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Several Potential Recombinants in China #108

Closed Over-There-Is closed 1 year ago

Over-There-Is commented 1 year ago

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

Over-There-Is commented 1 year ago

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 commented 1 year ago

Thx great work!

Over-There-Is commented 1 year ago

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.

Over-There-Is commented 1 year ago

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 commented 1 year ago

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

Over-There-Is commented 1 year ago

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.

Over-There-Is commented 1 year ago

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)

Over-There-Is commented 1 year ago

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 commented 1 year ago

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

Over-There-Is commented 1 year ago

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

Over-There-Is commented 1 year ago

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

Over-There-Is commented 1 year ago

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

Over-There-Is commented 1 year ago

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 commented 1 year ago

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:

Schermata 2023-06-17 alle 16 00 07

FedeGueli commented 1 year ago

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

FedeGueli commented 1 year ago

Schermata 2023-06-17 alle 16 21 42 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 commented 1 year ago

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

FedeGueli commented 1 year ago

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

Over-There-Is commented 1 year ago

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*

Over-There-Is commented 1 year ago

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

Over-There-Is commented 1 year ago

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.

Over-There-Is commented 1 year ago

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 commented 1 year ago

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

Over-There-Is commented 1 year ago

Guangdong/GDCDC_MZ_0055/2023|EPI_ISL_17697694|2023-05-05 XBB.1.9.1* / DY.3

Over-There-Is commented 1 year ago

Yunnan/YNCDC-1334/2023|EPI_ISL_17830364|2023-06-06 EG.5.1.1 / BQ.1.1.18*? But BQ series have not been circulated in China. Yunnan/YNCDC-1333/2023|EPI_ISL_17830371|2023-06-05 GB.2 / BA.5.2 Yunnan/YNCDC-1341/2023|EPI_ISL_17830436|2023-06-09 BA.5.2 / XBB.2.3.2 Yunnan/YNCDC-1314/2023|EPI_ISL_17830358|2023-06-01 FR.1.2 / FY.3 Yunnan/YNCDC-1245/2023|EPI_ISL_17830484|2023-06-06 XBB.1.16 / EG.5.1.1

Over-There-Is commented 1 year ago

Xinjiang/XJCDCAKS-041/2023|EPI_ISL_17836425|2023-04-27 FL.5 / BF.7.14 Shanghai/SCDC-HG0609-1870/2023|EPI_ISL_17836973|2023-06-07 XBB.1.9.1 / BQ.1 Import from Russia Shanghai/SCDC-XG06-8261/2023|EPI_ISL_17836674|2023-06-07 GF.1/ XBB.1.16 Anhui/AQCDC-083/2023|EPI_ISL_17837073|2023-05-30 FY.3.1 / FR.1 Shanghai/SCDC-XG06-8176/2023|EPI_ISL_17836695|2023-06-04 XBB.1.5*+T10204C / XBB.1.16 Xinjiang/XJCDCHM-059/2023|EPI_ISL_17836351|2023-04-29 XBB.1.9.1 / FR.1.3

Over-There-Is commented 1 year ago

Hubei/HCDC-SY1865/2023|EPI_ISL_17794178|2023-05-29 GW.1+C4586T+C10030T / FL.4+N:K256R(#117)

Mutations based on GW.1: T541Crev, (T4586Crev), C10030T, A10465Grev, T20823Crev, C21363Trev, G27915T(Orf8:G8), T28297C(Orf9b:I5T), A29040G(N:K256R), G29237Arev Mutations base on FL.4+N:K256R: G1055A(GW.1), A5720Grev, C10030T, A10042G(XBB.1.19), C10186T(GW.1), T11956Crev, C15960T(GW.1), T12789Crev, T16741Grev, C28519T(GW.1) And 169/174 of sequences have all of G27915T(Orf8:G8), T28297C(Orf9b:I5T), A29040G(N:K256R) are FL.4.

Over-There-Is commented 1 year ago

Jiangxi/JXNC-174/2023|EPI_ISL_17794675|2023-05-02 FL.21+Orf1a:V1019F,I2873M / FL.2.3? Jiangxi/JXYT-038/2023|EPI_ISL_17794976|2023-05-06 FL.21+Orf1a:V1019F,I2873M / XBB.1.9.1 Jiangxi/NCCDC-HG-014/2023|EPI_ISL_17808160|2023-05-24(Import from Vietnam) FL.21+Orf1a:V1019F,I2873M / XBB.1.16+Orf1a:P804L,Orf3a:E242Q Jiangxi/JXJDZ-067/2023|EPI_ISL_17808160|2023-05-24 FL.21+Orf1a:V1019F,I2873M / XBB.1.16

Over-There-Is commented 1 year ago

Guangdong/GDCDC_JM_0096/2023|EPI_ISL_17698188|2023-05-10 XBB.1.5.15+Orf1a:P2046L,L3829F / XBL.3+C18888T,T15651C

FedeGueli commented 1 year ago

@Over-There-Is has some of them still spread beyond one single sequence?

Over-There-Is commented 1 year ago

Liaoning/LNCDC-202-4/2023|EPI_ISL_17972913|2023-06-06 FR.1.1 / XBB.1*+Orf9b:I5T Shanxi/JCCDC-JCCX0272/2023|EPI_ISL_17972998|2023-06-08 FU.1 / EG.5.1.1

Over-There-Is commented 1 year ago

@Over-There-Is has some of them still spread beyond one single sequence?

