XBB.1.9* Lineage Tracker

[NkRMnZr]

XBB.1.9* Lineage Tracker

L455F

• [ ] FL.16 > T22928C(S:F456L) > A13913G(ORF1b:N149S), T16029C > G960A(ORF1a:R232H), A2589G(ORF1a:E775G), C2892T(ORF1a:A876V), _revT3511C, T4008A(ORF1a:F1248Y), T5134C, C6026T(ORF1a:P1921S), G7736A(ORF1a:V2491I), C10386T(ORF1a:T3374I), G18756T, G22927T(S:L455F), G26640T(M:A40S) [Query: A13913G, T16029C, G22927T, Nov30] Sichuan/YBCDC-XGCX481/2023|EPI_ISL_18564312|2023-11-10

F456L

• [ ] XBB.1.9.1 > C10156T > C13881A, T22928C(S:F456L), G28041T(ORF8:G50*) [Query: C10156T, C13881A, T22928C, 8, Oct11]
• [ ] FL.2 > A14355G > C556T, G2527A, C6472A, A21137G(ORF1b:K2557R), T22928C(S:F456L) [Query: T4579A, A14355G, T22928C, 7, Sep6]
• [ ] sars-cov-2-variants/lineage-proposals#526, Branch 2: FL.2.3 > G28839T(N:R189L) > T16977C > T22928C(S:F456L)
• [ ] FL.13 > C5241T(ORF1a:P1659L) > A22106G(S:K182E) > C12499T > T22928C(S:F456L) [Query: C5241T, T22928C, 10, Sep29]
• [ ] sars-cov-2-variants/lineage-proposals#692 FL.13 > C27297T > C3264T(ORF1a:T1000I), A3754G, T4507C > A6626G(ORF1a:T2121A), C7844A(ORF1a:L2527M), C10474T, C15774T, G21142T(ORF1b:A2559S), T21976C, T22928C(S:F456L), C23929T
• [ ] EG.1.5 > C22978T > C19366T(ORF1b:P1967S) > T22928C(S:F456L) [Query: C22978T, C19366T, T22928C, 14, Sep29]

