Several Potential Recombinants in China

[Walde1nsamkeit]

Guangdong/GDCDC_GZ_0351/2023|EPI_ISL_17698183|2023-05-05
XBB.1.16.1 / FL.2.3+N:R189L
Mutations based on XBB.1.16.1: G5720A (Orf1a:G1819S, XBB.1.9), T7194T, T11750Crev, A17615G(Orf1b:K1383R, FL.2.3), T18703Grev, C22050T, G28447Arev, G28839T(N:R189L), T29386Crev

Guangdong/GDCDC_GZ_0352/2023|EPI_ISL_17698156|2023-05-05
XBB.1.16 / FL.2.3
Mutations based on XBB.1.16: T326C, G5720A (Orf1a:G1819S, XBB.1.9), T8835C (a common sequencing error in sequences uploaded by Guangzhou), T11750Crev, A17615G(Orf1b:K1383R, FL.2.3), G28447Arev

Guangdong/GDCDC_JM_0092/2023|EPI_ISL_17698225|2023-05-10
Reported by @NkRMnZr firstly.
XBB.1.9(.2?)* / FU.1+A460G(#50)
Mutations based on XBB.1.9+F486P:
A460G, T12730A (XBB.1.16), T12789Crev, G18703T (XBB.1.16), C29386T (XBB.1.16)
Since it does not contain C11956T (both contained in XBB.1.9.1 and XBB.1.16), the XBB.1.9* donor would not be XBB.1.9.1*.

Guangdong/GDCDC_FS_0044/2023|EPI_ISL_17698261|2023-05-10
Reported by @NkRMnZr firstly.
DY.3 / FL.2.3+N:R189L
Mutations based on DY.3:
T1627Crev, T5628Crev, G5720A (Orf1a:G1819S, XBB.1.9), C9866T (Main branch of BA.2), T11824Crev, C11956T(XBB.1.9.1), A12160Grev, A12310Grev, C15738T (BJ.1), T15939C (BJ.1), T16342C (BJ.1), A16616Crev, T17859C (BJ.1 & XBB*), ins21765TACATGrev(S:ins69HVrev), del21992-21994(S:Y144del), C22000A (BJ.1), C22109G (BJ.1), G22200A (BJ.1), G22317T(XBB.1), G22577C (BJ.1 & BA.2.75), A26529Grev, T27012Crev, G27505C (Orf8:G8*, Main branch of XBB.1), T27513Crev, T27889Crev, T28297C(Orf9b:I5T, XBB.1.9*/16*/22*/25/26), G28330Arev,G28839T(N:R189L)
Alternatively, mutations based on FL.2.3:
G405Arev, C2710T (BA.5.2.48), C4573T (DY.3), A4579Trev, T12789Crev, A15451Grev, C16887T(BA.5.2.48), G17615Arev, G19326Arev, C22599Grev, A22664Crev, C22895Grev, C22896Trev, A22898Grev, T22917G(BA.4/5), G22942Trev, C23019Trev, C23031Trev, T25416Crev, T26858Crev, C27259Arev, C27382Grev, T27383Arev, C27384Trev, G27505C, G28839T(N:R189L), G29868A(BA.5)

Guangdong/GDCDC_SZHG_0193/2023|EPI_ISL_17697616|2023-04-24
BF*+T6979G / FL.2?
Mutation base on BA.5.2.1: C44T, C106T, C1594T, C2110A, T2112C, C3177T, T4579A(FL.2), A4851G, C6224T, T6394C, T6673C, C6968T, T6979G(the mutation of a large branch of BF*), C7329G, C8290T, C8299T, A8992G, C12789T(XBB.1.9*/XBB.1.23), G15451A(BJ.1 & BA.2.75), C18431T, C19854T, C21440T, C22120T, C22295T, G22599C, C22664A (BJ.1), A22881G, G23018Trev, C23802T, G24386A, G26416A, C26625T, G28085A, G28330Arev, T29417C, C29838T
But it has neither F486V nor F486P but 486F. And it is seemed that a saltation was happened.
Probably not recombinant, proposed in cov-lineages/pango-designation#1919

