Multiple EG.5.1* Lineages with S:L455F

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Multiple EG.5.1* Lineages with S:L455F or S:L455S

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1. Branch 1: Designated as HK.8 via cov-lineages/pango-designation@9527e15 , after transferred to EG.5.1.1 on C11779T with S:L455F (15 seqs, mainly in China, 3 countries) cov-lineages/pango-designation#2230 , Phylogenetic order follows: EG.5.1.1 > C11779T > G22927T(S:L455F)
2. Branch 2: Transferred to EG.5.1.1 with ORF1a:L3930F, ORF1a:P80S, ORF1b:P1570S and S:L455F (774 seqs, 31 countries) cov-lineages/pango-designation#2229 EG.5.1.1 > C12053T(ORF1a:L3930F) > C503T(ORF1a:P80S) > C7732T, C18175T(ORF1b:P1570S), G22927T(S:L455F)
3. Branch 3: Designated as HK.14 via cov-lineages/pango-designation@c7550b1 , after transferred to Another EG.5.1.1 with S:L455F via G22927C (90 seqs, China, South Korea) cov-lineages/pango-designation#2194 , Phylogenetic order follows: EG.5.1.1 > C11779T > C6781T, C17802T, G22927C(S:L455F)
4. Branch 4: Designated as EG.5.1.8 via cov-lineages/pango-designation@072c887 after transferred to EG.5.1 with S:L455F (41+3+1 seqs, 9 countries) cov-lineages/pango-designation#2224 , Phylogenetic order follows: EG.5.1 > G22927T(S:L455F)
5. Branch 5: Designated as HK.13 via cov-lineages/pango-designation@49cdcb4 , after transferred to EG.5.1.1 with S:L455F via G22927C (171 seqs, 13 countries) cov-lineages/pango-designation#2250 , Phylogenetic order follows: EG.5.1.1 > G22927C(S:L455F)
6. Branch 7: EG.5.1.1 > C6627T(ORF1a:T2121I) > T17147C(ORF1b:I1227T) > G22927T(S:L455F) [Query: C6627T, T17147C, G22927T, 51 seqs, 01/19] Slow
7. Branch 8: EG.5.1.1 > C5284T > T14655C > C15951T, G22927T(S:L455F) [Query:C5284T, T14655C, G22927T, 68 seqs, 01/18]
8. Branch 9: WITHDRAWN ex-HK.10 (EG.5.1.1.10) via cov-lineages/pango-designation@f655671 Phylogenetic order follows: EG.5.1.1 > C19983T > G22927T(S:L455F) ⚠️ No Longer tracking, there are now a lot of HK.3 sublineages with C19983T, this seems weirdly homoplastic.
9. Branch 10: Retracted from EG.5.1.1 with S:L455F on C11173T branch (708 seqs, 25 countries) cov-lineages/pango-designation#2251 EG.5.1.1 > C11173T > G22927T(S:L455F) [Query: C11173T, G13627A, G22927T, -T10837G, -T15042C, -T22228C, -C27406T, -T28157C, 739 seqs, 01/19]
10. Branch 11: EG.5.1 > C9430T > C20873G(ORF1b:A2469G), G22927T(S:L455F) [Query: C9430T, G21718T, G22927T, -C1889T, -G13627A, -C21622A, 53, 01/12]
11. Branch 12: Designated as EG.5.1.17, phylogenetic order follows: EG.5.1 > G22927C(S:L455F) [Query: C2334T, A18492G, G22927C, -G1069A, -A22106C, -C22570T, -C25572T]
12. Branch 13: Transferred to EG.5.1.1 with ORF1a:A2909V (nsp4_A146V) and S:L455F (91 seqs, 11 countries) cov-lineages/pango-designation#2364 EG.5.1.1 > C19011T > C8991T(ORF1a:A2909V) > G22927T(S:L455F)
13. Branch 14: EG.5.1.1 > A8443G > G22927T(S:L455F) [Query: C6541T, A8443G, G22927T, -T4579A, 7 seqs, 10/12] Dead
14. Branch 15: Designated with three levels: HK.23, HK.23.1 and HK.23.1.1 after Transferred to EG.5.1.1 with ORF8:A65V and S:L455F (224 seqs, 13 countries) further gained S:A348S (54 seqs, 4 countries) cov-lineages/pango-designation#2340 EG.5.1.1 > C28087T(ORF8:A65V) > G22927T(S:L455F), many with further S:A348S
15. Branch 16: EG.5.1.1 > C8074T, T17811C > C7604T, C10789T, C10834T, C12815T, G20348T(ORF1b:S2294I), G22927C(S:L455F), A25998G [Query: C6541T, C8074T, G22927C, 13 seqs, 01/19] Slow
16. Branch 17: Transferred to EG.5.1.1 with S:L455F on C9118T Branch (124 seqs, mainly in Japan, 11 countries) cov-lineages/pango-designation#2341 EG.5.1.1 > C9118T > G16813T(ORF1b:V1116L), G22927T(S:L455F)
17. Branch 20: Designated HK.33, phylogenetic order follows: EG.5.1.1 > C2644T > T7957C, G22927T(S:L455F), G29348T(N:A359S) [Query: C2644T, G13627A, G22927T]
18. Branch 23: Designated as HK.2.1 via cov-lineages/pango-designation@d75dabe after transferred to HK.2 with S:L455F (51 seqs, Singapore, China) cov-lineages/pango-designation#2319 , phylogenetic order follows: HK.2 (EG.5.1.1.2) > G22927T(S:L455F)
19. Branch 24: Designated as HK.20 via cov-lineages/pango-designation@71cf97b after transferred to EG.5.1.1 with ORF1a:P2144S (nsp3_P1326S) and S:L455F, many with follow-up S:G482R (52 seqs, 13 countries) cov-lineages/pango-designation#2353 , phylogenetic order follows: EG.5.1.1 > C6695T(ORF1a:P2144S) > C9448A > C5575T, G22927T(S:L455F)
20. Branch 25: EG.5.1.1 > C29296T > G22927T(S:L455F) [Query: C6541T, G22927T, C29296T, 70 seqs, 01/17] (Mostly with S:A684V)
21. Branch 26: Designated as HK.11.1 via cov-lineages/pango-designation@e268dbf after transferred to HK.11 with S:L455F (52 seqs, 14 countries) cov-lineages/pango-designation#2320 , phylogenetic order follows HK.11 > T13228C > T4789A > G22927T(S:L455F)
22. Branch 27: Transferred to EG.5.1.1 with ORF3a:T34K, N:G204P (G>R>P) and S:L455F (196 seqs, 19 countries) cov-lineages/pango-designation#2342 EG.5.1.1 > C25493A(ORF3a:T34K) > G28884C(N:G204P) > G22927T(S:L455F)
23. Branch 28: Transferred to EG.5.1.1 with S:L455F on C5812T branch, mostly with M:K15Q and N:T166R (159 seqs, mainly in South Korea, 10 countries) further with S:A475V (50 seqs, 5 countries) cov-lineages/pango-designation#2398 EG.5.1.1 > C5812T > G22927T(S:L455F) > A26565C(M:K15Q), C28770G(N:T166R)
24. Branch 31: Transferred to EG.5.1.1 with ORF1a:L3919F (nsp7_L60F), ORF1a:A656V (nsp2_A476V) and S:L455F (215 seqs, 25 countries) cov-lineages/pango-designation#2321 , follows EG.5.1.1 > C12020T(ORF1a:L3919F), T24496C > C2232T(ORF1a:A656V), C21516T, G22927T(S:L455F)
25. Branch 32: EG.5.1.1 > T4579A > G2329A, A8443G > G22927T(S:L455F) [Query: T4579A, A8443G, G22927T, 73 seqs, 01/17]
26. Branch 33: Designated as EG.5.1.19 after transferred to EG.5.1 with ORF3a:M260K, ORF1b:K1383R (nsp13_K460R) and S:L455F (130 seqs, 17 countries) cov-lineages/pango-designation#2322 , phylogenetic order follows EG.5.1 > T26171A(ORF3a:M260K) > A17615G(ORF1b:K1383R), G22927T(S:L455F)
27. Branch 34: EG.5.1.3 > G2946A(ORF1a:G894D), T15264C, T22926C(S:L455S) [Query: C1889T, C2334T, T22926C, -A4340G, -A10703C, 12 seqs, 01/03] Slow
28. Branch 35: Transferred to Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (383 seqs, mainly in Canada, 9 countries) cov-lineages/pango-designation#2354 EG.5.1.4 > C26111T(ORF3:P240L) > C18555T > T17268C > G22927T(S:L455F)
29. Branch 36: Transferred to EG.5.1.1 with S:L455F on C22388T branch (128 seqs, 22 countries) cov-lineages/pango-designation#2399 EG.5.1.1 > C22388T > C1853T, G22927T(S:L455F)
30. Branch 37: EG.5.1.1 > C29095T > G22927T(S:L455F) C29095T became homoplastic across the EG.5.1+L455F tree, no longer tracking.
31. Branch 38: EG.5.1.1 > T24583C > G22927T(S:L455F) [Query: C6541T, G22927T, T24583C, 47 seqs, 01/19]
32. Branch 39: Designated as HK.1.1 and retracted , Phylogenetic order follows: HK.1 (EG.5.1.1.1) > G22927T(S:L455F) [Query: C6541T, G13627A, G22332, G22927T, 132 seqs, 01/19] this query already included further mutated S:G257D
33. Branch 40: EG.5.1.1 > C10615T > G22927T(S:L455F) > C1426T, G25691T(ORF3a:G100V) [Query: C1426T, C10615T , G22927T, 48 seqs, 01/19]
34. Branch 41: EG.5.1.1 > C24023T > C2485T, G15025A(ORF1b:A520T), G22927C(S:L455F) [Query: C6541T, G22927C, C24023T, 15 seqs, 01/17] Slow
35. Branch 42: Transferred to EG.5.1.1 with S:L455F on C22687T branch (336 seqs, 17 countries) cov-lineages/pango-designation#2355 EG.5.1.1 > C22687T > G22927T(S:L455F)
36. Branch 43: EG.5.1.1 > C19524T > G22927T(S:L455F), A28254Δ Seems pulled under HK.3, no longer tracking
37. Branch 44: Designated with 3 levels: EG.5.1.11, JR.1 and JR.1.1, Phylogenetic order follows: EG.5.1 > A22106C(S:K182Q) > C22995G(S:T478R), A25664G(ORF3a:Y91C) > C1613T(ORF1a:L450F), G20995T(ORF1b:G2510C), G22927C(S:L455F), A27388C
38. Branch 45: Transferred to EG.5.1.1 with S:L455F and N:Q289H (383 seqs, 23 countries) cov-lineages/pango-designation#2308 EG.5.1.1 > C13968A, A15885G > T11449C > C10369T, G22927T(S:L455F), C29077T, G29140T(N:Q289H)
39. Branch 46: Designated as HK.22 via cov-lineages/pango-designation@2d3115a , phylogenetic order follows: EG.5.1.1 > G25407T(ORF3a:M5I) > C2662T > G22927T(S:L455F) > T15408C, T24709C > T2698C, A3019G, G18332A(ORF1b:R1622K), T22917A(S:L452Q) [Query: C2662T, G22927T, G25407T]
40. Branch 47: EG.5.1.1 > C7600T > G22927T(S:L455F) > T10216C [Query: C7600T, T10216C, G22927T, 52 seqs, 01/15]
41. Branch 48: Transferred to EG.5.1.1 on A23539T branch with S:L455F (264 seqs, mainly in Australia, 10 countries) cov-lineages/pango-designation#2360 EG.5.1.1 > A23539T > G22927T(S:L455F) ⚠️ Please check potential misplacement.
42. Branch 49: EG.5.1.4 > C8407T, C11008A(ORF1a:H3581Q), G22927T(S:L455F), G25538T(ORF3a:G49V), C25572T [Query: A18492G, A21137G, G22927T, -C6120T, -G13627A, -C26111T, 76 seqs, 01/20] Now at least 3 smaller clusters seems pulled together a S:L455F branch right under EG.5.1.4 polytomy, hard to catch by proper query now.
