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Another BA.2.86* sublineage with S:A475V (26 seqs in 5 countries, including Belgian hospital cluster) #1009

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HynnSpylor opened this issue Oct 24, 2023 · 23 comments
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Another BA.2.86* sublineage with S:A475V (26 seqs in 5 countries, including Belgian hospital cluster) #1009

HynnSpylor opened this issue Oct 24, 2023 · 23 comments
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BA.2.86 designated S:475
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JN.4

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@HynnSpylor
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HynnSpylor commented Oct 24, 2023 •
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Defining mutations:

BA.2.86>A6183G (ORF1a:K1973R, but without C12815T)>C22986T (S:A475V)
GISAID query: A6183G, C22986T, -T3565C, -C22978T
Earliest seq: 2023-09-18 (Netherlands- EPI_ISL_184331408)
Most recent seq: 2023-10-19 (Belgium- EPI_ISL_18429484)
Countries detected: Belgium (4), Netherlands (1)
**The 4 Belgian sequences are submitted by @kdurkin. Thanks for the work!

Usher Tree:
QQ截图20231024215024
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1ab4b_7c3a50.json

Notice that another Spanish branch of BA.2.86.1* also gets S:A475V (has been proposed in #954)

Recently, S:A475V is increasing rapidly in some XBB* sublineages. We can monitor whether it can work well in BA.2.86*.

Genomes:
EPI_ISL_18331408, EPI_ISL_18429476-18429477, EPI_ISL_18429481, EPI_ISL_18429484
@kdurkin
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kdurkin commented Oct 24, 2023 •
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You did not give me much time to post this myself, some context for the 4 Belgian sequences, all come from the same small healthcare centre so its probably an outbreak in that centre.

@HynnSpylor
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HynnSpylor commented Oct 24, 2023 •
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Ah sorry for that @kdurkin I just notice that you are the submitter!
I'm tracking the BA.2.86*+RBD key points (455, 456, 475, 490, etc.) so I proposed it at once

@kdurkin
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kdurkin commented Oct 24, 2023

no problem

@Huachuan1120
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France+1, EPI_ISL_18441084

@HynnSpylor HynnSpylor changed the title Another BA.2.86* sublineage with S:A475V (5 seqs in Belgium and Netherlands) Another BA.2.86* sublineage with S:A475V (6 seqs in Belgium, Netherlands and France) Oct 28, 2023
@Memorablea Memorablea mentioned this issue Oct 30, 2023
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@kdurkin
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kdurkin commented Oct 30, 2023

14 additional samples from Belgian, all belong to the same healthcare centre cluster as the first 4 Belgian samples.
EPI_ISL_18445514
EPI_ISL_18445515
EPI_ISL_18445516
EPI_ISL_18445517
EPI_ISL_18445518
EPI_ISL_18445519
EPI_ISL_18445520
EPI_ISL_18445521
EPI_ISL_18445522
EPI_ISL_18445523
EPI_ISL_18445524
EPI_ISL_18445525
EPI_ISL_18445545
EPI_ISL_18445550

@JosetteSchoenma
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Indeed. The 13 black dots all say 'Hospital cluster' on GISAID.
Screenshot_20231030_161418_X.jpg

@JosetteSchoenma
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I say 13, but it's indeed probably 14. EPI_ISL_18445525 has N at S:A475V and several other nucleotides.

@HynnSpylor HynnSpylor changed the title Another BA.2.86* sublineage with S:A475V (6 seqs in Belgium, Netherlands and France) Another BA.2.86* sublineage with S:A475V (20 seqs in Belgium, Netherlands and France, including Belgian hospital cluster) Oct 30, 2023
@kdurkin
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kdurkin commented Oct 30, 2023

I did the sequencing, all 14 samples came from the same facility, a few have high Ns.

@JosetteSchoenma
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I did the sequencing, all 14 samples came from the same facility, a few have high Ns.

Did the ones that were found earlier also come from the same hospital? They aren't tagged 'hospital cluster' but are in the same branch. White dots. Ending in 476, 477, 481 and 484. Or were they only sequenced in the same lab?
Screenshot_20231030_161418_X.jpg

@kdurkin
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kdurkin commented Oct 30, 2023

I did the sequencing, all 14 samples came from the same facility, a few have high Ns.

Did the ones that were found earlier also come from the same hospital? They aren't tagged 'hospital cluster' but are in the same branch. White dots. Ending in 476, 477, 481 and 484. Or were they only sequenced in the same lab? Screenshot_20231030_161418_X.jpg

Yes they came from the same hospital, I only became aware that they were part of a cluster after they were submitted to GISAID.