Guangdong/GDCDC_CZ_0114/2023|EPI_ISL_17697708|2023-04-24
BF.7.14 / BA.5.2+C27012T, C27513T (Main branch of BA.5.2)
Mutation base on BF.7.14: T1Arev, C44T, G653A, T1602G, C3646T, C7834T, G18318T, G24998T(DZ.1?), T25290Grev, C27012T, G27038Arev, C27513T, T27532Crev, T28361Grev, G28371Trev

[Walde1nsamkeit]

Currently, except GDCDC_GZ_0351 and GDCDC_FS_0044, all sequences with N:R189L in China are XBB.1.9.1*. And except those two and Hubei/HCDC-1181, all these sequences have A17615G. Two of these sequences lost T4579A due to sequencing error or reversion mutation, but they should be FL.2 too.

[FedeGueli]

Thx great work!

[Walde1nsamkeit]

Hubei/HCDC-1000/2023|EPI_ISL_17625385|2023-04-27
HCDC-0999 FR.1.4 / DY.4+Orf1a:S3949N, T4175I
Mutations based on FR.1: T337Crev (0999), C1627T (BA.5.2/10/11), C2061T (0999), T2372C (FR.1.1/4), C8626T (BA.5.2.48), C11515Trev, G12111A (Orf1a:S3949N, common in DY.4), G12160A(BA.4/5), C12789T(Orf1a:T4175I, common in BA.5.2.48 or DY.4), T14961C (FR.1.1/4), C15960T (FR.1.4), C16887T(BA.5.2.48), del21765-21770(BA.1/4/5), G22121Arev, G22190Arev, A22331Grev, G22942Trev, T25416Crev, G26459Arev, G26529A(BA.5), A28330G(BA.5.2), T29370Crev

Hubei/HCDC-1001/2023|EPI_ISL_17625388|2023-04-27
FL.2 / DY.4+Orf1a:S3949N, T4175I
Mutations based on FL.2: G405Arev, C920T, C8626T (BA.5.2.48), G12111A (Orf1a:S3949N, common in DY.4), T15738Crev, G12160A (BA.4/5), G22109Crev, A22200G (BA.2/4/5), T22317Grev, C23191T, T28245G

Hubei/HCDC-1002/2023|EPI_ISL_17625384|2023-04-27
FL.2+Orf1b:K1383R+C25803T / DY.4+Orf1a:S3949N, T4175I
Mutations based on FL.2: G12111A (Orf1a:S3949N, common in DY.4), G12160A(BA.4/5), A17615G (Orf1b:K1383R), A22200G(BA.2/4/5), T22317Grev, C25803T.

Hubei/HCDC-1003/2023|EPI_ISL_17625389|2023-04-27
FL.2+Orf1b:K1383R+S:H146K / DY.4+Orf1a:S3949N, T4175I
Mutations based on FL.2: G12111A (Orf1a:S3949N, common in DY.4), G12160A(BA.4/5), A17615G (Orf1b:K1383R), C21998A (S:Q146K),G22109Crev, A22200G(BA.2/4/5), T22317Grev.

[Walde1nsamkeit]

GDCDC_SZHG_0193 is quite similar to several sequences collected in Shenyang, Liaoning since 2023-02-21.

Sequences: EPI_ISL_17493027, EPI_ISL_17495186, EPI_ISL_17495358,
EPI_ISL_17495368-17495369, EPI_ISL_17652380, EPI_ISL_17697616

Mutations based on BA.5.2.1: T6979G> C26625T> T2112C> T6394C> C23802T> C3177T> C1594T> C2110A, A4851G, T6673C, C6968T, C7329G, C8290T, A8992G, C12789T, G15451A, C21440T, C22120T, C22295T, G22599C, C22664A, A22881G, G23018Trev, G24386A, G26416A, G28330Arev, T29417C
> T4579A, C6224T> C106T, C8299T> T22981C or C18431T, C19854T, G28085A

The bolded mutations are included in XBB.1.9*/25.
These sequences seem unrelated to FL.2.

