Several Potential Recombinants in China

[Over-There-Is]

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]

Did not found new recombinant recently, so close it.

[Over-There-Is]

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?

[Over-There-Is]

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.

[Over-There-Is]

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.

[Over-There-Is]

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)

[Over-There-Is]

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

[Over-There-Is]

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)

[Over-There-Is]

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.

[Over-There-Is]

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

[Over-There-Is]

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

[Over-There-Is]

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

[Over-There-Is]

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

[Over-There-Is]

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

[Over-There-Is]

Singapore/R3MQ54/2024|EPI_ISL_18771091|2024-01-10 from HKSAR, China

BA.2.86.1+ G210A, G2331T, C6310T, C7420T, T8670G FL.15+A27980G, T29023C

breakpoint: 23604\~24378

C6310T and T29023C are potential inherited