43. Branch 50: EG.5.1.1 > G28904T(N:A211S) > G22927T(S:L455F), G27261T, C28744T [Query: C6541T, G22927T, G28904T, 27 seqs, 01/19] Slow
44. Branch 51: Transferred to EG.5.1.1 with S:L455F on C10015T branch (286 seqs, 23 countries) cov-lineages/pango-designation#2365 EG.5.1.1 > C10015T > G22927T(S:L455F)
45. Branch 53: Transferred to EG.5.1.1 with ORF1a:T568I (nsp2_T388I), ORF1b:Q2181H (nsp15_Q130H), S:L455F (via G22927C) and ORF8:S67F (238 seqs, 22 countries) cov-lineages/pango-designation#2366 EG.5.1.1 > C27741T > C1912T, C1968T(ORF1a:T568I), T7111C, A20010T(ORF1b:Q2181H), T20592C, G22927C(S:L455F), C28093T(ORF8:S67F)
46. Branch 54: EG.5.1.1 > G24368T(S:D936Y) > G22927T(S:L455F) [Query: G13627A, G22927T, G24368T, -G3567A, -C4012T, -C5031T, -T13234C, -C17976T, 72 seqs, 01/19]
47. Branch 55: Designated with 2 levels: HK.24 and HK.24.1 , phylogenetic order follows EG.5.1.1 > G23522A(S:E654K) > G22927T(S:L455F)
48. Branch 56: EG.5.1.1 > A22582G > G22927T(S:L455F) [Query: G13627A, A22582G, G22927T, -G3153A, 39 seqs, 01/16]
49. Branch 57: EG.5.1.1 > A22582G > G3153A(ORF1a:G963D) > G22927T(S:L455F) [Query: G3153A, A22582G, G22927T, 57 seqs, 01/17]
50. Branch 58: EG.5.1 > T26972C > C28909T > C2106A(ORF1a:T614N), G28423T(ORF9b:R47L) > A21759G(S:H66R), G22927T(S:L455F), G24004A, C25572T [Query: A18492G, G22927T, C28909T, 46 seqs, 01/19]
51. Branch 59: EG.5.1.1 > G20134T(ORF1b:V2223L) > G22927T(S:L455F) [Query: G13627A, G20134T, G22927T, 46 seqs, 01/18] ⚠️ Please check potential reversion/artifact/misplacement
52. Branch 60: EG.5.1.1 > T16545G > C1471T, G22927T(S:L455F) [Query: G13627A, T16545G, G22927T, 67 seqs, 01/19]
53. Branch 62: EG.5.1.1 > C18559T(ORF1b:L1698F) > T15927C, G22927T(S:L455F) [Query: C6541T, C18559T, G22927T, 16 seqs, 01/16] Slow
54. Branch 63: Transferred to EG.5.1.1 with S:L455F on T14034C branch (130 seqs, mainly in South Korea, 9 countries) cov-lineages/pango-designation#2400 EG.5.1.1 > T14034C > T6556C, G22927T(S:L455F) ⚠️ Please check potential misplacement
55. Branch 64: EG.5.1.6 > C28236T(ORF8:R115C) > C16092T > C10969T > G526T(ORF1a:E87D) > C23380T > A12485G(ORF1a:I4074V) > T877C, A15270T(ORF1b:E601D), G22927T(S:L455F) [Query: G526T, A15270T, G22927T, 35 seqs, 01/19], thanks to @aviczhl2 and @FedeGueli
56. Branch 65: EG.5.1 > A3210G(ORF1a:D982G) > G26888A >G26227T, C28720T > T8909C> G22927T(S:L455F) [Query: A3210G, T8909C, G22927T, 25 seqs, 01/19]
57. Branch 66: EG.5.1.1 > C11779T > C12525T(ORF1a:T4087I) > G22927T(S:L455F) [Query: C11779T, C12525T, G22927T, 45 seqs, 01/19]
58. Branch 67: EG.5.1.1 > C25613T(ORF3a:S74F) > G22927C(S:L455F) [Query: C6541T, G22927C, C25613T, -C26681T, -G26840A, 51 seqs, 01/16]
59. Branch 68: EG.5.1.1 > G16710A > G22927T(S:L455F) [Query: G16710A, G13627A, G22927T, -G28904T, 72 seqs, 01/19]
60. Branch 69: EG.5.1.1 > G1085T(ORF1a:V274L) > G1535A(ORF1a:V424I), G22927T(S:L455F) [Query: G1085T, G13627A, G22927T, -A11000G, -C29375T, 69 seqs, 01/20]
61. Branch 70: EG.5.1.1 > T21748C > A16225G(ORF1b:T920A), T25036C > G22927C(S:L455F) [Query: A16225G, T21748C, G22927C, 42 seqs, 01/19]
62. Branch 71: EG.5.1.1 > C6638T(ORF1a:H2125Y) > G22927T(S:L455F) [Query: C6638T, G13627A, G22927T, -C14889T, 28 seqs, 01/19]
63. Branch 72: EG.5.1.1 > C11779T > G10261A > C9611T(ORF1a:L3116F), C18348T > G22927T(S:L455F) [Query: C9611T, C11779T, G22927T, 47 vseqs, 01/19]
64. Branch 73: HK.28 (C19170T) > G22927T(S:L455F) [Query: G13627A, C19170T, G22927T, -C1909T, -C3736T, -C5031T, -C7504T, -A18153G, 57 seqs, 01/19]
65. Branch 74: EG.5.1.3 > A28032G(ORF8:I47V) > A1047C(ORF1a:K261T) > C3608A(ORF1a:L1115I), C18261T, G22927T(S:L455F) [Query: A1047C, C1889T, G22927T, 6 seqs, 11/22] dead
66. Branch 75: EG.5.1.1 > C29253T(N:S327L) > G22927T(S:L455F) [Query: G13627A, G22927T, C29253T, -G1067T, -C2110T, -A2730C, 38 seqs, 01/19] ⚠️ Please check potential misplacement
67. Branch 76: HK.30 (EG.5.1.1 + T26609C) > C5907T(ORF1a:T1881I), T17454A > G22927T(S:L455F) [Query: G13627A, G22927T, T26609C, -C24616T, 40 seqs, 01/16]
68. Branch 77: Designated HV.2 after transferred to EG.5.1.6 with S:L455F (96 seqs, mainly in Canada, 12 countries) cov-lineages/pango-designation#2401 EG.5.1.6 > C925T, C27161T > C14919A > G14559A > G22927T(S:L455F)
69. Branch 78: EG.5.1.1 > C18395T(ORF1b:A1643V) > G22927T(S:L455F) [Query: C6541T, C18395T, G22927T, 47 seqs, 01/16]
70. Branch 79: EG.5.1.1 > T6736C > T23287C > C22075T > C8389T, A16668G, C17474T(ORF1b:T1336I), G22927T(S:L455F), G26416T(E:V58F) [Query: T6736C, G13627A, G22927T, 16 seqs, 01/04] (Mostly with S:Q14H/G21604C) Slow
71. Branch 80: EG.5.1.1 > C8146T > G2035A, G6373T(ORF1a:M2036I), G22927T(S:L455F) [Query: C8146T, G13627A, G22927T, -C27557T, 19 seqs, 01/17]
72. Branch 81: EG.5.1.1 > C2857T > G22927T(S:L455F) [Query: C2857T, G13627A, G22927T, -C5031T, -T17475C, 50 seqs, 01/19]
73. Branch 82: EG.5.1.1 > T16494C, T22307C > G22927C(S:L455F) [Query: G13627A, T16494C, G22927C, 18 seqs, 01/17]
74. Branch 83: EG.5.1.1 > C29358T(N:T362I) > T23803C > C842T(ORF1a:P193S), C15141T, T16743C, C22450T, G22927T(S:L455F), C24442T, C25916T(ORF3a:T175I), C28232T [Query: G22927T, T23803C, C29358T, 28 seqs, 01/10], thanks to @aviczhl2
75. Branch 84: HK.19 > C2455T > G22927T(S:L455F), C23533T [Query: C2455T, C22033A, G22927T, -G25606A, 20 seqs, 01/19]
76. Branch 85: EG.5.1.1 > C7390T > G22927T(S:L455F) [Query: C7390T, G13627A, G22927T, 49 seqs, 01/15] Mostly with ORF6:N34K/C27303A
77. Branch 86: EG.5.1.1 > G25855T(ORF3a:D155Y) > G22927T(S:L455F) > T4063C, C13405T, A21612C(S:N17T) [Query: A21612C, G22927T, G25855T, 79 seqs, 01/29]
78. Branch 87: EG.5.1 > C15960T > C16260T > G22927T(S:L455F), C24771T(S:A1070V), C25658T(ORF3a:T89I) [Query: C15960T, C16260T, A18492G, G22927T, 19 seqs, 01/19]
79. Branch 88: EG.5.1.1 > T4579A > A4576T > G22927T(S:L455F), [Query: A4576T, G13627A, G22927T, 118 seqs, 01/29] (Sibling to Branch 32)
80. Branch 89: EG.5.1.1 > C27406T(ORF7a:L5F) > G22927T(S:L455F) [Query: C6541T, G13627A , G22927T, C27406T, 11 seqs, 01/08]
81. Branch 90: EG.5.1.1 > C13724T(ORF1a:A4487V), A25636T(ORF3a:N82Y) > T10750C, G22927T(S:L455F) [Query: G13627A, C13724T, G22927T, -C5031T, 28 seqs, 01/12]
82. Branch 91: EG.5.1.1 > C22987T >G22927T(S:L455F) > G19419A, G21974C(S:D138H) [Query: G13627A, G19419A, G21974C, 12 seq, 12/26]
83. Branch 92: EG.5.1.1 > C629T(ORF1a:L122F) > A1168G > C22987T > T595C, C20148T, G22927T(S:L455F) [Query: A1168G, G22927T, C22987T, 11 seqs, 01/09]
84. Branch 93: EG.5.1.18 > T1216C, A9034G, A12121T, A12519G(ORF1a:D4085G), G22927T(S:L455F) [Query: G9269A, G22927T, G26051T, 8 seqs, 12/19] Slow
85. Branch 94: EG.5.1.13 > G670T_rev(ORF1a:R135S_rev) > T28861C > G8889A(ORF1a:R2875H) > C13381T > G22424T(S:A288S) > C25047T(S:P1162L) > G25855T(ORF3a:D155Y) > G22927T(S:L455F) [Query: G8889A, C13381T, G22927T, 49 seqs, 01/15], a sub-branch of EG.5.1.13+Orf1a:R135S(rev) (1314 seqs global > 30 countries，further gaining Flip+S:A288S,P1162L 42 Seqs) #1074 proposed by @aviczhl2
86. Designated with 2 levels: HK.27 and HK.27.1 from EG.5.1.1 branch with orf1a:T1589I (NSP3_T771I = PLPro_T26I )that acquired then S:L455F FLip lineage - 772samples ( as Nov 21) cov-lineages/pango-designation#2226 proposed by @FedeGueli , phylogenetic order follows: EG.5.1.1 > C5031T(ORF1a:T1589I) > G22927T(S:L455F) [Query: C5031T, G22927T]
87. Designated as HK.1.2 via cov-lineages/pango-designation@2ee937c , formerly doublet, now proposed by @aviczhl2 : HK.1+Orf1a:V2019I+S:T307I,L455F (42 seqs, 6 countries 4% in NZL 4% Xinjiang) cov-lineages/pango-designation#2310 , Phylogenetic order follows: HK.1 (EG.5.1.1.1) > G6320A(ORF1a:V2019I) > C11704T, C22482T(S:T307I), G22927C(S:L455F) [Query: G6320A, G22332T, G22927C]
88. Designated as JJ.1 (EG.5.1.4.1) via cov-lineages/pango-designation@36e3fb0 , EG.5.1.4+Orf3a:P240L+S:L455F,Orf3a:I47V Exploding in Japan(27 seqs, 2 countries) cov-lineages/pango-designation#2208 formerly a singlet, proposed by @aviczhl2 , Phylogenetic order follows: EG.5.1.4 > C26111T(ORF3:P240L) > G22927T(S:L455F), A25531G(ORF3a:I47V) [Query: A21137G, G22927T, A25531G]
89. Designated as JG.3 (EG.5.1.3.3) via cov-lineages/pango-designation@b084562, proposed by @aviczhl2 , EG.5.1.3+Orf1a:T2274I+S:L455F,S704L(70 seqs, 15 countries) cov-lineages/pango-designation#2231 Phylogenetic order follows: EG.5.1.3 > C7086T(ORF1a:T2274I), G22927T(S:L455F), C23673T(S:S704L) [Query: C1889T, G22927T, C23673T]
90. New EG.5.1.1-Flip lineage with insertion on Orf8(104 seqs, 11 countries, 26 seqs with S:G184S) cov-lineages/pango-designation#2434 proposed by @aviczhl2 , Phylogenetic order follows: EG.5.1.1 >T14988C, A23014T(S:A484A) > C1471T > C12823T > G25459T(ORF3a:A23S) > G22927T(S:L455F), ins28214T [Query: C1471T, T14988C, G22927T, 89 seqs, 01/19]
91. HK.3 (EG.5.1.1.3) designated via cov-lineages/pango-designation@39a35ba , Phylogenetic order follows: EG.5.1.1 > G22927T(S:L455F)