[FedeGueli]

Yes this cluster already proposed abd discussed in the main pango page (Search: Liaoning)

[Walde1nsamkeit]

Almost all sequences with G12111A and C12789T mutations assigned as "BA.5.2.48" by GISAID actually have also C20762T and A29868Grev mutations, it means all of these sequences are actually DY.4.
More than a half of DY.4 sequences in China and 3/4 in Hubei have both G12111A and C12789T mutations, which is related to the sublineage proposed in cov-lineages/pango-designation#1620.

[Walde1nsamkeit]

Sichuan/DZCDC-CX0023/2023|EPI_ISL_17684194|2023-04-30

DZCDC-CX0024 related FL.13.1+A2611G / DZCDC-CX0017 related (BF.7.14 / BA.5.2.48)?

Mutations Base on FL.13.1:
G1Arev, C44T, C1627T(BA.5.2/10/11), C1848T(0024), A2611G(common in FL.13.1, also contained in 0024), C2710T(BA.5.2.48), C4573T(DY.3), A5720Grev, G10658A(0024), G12160A(BA.4/5), G12310A(BA.5.2), C13011T(0024), C13436T, T15738Crev, C15939Trev, C16616A(BA.5.2), C16887T(BA.5.2.48), C17010G, T17208C(BA.5.2.48), C18962T(0017), del21765-21770(BA.1/4/5), A21801G(0017), T22159C(0017), T22304A, T22317Grev, C27889T(BA.4/5), C28297Trev, A28330G(BA.5.2), A28338G(0017), G28361T(BA.5.2.1), G28371T(BA.5.2.1)

[Walde1nsamkeit]

A potential recombinant is found while finding the DY.3 donor of DZCDC-CX0023.
Sichuan/DZCDC-CX0017/2023|EPI_ISL_17563623|2023-04-12
BF.7.14 / BA.5.2.48
Mutations based on BF.7.14:
C1077A, A1596C, C2710T(BA.5.2.48), C8626T(BA.5.2.48), C10702T, G12310A(main branch of BA.5.2), C16616A(main branch of BA.5.2), C16887T(BA.5.2.48), T16974C, T17208C(BA.5.2.48), C18962T, T19955Crev, A21801G, T22159C, G25471C, C27513T(main branch of BA.5.2), A28338G

Mutations based on BA.5.2.48:
C1077A, G1085T(BF.7.14), A1596C, C7528T(BF.7), C10702T, G14181C(BF.7.14/27), T16974C, C18962T, A21801G, T22159C, G22599C(BF.7), G25290T(BF.7.14), G25471C, C27532T(BF.7.14/27), A28338G, G28361T(BA.5.2.1), G28371T(BA.5.2.1), C29632T(BF.7.14)

[FedeGueli]

If a lineage from this list starts growing please propose separately. thx

[Walde1nsamkeit]

Sichuan/YBCDC-XGCX238/2023|EPI_ISL_17808220|2023-05-24 XBB.1.5.62+A9922C, C11565T / FR.1.3
Yunnan/YNCDC-1164/2023|EPI_ISL_17808317|2023-05-27 EG.5.1 / FR.1.3
Yunnan/YNCDC-1163/2023|EPI_ISL_17808316|2023-05-27 EG.5.1 / FR.1.3

[Walde1nsamkeit]

Jiangxi/JXJDZ-018/2023|EPI_ISL_17794481|2023-04-25 FL.4 / FR.1*
Jiangxi/JXNC-195/2023|EPI_ISL_17794681|2023-05-02 FU.1+A460G / FR.1.2
Jiangxi/JXYT-078/2023|EPI_ISL_17795007|2023-05-29 EG.5.1 / GJ.1
Jiangxi/JXYC-161/2023|EPI_ISL_17794942|2023-05-07 XBL.3 / FU.1+A460G

[Walde1nsamkeit]

Inner_Mongolia/NMCDC-HHH-022/2023|EPI_ISL_17785537|2023-03-20 BF.7.14 / DY.2?

[Walde1nsamkeit]

Beijing/BJCDC-0966/2023|EPI_ISL_17784968|2023-04-06 XBB.1.19.1 / BF.7.14
Beijing/BJCDC-0848/2023|EPI_ISL_17784897|2023-03-30 XBB.1.16 / BF.7.14
Beijing/BJCDC-1261/2023|EPI_ISL_17785150|2023-04-25 FL.4 / BA.5.2*?
Beijing/BJCDC-0851/2023|EPI_ISL_17784900|2023-03-27 DZ.1 / BF.7.14?