@JosetteSchoenma
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Thanks!

@Huachuan1120

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@Huachuan1120
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England,UK+1, EPI_ISL_18457932
Finland+1, EPI_ISL_18458444

@HynnSpylor
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HynnSpylor commented Nov 2, 2023 •
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The UK and Finland seqs are indeed on the branch. But the Spanish seq updated yesterday is not.
Also notice that Finland seq gets S:S680F
QQ截图20231102212602

@HynnSpylor HynnSpylor changed the title Another BA.2.86* sublineage with S:A475V (20 seqs in Belgium, Netherlands and France, including Belgian hospital cluster) Another BA.2.86* sublineage with S:A475V (22 seqs in 5 countries, including Belgian hospital cluster) Nov 2, 2023
@Huachuan1120
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Thanks to @HynnSpylor for correction!

@HynnSpylor
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One more seq in France.

@HynnSpylor HynnSpylor changed the title Another BA.2.86* sublineage with S:A475V (22 seqs in 5 countries, including Belgian hospital cluster) Another BA.2.86* sublineage with S:A475V (23 seqs in 5 countries, including Belgian hospital cluster) Nov 3, 2023
@Huachuan1120
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Netherlands+1，EPI_ISL_18463265

@Huachuan1120
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Denmark+1, EPI_ISL_18472838

@FedeGueli FedeGueli changed the title Another BA.2.86* sublineage with S:A475V (23 seqs in 5 countries, including Belgian hospital cluster) Another BA.2.86* sublineage with S:A475V (24 seqs in 5 countries, including Belgian hospital cluster) Nov 7, 2023
@kdurkin
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kdurkin commented Nov 9, 2023 •
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12 additional samples, Belgium and Spain

9 from ULG Belgium

3 are form the same facility as the 18 in the "Belgian hospital cluster" and are labelled in GISAID as active surveillance
hCoV-19/Belgium/ULG-301442/2023|EPI_ISL_18487847
hCoV-19/Belgium/ULG-301443/2023|EPI_ISL_18487848
hCoV-19/Belgium/ULG-301444/2023|EPI_ISL_18487849

4 cluster with the "Belgian hospital cluster" but do not have a know connection, sampled in different hospital, labelled in GISAID as baseline surveillance
hCoV-19/Belgium/ULG-301446/2023|EPI_ISL_18487851
hCoV-19/Belgium/ULG-301452/2023|EPI_ISL_18487857
hCoV-19/Belgium/ULG-301456/2023|EPI_ISL_18487861
hCoV-19/Belgium/ULG-301467/2023|EPI_ISL_18487872

Other 2 do not cluster with the "Belgian hospital cluster", sequenced as part as baseline surveillance
hCoV-19/Belgium/ULG-301468/2023|EPI_ISL_18487873
hCoV-19/Belgium/ULG-301476/2023|EPI_ISL_18487881

2 samples from other Belgian labs
hCoV-19/Belgium/AZDelta-2343-04107/2023|EPI_ISL_18486570|2023-11-02
hCoV-19/Belgium/Jessa_11-2343-007069/2023|EPI_ISL_18486684|2023-10-29

Spanish sample
hCoV-19/Spain/CT-LabRefCat-079590328300/2023|EPI_ISL_18485651|2023-10-10
BA 2 86

@FedeGueli FedeGueli changed the title Another BA.2.86* sublineage with S:A475V (24 seqs in 5 countries, including Belgian hospital cluster) Another BA.2.86* sublineage with S:A475V (26 seqs in 5 countries, including Belgian hospital cluster) Nov 9, 2023
@Over-There-Is
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JN.4

@NkRMnZr NkRMnZr mentioned this issue Nov 12, 2023
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@Over-There-Is
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Over-There-Is commented Nov 12, 2023 •
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USA/MD-MDH-9068/2023|EPI_ISL_18403840|2023-10-03 & USA/MD-MDH-9069/2023|EPI_ISL_18403841|2023-10-03
dropout or convergence?

@Over-There-Is
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2023-11-12 (5)
@corneliusroemer

FedeGueli referenced this issue in cov-lineages/pango-designation Nov 12, 2023
@corneliusroemer
Designate JN.4 (BA.2.86.1 with S:A475V but lacking C12815T), with 35 …
8c291c7 
…seqs
@FedeGueli FedeGueli added this to the JN.4 milestone Nov 12, 2023
@FedeGueli
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Designated JN.4 via cov-lineages/pango-designation@8c291c7

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