CR.1 (BA.5.2.18.1) x XBB.1 recombinant [5 seq, 2x UK, 1x US, 1x FR, 1x DK]

[corneliusroemer]

I've come across a BA.5 - XBB.1 recombinant with BA.5 5' end and breakpoint before Spike, around nt pos 20000.

hCoV-19/England/QEUH-325F8DE8/2022|EPI_ISL_15939141|2022-11-18
hCoV-19/USA/CA-HLX-STM-DF65Z7QDY/2022|EPI_ISL_16087814|2022-11-14
hCoV-19/France/ARA-HMN-22122070507/2022|EPI_ISL_16234849|2022-11-21
hCoV-19/Scotland/LSPA-32629512/2022|EPI_ISL_16236725|2022-12-07
hCoV-19/Denmark/DCGC-626678/2022|EPI_ISL_16238389|2022-12-14

There are extra Spike mutations: P521T, E554G, I870V

https://next.nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_216f9_487820.json?label=id:node_9106096

[corneliusroemer]

Putting the BA.5 mutations into covSpectrum landed a hit for CR.1 - so that seems to be the BA.5-side donor: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=A8040G%2CG15957T%2C12160A%2C12310A%2C16616A&

[FedeGueli]

Wow @corneliusroemer great catch. It has Orf1b:1050N doesnt look at all. Also interesting private spike mutations

[FedeGueli]

Gisaid query: E_T11A,Spike_E554G,Spike_P521T,NSP13_T127N

or easier : Spike_E554G,Spike_P521T,Spike_I870V

[FedeGueli]

One more sequence from Michigan, a young girl, so i presume it is possible that it is circualting more widely than we see

[FedeGueli]

Seventh sequence comes from Brunei.

[FedeGueli]

8 sequences, the 8th sample came from Canada.

[FedeGueli]

10 as today. 2 last from France cc @corneliusroemer

[corneliusroemer]

That's what it looks like on Usher:

https://next.nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2e4c4_b70630.json?f_userOrOld=uploaded%20sample&label=id:node_7751250

[FedeGueli]

11 sequences as today

[FedeGueli]

12 sequences as today last one uploaded yesterday from Austria

[FedeGueli]

14 as today

[FedeGueli]

one more sequence , total count is 17, 2 of the last 5 samples submitted are from Indonesia , @corneliusroemer maybe this recombination happened there? still not going anywhere as today

[c19850727]

total count is 31 (or 30?) as of 2023-03-12.

Interestingly, this proposed recombinant further recombined with a BQ.1*:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1ba33_dfc590.json?c=gt-nuc_8040,25455&label=id:node_7771803

[FedeGueli]

@corneliusroemer @InfrPopGen @thomaspeacock @AngieHinrichs maybe worth a designation, 30 sequences and the 31th found by great @c19850727 is very unique: it has; 1 orf1ab from BA.5.2/1050N 2 Spike from.XBB.1 with 3 unique S mutations (521,554,870) 3 E to N from BQ.1 with all proposed as attenuating mutations gone.

[JosetteSchoenma]

XBV