Lineage Special tracking （Thx @FedeGueli #22

Memorablea · 2023-05-09T06:18:00Z

专项追踪

各个分支的跃迁演化
FL.2.3.1 + S:Q14R A21603G, G29543T
EG.5.1.1 with S:P681R
S：403K
等待更新......

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Outpfmance · 2023-05-21T15:32:21Z

这也是一个还在增长的中国本土跃迁分支，为【BA.2.75*】系的【BN.1*】的分支

Memorablea · 2023-06-05T10:51:54Z

关闭，等待有必要的更新

Memorablea · 2023-06-07T11:40:38Z

EPI_ISL_17703983疑似为XBB.1.19和XBB.1.22的重组

FedeGueli · 2023-06-15T14:09:20Z

Thx @Memorablea and @over_There_is i have proposed it : sars-cov-2-variants/lineage-proposals#196

Sorry i ve missed that this was the right place to discuss. i hev deleted msg in # 25

Memorablea · 2023-06-16T04:48:49Z

Sorry i ve missed that this was the right place to discuss. i hev deleted msg in # 25

Thank you for understanding!

Memorablea · 2023-06-17T05:17:54Z

Thank you @FedeGueli , this item has been changed to a dedicated tracking.

FedeGueli · 2023-06-17T06:09:08Z

Thank you very much @Memorablea !

Memorablea · 2023-06-17T12:32:43Z

@FedeGueli 这里发现了几个，不太了解是否重复

Memorablea · 2023-06-18T05:13:28Z

专项追踪

等待更新......

上海的FU.1大量更新，仅6月16日一天上报123例。

Over-There-Is · 2023-06-18T20:30:46Z

上海DY.2跃迁突变涉及14碱基和10氨基酸变化

Shanghai/SCDC-XG06-7545/2023|EPI_ISL_17811279|2023-05-28

DY.2> T9160A> C745T, C6936T(Orf1a:S2224F), G8264A(Orf1a:G2667S), C12763T, G13385A(Orf1a:G4374S), C20404T(Orf1b:P2313S), G22200A(S:G213E), C22295T(S:H245Y), G23018Trev(S:V486Frev), G24368C(S:D936H), C26408T(E:S55F), C28512G(N:P80R), A28795G, C29149T

带有长期感染标志突变S:H245Y, V486Frev

                 /organism="Severe acute respiratory syndrome coronavirus 2"
                 /mol_type="genomic RNA"
                 /isolate="SARS-CoV-2/human/CHN/SH-XG2306-7545/2023"
                 /isolation_source="Nasopharyngeal swab"
                 /host="Homo sapiens; Host_age: 71; Host_sex: Male"
                 /country="China:Shanghai"
                 /collection_date="2023-05-28"
                 /note="Passage_details/history: Original"

Over-There-Is · 2023-06-20T11:21:47Z

河南驻马店BF.7.14跃迁突变涉及16碱基和4氨基酸变化

Henan/ZMDCDC-131/2023|EPI_ISL_17817003|2023-04-27

BF.7.14> G28376A(N:A35T)
> C7093T, T7453C, C11962A, G14126A(Orf1b:S220N), T24763C, C26276T(E:T11M)
> C19269T, T28251G(Orf8:F120V), A28254C(Orf8:I121L)
> A812G(Orf1a:T183A), C3787T, C9073T, C10798T, C10868T, C11747T, C11750T(Orf1a:L3829F), C12789T(Orf1a:T4175I), T13644C, C17745T, A18600G, C20629T(Orf1b:H2388Y), C21727T, G22200Trev(S:G213Vrev), C29679T, C29732T

                 /organism="Severe acute respiratory syndrome coronavirus 2"
                 /mol_type="genomic RNA"
                 /isolate="SARS-CoV-2/human/CHN/ZMDCDC-131/2023"
                 /isolation_source="Oro-pharyngeal swab"
                 /host="Homo sapiens; Host_age: 16; Host_sex: female"
                 /country="China:Henan,Zhumadian"
                 /collection_date="2023-04-27"
                 /note="Passage_details/history: Original"

