XDG (Branch 2 ) : EG.5.2 sublineage with S:K679R (sibling of EG.5.2.1, 26 seqs, 13 countries) and its 2 recombinants with XBB.1.9* (14 seq, 4 countries / 25 seq, 6 countries)

[Over-There-Is]

Credit to @NkRMnZr

EG.5.2+S:K679R

EG.5.2> A6729G(Orf1a:N2155S)> C11518T> C3602T(Orf1a:H1113Y)> A25744G(Orf3a:I118V, shared with EG.5.2.1)> A23598G(S:K679R) Query: A6729G, A23598G Earliest sequence: 05-12 Noord Holland, Netherlands EPI_ISL_17787266 Latest sequence: 09-23 Basque, Spain EPI_ISL_18366383 Regions detected: Spain 6(Catalunya 2, Balearic Islands 1, Basque 1, Canary Islands 1, Castilla y León 1), UK 4(Scotland 3, England 1), Belgium 2(Londerzeel 1, Gingeleon 1), Austria 1(Wien), Denmark 1, Luxembourg 1, Netherlands 1(Noord Holland), Portugal 1, Sweden 1(Kalmar); Israel 2, South Korea 2, Georgia 1(Tbilisi); Peru 3(Lima)

https://nextstrain.org/fetch/github.com/Over-There-Is/subtreeAuspice/raw/main/subtreeAuspice_genome_20424_7b8a0.json

And its C583T, T16905C branch (3 seq, 3 countries) recombines with two different XBB.1.9* donors and forms two different recombinants.

Sequences: EPI_ISL_17787266, EPI_ISL_17827046, EPI_ISL_17960339, EPI_ISL_18042094, EPI_ISL_18052049, EPI_ISL_18052445, EPI_ISL_18096783, EPI_ISL_18134870, EPI_ISL_18147777, EPI_ISL_18167899, EPI_ISL_18168067, EPI_ISL_18209149, EPI_ISL_18214053, EPI_ISL_18226771, EPI_ISL_18273765, EPI_ISL_18286676, EPI_ISL_18293080, EPI_ISL_18322861, EPI_ISL_18337011, EPI_ISL_18337025, EPI_ISL_18366383, EPI_ISL_18370626, EPI_ISL_18370924, EPI_ISL_18379250, EPI_ISL_18385349, EPI_ISL_18414631

Recombinant 1:

XBB.1.9 / EG.5.2 / XBB.1.9 Query: 4060, 4086, C11518T or C11518T, G27390C or A23598G, G27390C

Earliest sequence: 07-24 Iceland EPI_ISL_18094123 Latest sequence: 08-28 California, US EPI_ISL_18267315 Regions detected: US 10(California), Iceland 2, France 1(Nouvelle-Aquitaine), UK 1(England)

Breakpoint 1: 6729\~9693 Breakpoint 2: 28754\~29625 EG.5.2> A6729G> C11518T> C3602T> A25744G(Orf3a:I118V, shared with EG.5.2.1)> A23598G(S:K679R)> C583T, T16905C> A79G, T583Crev, T2334Crev(Orf1a:V690Arev), T3602Crev, A4060C, T4086C(Orf1a:I1274T), C5152Trev, G6729Arev, G27390C, T29625Crev(Orf10:F23Srev)

Since it has G5720A and G6729Arev, the other one donor should be an XBB.1.9. Any 2 of A79G, A4060C, T4086C, G27390C gives no sequence except this recombinant. A79G, G5720A, -16905 gives no sequence. A4060C, G5720A, -16905 gives 1 sequence, a French FL.8 with several mutations between 5' to 5720, and its 405 is reversed. T4086C, G5720A, -16905 gives 3 sequences, 1 is an Indian low-quality sequence, and 2 are American FL.4> A28615G> A6646G> T4086C. G27390C, G5720A, -16905 gives 23 sequences, but most of they are too messy, and 27390 is on the upstream of 28754, it seems impossible to inherit 27390 from the XBB.1.9 donor. And this recombinant is also possible to be more complex and twisted? But in this case, the non-EG.5.2 donor could be from the other strains.

