XCU:Potential recombination between XBB and XBC (3. seq., Philippines, Singapore)

[agamedilab]

Proposal for a sublineage of XBB and XBC
Earliest sequence: 04.09.2023 (Philippines)
Countries detected: Philippines; Singapore

nuc unique G7058A, G22577C, C22664A, G22895C, G22927A, T23042C, C25584T, A26275G, C26577G, G26709A, C26767T, G27915T, A29510C
nuc homoplasies T3478C, C4586T, A7766G, A10449C, T15030C, A17207G, A19890G, T21846C, A22116G, C22329T, G22599C, T22896C, G22898A, T22942G, T23018C, T23019C, T23031C, C23123A, C25416T, C26060T, C26270T, C26606T, C26858T, A27259C, G27382C, A27383T, T27384C, T28297C, G28376A, C29762T
nuc reversionsToRoot A10449C, T21846C, C26767T
S unique D339H, L368I, V445P, S494P
S homoplasies I95T, N185S, S256L, R346T, G446S, N460K, F486P, F490S, P521T
S reversionsToRoot I95T
ORF3a homoplasies T223I
E unique T11A
E homoplasies T9I
M unique Q19E, A63T, T82I
M reversionsToRoot T82I
ORF6 homoplasies D61L
ORF8 unique G8*
N unique S413R
N homoplasies A35T
ORF1ab unique G2265S
ORF1ab homoplasies I2501V, H3395P, Y5648C
ORF1ab reversionsToRoot H3395P

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1d9a8_3dc3e0.json?f_userOrOld=uploaded%20sample

EPI_ISL_18342927
EPI_ISL_18361826
EPI_ISL_18361978

Gisaid query: G22927A, T23042C, C25584T

[FedeGueli]

I think there i third from Philippines EPI_ISL_18342927 that was spotted alst week by @NkRMnZr

[FedeGueli]

oh already modified thx

[HynnSpylor]

Yes the Usher and GISAID temporarily classified it as "B.1.1.529"
The breakpoint may be between S:256 and S:339 (Before =XBC, After= XBB)
The XBB* part is likely from XBB.1.16.11* (with T28297C, G27915T, C23123A etc.)

[FedeGueli]

Yes the Usher and GISAID temporarily classified it as "B.1.1.529" The breakpoint may be between S:256 and S:339 (Before =XBC, After= XBB) The XBB* part is likely from XBB.1.16.11* (with T28297C, G27915T, C23123A etc.)

misisng T478R tough. so maybe it got reverted :? Philippines has had already some lineages with reversion to T at 478

[corneliusroemer]

You guys are fast! Just came across this one independently. Looks pretty solid to me, given the fact it's two countries, they cluster well, there are clear private mutations etc.

The XBC is likely XBC.1.7 - matches quite well with some XBC.1.7 sequences from the Phillipines

[corneliusroemer]

XBC donor is a direct descendant of Philippines/PH-PGCMIN3313/2023|EPI_ISL_17948931|2023-05-26 (XBC.1.7.1)

XBB part is likely FL.23.2.1 (has both 494P and 521T, was seen most commonly in Philippines and doesn't require any reversions)

=> designated XCU

[FedeGueli]

Designated XCU via cov-lineages/pango-designation@4806a9b

[FedeGueli]

XBC donor is a direct descendant of Philippines/PH-PGCMIN3313/2023|EPI_ISL_17948931|2023-05-26 (XBC.1.7.1)

XBB part is likely FL.23.2.1 (has both 494P and 521T, was seen most commonly in Philippines and doesn't require any reversions)

=> designated XCU

Thx Cornelius great catches for donors.

[JosetteSchoenma]

XCU

[FedeGueli]

12 now but 4/36 in Philippines

[ryhisner]

8/17 sequences from the Philippines uploaded today—collection dates Nov 4 to Nov 14—are XCU.

[FedeGueli]

Thx @ryhisner for the head up it is growing a lot. i found 20 samples seuqenced in or from philippines in November and the variant scenario is the following:
8 XCU
7 XBB.2.3.3/GJ/JE
3 JD.1.1
1 JN.1
1 HN.5