EG.5.1/XBB.1.5.70 recombinants, Belgium/France/Spain/Denmark (9 seqs)

[corneliusroemer]

Came across some potential undesignated recombinants that share properties of both EG.5.1 and XBB.1.5.70

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_123b8_fc5810.json?label=id:node_3717968

hCoV-19/Belgium/UGent-1524/2023
hCoV-19/Denmark/DCGC-661082/2023
hCoV-19/Belgium/AZDelta-2340-02185/2023
hCoV-19/Belgium/AZDelta-2340-02136/2023
hCoV-19/Belgium/AZDelta-2339-05890/2023
hCoV-19/Spain/CT-HUVH-M26038/2023
hCoV-19/France/PAC-HCL723000936001/2023

GISAID Query: T28297C, C29625T,C1889T, C2334T, G12467T

Probably multiple recombinants, the top one is likely a single one (3x Belgium, 1x Spain) - if someone wants to do a breakpoint analysis, be my friend!

[xz-keg]

The top one is #947

Others seem to be different new recombs.

[corneliusroemer]

Thanks @aviczhl2! I wonder how we can make it easier to find recombinants that have already been analyzed.

Maybe a google sheet where we have a list of strain names associated with each proposed recombinant.

Also, would be great to have some more structured format for analysis of proposed recombinants to make it easier to check if a recombinant has already been described and to which extent (e.g. fine grained breakpoint and donor analysis or not)

[xz-keg]

Thanks @aviczhl2! I wonder how we can make it easier to find recombinants that have already been analyzed.

It seems difficult.

Firstly we shouldn't rely on fixed usher tree placements(eg under which variant) as they may change. As far as I know XCV experienced at least 2 placement changes, and other recombs also.

Maybe we can use private mutations but it is not easy to figure out private mutations at the first glance too.

There are some manual labels like mixBA1BA2postspike for past BA.1/BA.2 recombs on usher, is it easy to create such labels so that each recomb is tied to a label #n when proposed?

[xz-keg]

Maybe we can maintain a google sheet for labels on usher tree. Everyone just add seq IDs to that sheet? With only that sheet we still get nothing but if that can be added to usher tree it will be helpful.

@AngieHinrichs, is it possible to process such a sheet automatically every day and assign labels to the correlating variants accordingly?

[corneliusroemer]

I think it would be best to keep it light for a start and not wire it into Usher (unless this is easy for Angie).

What we'd want is essentially something similar to lineages.csv but for not-yet-designated recombinants.

We could maintain it in this repo here and call it recombinants.csv and a simple format:

strain,issue_URL

I will create an example for the top cluster. This could then be easily searched by anyone using e.g. grep and a list of strain names to see if the recombinant has been proposed.

[corneliusroemer]

@aviczhl2 I've created a recombinants.tsv in the root of the repo

One can easily add the recombinants with the helper script utils/add_to_recombinants.sh with the tsv that one gets from Usher/Auspice through the "Download metadata interface"

See: https://github.com/sars-cov-2-variants/lineage-proposals/blob/main/recombinants.tsv

[xz-keg]

@aviczhl2 I've created a recombinants.tsv in the root of the repo

One can easily add the recombinants with the helper script utils/add_to_recombinants.sh with the tsv that one gets from Usher/Auspice through the "Download metadata interface"

See: https://github.com/sars-cov-2-variants/lineage-proposals/blob/main/recombinants.tsv

Currently only @FedeGueli has the access to edit anything in the repo, others have to create merge requests and that may cause conflicts if multiple people push at the same time.

I guess we shall attach the .tsv in the proposal and let Fede add them.

[corneliusroemer]

@aviczhl2 I'll give you write access to the repo then you can add them directly!

[xz-keg]

@aviczhl2 I'll give you write access to the repo then you can add them directly!

Sure.

[xz-keg]

I'm start maintaining that .tsv now.

For this issue besides what proposed in #947 I'd like to separate the rest into 3 branches (as they're 3 different recombs)

Branch 1 for France/GES-IPP16300/2023|EPI_ISL_18076084|2023-07-10
Branch 2 for France/PAC-HCL723000936001/2023|EPI_ISL_18228989|2023-08-07
Branch 3 for
Belgium/UGent-1524/2023|EPI_ISL_18403134|2023-10-01 and
Denmark/DCGC-661082/2023|EPI_ISL_18377615|2023-09-25

[corneliusroemer]

Yep great! For a start it's fine to just have the issue url as opposed to the exact branch number.

[FedeGueli]

I'm start maintaining that .tsv now.

For this issue besides what proposed in #947 I'd like to separate the rest into 3 branches ,

Branch 1 for France/GES-IPP16300/2023|EPI_ISL_18076084|2023-07-10 Branch 2 for France/PAC-HCL723000936001/2023|EPI_ISL_18228989|2023-08-07 Branch 3 for Belgium/UGent-1524/2023|EPI_ISL_18403134|2023-10-01 and Denmark/DCGC-661082/2023|EPI_ISL_18377615|2023-09-25

thank you

[NkRMnZr]

the XBB.1.5.70* side donor for Belgium/UGent-1524/2023|EPI_ISL_18403134|2023-10-01 is probably GK.4 (C14396T, C18807T, C22986T)

[AngieHinrichs]

See: https://github.com/sars-cov-2-variants/lineage-proposals/blob/main/recombinants.tsv

That is perfect! I will start importing that into the build tomorrow (2023-10-19). Thanks @corneliusroemer and @aviczhl2 !

[FedeGueli]

9 now with one sample uploaded today from Denmark. it seems slow.

[xz-keg]

The usher tree seems completely altered for the proposal and the 4 recombs seem separated apart now,

[FedeGueli]

The usher tree seems completely altered for the proposal and the 4 recombs seem separated apart now,

closing it for now.

[FedeGueli]

the two usher are :
1
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_55db7_7be930.json?label=id:node_3604994

2
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_55db7_7be930.json?f_userOrOld=uploaded%20sample&label=id:node_3721821