Not yet.

NkRMnZr commented 1 year ago

recomb

There's quite a lot of recombinant of BA.2.75 (CH.1.1 or BN.1) and XBB.1+ORF8:G8+S:F486P(+ some with S:Q613H, and some with S:D253G and S:P521S, probably from XBB.2.3*) caught by UShER under BY.1 assignment, they may be from different recombinant events.

ryhisner commented 1 year ago

This looks like a very believable FR.1.1/XBB.2.3 recombinant from Shanghai. Breakpoint between K356T and L368I, which seems pretty ideal for a recombinant between these two. Has a handful of private mutations, including M:T30I and ORF3a:A33E.

EPI_ISL_17987802

Over-There-Is commented 1 year ago

This looks like a very believable FR.1.1/XBB.2.3 recombinant from Shanghai. Breakpoint between K356T and L368I, which seems pretty ideal for a recombinant between these two. Has a handful of private mutations, including M:T30I and ORF3a:A33E.

EPI_ISL_17987802

I got noticed to that sequence yesterday. It is assigned as BY.1 by usher, but BY.1 have not ever circulated in China. Additionally, rather than FR.1.1, I think the FR* donor would be FR.1.4.

Over-There-Is commented 1 year ago

Beijing/BJCDC-1618/2023|EPI_ISL_18009877|2023-05-08 FU.1+A460G / GW.1 Beijing/BJCDC-1446/2023|EPI_ISL_18009716|2023-05-01 FU.1+A460G / BA.5 Beijing/BJCDC-1461/2023|EPI_ISL_18009731|2023-05-01 same as BJCDC-1446 Beijing/BJCDC-1651/2023|EPI_ISL_18009923|2023-05-08 XBB.1.16/ BA.5 Beijing/BJCDC-1651/2023|EPI_ISL_18009923|2023-05-08 GY.6 / BA.5 Beijing/BJCDC-1644/2023|EPI_ISL_18009916|2023-05-04 EG.5.1.1 / BA.5 Beijing/BJCDC-1658/2023|EPI_ISL_18009930|2023-05-09 FY.3 / FR.1 Beijing/BJCDC-1665/2023|EPI_ISL_18009937|2023-05-09 XBB.1 / FR.1 Beijing/BJCDC-1590/2023|EPI_ISL_18009849|2023-05-08 XBB.1.16.2 / BA.5 Beijing/BJCDC-1577/2023|EPI_ISL_18009835|2023-05-06 GY.1 / BA.5 Beijing/BJCDC-1578/2023|EPI_ISL_18009836|2023-05-06 GY.1 / BA.5 Beijing/BJCDC-1611/2023|EPI_ISL_18009870|2023-05-03 XBB.1.5 / BA.5 Beijing/BJCDC-1634/2023|EPI_ISL_18009906|2023-05-01 XBB.1.5 / BA.5 Beijing/BJCDC-1649/2023|EPI_ISL_18009921|2023-05-08 XBB.1.5 / BA.5*

Over-There-Is commented 1 year ago

Guangdong/GDCDC_SZHG_1962/2023|EPI_ISL_18036528|2023-06-13 Assigned as XCC by usher, but seems not related to it. FR.1.1 + C3927T / FY.3 + A11556G + A29812G Breakpoint: 4586~5183

Mutations from FR.1.1: C337T, C1142T(ORF1a:L293F), C1471T, C1513T, T2372C, C3796T, C3923T(ORF1a:P1220S), *C3927T(ORF1a:S1221L), C4586T Mutations from FY.3: *A11556G(ORF1a:E3764G), C15738T T15939C, T16342C(ORF1b:S959P), T17859C, A19326G, T21810C(S:V83A), del21992-21994(S:Y144-),C22000A(S:H146Q), C22109G(S:Q183E), A22161G(S:Y200C), T22200A(S:V213E), G22317T(S:G252V), C22664A(S:L368I), G22895C(S:V445P), T22896C(S:V445P), T23018C(S:F486P), T23019C(S:F486P), C23191T, G27915T(ORF8:G8), T28297C(ORF9b:I5T), \A29812G Private mutations: A1740C(ORF1a:K492T), C28732T

xz-keg commented 1 year ago

Ins27791T seems to appear in a lot of different Hubei XBB seqs. It seems not a symbol of FR.1-related recombinations but some artifacts, as they only appear in Hubei.

FedeGueli commented 1 year ago

Ins27791T seems to appear in a lot of different Hubei XBB seqs. It seems not a symbol of FR.1-related recombinations but some artifacts, as they only appear in Hubei.

@ryhisner please take a look

Over-There-Is commented 1 year ago

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

Over-There-Is commented 1 year ago

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

FedeGueli commented 1 year ago

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

Over-There-Is commented 1 year ago

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

Over-There-Is commented 1 year ago

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

Over-There-Is commented 1 year ago

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)

Over-There-Is commented 1 year ago

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 commented 1 year ago

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

Over-There-Is commented 1 year ago

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

Over-There-Is commented 1 year ago

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 commented 1 year ago

@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!