• A few Singlets, Doublets , Triplets , Quadruplets or Quintuplets , see below. Credit to @BorisUitham who was the first to notice the high homoplasy of S:L455F in EG.5.1 backbone. Checking updates.
• Known homoplastic/misplacement/artificial/flip-flop banches that are no longer tracking: C66T, C346T, G598A, G1820A, C4423T, C6843T, A10323G(ORF1a:K3353R), C12651T(ORF1a:T4129I), C13860T, A15159G, C19983T, C22096T(S:D178D), C22264T(S:N234N), C22792T(S:I410I), C22998T(S:P479L), C26681T, C27059T, C27507T, C27884T, A29700G

Branch 1:

Transferred to main repo. Designated as HK.8

Designated as HK.8 (EG.5.1.1.8) via cov-lineages/pango-designation@9527e15

Transferred to cov-lineages/pango-designation#2230

Defining Mutations: EG.5.1.1 > C11779T > G22927T(S:L455F)
Query: C6541T, C11779T, G22927T
Earliest seq: 2023-06-27 (EPI_ISL_18060870, Yibin, Sichuan, China)
Latest seq: 2023-07-17 (EPI_ISL_18060877, Zi'yang, Sichuan, China)
Sampled Countries: China (2, Sichuan)

Genomes:

EPI_ISL_18060870, EPI_ISL_18060877

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_202eb_c2cf60.json?f_userOrOld=uploaded%20sample

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---

Branch 2:

Transferred to main repo:

Transferred to cov-lineages/pango-designation#2229

Defining Mutations: EG.5.1.1 > C12053T(ORF1a:L3930F) > C503T(ORF1a:P80S) > C7732T, C18175T(ORF1b:P1570S), G22927T(S:L455F)
Query: C503T, C6541T, G22927T
Earliest seq: 2023-07-15 (EPI_ISL_18060497, Tokyo, Japan)
Latest seq: 2023-07-18 (EPI_ISL_18065046, Miyagi, Japan)
Sampled Countries: Japan (2)

Genomes:

EPI_ISL_18060497, EPI_ISL_18065046

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_22c78_c2e570.json?f_userOrOld=uploaded%20sample

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Branch 3

Transferred to main repo

Transferred to cov-lineages/pango-designation#2194

Defining Mutations: EG.5.1.1 > C11779T > C6781T, C17802T, G22927C(S:L455F)
Query: C6781T, C17802T, G22927C
Earliest seq: 2023-07-04 (EPI_ISL_17994488, Shanghai, China)
Latest seq: 2023-07-18 (EPI_ISL_18074754, Shanghai, China)
Sampled Countries: China (3, Shanghai)

Genomes:

EPI_ISL_17994488, EPI_ISL_18074751, EPI_ISL_18074754

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_13292_36d050.json?f_userOrOld=uploaded%20sample

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---

Branch 4

Transferred to main repo

Transferred to cov-lineages/pango-designation#2224

Defining Mutations: EG.5.1 > C12100G, G22927T(S:L455F)
Query: C12100G, G22927T
Earliest seq: 2023-07-09 (EPI_ISL_18060822, Shanghai, China)
Latest seq: 2023-07-31 (EPI_ISL_18094969, Washington, USA with Travel History to: Japan)
Sampled Countries: China (2, Shanghai, 1 ex. Thailand), USA (2, Washington, ex. Japan)

Genomes:

EPI_ISL_18060822, EPI_ISL_18075026, EPI_ISL_18094946, EPI_ISL_18094969

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1ebd2_7501c0.json?f_userOrOld=uploaded%20sample&label=id:node_6794320

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Branch 5

Transferred to main repo

Transferred to cov-lineages/pango-designation#2250

Defining Mutations: EG.5.1.1 > G22927C(S:L455F, different to HK.3's G22927T)
Query: C6541T, G22927C, -C3653T, -C6317T, -C6327T, -A6659G, -T7111C, -C8074T, -G8768A, -C10702T, -C11779T, -C13968A, -T17811C, -A21137G, -T21748C, -C22482T, -C24023T, -C27741T, -G29734T
Earliest seq: 2023-07-08 (EPI_ISL_18012368, Sichuan, China)
Latest seq: 2023-07-27 (EPI_ISL_18105834, Shanghai, China)
Sampled Countries: China (3: Shanghai/2; Sichuan/1)

