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Memorablea / COVID-19-

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Lineage Special tracking （Thx @FedeGueli #22

Closed Memorablea closed 6 months ago

Memorablea commented 1 year ago

专项追踪

Memorablea commented 1 year ago

XBB.1.16带有S：V551I 最早：2023-04-05 最近：2023-04-19 （请注意，我指的时间为上报时间，故仍然应进行监控） 分布：上海、印度 序列：EPI ISL 17591908、EPI ISL 17530314、EPI ISL 17536936、EPI ISL_17511858、EPI ISL_17619227、EPI ISL_17618926 image image

XBB.1.16 with S: V551I Earliest: April 5th, 2023 Recently: April 19, 2023 (Please note that the time I am referring to is the reporting time, so monitoring should still be carried out) Distribution: Shanghai, India sequence：EPI ISL 17591908、EPI ISL 17530314、EPI ISL 17536936、EPI ISL_17511858、EPI ISL_17619227、EPI ISL_17618926 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_30876_9e30b0.json?label=id:node_3155738 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_30876_9e30b0.json

Memorablea commented 1 year ago

T10810C FY.3 19 sequences image

Memorablea commented 1 year ago

我建议对中国的XBB.1.22.1进行指定

经过观察，我已经在Pango Issues发布FY.3和A11556G的内容，希望这条可以对将要进行指定的人有帮助

Outpfmance commented 1 year ago

IMG_0392 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 commented 1 year ago

关闭，等待有必要的更新

Memorablea commented 1 year ago

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

FedeGueli commented 1 year ago

Thx @Memorablea and @over_There_is i have proposed it : https://github.com/sars-cov-2-variants/lineage-proposals/issues/196

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

Memorablea commented 1 year ago

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

Thank you for understanding!

Memorablea commented 1 year ago

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

FedeGueli commented 1 year ago

Thank you very much @Memorablea !

Memorablea commented 1 year ago

@FedeGueli 这里发现了几个，不太了解是否重复 image

Memorablea commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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"

2023-06-20 (10)

Over-There-Is commented 1 year ago

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"

2023-06-22 (9)

Memorablea commented 1 year ago

专项追踪

  • XBB.1.9.1 + Orf1a：L3588F （NSP6_L19F）

There are currently 72 sequences from 6 countries.

Memorablea commented 1 year ago

FU.1+A460G 116条 image

Over-There-Is commented 1 year ago

新疆阿克苏BA.5.2.48跃迁 两条位于同一分支，均带V486Frev 2023-06-26 (5)

FedeGueli commented 1 year ago

Hi i would like to highlight this FL.2.3 with S:K356T likely emerged in China: Schermata 2023-07-01 alle 18 25 56 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_53fb_3c360.json?label=id:node_10475998

FedeGueli commented 1 year ago

And also this FU.1 sequence with S:N354K https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice7_genome_5aee_3c8a0.json Schermata 2023-07-01 alle 18 28 16

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 commented 1 year ago

Shanxi/TYCDC-096/2023|EPI_ISL_17951387|2023-04-21 BF.7.14.5>T27532Crev(Orf7a:Y47Hrev) >C13883T(Orf1b:T139I) >C2509T, T4930C, C10228T >G704A(Orf1a:D147N), C1404A(Orf1a:P380H), A2380G, A3342G(Orf1a:N1026S), A3647G(Orf1a:I1128V), A3829C, C12623T(Orf1a:P4120S), T12862C, C27999T(Orf8:P36S), A28482G(N:Q70R)

FedeGueli commented 1 year ago

I suggest very much to add this to the tracking list, in my math its doubling time is short. https://github.com/sars-cov-2-variants/lineage-proposals/issues/191

Memorablea commented 1 year ago

I suggest very much to add this to the tracking list, in my math its doubling time is short. sars-cov-2-variants/lineage-proposals#191

Understand

Memorablea commented 1 year ago

196 and #117 @Over-There-Is continues to track the issue interface, and I mark it as complete. Thank you @FedeGueli .