Over-There-Is · 2023-06-22T11:48:57Z

云南DY.1跃迁
Yunnan/YNCDC-1366/2023|EPI_ISL_17830456|2023-06-03
DY.1> C12970T
> C27707T(Orf7a:A105V)
> C3902T(Orf1a:P1213S), C5314T, C6573T(Orf1a:S2103F), C6681T(Orf1a:A2139V), C7874T(Orf1a:P2537S), C17130T
> C1479T(Orf1a:A405V), C3157T, C3653T(Orf1a:L1130F), T12136C, C13197T(Orf1a:T4311I), C13501T(Orf1b:P12S), G15451A(Orf1b:G662S), C23315T(S:L585F), A26709Grev(M:T63Arev), T27522A(Orf7a:N43K), G28027A(Orf8:W45*), G28134A(Orf8:~~V81I~~), C29098T, C29627T(Orf10:R24C)

                 /organism="Severe acute respiratory syndrome coronavirus 2"
                 /mol_type="genomic RNA"
                 /isolate="SARS-CoV-2/human/CHN/YNCDC-1366/2023"
                 /isolation_source="Oro-pharyngeal swab"
                 /host="Homo sapiens; Host_age: 69; Host_sex: Male"
                 /country="China:Yunnan"
                 /collection_date="2023-06-03"

Memorablea · 2023-06-23T08:26:33Z

专项追踪

XBB.1.9.1 + Orf1a：L3588F （NSP6_L19F）

There are currently 72 sequences from 6 countries.

Memorablea · 2023-06-26T09:12:46Z

FU.1+A460G 116条

Over-There-Is · 2023-06-26T12:32:36Z

新疆阿克苏BA.5.2.48跃迁两条位于同一分支，均带V486Frev

FedeGueli · 2023-07-01T16:26:19Z

Hi i would like to highlight this FL.2.3 with S:K356T likely emerged in China:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_53fb_3c360.json?label=id:node_10475998

FedeGueli · 2023-07-01T16:30:07Z

And also this FU.1 sequence with S:N354K https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice7_genome_5aee_3c8a0.json

Very recent . In the past there has been one quite successful BA.4 (i think BA.4.10) with S:N354D so maybe worth keeping tracked

Over-There-Is · 2023-10-26T15:06:42Z

South_Korea/KDCA268339/2023|EPI_ISL_18435652|2023-10-01 FL.2.3+Q14H, A653V

Over-There-Is · 2023-10-26T15:57:17Z

Canada/MB-CPL-653580/2023|EPI_ISL_18429933|2023-09-26 GW.1+C6525T(T2087I, Definition of JN.3)

Over-There-Is · 2023-10-27T04:16:12Z

Beijing/BJCDC-2781/2023|EPI_ISL_18438180|2023-06-04 GW.1.1+G184S
Beijing 06-04
Seems stopped growing

Over-There-Is · 2023-10-27T04:20:35Z

Beijing/BJCDC-4318/2023|EPI_ISL_18438229|2023-08-31 XBB.1.42.2+Q14H, A626V

Over-There-Is · 2023-10-28T14:44:00Z

FL.1.5.1> C26894T> C25931T(Orf3a:S180F)> A17615G(Orf1a:K1383R) 6seq, US

Over-There-Is · 2023-11-05T05:59:39Z

FL.2.3.1+Q14R 2 seq T1270C, T3883C, A21603G China 1(Heilongjiang), Switzerland 1(Ticino) EPI_ISL_18384445 EPI_ISL_18397929

5 seq now, China 4:Heilongjiang 3, Xinjiang 1(Urumqi); Switzerland 1(Ticino)
Heilongjiang/HLJCDC-2366/2023|EPI_ISL_18465045|2023-09-19 E309Q(2 seq)
Heilongjiang/HLJCDC-2456/2023|EPI_ISL_18465139|2023-10-05 A484S

Over-There-Is · 2023-11-05T06:01:52Z

Shanghai/SCDC-XG10-14604/2023|EPI_ISL_18465384|2023-09-30 under FL.2.3>N:R189L>S:F456L branch
Q14R, L455F