[FedeGueli]

Sichuan/YBCDC-XGCX238/2023|EPI_ISL_17808220|2023-05-24 XBB.1.5.62+A9922C, C11565T /

this is in the same tree of one proposed (the one at the top) in this repo:

[FedeGueli]

Great work @Over-There-Is i m impressed!

[FedeGueli]

Always hard to tell with recombinant but this has everything to go well https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_461fd_dbced0.json?label=id:node_7109121

[FedeGueli]

@Over-There-Is i suggest a cutoff after 1st of may to reduce your load of work

[FedeGueli]

EPI_ISL_17794681
Please keep these three tracked if also one or two more sequences will pop up somewhere propose them as single lineage here in the preproposal for a rapid review. Thank you for your efforts.

Sichuan/YBCDC-XGCX238/2023|EPI_ISL_17808220|2023-05-24 XBB.1.5.62+A9922C, C11565T / FR.1.3
Yunnan/YNCDC-1164/2023|EPI_ISL_17808317|2023-05-27 EG.5.1 / FR.1.3
Yunnan/YNCDC-1163/2023|EPI_ISL_17808316|2023-05-27 EG.5.1 / FR.1.3

[Walde1nsamkeit]

Thanks to @NkRMnZr and @Memorablea!
Xinjiang/XJCDC-TC-082/2023|EPI_ISL_17775584|2023-05-16 FR.1 / XBB.1.42
Liaoning/LNCDC-131-8/2023|EPI_ISL_17775080|2023-04-26 BN.1* / BA.5.2.48*
Xinjiang/XJCDC-TC056/2023|EPI_ISL_17775234|2023-04-29 XBB.1.5* / DY.3 ?
Liaoning/LNCDC-131-6/2023|EPI_ISL_17775077|2023-04-26 XBB.1.9.1 / FR.1
Xinjiang/XJCDC-KLMY-102/2023|EPI_ISL_17775383|2023-05-06 XBB.1* / FR.1
Xinjiang/XJCDC-BAZ-090/2023|EPI_ISL_17775563|2023-05-04 XBB.1* / FR.1
Taiwan/CDC-F80278/2023|EPI_ISL_17766861|2023-04-19 XBB.1.9.2 / DV.6.2 ?
Liaoning/LNCDC-131-3/2023|EPI_ISL_17775091|2023-04-26 FD.2 / XBB.1.16* ?
Xinjiang/XJCDC-KS-101/2023|EPI_ISL_17775197|2023-05-20 XBB.1.44.1 / XBB.1.16*

[Walde1nsamkeit]

Jiangxi/JXNC-174/2023|EPI_ISL_17794675|2023-05-02 #187 / FL.2.3?

[Walde1nsamkeit]

Fujian/FCDC-LYCX099/2023|EPI_ISL_17703983|2023-05-16
Contains all defining mutations of XBB.1.19.1 and FY.3.1 except T44Crev

Mutations based on XBB.1:
Homoplastic mutation: T23018C
Mutations from XBB.1.19.1: C541T, C6701T, A10042G, G10105T, C15763T, T21363C, G23222A, G26277A, A29712T, G29810T (7 seq)
Mutations from FY.3.1: C245A, G2513A, G4109T, C5544T, A22161G, T22191C, C23191T, G27915T, T28297C (91 seq)
Private mutations: C16989T, G19480T, C26681T
C26681T is also contained in some Israeli XBB.1.19.1 sequences, but not contained in Sichuan sequences which related to this one.

[Walde1nsamkeit]

EPI_ISL_17794681
Please keep these three tracked if also one or two more sequences will pop up somewhere propose them as single lineage here in the preproposal for a rapid review. Thank you for your efforts.

Sichuan/YBCDC-XGCX238/2023|EPI_ISL_17808220|2023-05-24 XBB.1.5.62+A9922C, C11565T / FR.1.3
Yunnan/YNCDC-1164/2023|EPI_ISL_17808317|2023-05-27 EG.5.1 / FR.1.3
Yunnan/YNCDC-1163/2023|EPI_ISL_17808316|2023-05-27 EG.5.1 / FR.1.3

although EPI_ISL_17808316 and EPI_ISL_17808317 are both EG.5.1 / FR.1.3, they have different breakpoint.