FedeGueli commented 1 year ago

Just a singlet but worrisome from Singapore an EG.5.1.1 with S:K356T it clusters with samples from Shanghai early in June while this has been collected on 26th of June in Singapore: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_33e08_5c8800.json?c=gt-ORF1ab_2092 this may point to an ongoing circualtion in Shanghai (or maybe not , cause there already more than 100 seqs from Shanghai after June 20th and none of this lineage)

FedeGueli commented 1 year ago

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4a392_651b30.json?c=userOrOld&label=id:node_10505271 singlet from Shanghai with S:V70A , S:F490P (reached with a trilple nuc mutation) and a large del between 139-146

Memorablea commented 1 year ago

OK

Over-There-Is commented 1 year ago

国内流通的XBB.1.5.15以G1820A(Orf1a:G519S)分支为主，但没有FD.2定义中的C21998A(S:Q146K) G15957T, G1820A, -C21998A可以搜索到112条序列 而G15957T, G1820A, C21998A仅能搜索到新疆博尔塔拉蒙古族自治州的两条序列 与国外的XBB.1.5.15+G1820A少、FD.2多完全相反 其他株系常常出现Q146K变异，不大可能出现反向的K146Q测序错误(?) 数量差异足够悬殊，基本可排除测序错误的原因 该支系是否FD.2的邻近支系？

Over-There-Is commented 1 year ago

369 现流通于新西兰 疑似国产

Memorablea commented 1 year ago

由 @Outpfmance 发现：湖北省一条EG.5.1(.1)带有S:P681R

Over-There-Is commented 1 year ago

Ukraine/80095/2023|EPI_ISL_18131053|2023-07-27 Dnipropetrovsk Oblast, Ukraine This singlet has been uploaded for days, but it's too hard to analyze. I am also not sure if this sequence really a recombinant. It has feature of both BA.1 and BA.2, but it has too many breakpoints, seems the sample is contaminated. But it also nearly impossible to find two chronic infectors at the same time and collect their sample. Somebody said it is possible for a chronic co-infection to lead to recombine multiple times and forms multiple breakpoints, but I forgot who he is. Nekromanzer? Outpfmance? Or Paibangzhu[potential another identity of Sakaguchi]? And I forgot where I saw that BA.1 has ins214EPE and remembered this sequence, I did not notice this ever. This sequence seems gained lots of mutations through saltation, including some convergent mutations nowadays. It seems this singlet is not spreading yet, but Ukraine has not uploaded sequence for half a month.

BA.1.1 / BA.2+C9866T Mutations based on the common ancestor of BA.1/2: C44T, T670G, A761G, C2455T, C2790T, G4184A, C4321T, C5183T, A6505G, G7553A, C8016T, G8393A, C8626T, C9042T, G9753A, C9866T, C10198T, G10447A, C10507T, C12400T, C12880T, T13195C, G13459T, A14226G, C15240T, C17676T, A19443G, A20055G, C20930T, C21588T, C21762T, 21765..21770 (6 bp), C21846T, 21987..21995 (9 bp), G22132T, 22194..22196 (3 bp), ins22204GAGCCAGAA, C22212T, G22599A, A22688G, G22775A, A22786C, A22812C, A22881G, T22896C, A22941C, C22971A, T22977C, T23030G, G23040A, G23222A, C23230T, C23453T, A23534G, C24130A, G24368T, C24503T, A25326G, G25681A, C26060T, C26600T, T26494G, T26551C, C26728T, A26739G, C26858T, A27403G, T27837G, A29510C, 29734..29759 (26 bp)

Breakpoint 1: BA.2 6515\~8393 BA.1.1 Breakpoint 2: BA.1.1 9534\~9866 BA.2 Breakpoint 3: BA.2 12880\~13195 BA.1.1 Breakpoint 4: BA.1.1 19955\~20055 BA.2 Breakpoint 5: BA.2 20055\~21618 BA.1.1 Breakpoint 6: BA.1.1 22599\~22673 BA.2 Breakpoint 7: BA.2 23202\~24130 BA.1.1 Breakpoint 8: BA.1.1 24503\~26060 BA.2 This sequence does not have G27382C, A27383T, T27384C, there are potentially 2 more breakpoint: 26858\~27382 and 27382\~29510. Extra Mutations: A761G, C2455T, C5183T, A6505G, G7553A, C8016T, C8626T, C9042T, G9753A, C9866T(Main branch of BA.2), C10507T, C12400T, G13459T, A14226G, C17676T, A19443G, C20930T, C21588T, G22132T, C22212T, G22599A(BA.1.1), A22812C, A22881G, T22896C, A22941C, C22971A, T22977C, T23030G, G23040A, G23222A, C23230T, C23453T, A23534G, G24368T, A25326G, G25681A, C26600T, T26494G, T26551C, C26728T, A26739G, A27403G, T27837G

ryhisner commented 1 year ago

There were a number of extremely divergent and unusual sequences uploaded from Ukraine a few weeks ago. They were all uploaded by the "Reference laboratory for diagnostics of HIV/AIDS", so I think there can be little doubt these sequences came from individuals with HIV who have been chronically infected for a very long time, possibly complicated by coinfection with multiple variants and an untold amount of intrahost recombination.