T478X

• [ ] XBB.1.9.1 > T27530C(ORF7a:F46S) > T22885A(S:L441) > T25496C(ORF3a:I35T) > C22995G(S:T478R), C27002T [Query: T22885A, C22995G, T25496C, 6, Oct11]
• [ ] XBB.1.9.1 > C28846T > G2174A(ORF1a:E637K) [Sibling to FL.15] > C22995G(S:T478R) [Query: C28846T, G2174A, C22995G, 22, Sep29]
• [ ] FL.1 > C706T, A15936G > C22995G(S:T478R), C25487T(ORF3a:T32I) [Query: C706T, A15936G, C22995G, 16, Sep28]
• [ ] sars-cov-2-variants/lineage-proposals#1058 FL.1 > C7164T(ORF1a:T2300I), A13308G(ORF1a:K4348R), C14877T > C22995G(S:T478R), C23123A(S:P521T) > G5917A, A26544G(M:I8V)
• [ ] FL.2.3.1 > A1842G(ORF1a:Q526R), C22995G(S:T478R), C26305T(E:L21F) [Query: A11188G, A17615G, C22995G, 4, Sep15]
• [ ] FL.2.6 > A29683T > T181C, T12811C, G13624T(ORF1b:D53Y), C22033A(S:F157L), A22405C(S:E281D), C22995G(S:T478R), A23223G(S:E554G) [Query: C22995G, T23485A, A29683T, 1+1, Oct11]
• [ ] FL.4 > A28615G > C2939T(ORF1a:P892S) > C27741T > C22995G(S:T478R) [Query: C2939T, G16741T, C22995G, 33, Sep23]
• [ ] FL.4 > A28615G > C25006T(S:F1148) > C1594T, C4534T, C22995G(S:T478R) [Query: C22995G, C25006T, A28615G, 12, Oct12]
• [ ] FL.5 > C3177T(ORF1a:P971L) > G18105T(ORF1b:Q1546H) > A29443G > C22995G(S:T478R) [Query: C22995G, A29443G, 8, 08/29]
• [ ] FL.5 > A29020G > C22995G(S:T478R) [Query: A29020G, C22995G, C29358T, 16, Sep8]
• [ ] FL.5.1 > C2695T, C11455T > C8616T(ORF1a:A2784V), C22995G(S:T478R) [Query: C2695T, C11455T, C22995G, 13, Aug28]
• [ ] XBB.1.9.1 / FL.7 (C21714T(S:T51I) > G2162A(ORF1a:E633K), C15857T(ORF1b:T1645I) > _T21714C_rev(S:I51Trev) > T15096C > A1378G > T12847C, C13366T, C22995G(S:T478R), C23123T(S:P521S), T27408G [Query: A1378G, T15096C, C22995G, 11, Oct19]
• [ ] FL.7 > T2911G > G1857A(ORF1a:S531N) > T8158C > T13114C > T12505C > C22995T(S:T478I) [Query: T8158C, T13114C, C22995T, 3, Oct3]
• [ ] FL.10 > C22995G(S:T478R) [Query: G5720A, G2235A, C22995G, C11956T, -T20337C, -G29717A, 27, Sep23]
• [ ] FL.10.1 > T24352C > C22995G(S:T478R), A24791G(S:T1077A), G25437T(ORF3a:L15F), A26603G [Query: C4234T, C22995G, T24352C, 5, Sep14]
• [ ] sars-cov-2-variants/lineage-proposals#789 FL.24 > C22995G(S:T478R)
• [ ] FL.26 > G6669T(ORF1a:W2135L) > C14805T, T23030C(S:F490P) > A3184G, C6027T(ORF1a:P1921L), C7851T(ORF1a:A2529V), T15375C, C16178T(ORF1b:S904L), C22995G(S:T478R) [Query: G6669T, C14805T, C22995G, 4, Sep19]
• [ ] EG.1 > T25496C(ORF3a:I35T) > C186T, A7201G, C11103T(ORF1a:P3613L), T16521C, C22208T(S:L216F), G22487C(S:E309Q), C22995G(S:T478R), A23440G, G26235T, C27110T, C28146T(ORF8:P85S), G28904T(N:A211S), C29098T [Query: C22995G, T25496C, C28928T, 4 seqs, Sep23]
• [ ] EG.4 > C19186A(ORF1b:L1907I), G25538T(ORF3a:G49V) > T10387C, C22995G(S:T478R), G26648A [Query: C19186A, C22995G, G25538T, 15, Oct11]
• [ ] EG.4 > T23590C > C27335T(ORF6:T45I) > C22995G(S:T478R), C29659T [Query: C22995G, T23590C, C27335T, 15, Aug28]

Q613H

• [ ] XBB.1.9.1 > G21019A(ORF1b:A2518T) > C27600T > A8773G, G23401T(S:Q613H), G26428T(E:V62F), C29311T [Query: G21019A, G23401T, C27600T, 16, Sep13]
• [ ] sars-cov-2-variants/lineage-proposals#1001 XBB.1.9.1 > C28846T > G2174A(ORF1a:E637K) > C25482T > A2821G, C14670T, C22995G(S:T478R), T23158C, G23401T(S:Q613H)
• [ ] FL.2 > A14355G > T3724C, T17007C > A10323G(ORF1a:K3353R) > G1274T(ORF1a:V337F), C6896T, C11824T, G23401T(S:Q613H), C23638T [Query: T3724C, A14355G, G23401T, 4, Aug22]
• [ ] FL.4 > A28615G > C23635T > G22113T(S:G184V), A25983G > G7059A(ORF1a:G2265D), G23401T(S:Q613H) [Query: G7059A, G22113T, G23401T, 5, Sep6]
• [ ] FL.4.5 > C21772T > C11671T, C18744T > C5467T, C22624T > C4202T, C18267T, G22021T(S:M153I), G23401T(S:Q613H) [Query: C5467T, C11671T, G23401T, 7, Sep27]
• [ ] FL.4.6 > C12781T > C18129T > G18382A(ORF1b:V1639I), T24796C > G3250A, C6636T(ORF1a:T2124I), G18937A(ORF1b:G1824S), G21901A, C22329T(S:S256L), G23401T(S:Q613H), G23611T, C29358T(N:T362I) [Query: C12781T, G18382A, G23401T, 16, Sep19]
• [ ] FL.19 > C16376T(ORF1b:P970L), G23401T(S:Q613H) [Query: C16376T, G23401T, T24505G, 9, Oct13]
• [ ] sars-cov-2-variants/lineage-proposals#516 EG.2 > C26110T(ORF3a:P240S) > T19138C(ORF1b:F1891L), G23401T(S:Q613H), G24116T(S:A852S)