Genomes:

EPI_ISL_18012368, EPI_ISL_18074450, EPI_ISL_18105834

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_a8d5_ccb160.json?branchLabel=nuc%20mutations&f_userOrOld=uploaded%20sample&label=id:node_6794516

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Branch 6

Many sequences pulled back to HK.3, the reversion probably due to dropout rather than recombinant

Defining Mutations: EG.5.1.1 > T22480C_Reversion > G22927T(S:L455F)
Query: C6541T, G13627A, G22927T, -C7948T, -C22480T
Earliest seq: 2023-07-05 (EPI_ISL_17988079, Xiangyang, Hubei)
Latest seq: 2023-08-07 (EPI_ISL_18105560, Xiangyang, Hubei)
Sampled Countries: China (4, Hubei)

Genomes:

EPI_ISL_17988079, EPI_ISL_18105559-18105560, EPI_ISL_18105562

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_100ff_ccdc70.json?f_userOrOld=uploaded%20sample&label=id:node_6791410

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Branch 7

Defining Mutations: EG.5.1.1 > C6627T(ORF1a:T2121I) > T17147C(ORF1b:I1227T) > G22927T(S:L455F)
Query: C6627T, T17147C, G22927T
Earliest seq: 2023-07-06 (EPI_ISL_18074610, Shanghai)
Latest seq: 2023-08-05 (EPI_ISL_18108436, Shanghai, Travel history: Singapore)
Sampled Countries: China (3: Shanghai)

Genomes:

EPI_ISL_18074610, EPI_ISL_18108436, EPI_ISL_18108490

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1999b_eabba0.json?f_userOrOld=uploaded%20sample&label=id:node_10741278

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Branch 8

Defining Mutations: EG.5.1.1 > C5284T > T14655C > C15951T, G22927T(S:L455F)
Query: C5284T, T14655C, G22927T
Earliest seq: 2023-07-23 (EPI_ISL_18105571, Shanghai)
Latest seq: 2023-08-11 (EPI_ISL_18114886, Shanghai)
Sampled Countries: China (3, Shanghai)

Genomes:

EPI_ISL_18105571, EPI_ISL_18108625, EPI_ISL_18114886

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_28a92_b9eb0.json?f_userOrOld=uploaded%20sample&label=id:node_6895881

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Branch 9

Defining Mutations: EG.5.1.1 > C19983T > G22927T(S:L455F)
Query: C6541T, G13627A, C19983T, G22927T, -C6695T **Earliest seq:** 2023-06-30 (EPI_ISL_18074254, Liaoning, China) **Latest seq:** 2023-08-27 (EPI_ISL_18239976`, Utah, USA)
Sampled Countries: China (3: Liaoning/2; Shanghai/1)

Genomes:

EPI_ISL_18074249, EPI_ISL_18074254

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2cc80_bc030.json?f_userOrOld=uploaded%20sample&label=id:node_6895986

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Branch 10

Transferred to main repo

Transferred to cov-lineages/pango-designation#2251

Defining Mutations: EG.5.1.1 > C11173T > G22927T(S:L455F)
Query: C11173T, G13627A, G22927T, -T22228C, -C27406T, -T28157C
Earliest seq: 2023-07-16 (EPI_ISL_18049850, Qinghai)
Latest seq: 2023-08-01 (EPI_ISL_18114762, Shanghai)
Sampled Countries: China (3, Qinghai, Shanghai, Xinjiang)

Genomes:

EPI_ISL_18049850, EPI_ISL_18108872, EPI_ISL_18114762

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_33d9d_bf590.json?f_userOrOld=uploaded%20sample&label=id:node_10744521

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Branch 11

Defining Mutations: EG.5.1 > C9430T > T1939C, C10039T, C20873G(ORF1b:A2469G), G22927T(S:L455F)
Query: C9430T, G21718T, G22927T, -C1889T, -G13627A, -C21622A
Earliest seq: 2023-07-31 (EPI_ISL_18127303, Tokyo, Japan)
Latest seq: 2023-08-07 (EPI_ISL_18127606, Kanagawa, Japan)
Sampled Countries: Japan (3: Tokyo/2; Kanagawa/1)

Genomes:

EPI_ISL_18127215, EPI_ISL_18127303, EPI_ISL_18127606

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice4_genome_1293d_792f00.json?f_userOrOld=uploaded%20sample

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---

Branch 12:

Designated EG.5.1.17

Designated as EG.5.1.17 via cov-lineages/pango-designation@5a8103c

Defining Mutations: EG.5.1 > G22927C(S:L455F)
Query: C2334T, A18492G, G22927C, -G1069A, -A22106C, -C22570T, -C25572T
Earliest seq: 2023-07-09 (EPI_ISL_18108295, Anhui, China)
Latest seq: 2023-08-15 (EPI_ISL_18138165, Shanghai, China)
Sampled Countries: China (4: Shanghai/3; Anhui/1)

Genomes:

EPI_ISL_18108295, EPI_ISL_18114797, EPI_ISL_18138165, EPI_ISL_18138282

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_289ba_a2e580.json?f_userOrOld=uploaded%20sample&label=id:node_6920519

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Branch 13:

Transferred to main repo

transferred to cov-lineages/pango-designation#2364

Defining Mutations: EG.5.1.1 > C19011T > C8991T(ORF1a:A2909V) > G22927T(S:L455F)
Query: C8991T, C19011T, G22927T
Earliest seq: 2023-08-14 (EPI_ISL_18146054, Hubei, China)
Latest seq: 2023-10-31 (EPI_ISL_18473645, Singapore, travel history: India)
Sampled Countries: China (38: HB/23; SH/4; AH/3; BJ/2; YN/2; GS/1; HA/1; QH/1; XJ/1), Singapore (5: Local/2; ex. China/2; ex. India/1), Netherlands (3), Australia (2: NSW), Austria (1), Croatia (1), France (1), Laos (1)

Genomes:

EPI_ISL_18141179, EPI_ISL_18146054, EPI_ISL_18146087, EPI_ISL_18217222, EPI_ISL_18217236, EPI_ISL_18254205, EPI_ISL_18268148-18268149, EPI_ISL_18268153, EPI_ISL_18268244, EPI_ISL_18284712, EPI_ISL_18284755, EPI_ISL_18306934, EPI_ISL_18313098, EPI_ISL_18313105, EPI_ISL_18313198, EPI_ISL_18313226, EPI_ISL_18349877, EPI_ISL_18354962, EPI_ISL_18363349, EPI_ISL_18376465, EPI_ISL_18376494, EPI_ISL_18384477, EPI_ISL_18384508, EPI_ISL_18388887, EPI_ISL_18388889, EPI_ISL_18388891, EPI_ISL_18438085, EPI_ISL_18438311, EPI_ISL_18438356, EPI_ISL_18438359, EPI_ISL_18438427, EPI_ISL_18441693, EPI_ISL_18442727, EPI_ISL_18442730, EPI_ISL_18447747, EPI_ISL_18457659, EPI_ISL_18461703, EPI_ISL_18461971, EPI_ISL_18463327, EPI_ISL_18463426, EPI_ISL_18464919, EPI_ISL_18464984, EPI_ISL_18465193, EPI_ISL_18465381, EPI_ISL_18465391, EPI_ISL_18466345, EPI_ISL_18473414, EPI_ISL_18473645, EPI_ISL_18475163, EPI_ISL_18475178

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_16441_b42970.json?label=id:node_3500994

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Branch 14

Defining Mutations: EG.5.1.1 > A8443G > G22927T(S:L455F)
Query: C6541T, A8443G, G22927T
Earliest seq: 2023-07-22 (EPI_ISL_18060879 Ziyang, Sichuan)
Latest seq: 2023-08-09 (EPI_ISL_18146071, Xiaogan, Hubei)
Sampled Countries: China (3: Sichuan/2; Hubei/1)

Genomes:

EPI_ISL_18060879, EPI_ISL_18146071, EPI_ISL_18166195

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_140e3_db750.json?f_userOrOld=uploaded%20sample

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Branch 15

Designated with levels: HK.23, HK.23.1 and HK.23.1.1

Designated as three levels: HK.23, HK.23.1 and HK.23.1.1

Transferred to cov-lineages/pango-designation#2340

Defining Mutations: EG.5.1.1 > C28087T(ORF8:A65V) > G22927T(S:L455F)
Query: C6541T, G22927T, C28087T, -A4306G, -G4444A, -A6889G, -G8171A, -T8305C, -C10039T, -C19185T, -C25207T
Earliest seq: 2023-08-10 (EPI_ISL_18138246, Shanghai)
Latest seq: 2023-08-14 (EPI_ISL_18208534, Shanghai)
Sampled Countries: China (3: Shanghai)

Genomes:

EPI_ISL_18138040, EPI_ISL_18138246, EPI_ISL_18208534

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_192a8_20dc90.json?f_userOrOld=uploaded%20sample

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Branch 16

Defining Mutations: EG.5.1.1 > C8074T > T17811C > C7604T, C10789T, C10834T, C12815T, G20348T(ORF1b:S2294I), G22927C(S:L455F), A25998G
Query: C6541T, C8074T, G22927C
Earliest seq: 2023-08-22 (EPI_ISL_18217203, Hubei, China)
Latest seq: 2023-08-22 (EPI_ISL_18217204, Hubei, China)
Sampled Countries: China (3)

Genomes:

EPI_ISL_18217202-18217204

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1c2cf_6feba0.json?c=gt-S_455&gmax=25384&gmin=21563&label=id:node_6949824