Sequences: EPI_ISL_18094123, EPI_ISL_18094138, EPI_ISL_18118869, EPI_ISL_18121231, EPI_ISL_18121255, EPI_ISL_18144691, EPI_ISL_18215145, EPI_ISL_18222944, EPI_ISL_18267315, EPI_ISL_18267640, EPI_ISL_18270057, EPI_ISL_18270377, EPI_ISL_18317736, EPI_ISL_18347338

Recombinant 2:

XBB.1.9.1 / EG.5.2 Query: T4690C, A23598G

Earliest sequence: 08-21 Denmark EPI_ISL_18210614 Latest sequence: 09-29 New York, US EPI_ISL_18394164 Regions detected: Italy 8(Sicily 4, Apulia 3, Veneto 1), US 8(NY 4, California 2, Minnesota 2),Canada 2(BC 1, Ontario 1), Denmark 1, France 1(ARA), Greece 1(Central Greece)

Breakpoint: 6729\~9693 EG.5.2> A6729G> C11518T> C3602T> A25744G(Orf3a:I118V, shared with EG.5.2.1)> A23598G(S:K679R)> C583T, T16905C> C547T, T583Crev, C1758T(Orf1a:A498V, Private), T2334Crev(Orf1a:V690Arev), T3602Crev, T4579A, T4690C, T4930C, C5152Trev, G6729Arev The donor should be from XBB.1.9.1> C29614T> C547T> T15309C> T4690C, T4930C, G10540T, C26054T branch. (2 seq, and 1 seq has further T4579A.)

Sequences: EPI_ISL_18210080, EPI_ISL_18210109, EPI_ISL_18210181, EPI_ISL_18210614, EPI_ISL_18218428, EPI_ISL_18300257, EPI_ISL_18314673, EPI_ISL_18330426, EPI_ISL_18344025, EPI_ISL_18357726, EPI_ISL_18363919, EPI_ISL_18364276, EPI_ISL_18368928, EPI_ISL_18389364, EPI_ISL_18394164, EPI_ISL_18404126, EPI_ISL_18419443, EPI_ISL_18419447, EPI_ISL_18419462, EPI_ISL_18419489, EPI_ISL_18422941

[FedeGueli]

is it the EG.5.2 + 679R sonor proposed yet?

[Over-There-Is]

is it the EG.5.2 + 679R sonor proposed yet?

not proposed yet.

[FedeGueli]

I suggest to propose it having recombined two times means it has some ability in coinfect (679R) or prevalence somewhere

[FedeGueli]

Query for it : A23598G,A25744G, -A4060C , -C547T

Defining : EG.5.2 (S:F456L) > ORF1a:N2155S (A6729G) > C11518T > ORF1a:H1113Y (C3602T) >Orf3a:I118V (A25744G) > S:N>K679R (A23598G)

17 samples EPI_ISL_10729647, EPI_ISL_17787266, EPI_ISL_17827046, EPI_ISL_17960339, EPI_ISL_18042094, EPI_ISL_18052049, EPI_ISL_18052445, EPI_ISL_18094138, EPI_ISL_18096783, EPI_ISL_18121255, EPI_ISL_18134870, EPI_ISL_18147777, EPI_ISL_18167899, EPI_ISL_18168067, EPI_ISL_18209149, EPI_ISL_18214053, EPI_ISL_18226771

--

[Over-There-Is]

Query for it : A23598G,A25744G, -A4060C , -C547T

Defining : EG.5.2 (S:F456L) > ORF1a:N2155S (A6729G) > C11518T > ORF1a:H1113Y (C3602T) >Orf3a:I118V (A25744G) > S:N>K679R (A23598G)

17 samples EPI_ISL_10729647, EPI_ISL_17787266, EPI_ISL_17827046, EPI_ISL_17960339, EPI_ISL_18042094, EPI_ISL_18052049, EPI_ISL_18052445, EPI_ISL_18094138, EPI_ISL_18096783, EPI_ISL_18121255, EPI_ISL_18134870, EPI_ISL_18147777, EPI_ISL_18167899, EPI_ISL_18168067, EPI_ISL_18209149, EPI_ISL_18214053, EPI_ISL_18226771

--

Two sequences of recombinant 1 have M on 4060, so -G27390C would be better.

[FedeGueli]

+4 lineage 1

[Over-There-Is]

Sorry for forgetting tracking this issue.

[Over-There-Is]

Lineage 2 also has a new sequence.

[Over-There-Is]

Common query for the EG.5.2 donor and both recombinant: C11518T, T16905C, A23598G 21 seq or including non T16905C branch: C11518T, A23598G, A25744G 35 seq

[Over-There-Is]

2 of recombinant 1 have P445S. Artefact?

[FedeGueli]

Only Recombinant 2 is fast the other two very slow.

[Over-There-Is]

Branch 2 is also in France now.

[FedeGueli]

Please propose branch 2 it seems fast https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1f872_6e1f90.json?label=id:node_3421384

[FedeGueli]

And then close this one.

[Over-There-Is]

EG.5.2.4 & XDG

[FedeGueli]

Designated EG.5.2.4 donor EG.5.2.4 è FL.37 >> XDG

via https://github.com/cov-lineages/pango-designation/commit/d7b0265b8f5d95db0be543300f7402653c1d7b09