XCQ: Another XBB.2.3 and XBB.1.5 recombinant, with S:T732I (79 seqs, mainly in Guatemala, 8 countries)

[NkRMnZr]

Transferred from sars-cov-2-variants/lineage-proposals#711, it's a different recombinant to sars-cov-2-variants/lineage-proposals#604

Query: A13187G, C22388T, C23757T (if considering potential ORF1a:G2091S dropout)
Earliest seq: 2023-06-30 (EPI_ISL_18080753, California, USA)
Latest seq: 2023-09-03 (EPI_ISL_18258876, Liège, Belgium)
Sampled Countries: Guatemala (21), USA (12, Many with foreign travel history), Spain (3), Belgium (6), Mexico (1), UK (1: England)

Recombinant Profile:

• Nearest Branch on Phylogenetic Tree: XBB.2.3 > T27431C_reversion(ORF7a:V13A_reversion) > T29706G_reversion > A13187G(ORF1a:I4308V/nsp10_I55V), C22388T, C23757T(S:T732I) > G6536A(ORF1a:G2091S) > G27915T(ORF8:G8*)
• Donor A: XBB.2.3, upstream from 5' end to breakpoint
• Breakpoint: Between nuc 23123/spike_521 to nuc 27431/ORF7a_13
• Donor B: Any XBB.1* with ORF8:G8* and without ORF9:I5T, most likely XBB.1.5, downsteram from breakpoint to 3' end.
• Private mutations: ORF1a:I4308V, C22388T, S:T732I
  

Genomes:

EPI_ISL_17954534, EPI_ISL_17954569, EPI_ISL_17982568, EPI_ISL_17982581, EPI_ISL_17982586, EPI_ISL_18011156, EPI_ISL_18023025, EPI_ISL_18037651, EPI_ISL_18080753, EPI_ISL_18081441, EPI_ISL_18090453, EPI_ISL_18094954, EPI_ISL_18099400, EPI_ISL_18099404, EPI_ISL_18099406, EPI_ISL_18099415, EPI_ISL_18099422, EPI_ISL_18099424, EPI_ISL_18099433, EPI_ISL_18104413, EPI_ISL_18118410, EPI_ISL_18136401, EPI_ISL_18137317, EPI_ISL_18138518, EPI_ISL_18139698, EPI_ISL_18139701, EPI_ISL_18139731, EPI_ISL_18139754, EPI_ISL_18139756, EPI_ISL_18144338, EPI_ISL_18163511, EPI_ISL_18163519, EPI_ISL_18163522, EPI_ISL_18163581, EPI_ISL_18168281-18168282, EPI_ISL_18227406, EPI_ISL_18234086, EPI_ISL_18243314, EPI_ISL_18252808, EPI_ISL_18258869, EPI_ISL_18258871, EPI_ISL_18258876, EPI_ISL_18260691

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_9fd0_844560.json?label=id:node_7422389

[NkRMnZr]

Tracking updates:

09-23, 5 seqs from Canada and Guatemala EPI_ISL_18277421, EPI_ISL_18277815, EPI_ISL_18277817, EPI_ISL_18291430, EPI_ISL_18291449

09-29, 19 seqs from Belgium, Canada, Italy and USA

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_98c_688710.json?f_userOrOld=uploaded%20sample&label=id:node_7323805

EPI_ISL_18299714, EPI_ISL_18300315, EPI_ISL_18305267-18305269, EPI_ISL_18305271, EPI_ISL_18305403-18305404, EPI_ISL_18305406, EPI_ISL_18305482-18305485, EPI_ISL_18305641, EPI_ISL_18305643, EPI_ISL_18305650, EPI_ISL_18308458, EPI_ISL_18317522, EPI_ISL_18318172

10-08, 11 seqs from Canada, Spain and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_9d4_2c7c20.json?f_userOrOld=uploaded%20sample&label=id:node_3874558

EPI_ISL_18328332, EPI_ISL_18340153, EPI_ISL_18340972-18340973, EPI_ISL_18343646, EPI_ISL_18343661-18343662, EPI_ISL_18343808, EPI_ISL_18344462, EPI_ISL_18352237, EPI_ISL_18359519

[JosetteSchoenma]

I am putting XCQ here, to see if that would help with searching GItHub for it.

And maybe the designated name could be put in the title as well? I think that will make searching for things a lot easier.

[JosetteSchoenma]

Yes, it helps! Now I can find it with searching for 'XCQ', while before my comment, it wasn't found.