G28839T(N:R189L)> T16977C> T22928C(S:F456L) or FL.2.3> G28839T(N:R189L)> T22928C(S:F456L)> T16977C?

Branch C: A17615G, G4881A, T22928C
2 seq, South Korea, new branch.
FL.2.3> G4881A(Orf1a:S1539N)> T7633C, C12754T, C17403T, T22928C(S:F456L), C26936T, C28087T(Orf8:A65V)

Singlet a: Guangdong/GDCDC_SZHG_1719/2023|EPI_ISL_18036297|2023-06-03 inactive
T9076C, C28717A
FL.2.3> G28980T(N:G236V)> T9076C, T28157G(Orf8:I88M) recombined with
XBB.2.3.7> G11042A(Orf1a:V3593I)> G1401A(Orf1a:G379E)> A3503G(Orf1a:N1080D), C8950T> C28717A> C26447T(E:S68F)
then A4479C(Orf1a:K1405T), C12853T, T22928C(S:F456L)

Singlet b: Henan/PYCDC-LG23695/2023|EPI_ISL_18105470|2023-07-18 inactive
A17615G, T14961C, T22928C
FL.2.3> T14961C> C2704T, C22388T, T22928C(S:F456L), A25201C

Singlet c: France/GES-IPP15690/2023|EPI_ISL_17831356|2023-06-05 inactive
G5720A, A17615G, T22928C, -G28839T, -G4881A, -A22320G, -T14961C
FL.2.3> G3197A(Orf1a:D978N), C4890A(Orf1a:T1542N), T22928C(S:F456L), C27247A(Orf6:L16I)

@NkRMnZr
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NkRMnZr commented Sep 9, 2023

@FedeGueli
We could add them as branches if you agee just give me the queries and the defining mutations for each branch.

Now things got complicated, as it is when FL.2.3 designated (homoplastic and spike_146-148 mutation-or-artifact involved). If N:R189L did happen before S:F465L, Branch 1 and 2 could be merged, and the French lineage will be decided whether it has dropout or not; if current path of S:F456L > N:R189L is correct, it would be the situation @Over-There-Is listed above with multiple very similar lineages with S:F456L

@FedeGueli
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@FedeGueli
We could add them as branches if you agee just give me the queries and the defining mutations for each branch.

Now things got complicated, as it is when FL.2.3 designated (homoplastic and spike_146-148 mutation-or-artifact involved). If N:R189L did happen before S:F465L, Branch 1 and 2 could be merged, and the French lineage will be decided whether it has dropout or not; if current path of S:F456L > N:R189L is correct, it would be the situation @Over-There-Is listed above with multiple very similar lineages with S:F456L

@AngieHinrichs what do you think?

@Over-There-Is
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A405G, A17615G, G28839T gives 651 sequences, and A405G, -A17615G, G28839T only gives 38, and 24 Indian low-quality sequences are included. That means, for XBB* variants, G28839T is not homoplastic. So, it is more likely for N:R189L to come before S:F456L.

@FedeGueli
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A405G, A17615G, G28839T gives 651 sequences, and A405G, -A17615G, G28839T only gives 38, and 24 Indian low-quality sequences are included. That means, for XBB* variants, G28839T is not homoplastic. So, it is more likely for N:R189L to come before S:F456L.

That is what i recalled too. Thx.

@Over-There-Is
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FLip +1
2023-09-15 (1)

@NkRMnZr NkRMnZr changed the title Multiple FL.2.3 lineages with S:F456L (17/5) Multiple FL.2.3 lineages with S:F456L (Branch 1 with further S:L455F) Sep 15, 2023
@Over-There-Is Over-There-Is mentioned this issue Sep 15, 2023
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@AngieHinrichs
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So, it is more likely for N:R189L to come before S:F456L.

I think this is fixed in the 2023-09-15 tree which will be on the main site in about an hour.

@Over-There-Is
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New singlet: USA/KY-CDC-QDX84229412/2023|EPI_ISL_18265617|2023-08-21
FL.2.3> G28980T(N:G236V)> C7948T> C13366T> T22930G(S:F456L), T25496C(Orf3a:I35T), C27752T(Orf7a:T120I)
Rather than T22928C, this one is T22930G.

@FedeGueli FedeGueli added Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. and removed Rapid review needed labels Sep 18, 2023
@FedeGueli
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23 for Branch 1 now. but still it seems slow to me.

@Over-There-Is
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New singlet: Canada/NS-NSH-644347/2023|EPI_ISL_18282191|2023-09-01
FL.2.3> G28839T(N:R189L)> C19970T(Orf1b:A2168V)> C6636T(Orf1a:T2124I), G22927C(S:L455F), T22930A(S:F456L), A29499T(N:Q409L)

@Over-There-Is
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One more sequence from FL.2.3> G4881A(Orf1a:S1539N)> T7633C, C12754T, C17403T, T22928C(S:F456L), C26936T branch, without Orf8:A65V

@Over-There-Is
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env/Germany/BY-LGL-5992988/2023|EPI_ISL_18343249|2023-09-11
N:R189L> S:F456L branch, but contaminated by XBB.1.16* and dropped out S:F456L.

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NkRMnZr commented Oct 9, 2023

Too slow, tracking it privately

@NkRMnZr NkRMnZr closed this as not planned Won't fix, can't repro, duplicate, stale Oct 9, 2023
@Over-There-Is
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USA/NY-CDC-QDX84402965/2023|EPI_ISL_18375139|2023-08-25

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Canada/BC-BCCDC-661172/2023|EPI_ISL_18453145|2023-10-14 new singlet?

@FedeGueli FedeGueli mentioned this issue Nov 13, 2023
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@Over-There-Is Over-There-Is mentioned this issue Nov 14, 2023
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@Over-There-Is
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Over-There-Is commented Nov 14, 2023 •
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One more sequence from FL.2.3> G4881A(Orf1a:S1539N)> T7633C, C12754T, C17403T, T22928C(S:F456L), C26936T branch, without Orf8:A65V

+2

@Over-There-Is
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Canada/BC-BCCDC-661172/2023|EPI_ISL_18453145|2023-10-14 new singlet?

+3

@FedeGueli
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generally it looks still much slower than Hk.3 : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=4579A%2CA17615G%2CT22928C&analysisMode=CompareToBaseline&

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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. S:456
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