R403K

• [ ] sars-cov-2-variants/lineage-proposals#988 FL.4 > A28615G > C2939T(ORF1a:P892S) > T3118C > T14127C > C27864T(ORF7a:H37Y) > T1211C(ORF1a:C316R), C7006A, T15790G(ORF1b:S775A), T18426C > C18395T(ORF1b:A1643V) > C20233T(ORF1b:P2256S), G22770A(S:R403K)

RBD Levels

• [ ] XBB.1.9.1 > G7042T(ORF1a:M2259I) > G24356A(S:G932S) > C22313T(S:P251S), A22629C(S:K356T), T29577G(ORF10:F7C) [Query: G5720A, G7042T, A22629C, G24356A, 9, Oct16]
• [ ] FL.2.2.1 > C4633T > G21785A(S:G75S) > A6475T(ORF1a:E2070D), A8475G(ORF1a:N2737S), G17721T, A22629C(S:K356T), G29086A_rev [Query: C4633T, C22482T, A22629C, 10, Sep29]
• [ ] FL.5 > A10103G(ORF1a:M3280V) > C12049T, C21304A(ORF1b:R2613S), A22629C(S:K356T), G24368T(S:D936Y), G26074A(ORF3a:V228I), T26294C(E:V17A), G29239A(N:M322I) [Query: A10103G, A22629C, C29358T, 9, Sep22]
• [ ] FL.10.1 > T24352C(S:A930) > C4784T(ORF1a:L1507F), C21145T(ORF1b:L2560F), C27600T > G22820A(S:D420N), G29260T [Query: C4784T, G22820A, T24352C, 2, Oct12]
• [ ] sars-cov-2-variants/lineage-proposals#981 FL.20 > A9052T > T29785C > C25692T > A23746T(S:P728) > A8147G(ORF1a:N2628D), C9778T, C15951T, A22629C(S:K356T), C28714A, A29115T(N:Q281L) [Query: A9052T, A22629C, T29785C, 8, Oct17]
• [ ] FL.20.2 > C22916A(S:L452M) [Query:T19755C, C22916A, C22995G, 10, Oct23]
• [ ] FL.25 > A21137G(ORF1b:K2557R) > C27741T > C3261T(ORF1a:T999I), C3318T(ORF1a:P1018L), A5720G_rev(ORF1a:S1819G_rev), A12556T(ORF1a:E4097D), T23042C(S:S494P), T26497C [Query: T23042C, G23222A, C27741T, 6, Aug28]
• [ ] sars-cov-2-variants/lineage-proposals#713 EG.1 > C21306T > G1400A(ORF1a:G379R) > T22917G(S:L452R), C29218T
• [ ] EG.1.4 > C25339T > T1591C, T7396C > G472A, C21721T > C27128T > A1124C, A22893G(S:K444R) [Query: A1124C, A22893G, 6, Aug28]
• [ ] EG.1.6 > A16882G(ORF1b:T1139A) > C11591T(ORF1a:L3776F), A17233C(ORF1b:I1256L) > C27519T > T22917A(S:L452Q) [Query: C11591T, T22917A, G26235T, 7, Sep22]
• [ ] EG.2 > G4561A, G23587C(S:Q675H) > C24748T > A5725G > C7926T(ORF1a:A2554V), A10132T, T10135A, T23030C(S:F490P) [Query: A10132T, T10135A, T23030C, 28, Sep26], Sub-lineage of sars-cov-2-variants/lineage-proposals#445
• [ ] EG.2 > T23449C > G27604A(ORF7a:V71I) > A2560G, C23185T > C22264T > C7728T(ORF1a:S2488F), C17747T(ORF1b:P1427L) > T23042C(S:S494P) [Query: C7728T, C17747T, T23042C, 31, Sep29]
• [ ] EG.8 > C512T(ORF1a:H83Y) > T29288C > C952T, C5833T, A7050G(ORF1a:Y2262C), A22629C(S:K356T), C23475T(S:T638I) [Query: C512T, C7173T, A22629C, 21, Sep27]
• [ ] GD.1 (XBB.1.9.3) > T18099C > G14187T(ORF1b:R240S) > C6781T > A22629C(S:K356T), T24957C(S:I1132T), T28098C(ORF8:S69P) [Query: C6781T, T18099C, A22629C, 16, Sep8]