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Branch 17

Transferred to main repo

Transferred to cov-lineages/pango-designation#2341

Defining Mutations: EG.5.1.1 > C9118T > G22927T(S:L455F)
Query: C6541T, C9118T, G22927T, -C25546A
Earliest seq: 2023-08-14 (EPI_ISL_18214798, Osaka, Japan)
Latest seq: 2023-10-02 (EPI_ISL_18373543, England, UK)
Sampled Countries: Japan (37), USA (4: TX/2; NJ; SC), South Korea (2), UK (2: EN), Australia (1: WA), Canada (1: ON), France (1)

Genomes:

EPI_ISL_18162837, EPI_ISL_18166739, EPI_ISL_18214798, EPI_ISL_18214838, EPI_ISL_18226559, EPI_ISL_18235760, EPI_ISL_18236014, EPI_ISL_18242568, EPI_ISL_18243896, EPI_ISL_18247826-18247827, EPI_ISL_18253490, EPI_ISL_18261506, EPI_ISL_18271898, EPI_ISL_18279175, EPI_ISL_18279234, EPI_ISL_18285272, EPI_ISL_18285440, EPI_ISL_18294200, EPI_ISL_18300272, EPI_ISL_18338985, EPI_ISL_18342460, EPI_ISL_18354762, EPI_ISL_18354776, EPI_ISL_18362312, EPI_ISL_18370698, EPI_ISL_18370761, EPI_ISL_18371874, EPI_ISL_18372806, EPI_ISL_18373146, EPI_ISL_18373543, EPI_ISL_18376280, EPI_ISL_18376286, EPI_ISL_18377931, EPI_ISL_18382356, EPI_ISL_18382437, EPI_ISL_18382737, EPI_ISL_18385259, EPI_ISL_18387636, EPI_ISL_18390707, EPI_ISL_18390782, EPI_ISL_18390836, EPI_ISL_18397002, EPI_ISL_18402105, EPI_ISL_18402112, EPI_ISL_18411313, EPI_ISL_18413797, EPI_ISL_18413896

UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1f50e_2e6ab0.json?f_userOrOld=uploaded%20sample&label=id:node_3461917

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Branch 18

Merged into HK.3

Defining Mutations: EG.5.1.1 > C22264T > G22927T(S:L455F)
Query: G13627A, C22264T, G22927T
Earliest seq: 2023-07-30 (EPI_ISL_18129236, British Columbia, Canada)
Latest seq: 2023-08-28 (EPI_ISL_18213253, Fujian, China)
Sampled Countries: Canada (1, BC), China (1, Fujian), UK (1, England)

Genomes:

EPI_ISL_18129236, EPI_ISL_18142517, EPI_ISL_18213253

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2fbb2_705f80.json?c=gt-nuc_22264&gmax=23264&gmin=21264&label=id:node_6943899

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Branch 19

Merged under HK.13, no longer tracking

Defining Mutations: EG.5.1.1 > C29167T > G1186A, T4871C(ORF1a:Y1536H), C7011T(ORF1a:A2249V), G17741A(ORF1b:R1425H), G22927C(S:L455F)
Query: T4871C, G17741A
Earliest seq: 2023-08-09 (EPI_ISL_18160385, New York, USA)
Latest seq: 2023-08-19 (EPI_ISL_18214905, Ibaraki, Japan)
Sampled Countries: China (1, Shanghai), Japan (1), USA (1, NY)

Genomes:

EPI_ISL_18160385, EPI_ISL_18208589, EPI_ISL_18214905

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_15b7_70e2f0.json?label=id:node_6948139

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Branch 20

Designated as HK.33

Designated as HK.33 via cov-lineages/pango-designation@7ad122e

Defining Mutations: EG.5.1.1 > C2644T > T7957C, G22927T(S:L455F), G29348T(N:A359S)
Query: C2644T, G13627A, G22927T
Earliest seq: 2023-08-21 (EPI_ISL_18222131, SEA airport, Washington, USA, travel history: UK)
Latest seq: 2023-08-25 (EPI_ISL_18208454, Shanghai, China)
Sampled Countries: USA (2, ex. UK), China (1, Shanghai)

Genomes:

EPI_ISL_18147035, EPI_ISL_18208454, EPI_ISL_18222131

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_172d3_85e8d0.json?f_userOrOld=uploaded%20sample&label=id:node_6951215

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Branch 21, now pulled under HK.3.8

Pulled under HK.3.8

Defining Mutations: EG.5.1.1 > C18747T > C643T, T13060C, G19723T(ORF1b:V2086F), G22927T(S:L455F)
Query: C643T, C18747T, G22927T
Earliest seq: 2023-08-11 (EPI_ISL_18208543, Shanghai)
Latest seq: 2023-08-28 (EPI_ISL_18232547, Shanghai Customs, travel history to Japan
Sampled Countries: China (3, SH)

Genomes:

EPI_ISL_18208543, EPI_ISL_18208548, EPI_ISL_18232547

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1d67e_99d900.json?label=id:node_10811725

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---

Branch 22, Now pulled under HK.3.2 > A708C(ORF1a:E148A) > C10969T, G23593T(S:Q677H), G28056A(ORF8:A55T), no longer tracking.

Pulled under HK.3.2

Defining Mutations: HK.5 > G22927T(S:L455F)
Query: spike_Q52H, spike_L455F, spike_Q677H
Earliest seq: 2023-08-13 (EPI_ISL_18146068, Hubei)
Latest seq: 2023-08-24 (EPI_ISL_18226161, Virginia)
Sampled Countries: USA (2, VA), China (1, HB)

Genomes:

EPI_ISL_18146068, EPI_ISL_18226161-18226162

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_34c06_9a5d70.json?f_userOrOld=uploaded%20sample&label=id:node_10811724

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---

Branch 23

Transferred to main repo:

Transferred to main repo cov-lineages/pango-designation#2319

Defining Mutations: HK.2 > G22927T(S:L455F)
Query: C6541T, G21604T, G22927T, -A518G, -C934T, -C1426T, -G3663A, -C5031T, -C7712T, -A7849G, -C8320T, -T16545G
Earliest seq: 2023-08-21 (EPI_ISL_18141161, Singapore)
Latest seq: 2023-08-23 (EPI_ISL_18232599, Shanghai)
Sampled Countries: Singapore (1), China (2, SH)

Genomes:

EPI_ISL_18141161, EPI_ISL_18232598-18232599

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_40e5c_9aa250.json?f_userOrOld=uploaded%20sample&label=id:node_10811725

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---

Branch 24, Designated as HK.20 via cov-lineages/pango-designation@71cf97b ; follow-up S:G482R/G23006C designated as HK.20.1

Designated as HK.20 and HK.20.1

Transferred to cov-lineages/pango-designation#2353

Defining Mutations: EG.5.1.1 > C6695T(ORF1a:P2144S) > C9448A > C5575T, G22927T(S:L455F)
Query: C6695T, C9448A, G22927T
Earliest seq: 2023-08-13 (EPI_ISL_18114870, Shanghai Customs, travel history to Japan)
Latest seq: 2023-10-20 (EPI_ISL_18448529, Ontario, Canada)
Sampled Countries: China (13, SH/6; SC/4; FJ/1; ex. Japan/1; ex. S. Korea/1), USA (12: CA/8; AZ/1; OH/1; TX/1; ex. Nepal/1), Singapore (6: Local/5; ex. China/1), Italy (5), UK (3: EN), Australia (2: NSW; QLD), Canada (2: ON), Japan (2), South Korea (2), Switzerland (2), Denmark (1), France (1), Spain (1)

Genomes:

EPI_ISL_18114870, EPI_ISL_18208555, EPI_ISL_18208592, EPI_ISL_18208601, EPI_ISL_18232643, EPI_ISL_18246292, EPI_ISL_18284706, EPI_ISL_18285031, EPI_ISL_18285192, EPI_ISL_18306956, EPI_ISL_18307066, EPI_ISL_18320793, EPI_ISL_18328004, EPI_ISL_18352555, EPI_ISL_18354001, EPI_ISL_18355023, EPI_ISL_18360344, EPI_ISL_18360616, EPI_ISL_18361723, EPI_ISL_18366403, EPI_ISL_18370066, EPI_ISL_18370200, EPI_ISL_18371411, EPI_ISL_18376528, EPI_ISL_18385607, EPI_ISL_18386446, EPI_ISL_18386489, EPI_ISL_18387133, EPI_ISL_18397207, EPI_ISL_18403093, EPI_ISL_18407761, EPI_ISL_18409112, EPI_ISL_18411495, EPI_ISL_18415804, EPI_ISL_18421982, EPI_ISL_18423702, EPI_ISL_18425050, EPI_ISL_18428715, EPI_ISL_18429030, EPI_ISL_18430106, EPI_ISL_18433978, EPI_ISL_18435244, EPI_ISL_18442967, EPI_ISL_18443714, EPI_ISL_18443742-18443744, EPI_ISL_18443746, EPI_ISL_18444154, EPI_ISL_18446641, EPI_ISL_18448416, EPI_ISL_18448529

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_11cc_c2b40.json?label=id:node_3485632

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---

Branch 25: Mostly with S:A684V

Defining Mutations: EG.5.1.1 > C29296T > G22927T(S:L455F)
Query: C6541T, G22927T, C29296T
Earliest seq: 2023-08-06 (EPI_ISL_18133933, Qinghai)
Latest seq: 2023-08-30 (EPI_ISL_18245873, Gansu)
Sampled Countries: China (4: SC/2; GS; QH)

Genomes:

EPI_ISL_18133933, EPI_ISL_18245873, EPI_ISL_18246316, EPI_ISL_18246328

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_fec3_1b4b0.json?label=id:node_10825408

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---

Branch 26

Transferred to main repo

Transferred to main repo cov-lineages/pango-designation#2320

Defining Mutations: HK.11 > T13228C > T4789A > G22927T(S:L455F)
Query: T4789A, T13228C, G22927T
Earliest seq: 2023-08-21 (EPI_ISL_18221467, Halland, Sweden)
Latest seq: 2023-08-21 (EPI_ISL_18244247, Denmark)
Sampled Countries: Denmark (2), Sweden (1)

Genomes:

EPI_ISL_18221467, EPI_ISL_18244233, EPI_ISL_18244247

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1d161_22300.json?f_userOrOld=uploaded%20sample&label=id:node_6955887

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---

Branch 27

Transferred to main repo

Transferred to cov-lineages/pango-designation#2342

Defining Mutations: EG.5.1.1 > C25493A(ORF3a:T34K) > G28884C(N:G204P) > G22927T(S:L455F)
Query: C6541T, G22927T, C25493A
Earliest seq: 2023-07-18 (EPI_ISL_18245992, Heilongjiang)
Latest seq: 2023-10-10 (EPI_ISL_18397223, Singapore)
Sampled Countries: China (18: HL/10; LN/2; SH/2; HB; SC; SX; YN), Singapore (14), Denmark (4), Italy (3), USA (3: CA/2; NY), France (2), Australia (1: NSW), Germany (1), South Korea (1), Sweden (1)

Genomes:

EPI_ISL_18138073, EPI_ISL_18232576, EPI_ISL_18244264, EPI_ISL_18245964, EPI_ISL_18245971, EPI_ISL_18245992, EPI_ISL_18246139, EPI_ISL_18246193, EPI_ISL_18282065, EPI_ISL_18300796, EPI_ISL_18306948, EPI_ISL_18306976, EPI_ISL_18306993, EPI_ISL_18307005-18307006, EPI_ISL_18307019, EPI_ISL_18307026, EPI_ISL_18313136, EPI_ISL_18320696, EPI_ISL_18324230, EPI_ISL_18329168, EPI_ISL_18330265, EPI_ISL_18339790, EPI_ISL_18352920, EPI_ISL_18356975, EPI_ISL_18361976, EPI_ISL_18362045, EPI_ISL_18376532, EPI_ISL_18376955, EPI_ISL_18377536, EPI_ISL_18377636, EPI_ISL_18382895, EPI_ISL_18384393, EPI_ISL_18384413, EPI_ISL_18384418, EPI_ISL_18384426, EPI_ISL_18384448, EPI_ISL_18384625, EPI_ISL_18384643, EPI_ISL_18391206-18391207, EPI_ISL_18397223, EPI_ISL_18397241, EPI_ISL_18397267, EPI_ISL_18397584, EPI_ISL_18401938, EPI_ISL_18405209, EPI_ISL_18406218

UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_58dd0_2eda30.json?f_userOrOld=uploaded%20sample&label=id:node_3458763

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---

Branch 28

Transferred to main repo:

Transferred to cov-lineages/pango-designation#2398

Defining Mutations: EG.5.1.1 > C5812T > G22927T(S:L455F), mostly with >> A26565C(M:K15Q), C28770G(N:T166R)
Query: C5812T, G22927T, C28770G (for major A26565C(M:K15Q), C28770G(N:T166R) sub-branch only)
Earliest seq: 2023-08-09 (EPI_ISL_18214077, South Korea)
Latest seq: 2023-11-09 (EPI_ISL_18547984, Nevada, USA)
Sampled Countries: South Korea (68), USA (5: NV/2; NC/1; ex. S. Korea/2), Australia (2: NSW; QLD), China (2: SC/1; ex. S. Korea/1), Denmark (2), Hungary (2), Finland (1), Japan (1)

Genomes:

EPI_ISL_18214077, EPI_ISL_18236938, EPI_ISL_18293068, EPI_ISL_18293497, EPI_ISL_18347905, EPI_ISL_18353940, EPI_ISL_18354370, EPI_ISL_18354403, EPI_ISL_18355265, EPI_ISL_18355547, EPI_ISL_18368528, EPI_ISL_18382157, EPI_ISL_18382304, EPI_ISL_18382505, EPI_ISL_18382615, EPI_ISL_18386641, EPI_ISL_18408701-18408702, EPI_ISL_18408814, EPI_ISL_18408878, EPI_ISL_18411301, EPI_ISL_18415920, EPI_ISL_18435710, EPI_ISL_18438964, EPI_ISL_18439203, EPI_ISL_18439262-18439263, EPI_ISL_18439368, EPI_ISL_18439436, EPI_ISL_18460639, EPI_ISL_18460726, EPI_ISL_18460826, EPI_ISL_18461023, EPI_ISL_18461030, EPI_ISL_18461109, EPI_ISL_18461117, EPI_ISL_18461139, EPI_ISL_18488790, EPI_ISL_18488878, EPI_ISL_18488904, EPI_ISL_18489119, EPI_ISL_18501908, EPI_ISL_18502007, EPI_ISL_18503617, EPI_ISL_18503624, EPI_ISL_18503755, EPI_ISL_18503952, EPI_ISL_18503974, EPI_ISL_18511170, EPI_ISL_18511222, EPI_ISL_18511248, EPI_ISL_18511257, EPI_ISL_18511484, EPI_ISL_18513699, EPI_ISL_18518361, EPI_ISL_18535616, EPI_ISL_18535618, EPI_ISL_18535641, EPI_ISL_18535643-18535644, EPI_ISL_18535683, EPI_ISL_18539076, EPI_ISL_18539319, EPI_ISL_18539641, EPI_ISL_18539827, EPI_ISL_18540358, EPI_ISL_18544082, EPI_ISL_18547609, EPI_ISL_18547984, EPI_ISL_18550336, EPI_ISL_18552522, EPI_ISL_18559930, EPI_ISL_18564453, EPI_ISL_18564477, EPI_ISL_18564533, EPI_ISL_18564565, EPI_ISL_18564603, EPI_ISL_18564701, EPI_ISL_18564813, EPI_ISL_18564892, EPI_ISL_18564897, EPI_ISL_18565136

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_356f8_c1a890.json?label=id:node_3518019

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---

Branch 29

Now pulled under HK.3

Defining Mutations: EG.5.1.1 > C16726T(ORF1b:H1087Y) > G9424T, A12472G, G22927T(S:L455F), T23030C(**S:F490P**), G27621T(ORF7a:Q76H)
Query: A12472G, G22927T, G27621T
Earliest seq: 2023-08-25 (EPI_ISL_18245860, Fujian, China)
Latest seq: 2023-09-06 (EPI_ISL_18243501, Singapore)
Sampled Countries: Singapore (2), China (1, FJ)

Genomes:

EPI_ISL_18243491, EPI_ISL_18243501, EPI_ISL_18245860

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_4007a_342f0.json?label=id:node_10825409

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---

Branch 30

Now pulled under HK.3

Defining Mutations: EG.5.1.1 > C4423T > G22927T(S:L455F)
Query: C4423T, G13627A, G22927T
Earliest seq: 2023-08-12 (EPI_ISL_18246284, Sichuan, China)
Latest seq: 2023-08-25 (EPI_ISL_18235973, Chiba, Japan)
Sampled Countries: China (2, SC), Japan (1)

Genomes:

EPI_ISL_18232772, EPI_ISL_18235973, EPI_ISL_18246284

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_5299_39270.json?f_userOrOld=uploaded%20sample&label=id:node_6954721

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---

Branch 31

Transferred to main repo

Transferred to cov-lineages/pango-designation#2321

Defining Mutations: EG.5.1.1 > C12020T(ORF1a:L3919F), T24496C > C2232T(ORF1a:A656V), C21516T, G22927T(S:L455F)
Query: C6541T, C12020T, G22927T, -G6337T, -C8982A, -G18445A, -C28087T
Earliest seq: 2023-08-21 (EPI_ISL_18216560, Galway, Ireland)
Latest seq: 2023-09-04 (EPI_ISL_18254216, Hubei)
Sampled Countries: China (1), Ireland (1), UK (1)

Genomes:

EPI_ISL_18216560, EPI_ISL_18244531, EPI_ISL_18254216

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_203fd_1904a0.json?label=id:node_6967052

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---

Branch 32

Defining Mutations: EG.5.1.1 > T4579A > G2329A, A8443G > G22927T(S:L455F)
Query: T4579A, A8443G, G22927T
Earliest seq: 2023-08-08 (EPI_ISL_18166186, Sichuan)
Latest seq: 2023-08-26 (EPI_ISL_18254268, Hubei)
Sampled Countries: China (5)

Genomes:

EPI_ISL_18166186, EPI_ISL_18232746, EPI_ISL_18245861, EPI_ISL_18246325, EPI_ISL_18254268

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_647e_1a2900.json?label=id:node_6956460

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---

Branch 33

Designated as EG.5.1.19

Designated as EG.5.1.19 via cov-lineages/pango-designation@0807c23 , after transferred to cov-lineages/pango-designation#2322

Defining Mutations: EG.5.1 > T26171A(ORF3a:M260K) > A17615G(ORF1b:K1383R), G22927T(S:L455F)
Query: G21718T, G22927T, T26171A
Earliest seq: 2023-08-09 (EPI_ISL_18134871, Daknam, Belgium)
Latest seq: 2023-09-03 (EPI_ISL_18252041, SEA airport, Washington, with travel hisotry: Netherlands)
Sampled Countries: Belgium (1), France (1), Romania (1), USA (1, ex. Netherlands)

Genomes:

EPI_ISL_18134871, EPI_ISL_18229094, EPI_ISL_18252041, EPI_ISL_18254718

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_107fe_1a6cd0.json?f_userOrOld=uploaded%20sample&label=id:node_6953659

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---

Branch 34, NOT FLip but with S:L455S

Defining Mutations: EG.5.1.3 > G2946A(ORF1a:G894D), T15264C, T22926C(S:L455S)
Query: C1889T, C2334T, T22926C, -A4340G, -A10703C
Earliest seq: 2023-07-27 (EPI_ISL_18248425, Zagreb, Croatia)
Latest seq: 2023-07-31 (EPI_ISL_18248430, Zagreb, Croatia)
Sampled Countries: Croatia (4)

Genomes:

EPI_ISL_18248425, EPI_ISL_18248427, EPI_ISL_18248429-18248430

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1ed45_24dab0.json?f_userOrOld=uploaded%20sample&label=id:node_10831638