Over-There-Is · 2023-11-05T06:07:28Z

EG.5.1.8+Orf1a:L3829F 2seq

FedeGueli · 2023-11-06T09:39:29Z

Shanghai/SCDC-XG10-14604/2023|EPI_ISL_18465384|2023-09-30 under FL.2.3>N:R189L>S:F456L branch Q14R, L455F

please propose this one if it turns 2

Over-There-Is · 2023-11-06T13:17:12Z

Hong_Kong/VB23204967/2023|EPI_ISL_18466251|2023-10-27
FQ.1> T6571C> C26537T> T378C(Orf1a:V38A), C503T(Orf1a:P80S), C629T(Orf1a:L122F), T1354C, A1818G(Orf1a:K518R), C2721T(Orf1a:A819V), G2897A(Orf1a:A878T), C3619T, A4233G(Orf1a:D1323G), C5178A(Orf1a:T1638N), A5227G, C7644T(Orf1a:A2460V), A7986T(Orf1a:Q2574L), C9073T, G9383T(Orf1a:A3040S), C10279T, A12762G(Orf1a:D4166G), C17626T(Orf1b:H1387Y), C17733T, G18340A(Orf1b:V1625I), G19282A(Orf1b:D1939N), G19480A(Orf1b:G2005S), C19524T, T22729C, G23429A(S:A623T), C23763T(S:T734I), C26198T(Orf3a:T269M), G27087A(M:G189S), C27208T(Orf6:H3Y), T27504C, T27780C(Orf7b:F9L), T27889Crev, del28254(Orf8:I121fs), C28957T, A29700G
34 sub and 1 del(frameshift) saltation

Over-There-Is · 2023-11-08T05:15:56Z

Shanghai/SCDC-XH1020-48_S48/2023|EPI_ISL_18475201|2023-10-13 FL.21.2+K356T, S704L

Over-There-Is · 2023-11-10T05:09:25Z

HCDC-SY3488/2023|EPI_ISL_18485310|2023-10-24 FL.15.2>L455F>D215N, A845V

Over-There-Is · 2023-11-12T08:19:32Z

Fujian/FCDC-QZ11S001/2023|EPI_ISL_18495156|2023-10-25 JH.1+F157L, K478R
/note="Passage_details/history: sample collected following
travel from Africa; Patient_status: Released"
But not mentioned which country.

Shanxi/TYCDC372/2023|EPI_ISL_18495303|2023-07-18 DY.2+T732I> P9L, R214H, R403S, K444M, V486Frev
Shanxi/TYCDC373/2023|EPI_ISL_18495304|2023-07-18 DY.2+P9L, D215G, K444N, A484V
Shanxi/TYCDC426/2023|EPI_ISL_18495357|2023-08-04 DY.2+T95I, E340K, R403K, K444N, R452Q, N460K, V483A, A484V, N658D
Shanxi/TYCDC485/2023|EPI_ISL_18495416|2023-09-01 BF.7.14+W152L, D339H, V455A, V486Frev, T547K, A570V, P1143S, D1260H
Shanxi/TYCDC445/2023|EPI_ISL_18495376|2023-08-11 BF.7.14.4+Y508H, D936H
Shanxi/TYCDC601/2023|EPI_ISL_18495532|2023-11-03 FL.2.3+Q146K> T20N, D428Y, H505Yrev

FedeGueli · 2023-11-12T10:17:20Z

Fujian/FCDC-QZ11S001/2023|EPI_ISL_18495156|2023-10-25 JH.1+F157L, K478R /note="Passage_details/history: sample collected following travel from Africa; Patient_status: Released" But not mentioned which country.

Shanxi/TYCDC372/2023|EPI_ISL_18495303|2023-07-18 DY.2+T732I> P9L, R214H, R403S, K444M, V486Frev Shanxi/TYCDC373/2023|EPI_ISL_18495304|2023-07-18 DY.2+P9L, D215G, K444N, A484V Shanxi/TYCDC426/2023|EPI_ISL_18495357|2023-08-04 DY.2+T95I, E340K, R403K, K444N, R452Q, N460K, V483A, A484V, N658D Shanxi/TYCDC485/2023|EPI_ISL_18495416|2023-09-01 BF.7.14+W152L, D339H, V455A, V486Frev, T547K, A570V, P1143S, D1260H Shanxi/TYCDC445/2023|EPI_ISL_18495376|2023-08-11 BF.7.14.4+Y508H, D936H Shanxi/TYCDC601/2023|EPI_ISL_18495532|2023-11-03 FL.2.3+Q146K> T20N, D428Y, H505Yrev

Thank you JH.1 is a dark horse in Africa. also the last one seems interesting lets see if 505 rev is real or not.