Known Potential Growth Boosters

• [ ] XBB.1.9.1 > A22215G(S:Q218R) > G22471A(S:L303) > G29422A > C10279T, C12781T, A22115G(S:N185D), G23222A(S:E554K), C23707A(S:P715), G25297A(S:K1245) [Query: C10279T, C12781T, G23222A, 9, Oct18]
• [ ] XBB.1.9.1 > C29679T > C16163T(ORF1b:T899I) > C24210T(S:T883I) [Query: C11956T, C16163T, C24210T, 37, Sep19]
• [ ] FL.2.2.1 > C6336T(ORF1a:S2024L) > C3903T(ORF1a:P1213L), G23224T(S:E554D) [Query: C6336T, G23401T, C28928T, 15, Aug27]
• [ ] FL.4 > C2416T > C676T, G3246A(ORF1a:S994N), G19999T(ORF1b:V2178F), G23222C(S:E554Q) [Query: G3246A, G19999T, G23222C, 19, Sep27]
• [ ] FL.18 > A17875G(ORF1b:T1470A) > C24210T(S:T883I) [Query: C24210T, A17875G, C6285T, 15, Sep14]
• [ ] XBB.1.9.2 > C1314T(ORF1a:T350I), A2521G, T10756C > T2584G > C18162T, G23309C(S:E583Q) [Query: C1314T, C18162T, G23309C, 16, Sep30]
• [ ] XBB.1.9.2 > G2659T(ORF1a:K798N) > C8752T > T6688C > C16596T > C5284T > C6539T(ORF1a:H2092Y) > T14067C, T14360C(ORF1b:I298T), G23222C(S:E554Q) [Query: T14067C, T14360C, G23222C, 4, Sep1]
• [ ] XBB.1.9.2 > C20016T > C25553T(ORF3a:A54V) > A17615G(ORF1b:K1383R) > G9441A(ORF1a:C3059Y), C24210T(S:T883I) [Query: C24210T, C25553T, A17615G, 13, Sep12]
• [ ] XBB.1.9.2 > T20407C(ORF1b:F2314L) > A12533G(ORF1a:T4090A) > C5482T > G22604T(S:A348S) [Query: C5482T, A12533G, G22604T, 21, Sep15]
• [ ] EG.1 > T29264C > T11457C(ORF1a:I3731T) > G6358T(ORF1a:E2031D) > T13157C > A16607G(ORF1b:N1047S), C28511T(N:P80S) > C22851T(S:T430I), C23673T(S:S704L) [Query: A16607G, C22851T, C23673T, 6, Sep26]
• [ ] sars-cov-2-variants/lineage-proposals#625 EG.2 > C28344T(N:T24I) > A17757G > G21718T(S:Q52H) [Query: A17757G, G21718T, C28344T, 23, Sep27]

Others

• [ ] XBB.1.9.1 > C12815T > C934T > ORF3a:V197A(T25982C), ORF7b:L32F(C27849T), nt:C28744T(ORF9c:S4L) > A22404T(S:E281V) > G12566A(ORF1a:V4101I) > C22971T(S:T470I) [Query: A22404T, C22971T, 17, Sep27]
• [ ] sars-cov-2-variants/lineage-proposals#626 XBB.1.9.1 > C28637T(N:P122S) > C11020T > T29131C > C21789T(S:T76I) [Query: C11020T, C21789T, C28637T, 41, Sep29]
• [ ] XBB.1.9.1 > C29614T > C547T > T15309C > C26111T(ORF3a:P240L) [Query: T15309C, C26111T, C29614T, 81, Aug31]
• [ ] FL.8 > C2662T > A23572T > C1441T > C2710A > C22329T(S:S256L) [Query: C2710A, C22329T, 116, Sep27]
• [ ] FL.18 > C15615T, C21742T, G21795T(S:R78M), T23293C [Query: C21742T, G21795T, T23293C, 44, Sep7]
• [ ] sars-cov-2-variants/lineage-proposals#463 XBB.1.9.2 > C21622T > A14673G > T9508C > C673T, G24926T(S:V1122L)
• [ ] XBB.1.9.2 > A29369G(N:T366A) [Query: A29369G, A27507C, A16878T, 120, Sep25]
• [ ] EG.1.3 > A18684G > C23635T > T16392C > C7564T, C25889T(ORF3a:S166L) > C18687T > A17148G(ORF1b:I1227M), C21516T, C24748T > C10525T, G22226T(S:A222S), C24023T [Query: C7564T, A18684G, G22226T, 12, Sep14]
• [ ] EG.1.4 > A25417G(ORF3a:T9A) > C7390T > A26924G > C3096T(ORF1a:S944L), C6573T(ORF1a:S2103F), T12133C, C14605T, G19254A, G22706T(S:V382L), T22951C [Query: G22706T, T22951C, 6, Sep1]
• [ ] EG.2 > C20806T, G22100C(S:E180Q) [Query: C20806T, G22100C, 26, Aug31]
• [ ] EG.4.5 > T7441C, C14649T, A22052C(S:N164H) [Query: T7441C, C14649T, A22052C, 20, Oct2]