[FedeGueli]

@Over_there_is where you see there are too breakpoints that points to contamination or coinfection rather true recombination

[Walde1nsamkeit]

The sequences with artefact ins27791T almost locate in Jingzhou. But for the sequences with other FR.1* significant mutations, it is believable.

[Walde1nsamkeit]

Sichuan/SCDC-0122/2023|EPI_ISL_18049857|2023-06-27
EG.5.1.1 / FY.3.1?

[FedeGueli]

Sichuan/SCDC-0122/2023|EPI_ISL_18049857|2023-06-27 EG.5.1.1 / FY.3.1?

I think it is the one proposed by Hynn Spylor

[Walde1nsamkeit]

Guangdong/GDCDC_GZ_0494/2023|EPI_ISL_18033830|2023-05-31 XBB.1.16 / FL.2.3
Guangdong/GDCDC_SZ_0796/2023|EPI_ISL_18035035|2023-05-14 XBB.1.16 / FL.2.3

[Walde1nsamkeit]

Guangdong/GDCDC_SZHG_1719/2023|EPI_ISL_18036297|2023-06-03 FL.2.3 / XBB.2.3.7
Mutations based on FL.2.3:
A4479C, T9076C, C12853T | T22317Grev, A22320G, T22928C, C23123T, C26447T, C27431T, T27915Grev, C28297Trev, C28717A, G29706T
Mutations based on XBB.2.3:
T4234Crev, A4479C, T4579A, G5720A, A6536Grev, T9076C, C11956T, C12789T, C12853T, T16342C, A17615G | T22928C, C26447T, C28717A

Breakpoint: 17615~22317

FL.2.3+T9076C 5 seqs (All in Nanping, Fujian, China)
FL.2.3> G28980T(N:G236V)> T9076C, T28157G(Orf8:I88M)

XBB.2.3+C26447T, C28717A 14seqs (Fujian 12[Nanping 10, Sanming 2], Singapore 1, Victoria, Australia 1)
XBB.2.3.7> G11042A(Orf1a:V3593I)> G1401A(Orf1a:G379E)> A3503G(Orf1a:N1080D), C8950T> C28717A> C26447T(E:S68F)

Private mutations: A4479C(Orf1a:K1405T), C12853T, T22928C(S:F456L)

Probably originates in Nanping, and exported to somewhere out of Chinese Mainland, and detected by Shenzhen Customs when entering.

@FedeGueli @ryhisner @JosetteSchoenma

Stopped growing

[Walde1nsamkeit]

SCDC-HG0803-2915-2/2023|EPI_ISL_18105656|2023-08-01
Imported from Indonesia
FR.1.1 / EG.5.1.1
Breakpoint: 22629~22664(S:356~456)
F157L+K356T+F456L+F486P
Extra mutations: C1686T(Orf1a: A474V), C8782T, G8849A(Orf1a:V2862M), G11966A(Orf1a:A3901T), C14790T, C21057T, C21910T / T23332C, C23453T(S:P631S), C27635T(Orf7a:S81L), C28253T(Artefact?), A28254C(Orf8:I121L, Artefact?)

Designated as XCN

Shanghai/SCDC-XG07-11369-2/2023|EPI_ISL_18105865|2023-07-20
EG.5.1.1 / XBB.1.16* / EG.5.1.1
Breakpoint: 5720~6541, 18703~21718
Extra mutations: T2377C(Private), C6336T(Orf1a:S2024L), C10030T, C14184T(Homoplastic), G20326A
EG.5.1.1+C6336T 3seq
XBB.1.16*+C6336T 73seq none have C10030T
EG.5.1.1+G20326A 8seq none have C6336T
XBB.1.16*+G20326A 10seq none in China, 1 FU.1 have C6336T