Over-There-Is commented 1 year ago

Yunnan/YNCDC-2534/2023|EPI_ISL_18241470|2023-08-16 FL.21.2+F456L Yunnan/YNCDC-2428/2023|EPI_ISL_18241448|2023-08-12 FL.21.2+Q14R

Over-There-Is commented 1 year ago

FL.2.3> N:R189L> S:N354K 9seq

Over-There-Is commented 1 year ago

FL.4.2+Q14H+P521S+A701V Heilongjiang/HLJCDC-2138/2023|EPI_ISL_18246167|2023-08-14 FL.4.2+K356T Heilongjiang/HLJCDC-2092/2023|EPI_ISL_18246080|2023-08-08 FL.4.2+F157L Heilongjiang/HLJCDC-1861/2023|EPI_ISL_18246168|2023-07-11

Over-There-Is commented 12 months ago

Shanghai/SCDC-XG09-13173/2023|EPI_ISL_18268466|2023-08-24 FL.2.3.1+K478R+T523I Shanghai/SCDC-XG09-12958/2023|EPI_ISL_18268444|2023-08-28 FL.2.3.1+Q14L

Over-There-Is commented 12 months ago

Hubei/HCDC-YC2844/2023|EPI_ISL_18268174|2023-08-23 FL.4(on N:K256R branch)+F456L+S494P+S691P

Over-There-Is commented 11 months ago

Fujian/FCDC-LY1864/2023|EPI_ISL_18277141|2023-09-11 EG.5.1.1> C26681T> T5327C, C5986T, T22032C(S:F157S), G22927T(S:L455F)

Over-There-Is commented 11 months ago

Sichuan/MYCDC-XGCX323/2023|EPI_ISL_18284777|2023-08-30 FE.1.1.3 saltation K356T, R403K, Y453F, S490P, K537E, A688V, K1045R

Over-There-Is commented 11 months ago

Japan/PG-564972/2023|EPI_ISL_18285429|2023-08-30 FL.2.3+S939F

FedeGueli commented 11 months ago

Sichuan/MYCDC-XGCX323/2023|EPI_ISL_18284777|2023-08-30 FE.1.1.3 saltation K356T, R403K, Y453F, S490P, K537E, A688V, K1045R

please propose it very bad looking. URGENT.

FedeGueli commented 11 months ago

Fujian/FCDC-LY1864/2023|EPI_ISL_18277141|2023-09-11 EG.5.1.1> C26681T> T5327C, C5986T, T22032C(S:F157S), G22927T(S:L455F)

Please post on # 537

Over-There-Is commented 11 months ago

Fujian/FCDC-LY1864/2023|EPI_ISL_18277141|2023-09-11 EG.5.1.1> C26681T> T5327C, C5986T, T22032C(S:F157S), G22927T(S:L455F)

Please post on # 537

Already included by Nekromanzer.

Over-There-Is commented 11 months ago

Anhui/AQCDC-147/2023|EPI_ISL_18289781|2023-08-27 FL.2.3.1+S490P

Over-There-Is commented 11 months ago

Anhui/AQCDC-133/2023|EPI_ISL_18289787|2023-08-20 FE.1.1+F157L Anhui/HFCDC-681/2023|EPI_ISL_18289827|2023-08 FU.1+Q14R Anhui/HFCDC-712/2023|EPI_ISL_18289858|2023-09 FU.1+Q14R Anhui/HCDC-150/2023|EPI_ISL_18289746|2023-08-14 FY.3.1+F157L Anhui/HFCDC-733/2023|EPI_ISL_18289879|2023-09 FY.3.3+G181A, F456L(already 2 seq) Henan/XYCDC-0271/2023|EPI_ISL_18289917|2023-08-03 FL.4+F456L

FedeGueli commented 11 months ago

That FY.3.3 if reaches 5 it is worth a proposal

Over-There-Is commented 11 months ago

Yunnan/YNCDC-2608/2023|EPI_ISL_18292741|2023-08-24 Yunnan/YNCDC-2610/2023|EPI_ISL_18292743|2023-08-27 XBB.1.16+L455F

Over-There-Is commented 11 months ago

Yunnan/YNCDC-2716/2023|EPI_ISL_18292849|2023-09-05 FL.15+W152R, F186S Yunnan/YNCDC-2585/2023|EPI_ISL_18292718|2023-08-28 FL.15+Q14H

FedeGueli commented 11 months ago

I have contacted you both on twitter please check dms

Over-There-Is commented 11 months ago

Japan/PG-564972/2023|EPI_ISL_18285429|2023-08-30 FL.2.3+S939F

Japan/PG-569108/2023|EPI_ISL_18294163|2023-08-29