High local prevalence and emerging branches

Saltation

Designated

• [x] sars-cov-2-variants/lineage-proposals#442 FL.19 > C19097T(ORF1b:A1877V) > T12145C > C12952T > T22928C(S:F456L), G24757T, designated as FL.19.1 via cov-lineages/pango-designation@1007720
• [x] sars-cov-2-variants/lineage-proposals#836 XBB.1.9.1 > G12769T, G15438T(ORF1b:M657I) > C28236T(ORF8:R115C) > C882T(ORF1a:A206V) > G25471C(ORF3a:D27H) > C16575T, G21800C(S:D80H) > G2265A(ORF1a:C667Y), A3417G(ORF1a:K1051R), C22995G(S:T478R), G23401T(S:Q613H), designated as FL.31 and FL.31.1 via cov-lineages/pango-designation@cc7f7fe
• [x] sars-cov-2-variants/lineage-proposals#719 XBB.1.9.1 > C21952T > G21578C(S:V6L), G23222C(S:E554Q), C28657T , designated as FL.32 and FL.32.1 via cov-lineages/pango-designation@73afbe1
• [x] sars-cov-2-variants/lineage-proposals#517 Branch 3 EG.2 > A6355T > C9430T, T18471C > A22474T(S:K304N) [Query: A6355T, T18471C, A22474T]
• [x] EG.4.5 designated via cov-lineages/pango-designation@3d3bfbb EG.4 > C22995G(S:T478R)

Losing Momentum

• [ ] FL.5 > A10103G(ORF1a:M3280V) > C8991T(ORF1a:A2909V) > C22995G(S:T478R) [Query: C8991T, A10103G, C22995G, 14, Sep29]
• [ ] sars-cov-2-variants/lineage-proposals#475 EG.4 > A4659G(ORF1a:Y1465C) > C16084T(ORF1b:H873Y) > C11095T > C6504T(ORF1a:A2080V), G22349A(S:A263T), G24914C(S:D1118H) [Query: C6504T, G22349A, G24914C, 22, Sep19]
• [ ] EG.4 > C5173T > C22995G(S:T478R) [Query: C5173T, C22995G, C28651T, 12, Sep26]

Inactive

• [ ] sars-cov-2-variants/lineage-proposals#341 FL.12 > T14472C > T24814G(S:D1084E) [Query: T24814G, T14472C, 219, Sep5]
• [ ] sars-cov-2-variants/lineage-proposals#190 FL.14 > C17766T > G23006A (S:G482S) [Query: C17766T, G23006A, G24926A, C22978T, 37, Sep5]
• [ ] XBB.1.9.2 > C28928T(N:L219F) > A21137G(ORF1a:K2557R) > C22995G(S:T478R), A26738G [Query: C22995G, A26738G, A21137G, 12, Aug04]

[Over-There-Is]

2144 Ukraine (and also Beijing, China?)

[NkRMnZr]

2144 Ukraine (and also Beijing, China?)

only to track smaller/slower lineages (when discovered and not proposed by others yet) here, will propose them if there's a sharp increment or local prevalence lineages started to be detected internationally.

[Over-There-Is]

*All the FL.2.3 + C8964T(ORF1a:S2900L), T23030C(S:F490P) and most of FL.2.3 + C23123T(S:P521S) sequences have also C21998A(S:Q146K).