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---

Branch 35, side-branch to JJ.1

Transferred to main repo

Transferred to cov-lineages/pango-designation#2354

Defining Mutations: EG.5.1.4 > C26111T(ORF3:P240L) > C18555T > T17268C > G22927T(S:L455F)
Query: T17268C, G22927T, C26111T
Earliest seq: 2023-08-08 (EPI_ISL_18132133, Newfoundland and Labrador)
Latest seq: 2023-10-23 (EPI_ISL_18448815, Ontario, Canada)
Sampled Countries: Canada (49: ON/22; NL/15; AB/10; BC/1; NS/1), US (7: CA/2; NY/2; AZ/1; UT/1; VA/1), France (1)

Genomes:

EPI_ISL_18132133, EPI_ISL_18256806, EPI_ISL_18258767, EPI_ISL_18258769-18258770, EPI_ISL_18258773, EPI_ISL_18258778, EPI_ISL_18291996, EPI_ISL_18291998, EPI_ISL_18292017, EPI_ISL_18292020-18292022, EPI_ISL_18292026-18292028, EPI_ISL_18333999, EPI_ISL_18344763, EPI_ISL_18357035, EPI_ISL_18372328, EPI_ISL_18372367, EPI_ISL_18383112, EPI_ISL_18383123-18383124, EPI_ISL_18383697, EPI_ISL_18388693, EPI_ISL_18395288, EPI_ISL_18395414, EPI_ISL_18395581, EPI_ISL_18404467, EPI_ISL_18425010, EPI_ISL_18425420, EPI_ISL_18425431, EPI_ISL_18425847, EPI_ISL_18425967, EPI_ISL_18426727, EPI_ISL_18427300, EPI_ISL_18427492, EPI_ISL_18427494, EPI_ISL_18427496, EPI_ISL_18427507, EPI_ISL_18427602, EPI_ISL_18431345, EPI_ISL_18436820, EPI_ISL_18437028, EPI_ISL_18437176, EPI_ISL_18438632, EPI_ISL_18438777, EPI_ISL_18448237, EPI_ISL_18448584-18448585, EPI_ISL_18448588, EPI_ISL_18448699-18448700, EPI_ISL_18448702, EPI_ISL_18448740, EPI_ISL_18448815

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_17f71_c79a0.json?f_userOrOld=uploaded%20sample&label=id:node_3447785

view from EG.5.1.4 polytomy

details

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---

Branch 36

Transferred to main repo:

Transferred to cov-lineages/pango-designation#2399

Defining Mutations: EG.5.1.1 > C22388T(S:L276L) > G22927T(S:L455F), mostly with >> C1853T sub-branch
Query: C1853T, G13627A, G22927T, -C4780T, -C5031T, -C6627T, -C8982A (for major C1853T sub-branch only)
Earliest seq: 2023-08-14 (EPI_ISL_18224087, Colorado, USA)
Latest seq: 2023-11-20 (EPI_ISL_18568071, SEA airport, travel history: France)
Sampled Countries: France (20), Norway (12), Germany (11), Switzerland (8), USA (6: CO/2; ex. France/2; ex.Germany/2), UK (4: EN), China (3: XJ/2; FJ/1), Denmark (3), Ukraine (3), Canada (2: NB; ON), Finland (2), Spain (2), Belgium (1), Italy (1), Japan (1), Singapore (1)

Genomes:

EPI_ISL_18224087, EPI_ISL_18224096, EPI_ISL_18233134, EPI_ISL_18239749, EPI_ISL_18263561, EPI_ISL_18263571, EPI_ISL_18263574, EPI_ISL_18263576, EPI_ISL_18272601-18272602, EPI_ISL_18280654, EPI_ISL_18280813, EPI_ISL_18290994, EPI_ISL_18291008, EPI_ISL_18291011, EPI_ISL_18308259, EPI_ISL_18313749, EPI_ISL_18326424, EPI_ISL_18326608, EPI_ISL_18327645, EPI_ISL_18337648, EPI_ISL_18337651, EPI_ISL_18338378, EPI_ISL_18373487, EPI_ISL_18373856, EPI_ISL_18380089, EPI_ISL_18380091, EPI_ISL_18388662, EPI_ISL_18388711, EPI_ISL_18411952, EPI_ISL_18412072, EPI_ISL_18421745, EPI_ISL_18421949, EPI_ISL_18428144, EPI_ISL_18428460, EPI_ISL_18428992, EPI_ISL_18433011, EPI_ISL_18441991, EPI_ISL_18451507, EPI_ISL_18464584, EPI_ISL_18464947, EPI_ISL_18468968, EPI_ISL_18476770, EPI_ISL_18485554, EPI_ISL_18486361, EPI_ISL_18486756, EPI_ISL_18493947, EPI_ISL_18494748, EPI_ISL_18495920, EPI_ISL_18496297, EPI_ISL_18496628, EPI_ISL_18496636, EPI_ISL_18496703, EPI_ISL_18499460, EPI_ISL_18505686, EPI_ISL_18505750, EPI_ISL_18519177-18519178, EPI_ISL_18525816, EPI_ISL_18530654, EPI_ISL_18530657-18530658, EPI_ISL_18530757, EPI_ISL_18530938, EPI_ISL_18530967, EPI_ISL_18538000, EPI_ISL_18540615, EPI_ISL_18540768, EPI_ISL_18540871, EPI_ISL_18540915, EPI_ISL_18544152, EPI_ISL_18552615, EPI_ISL_18553571, EPI_ISL_18556840, EPI_ISL_18568060, EPI_ISL_18568071, EPI_ISL_18568733-18568735, EPI_ISL_18570228

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_bd36_c24960.json?label=id:node_3504156

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---

Branch 37

⚠ C29095T became homoplastic across the EG.5.1+L455F tree, no longer tracking.

No longer tracking

Defining Mutations: EG.5.1.1 > C29095T > G22927T(S:L455F)
Query: G13627A, G22927T, C29095T
Earliest seq: 2023-08-28 (EPI_ISL_18246374, Sichuan, China)
Latest seq: 2023-08-31 (EPI_ISL_18264700, Texas, USA)
Sampled Countries: USA (2: TX), China (1: SC)

Genomes:

EPI_ISL_18246374, EPI_ISL_18264482, EPI_ISL_18264700

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_832a_59eef0.json?f_userOrOld=uploaded%20sample&label=id:node_10885350

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Branch 38

Defining Mutations: EG.5.1.1 > T24583C > G22927T(S:L455F)
Query: C6541T, G22927T, T24583C
Earliest seq: 2023-08-03 (EPI_ISL_18166149, Sichuan)
Latest seq: 2023-08-26 (EPI_ISL_18268462 Shanghai)
Sampled Countries: China (3: SC/2; SH/1)

Genomes:

EPI_ISL_18166149, EPI_ISL_18232692, EPI_ISL_18268462

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_f9a8_5a58c0.json?f_userOrOld=uploaded%20sample&label=id:node_10885352

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---

Branch 39

Defining Mutations: HK.1 (EG.5.1.1.1) > G22927T(S:L455F)
Query: C6541T, G13627A, G22332T, G22927T + C6541T, G13627A, G22332A, G22927T
Earliest seq: 2023-08-09 (EPI_ISL_18146086, Hubei)
Latest seq: 2023-08-28 (EPI_ISL_18254226, Hubei)
Sampled Countries: China (7)

Genomes:

EPI_ISL_18146086, EPI_ISL_18146100, EPI_ISL_18254226-18254227, EPI_ISL_18268425, EPI_ISL_18138066, EPI_ISL_18254258

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1cca6_5afd40.json?f_userOrOld=uploaded%20sample&label=id:node_6971951

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---

Branch 40

Defining Mutations: EG.5.1.1 > C10615T > G22927T(S:L455F) > C1426T, G25691T(ORF3a:G100V)
Query: C1426T, C10615T, G22927T
Earliest seq: 2023-08-08 (EPI_ISL_18138249, Shanghai)
Latest seq: 2023-08-25 (EPI_ISL_18268441, Shanghai)
Sampled Countries: China (4: SH)

Genomes:

EPI_ISL_18138249, EPI_ISL_18208636, EPI_ISL_18268441, EPI_ISL_18268482

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_20010_5b23f0.json?f_userOrOld=uploaded%20sample&label=id:node_6983332

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Branch 41

Defining Mutations: EG.5.1.1 > C24023T > C2485T, G15025A(ORF1b:A520T), G22927C(S:L455F)
Query: C6541T, G22927C, C24023T
Earliest seq: 2023-08-14 (EPI_ISL_18239206, South Korea)
Latest seq: 2023-08-24 (EPI_ISL_18254859, South Korea)
Sampled Countries: South Korea (3)

Genomes:

EPI_ISL_18239206, EPI_ISL_18254859, EPI_ISL_18271926

UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_26c10_8252f0.json?f_userOrOld=uploaded%20sample&label=id:node_10885690

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---

Branch 42

Transferred to main repo

Transferred to cov-lineages/pango-designation#2355

Defining Mutations: EG.5.1.1 > C22687T > G22927T(S:L455F)
Query: C6541T, C22687T, G22927T, -T2145C, -A16482C, -C21191T
Earliest seq: 2023-08-14 (EPI_ISL_18279039, Singapore, travel history: China)
Latest seq: 2023-09-01 (EPI_ISL_18278560, Alberta, Canada)
Sampled Countries: China (21: GS/4; HB/3; XJ/3; AH/2; SC/2; SX/2; FJ/1; HK/1; QH/1; SH/1; YN/1), Australia (12: NSW/5; SA/4; QLD/1; TA/1; VIC/1), South Korea (8), Canada (6: AB), USA (3: AZ/1; ex. Australia/2), Singapore (2: Local/1; ex. China/1), Japan (1)

Genomes:

