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BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in USA from travellers from Nigeria and Ghana and in China, England ,California and Canada (14 sequences) #2068

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FedeGueli opened this issue Jun 27, 2023 · 21 comments
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BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in USA from travellers from Nigeria and Ghana and in China, England ,California and Canada (14 sequences) #2068

FedeGueli opened this issue Jun 27, 2023 · 21 comments
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JH.1 JH.2

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@FedeGueli
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FedeGueli commented Jun 27, 2023 •
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Just cause I had issues with the pre proposal page (i ve tried to propose it multiple times but it never get saved) so i propose this here:

I think this could be quite urgent to be reviewed:
2 travellers entering United States via Virginia Washington Dalles airport coming from Nigeria have been sampled with this heavily mutated BQ.1.2.2 sublineage defined by 5 S1 Mutations , all known to be beneficial at least in the BQ.1 backbone:
Especially interesting it mutated the S:F486V defining of all BA.4/Ba.5 with S:V486A.
We have already saw S:F486A multiple times and it was succesfull in a BA.5.6 descendant BW.1.1 especially in Mexico.
S:P251L was succesfull in BQ.1.1.38 one of the more resilient lineages among the BQ. Clan
S:K182E popped up multiple times in BQ being the defining mutation of DN.3.1
S:E554K is uptrending globally (when emerging on the XBB backbone) and it was recently designated as defining mutation of FL.10.1
Schermata 2023-06-27 alle 15 25 49
S:S494P was defining of BQ.1.11.1 and BQ.1.19 and recently it is defining of FY.4.1 emerging in Kenya.

Defining mutations:
BQ.1.2.2 (S:K147E,S:V445A) > S:S494P (T23042C) > C10156T, Orf1b:E1888K (G19129A), S:K182E (A22106G),S:P251L (C22314T),S: F486A (T23019C), S:E554K (G23222A), C24865T, G29779T

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5dce0_addf70.json?label=id:node_10393485
Schermata 2023-06-27 alle 15 16 45

Gisaid query : EDITED: T22896C, G26951C,T23042C

Samples: 5 (as 07/07/2023)
EPI_ISL_17851464, EPI_ISL_17851591, EPI_ISL_17971795,
EPI_ISL_17971857, EPI_ISL_17971878

Fusogenicity:
Stuart Turville found BQ.1.2 to be over the average of other BA.5 lineages: see here
@FedeGueli FedeGueli changed the title BQ.1.2.2 with 5 spike mutations sampled in travellers from Nigeria (2) BQ.1.2.2 with 5 spike mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in travellers from Nigeria (2) Jun 27, 2023
@FedeGueli FedeGueli changed the title BQ.1.2.2 with 5 spike mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in travellers from Nigeria (2) BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in travellers from Nigeria (2) Jun 27, 2023
@MCB6
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MCB6 commented Jun 27, 2023 •
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Actually the point of entry to the US is marked as Washington Dalles Airport in Virginia near the nation's capital. On June 15. And these two samples were the only samples ever marked as imported from Nigeria at this location.
Er, corrected. Only one of the 2 samples has origination and vaccination info. The other has none. While there are two samples in this airport marked as from Nigeria, the other Nigeria specimen came moths earlier. Perhaps the two new samples come from the same individual...

@FedeGueli
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thx edited.

@FedeGueli FedeGueli reopened this Jun 27, 2023
@HynnSpylor
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HynnSpylor commented Jul 7, 2023 •
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Today US International Airport reports 3 seqs (from New York). 2 seqs show the travel history from Ghana with different last vaccinated date, then they are from different individuals

@FedeGueli FedeGueli changed the title BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in travellers from Nigeria (2) BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in travellers from Nigeria (5) Jul 7, 2023
@FedeGueli FedeGueli changed the title BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in travellers from Nigeria (5) BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in travellers from Nigeria and Ghana(5) Jul 7, 2023
@FedeGueli
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3 more samples of this one intercepted by airport surveillance (NYC) in travellers from Ghana.

@HynnSpylor
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Today Canada updated 2 samples (despite missing S:P251L)
Further watch needed

@FedeGueli
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There is also a ne Enlgish sequence:
England/CLIMB-CM7YR41G/2023|2023-07-14

@FedeGueli FedeGueli changed the title BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in travellers from Nigeria and Ghana(5) BQ.1.2.2 (S:K147E,S:V445A) with 8 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in USA from travellers from Nigeria and Ghana and in England and Canada Jul 25, 2023
@FedeGueli FedeGueli changed the title BQ.1.2.2 (S:K147E,S:V445A) with 8 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in USA from travellers from Nigeria and Ghana and in England and Canada BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in USA from travellers from Nigeria and Ghana and in England and Canada (8) sequences Jul 25, 2023
@FedeGueli
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ping @corneliusroemer @InfrPopGen @AngieHinrichs @thomaaspeacock i wont wait further to designate this one.

New tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_11a4a_f92df0.json?label=id:node_8114940&s=England/CLIMB-CM7YR41G/2023%7C2023-07-14
Schermata 2023-07-25 alle 11 22 38

Schermata 2023-07-25 alle 11 23 05

@HynnSpylor
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HynnSpylor commented Jul 25, 2023 •
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One more seq from Guangdong Province, China (EPI_ISL_18034523)

@FedeGueli FedeGueli changed the title BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in USA from travellers from Nigeria and Ghana and in England and Canada (8) sequences BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in USA from travellers from Nigeria and Ghana and in China, England and Canada (9) sequences Jul 25, 2023
@FedeGueli
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One more seq from Guangdong Province, China (EPI_ISL_18034523)

bad

@HynnSpylor
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1 more from England, UK

@FedeGueli
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1 more from England, UK

Is this the one already shown by usher or a new one?

@FedeGueli
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1 more from England, UK

@HynnSpylor it was the same mentioned above that wasnt on Gisaid until today.
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1fcda_817d40.json?label=id:node_8165400

@HynnSpylor
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A strange sample in Finland.
It shares S:F486A but without S:K182E, S:P251L, S:S494P and S:E554K, and with S:E484K, N188Y+Del186-187.

I temporarily classify it here
屏幕截图 2023-08-16 180004

屏幕截图 2023-08-16 175644

@FedeGueli
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Very interest one. Being Finland one of the worst hit by BQ.1.2 could be also convergent evo.

@FedeGueli FedeGueli mentioned this issue Aug 19, 2023
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@HynnSpylor
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Today US updates 2 samples, which is consistent with Finland sample

I suggest to open a new issue in preview page

@FedeGueli
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Today US updates 2 samples, which is consistent with Finland sample

I suggest to open a new issue in preview page
Thx!
already opened by @ryhisner . see the issue mentioned just above!

@FedeGueli
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FedeGueli commented Aug 29, 2023 •
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@ryhisner spotted a new one of this not yet on Gisaid from England /CLimb.
Schermata 2023-08-29 alle 23 31 42
tree by Ryan. (Thank you)

There are two more from US: EPI_ISL_18144683, EPI_ISL_18145459 .

@corneliusroemer i think this should be designated it is very likely it has some sort of incidence in western Africa

@FedeGueli FedeGueli changed the title BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in USA from travellers from Nigeria and Ghana and in China, England and Canada (9) sequences BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in USA from travellers from Nigeria and Ghana and in China, England and Canada (13) sequences Aug 29, 2023
@FedeGueli
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Updated tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4ede3_e70ee0.json?label=id:node_8387821
Schermata 2023-08-30 alle 00 38 09

cc @thomasppeacock @AngieHinrichs @corneliusroemer @InfrPopGen i suggest to designate it last sample is from 18/08 England.

@FedeGueli FedeGueli changed the title BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in USA from travellers from Nigeria and Ghana and in China, England and Canada (13) sequences BQ.1.2.2 (S:K147E,S:V445A) with 5 further S1 mutations (S:K182E,S:P251L,S:F486A,S:S494P,S:E554K) sampled in USA from travellers from Nigeria and Ghana and in China, England ,California and Canada (14 sequences) Aug 29, 2023
corneliusroemer added a commit that referenced this issue Aug 31, 2023
@corneliusroemer
Designate JH.1 (BQ.1.2.2.1, West Africa, S:K182E, S:P251L, S:486A, S:…
ebc32aa 
…S494P, S:E554K, from #2068) with 13 seqs

Resolves #2068
Note: It does not have the 22119-22124 deletion (S:186-187, S:N188Y) shared by most other BQ.1.2.2
corneliusroemer added a commit that referenced this issue Aug 31, 2023
@corneliusroemer
Designate JH.2 (BQ.1.2.2.2, S:A484T, S:V486A, USA/Canada/Finland, from …
9043731 
…#2068) with 4 seqs

Shares 22119-22124 deletion with most non-JH.1-BQ.1.2.2*
@corneliusroemer corneliusroemer added this to the JH.1 JH.2 milestone Aug 31, 2023
@AngieHinrichs AngieHinrichs mentioned this issue Aug 31, 2023
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@FedeGueli
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JH.1 tree slighty changed with a Branch with S:L249S that has not S:P251L and further gaiend S:T478R:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_21884_2b9030.json?c=country&label=id:node_8527662
Schermata 2023-09-26 alle 13 26 16

@Sinickle
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image

2 seqs from New Jersey USA collected 9/6 that are on the L249S branch, but do not have K478R

@FedeGueli
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@corneliusroemer that secondary branch is increasing i suggest or to broad JH.1 without S:P251L or to designate this branch with S:L249S

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