Hubei/HCDC-SY2459/2023|EPI_ISL_18105530|2023-08-01
EG.5.1.1 / XBB.1.16
Breakpoint: 25572~27507
Similar to Japan/PG-555753/2023|EPI_ISL_18106306|2023-08-03
Extra mutations: A1982G(Orf1a:I573V), C10408T, C22033A(S:F157L), T22480Crev(Artefact) / C28000T(Orf8:P36L), A28182G(Orf8:S97G)
The Japanese sequence does not have T22480Crev.

proposed by @aviczhl2 in #745, Latest sequence collected on 09-24

Hubei/HCDC-XY2528/2023|EPI_ISL_18105561|2023-08-07
EG.5.1.1 / XBB.1.16
Breakpoint: 22995~25572
Extra mutations: C3141T(Orf1a:P959L), T6178C, A17517G / T25825C(Orf3a:Y185H), C29311T(Homoplastic)

Jiangsu/TZCDC089-2024/2023|EPI_ISL_18105925|2023-07-03
FL.13.2 / EG.5.1.1
Breakpoint: 18492~21718
Extra mutations: G192A, G1401A(Orf1a:G379E), T3279G(Orf1a:I1005S), C7843T, T15354A

Shanghai/SCDC-660/2023|EPI_ISL_18105695|2023-07-20
FY.3.1 / XBB.1.16* / FY.3.1
Breakpoint: 5544~11750, 13960~18703
Extra mutations: C1912T, T1937G(Orf1a:S558A), C21998A(S:Q146K), G25166C(S:E1202Q)

2 seq, ~08-22

Shanghai/SCDC-632/2023|EPI_ISL_18105669|2023-07-13
FE.1.1 / EG.5.1 / FE.1.1
Breakpoint: 5720~8001, 28297~29625
Extra mutations: C832T

Shanghai/SCDC-XG07-11386-2/2023|EPI_ISL_18105882|2023-07-26
EG.5.1* / FY.3.1 / EG.5.1*
Breakpoint: 4109~5544, 27507~29625
Extra mutations: G347A(Orf1a:V28I), C18508T(Orf1b:L1681F), T23084C(S:Y508H)

Hubei/HCDC-XY2465/2023|EPI_ISL_18105551|2023-07-25
FR.1+C1142T / EG.5.1.1
Breakpoint: 1513~2344
Extra mutations: C4633T, C10582T, G16710A, T21388C, T22480Crev(Artefact), G25563C(Orf3a:Q57H)

[Walde1nsamkeit]

Hubei/HCDC-HG2675/2023|EPI_ISL_18217167|2023-08-16
EG.5.1.1 / FL.2.3.1
Breakpoint: 13627~16878
Mutations based on XBB.1.9+C23018T:
C2334T(Orfa1a:A690V, EG.5), C6541T(EG.5.1.1), C9693T(Orf1a:A3143V, EG.5), G13627A(Orf1b:D54N, EG.5.1.1) / A17615G(Orf1a:K1383R, FL.2.3), A21603G(S:Q14R, Private), A22629C(S:K356T, FL.2.3.1), C27128T(FL.2.3.1)

Query: C2334T, A17615G, A22629C
Stopped growing

[FedeGueli]

it exchanged 356 for 456 not sure if i was a good deal

[Walde1nsamkeit]

Anhui/HFCDC-602/2023|EPI_ISL_18133844|2023-08 FE.1.1.3 / XBB.1.16*
Breakpoint: 28093~28297
Private mutations: T1084C, C12781T
Stopped growing

[Walde1nsamkeit]

Henan/JZCDC-139/2023|EPI_ISL_18300568|2023-07-23
Henan/JZCDC-142/2023|EPI_ISL_18300571|2023-07-29
Henan/JZCDC-154/2023|EPI_ISL_18300583|2023-08-04
FL.4 / FL.13.2
Mutations based on XBB.1.9.1:
C5812T(A large branch under FL.4), G16741T(Orf1b:V1092F, FL.4) / C21904T(FL.13.2), C22329T(S:S256L, Private?), A22629C(S:K356T, FL.13.2)
Breakpoint: 16741~21904

Query: G16741T, C21904T, A22629C
Stopped growing

[FedeGueli]

@Over-There-Is are you still updating this one? i think it is a good thing to let it open .
My question is : did you routinely search if any of these ones had any sort of follow up? I would focus on doublets anyway or singlets with a mutational profile of interest to save your time. In the case you are not doing this anymore please close it!

