XBB.1.16/XBC.1.6 recombinant 18 samples Australia

[JosetteSchoenma]

EDITED: This was first spotted by @ryhisner in https://github.com/sars-cov-2-variants/lineage-proposals/issues/400 , then it seemed dying off until @JosetteSchoenma rediscovered it and analysed it further.

Query T3802C, G7091A, C25708T 9 samples EPI_ISL_18411395 EPI_ISL_18410952 EPI_ISL_18396131 EPI_ISL_18396104 EPI_ISL_18324919 EPI_ISL_18324890 EPI_ISL_17975448 EPI_ISL_17975402 EPI_ISL_17924212

Looks like more than 1 breaking point. I will run a Sc2rf and add more info later.

Compared to XBC.1.6

Rapid overview:(edited)

[JosetteSchoenma]

I think it has got 4 breaking points FU - |4321 - 6196 (ORF1a)| - XBC - |23670 (S) - 26060 (ORF3a)| - FU - |26275 (E) - 26767 (M)| - XBC - |27915 (no ORF8*) - 28297 (ORF9b)| - FU So, an XBC.1.6 Spike.

[JosetteSchoenma]

New one from Queensland. EPI_ISL_18435095 This makes 2 for Queensland, South Australia, and Australian Capital territory and 4 for New South Wales.

[JosetteSchoenma]

2 new ones from South Australia. Looks like GISAID held them back for a while. Recent EPI_ISL numbers but a week old submission dates. EPI_ISL_18453819 EPI_ISL_18453803 Last upload from NSW on the 20th of October, so expecting one in 2 days, if they do a biweekly upload.

[FedeGueli]

Josette i was looking a bit deeper into this it is very interesting it kept the orf8 not expressed via 27890T and Orf8:K2T (instead of the Orf8*) and also kept the new shorter Orf7b described by @Ryhisner gaining the double mutated XBB.1.16 Orf9b in this linegae triple mutated and instead it has Orf6 restored as XBC while keeping E:9/E:11 from BA.2.75 and instead M from Delta.

So if would like to divide its protein for ancestor we would have: NSp1-NSP3 from BA.2.10 (BJ.1) NSP3-NSP16 , from Delta NTD from Delta/XBC RBD from BA.2/XBC.1.6 FCS S2 from BA.2 ORF3A from BA.2 E from BA.2.75 M from Delta Orf7a from Delta Orf7b New shape via XBC Orf8 ablated via XBC Orf9b from XBB.1.16 with three mutations N = BA.2

[FedeGueli]

@ryhisner spotted this long time ago : https://github.com/sars-cov-2-variants/lineage-proposals/issues/400 then it seemed disappeared ! But it is the same. I think @JosetteSchoenma got right all the breakpoints so i leave this open ! i will add credit to Ryan! Sorry for not understanding it was the same but some difference in the proposal fooled me.

[FedeGueli]

+2 NSW

[JosetteSchoenma]

+2 NSW

[FedeGueli]

Pls propose once it reaches 25

[FedeGueli]

+3 QLD, NSw

[FedeGueli]

+1 VIC

@JosetteSchoenma lets wait next few uplaods from Australia to see if it is still there or not.

[FedeGueli]

re closing this