Over-There-Is · 2023-11-13T18:15:51Z

FL.2.3.1+Q14R 2 seq T1270C, T3883C, A21603G China 1(Heilongjiang), Switzerland 1(Ticino) EPI_ISL_18384445 EPI_ISL_18397929

5 seq now, China 4:Heilongjiang 3, Xinjiang 1(Urumqi); Switzerland 1(Ticino) Heilongjiang/HLJCDC-2366/2023|EPI_ISL_18465045|2023-09-19 E309Q(2 seq) Heilongjiang/HLJCDC-2456/2023|EPI_ISL_18465139|2023-10-05 A484S

Gansu +1, 6 now, without T1270C and T3883C
New query: A21603G, G29543T

FedeGueli · 2023-11-13T21:42:53Z

A21603G, G29543T

Thx for the new query
Lets wait for some more recent samples, it is enough one more from , to say, mid october to propose it.

Over-There-Is · 2023-11-14T14:30:05Z

Shanghai/SCDC-XG10-14604/2023|EPI_ISL_18465384|2023-09-30 under FL.2.3>N:R189L>S:F456L branch Q14R, L455F

No, sars-cov-2-variants/lineage-proposals#1068 is first mentioned here, and proposed on 8 Nov, and quoted by sars-cov-2-variants/lineage-proposals/issues/526 on 11 Nov. @FedeGueli

FedeGueli · 2023-11-14T22:47:48Z

Shanghai/SCDC-XG10-14604/2023|EPI_ISL_18465384|2023-09-30 under FL.2.3>N:R189L>S:F456L branch Q14R, L455F

No, sars-cov-2-variants/lineage-proposals#1068 is first mentioned here, and proposed on 8 Nov, and quoted by sars-cov-2-variants/lineage-proposals/issues/526 on 11 Nov. @FedeGueli

Sorry i dont get what are you responding to, what happened? i for sure mistook the issue if i ve credited soemone else.

FedeGueli · 2023-11-14T22:51:49Z

AH ok i see . i misunderstood the tracklist.

Over-There-Is · 2023-11-22T07:18:42Z

Fujian/FCDC-ND2157/2023|EPI_ISL_18523045|2023-10-22 EG.5.1.8+K356T

Over-There-Is · 2023-11-27T18:27:07Z

Singapore/R85MR218/2023|EPI_ISL_18544623|2023-11-18 from Japan
C27507Arev, T29555Crev, T29625Crev
Potential recombined with other Orf9b:I5T lineages like XBB.1.9.1* or XBB.1.22*

Over-There-Is · 2023-12-08T22:36:58Z

USA/NJ-CDC-QDX88030603/2023|EPI_ISL_18602256|2023-11-20
FL.2.3+S:F456L / EG.5.1.1
FL.2.3> T22928C> T14679C
EG.5.1.1> C12053T> C503T, A8116G> C18175T, G22927T> C7732T> G27962A> T26310C> T27713C
Brpt: 22930~25572
C7303T, C9430T, T15069C, C21459T, C21767T, A22005C, C23029T, C25066T, C27893T, C27942T are private

Over-There-Is · 2023-12-12T10:43:14Z

Hong_Kong/HKU-231211-039/2023|EPI_ISL_18604522|2023-01-31 BA.2.2 Saltation
H519Y, P621S on S494P> T470N> R346T> A222V branch (Potential single patient)

Over-There-Is · 2023-12-17T02:41:53Z

Russia/SPE-RII-MH150849S/2023|EPI_ISL_18638833|2023-11-13 HK.3.2/XBB.1.16*

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Outpfmance mentioned this issue May 21, 2023

包含中国的变异株提名（4月21日起） #10

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Memorablea closed this as not planned Won't fix, can't repro, duplicate, stale Jun 5, 2023

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GISAID China Report[202305-06] #25

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Memorablea changed the title ~~建议观察的血统Suggested bloodline for observation~~ 建议观察的血统Suggested Lineage Jun 16, 2023

Memorablea changed the title ~~建议观察的血统Suggested Lineage~~ Lineage Special tracking （Thx @FedeGueli Jun 17, 2023

Memorablea mentioned this issue Jun 29, 2023

XBB.1.33全球流行情况（230序列） #6

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Memorablea closed this as not planned Won't fix, can't repro, duplicate, stale Mar 17, 2024

Memorablea unpinned this issue Mar 17, 2024

Lineage Special tracking （Thx @FedeGueli #22

Lineage Special tracking （Thx @FedeGueli #22

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