[Walde1nsamkeit]

Did not found new recombinant recently, so close it.

[Walde1nsamkeit]

I didn't use XBB as root sequence to analyse sequences recently. It's quiet efficiently to find recombinants but I forgot to use it.

[FedeGueli]

I didn't use XBB as root sequence to analyse sequences recently. It's quiet efficiently to find recombinants but I forgot to use it.

is it on Nextclade?

[Walde1nsamkeit]

I didn't use XBB as root sequence to analyse sequences recently. It's quiet efficiently to find recombinants but I forgot to use it.

is it on Nextclade?

No on Nextclade, but it's modified based on the Nextclade reference sequence and tree.

[Walde1nsamkeit]

XBB.1.9+S:S486P+
C21T, G599A, C673T, C1385T, G1820A, A2109G, C3768T, T4579A / C6541T, A7150C, C9693T, C11173T, G13627A, A16878T, A18492G, G21718T, C22480T, G22927T, T22930A, C25572T / C28093T

FL.2.4 / EG.5.1.1+A7150C, C11173T, G22927T, G28212T / FL.2.4?

Sichuan/LZCDC-166/2023|EPI_ISL_18409297|2023-09-28
Australia/NSW-ICPMR-49586/2023|EPI_ISL_18411535|2023-09-23
Australia/NSW-ICPMR-49614/2023|EPI_ISL_18411563|2023-09-29
Australia/NSW-ICPMR-49647/2023|EPI_ISL_18411596|2023-09-30

Breakpoint 1: 4579~6541
Breakpoint 2: 25572~27507

C21T, T4579A, C28093T are from FL.2.4
C9693T, G13627A, A16878T, A18492G, G21718T, C22480T, T22930A, C25572T are from EG.5.1.1
HK.3 has G22927T too, but A7150C, C11173T seems from #537#branch_10

G599A, C673T, C1385T, G1820A, A2109G, C3768T seem private.

[Walde1nsamkeit]

Gansu/GSCDC-0503/2023|EPI_ISL_18464982|2023-10-24
XBB.1.42.2 / HK.1
Breakpoint: 9049~9693
Extra mutations: G3250A, C6114A(Orf1a:P1950H, a large branch with HL.2) / T21144C, A21603G(S:Q14R, maybe from HK.1> Orf1a:V2019I> S:Q14R branch?), G28202T, G28392A(N:R40H, Orf9b:V37I)

[Walde1nsamkeit]

Hubei/HCDC-WH3434/2023|EPI_ISL_18485331|2023-10-18
FL.15/HK.3.2
9693~11956

Mutations Based on XBB.1.9+S:S486P: C1174T, G1464T, G2174A, C3646T, C7735T, G11083T, G13627A, A16878T, A18492G, T20349G, C20759T, C21602A, G21718T, C22480T, C22786A, G22927T, T22930A, C25339T, C25572T, A27507C, A27669G, C29625T
Extra Mutations: C1174T, G1464T(Orf1a:G400V), C3646T, C7735T, G11083T(Orf1a:L3606F, potential artefact), T20349G(Orf1b:S2294R), C20759T(Orf1b:A2431V), C22786Arev(S:S408Rrev, potential artefact), C25339T, A27669G

FL.15> G1464T(Orf1a:G400V)> C12890T> C7735T
HK.3.2> A27669G> T8623C, C25339T
C1174T, C3646T, T20349G, C20759T are private

[Walde1nsamkeit]

Yunnan/YNCDC-3260/2023|EPI_ISL_18488078|2023-10-30
EG.5.1/BF.7.14/EG.5.1
23031~25290
27915~28297

Mutations Based on BA.2:
A405G, del686-694, C2334T, A2430G, C4012T, G5720A, C9693T, C9866T, A10323G, T12313A, C12789T, G15025A, G15451A, C15738T, T15939C, T16342C, A16878T, T17859C, A18492G, A19326G, G21718T, C21727T, C21767T, T21810C, C22000A, C22109G, G22200A, G22317T, C22480T, G22577C, G22599C, C22664A, G22895C, T22896C, G22898A, T22930A, T22942G, T23018C, T23019C, T23031C, G23040A, T24763C, C24766T, G25290T, C25509T, G26529A, T26858C, A27038G, C27259A, C27382G, T27383A, C27384T, C27889T, T28297C, C29625T

Extra Mutations:
del686-694(Orf1a:del141-143), A2430G(Orf1a:K722R), C4012T, A10323G(Orf1a:K3353R), T12313A, G15025A(Orf1b:A520T), C21727T, C21767T(S:H69Y), T24763C, C24766T, C25509T, C27532Trev(Orf7a:Y47Hrev, potential artefact), del28242-28252(Orf8:del117-120, fs)

[Walde1nsamkeit]

Gansu/GSCDC-0503/2023|EPI_ISL_18464982|2023-10-24 XBB.1.42.2 / HK.1 Breakpoint: 9049~9693 Extra mutations: G3250A, C6114A(Orf1a:P1950H, a large branch with HL.2) / T21144C, A21603G(S:Q14R, maybe from HK.1> Orf1a:V2019I> S:Q14R branch?), G28202T, G28392A(N:R40H, Orf9b:V37I)

Both XBB.1.42.2 and HK.1 are mainly in Xinjiang. but no recombinant in the latest batch. Maybe these 2 lineages also circulate in other Northwestern Chinese Provinces or Central Asia.

[Walde1nsamkeit]

Shanxi/TYCDC300/2023|EPI_ISL_18495231|2023-06-23
FR.1.4/EG.5.1
5720~7318
C22413T(S:T284I), C29762T

Shanxi/TYCDC352/2023|EPI_ISL_18495283|2023-07-07 FY.3.2/EG.5.1.1 potential contamination

Gansu/QYCDC-693/2023|EPI_ISL_18495563|2023-06-23 FY.3.3/EG.5.1.1 too many breakpoint and dropout, potential contamination

Gansu/QYCDC-897/2023|EPI_ISL_18495577|2023-09-01 EG.14/EG.5.1.1/FL.15.2/EG.5.1.1/FL.15.2 potential contamination

Gansu/QYCDC-704/2023|EPI_ISL_18495569|2023-06-28 EG.5.1.1 dropout contaminated by FY.3
Gansu/QYCDC-696/2023|EPI_ISL_18495566|2023-06-27 EG.5.1.1 dropout contaminated by FL.2.3+N:R189L
Shanxi/TYCDC350/2023|EPI_ISL_18495281|2023-07-07 EG.5.1.1 dropout?
Shanxi/TYCDC423/2023|EPI_ISL_18495354|2023-08-04 FU.1 dropout

[Walde1nsamkeit]

Gansu/QYCDC-0522/2023|EPI_ISL_18495868|2023-05-29 BA.5.2.48/BF.7.14.5/BA.5.2.48
14181~16616 22599~25290
BA.5.2.48> C11824T(The branch with DY.2/3)
BF.7.14.5> A25659T> T9229C> C21721T
Private mutations: A929G(Orf1a:I222V), C21721T, G23018Trev(S:V486Frev), G24570T(S:S1003I), C26907T

[Walde1nsamkeit]

Sichuan/ZGCDC-zgxg492/2023|EPI_ISL_18505570|2023-10-30
Sichuan/ZYCDC-YJ2188/2023|EPI_ISL_18505573|2023-10-19
FL.2.4/HK.13/FL.2.4
4579~6541 27507~28093
C2485T is from FL.2.4>C2485T branch
T11522C(Orf1a:F3753L), G12328A, C25810T(Orf3a:L140F) are private

Query: C2485T, T4579A, G22927C

[Walde1nsamkeit]

Xinjiang/XJCDCBAZ-313/2023|EPI_ISL_18505718|2023-09-06 EG.5.1.1/FL.4
25572~27507

EG.5.1.1> A4870G, C11455T
FL.4> C5812T> C29272T

C18490T(Orf1b:P1675S), T24934C, G25933C(Orf3a:E181Q), A27107G are private

[Walde1nsamkeit]

C12513T, A14010G, G18318T Potential EG.5.1/HV.1 recombinant, 3 seq