EPI_ISL_18146046, EPI_ISL_18213336, EPI_ISL_18217223, EPI_ISL_18278558, EPI_ISL_18278560, EPI_ISL_18279039, EPI_ISL_18289881, EPI_ISL_18293677, EPI_ISL_18293698, EPI_ISL_18311984, EPI_ISL_18312274, EPI_ISL_18312380, EPI_ISL_18313209, EPI_ISL_18327623, EPI_ISL_18327666, EPI_ISL_18346251, EPI_ISL_18346325, EPI_ISL_18347707, EPI_ISL_18350428, EPI_ISL_18360224, EPI_ISL_18361336, EPI_ISL_18361999, EPI_ISL_18365676, EPI_ISL_18365684, EPI_ISL_18365890, EPI_ISL_18366374, EPI_ISL_18382081, EPI_ISL_18382589, EPI_ISL_18382710, EPI_ISL_18384562, EPI_ISL_18388967, EPI_ISL_18389014, EPI_ISL_18389016, EPI_ISL_18390872, EPI_ISL_18396110, EPI_ISL_18401894, EPI_ISL_18401903, EPI_ISL_18401983, EPI_ISL_18404054, EPI_ISL_18408752, EPI_ISL_18411422, EPI_ISL_18411665, EPI_ISL_18411717, EPI_ISL_18411753, EPI_ISL_18425089, EPI_ISL_18427884, EPI_ISL_18435235, EPI_ISL_18438336, EPI_ISL_18438338, EPI_ISL_18438347, EPI_ISL_18439100, EPI_ISL_18447517, EPI_ISL_18447771

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_27ac0_cb920.json?f_userOrOld=uploaded%20sample&label=id:node_3487678

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---

Branch 43

now seems to be pulled under HK.3, no longer tracking

Pulled under HK.3

Defining Mutations: EG.5.1.1 > C19524T > G22927T(S:L455F), A28254Δ
Query: G13627A, C19524T, G22927T, -C5031T
Earliest seq: 2023-08-19 (EPI_ISL_18246322, Sichuan)
Latest seq: 2023-09-07 (EPI_ISL_18277156, Fujian)
Sampled Countries: China (3: FJ; HL; SC)

Genomes:

EPI_ISL_18246049, EPI_ISL_18246322, EPI_ISL_18277156

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_22869_97c570.json?f_userOrOld=uploaded%20sample&label=id:node_6973155

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---

Branch 44, "FLippeR"

Transferred to main Repo

Transferred to cov-lineages/pango-designation#2296

Defining Mutations: EG.5.1 > A22106C(S:K182Q) > C22995G(S:T478R), A25664G(ORF3a:Y91C) > C1613T(ORF1a:L450F), G20995T(ORF1b:G2510C), G22927C(S:L455F), C25803T, A27388C
Query: A22106C, G22927C, C22995G
Earliest seq: 2023-08-14 (EPI_ISL_18160020, Denmark, or, EPI_ISL_18278998, Singapore)
Latest seq: 2023-09-04 (EPI_ISL_18243476, Singapore)
Sampled Countries: Singapore (2), Denmark (1)

Genomes:

EPI_ISL_18160020, EPI_ISL_18243476, EPI_ISL_18278998

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_13bc1_9943e0.json?f_userOrOld=uploaded%20sample&label=id:node_6964487

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---

Branch 45

Transferred to main Repo

Transferred to cov-lineages/pango-designation#2308

Defining Mutations: EG.5.1.1 > C13968A, A15885G > T11449C > C10369T, G22927T(S:L455F), C29077T, G29140T(N:Q289H)
Query: T11449C, C13968A, G22927T
Earliest seq: 2023-09-06 (EPI_ISL_18273676, England)
Latest seq: 2023-09-07 (EPI_ISL_18284457, IAD Airport, DC, travel history: Italy)
Sampled Countries: UK (2: EN) USA (2, ex. Italy)

Genomes:

EPI_ISL_18273676, EPI_ISL_18281373, EPI_ISL_18284072, EPI_ISL_18284457

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2d447_b0ad70.json?f_userOrOld=uploaded%20sample&label=id:node_6985113

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---

Branch 46 with a sub-lineage of S:L452Q, designated as HK.22

parental lineage of HK.22

Branch 46 + S:L452Q designated as HK.22 via cov-lineages/pango-designation@2d3115a

Defining Mutations: EG.5.1.1 > G25407T(ORF3a:M5I) > C2662T > G22927T(S:L455F)
Query: C2662T, G22927T, G25407T
Earliest seq: 2023-08-06 (EPI_ISL_18114750, Shanghai)
Latest seq: 2023-09-06 (EPI_ISL_18284970, Shanghai)
Sampled Countries: China (4: SH)

Genomes:

EPI_ISL_18114750, EPI_ISL_18232688, EPI_ISL_18284888, EPI_ISL_18284970

UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_38b1_b0cc80.json?f_userOrOld=uploaded%20sample

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---

Branch 47

Defining Mutations: EG.5.1.1 > C7600T > G22927T(S:L455F) > T10216C
Query: C7600T, T10216C, G22927T
Earliest seq: 2023-08-22 (EPI_ISL_18246331, Sichuan)
Latest seq: 2023-09-04 (EPI_ISL_18284731, Hubei)
Sampled Countries: China (5)

Genomes:

EPI_ISL_18246331, EPI_ISL_18284731, EPI_ISL_18284776, EPI_ISL_18284783, EPI_ISL_18284960

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3ad47_b108e0.json?f_userOrOld=uploaded%20sample&label=id:node_10899080

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---

Branch 48

Transferred to main repo

Transferred to cov-lineages/pango-designation#2360 ⚠️ Please check potential misplacement.

Defining Mutations: EG.5.1.1 > A23539T(S:S659S) > G22927T(S:L455F)
Query: G13627A, G22927T, A23539T, -T899C, -C2662T, -C10015T, -T12865C, -G22332A
Earliest seq: 2023-08-16 (EPI_ISL_18141107, Singapore)
Latest seq: 2023-10-22 (EPI_ISL_18440472, Netherlands)
Sampled Countries: Australia (32: NSW/14; SA/8; QLD/4; VIC/3; TAS/1; WA/1), China (10: SC/4; HB/2; SH/2; FJ/1; XJ/1), New Zealand (9), Singapore (4), Netherlands (3), USA (2), France (1)

Genomes:

EPI_ISL_18141107, EPI_ISL_18246326, EPI_ISL_18278997, EPI_ISL_18279955, EPI_ISL_18292475, EPI_ISL_18300669, EPI_ISL_18307132, EPI_ISL_18320781, EPI_ISL_18324527, EPI_ISL_18324537, EPI_ISL_18324951, EPI_ISL_18346779, EPI_ISL_18346805, EPI_ISL_18346818, EPI_ISL_18347516, EPI_ISL_18347639, EPI_ISL_18347703-18347704, EPI_ISL_18347710, EPI_ISL_18352381, EPI_ISL_18355046, EPI_ISL_18360352, EPI_ISL_18365605, EPI_ISL_18365672, EPI_ISL_18365874, EPI_ISL_18376439, EPI_ISL_18388898, EPI_ISL_18396188, EPI_ISL_18411419, EPI_ISL_18411467, EPI_ISL_18411551, EPI_ISL_18411564, EPI_ISL_18411674, EPI_ISL_18411695, EPI_ISL_18423924, EPI_ISL_18427871, EPI_ISL_18428112, EPI_ISL_18435043, EPI_ISL_18438373, EPI_ISL_18440466, EPI_ISL_18440472, EPI_ISL_18440476, EPI_ISL_18442757, EPI_ISL_18442774, EPI_ISL_18447732, EPI_ISL_18454463, EPI_ISL_18454489, EPI_ISL_18457508, EPI_ISL_18459380, EPI_ISL_18459604, EPI_ISL_18459721, EPI_ISL_18459855, EPI_ISL_18459912, EPI_ISL_18459940, EPI_ISL_18461585, EPI_ISL_18461782, EPI_ISL_18461792, EPI_ISL_18461895, EPI_ISL_18461916, EPI_ISL_18461956, EPI_ISL_18464115

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e62_757100.json?label=id:node_3495970

Trivia:

• Please check potential misplacement: it seems only one seqs preceeding S:L455F branch, being Sichuan/BZCDC-043/2023|EPI_ISL_17988879|2023-06-12; however the mutations on the follow-up sub-branch G571A, C2263A, A28959G are "unique" to the EG.5.1.1* tree which may support it be a different lineage than HK.3.

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---

Branch 49

Now at least 3 smaller clusters seems pulled together a S:L455F branch right under EG.5.1.4 polytomy, hard to catch by proper query now.

Query failed

Defining Mutations: EG.5.1.4 > C8407T, C11008A(ORF1a:H3581Q), G22927T(S:L455F), G25538T(ORF3a:G49V), C25572T
Query: A18492G, A21137G, G22927T, -C6120T, -G13627A, -C26111T
Earliest seq: 2023-08-21 (EPI_ISL_18284756, Hubei)
Latest seq: 2023-09-03 (EPI_ISL_18284729, Hubei)
Sampled Countries: China (3)

Genomes:

EPI_ISL_18284721, EPI_ISL_18284729, EPI_ISL_18284756

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_176c9_b20830.json?f_userOrOld=uploaded%20sample&label=id:node_10899080

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Branch 50

Defining Mutations: EG.5.1.1 > G28904T(N:A211S) > G22927T(S:L455F), G27261T, C28744T
Query: C6541T, G22927T, G28904T
Earliest seq: 2023-08-30 (EPI_ISL_18268410, Shanghai)
Latest seq: 2023-09-03 (EPI_ISL_18254255, Hubei)
Sampled Countries: China (5)

Genomes:

EPI_ISL_18254255, EPI_ISL_18268410, EPI_ISL_18289864, EPI_ISL_18289874, EPI_ISL_18289889

UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_523af_c118f0.json?f_userOrOld=uploaded%20sample&label=id:node_6955662

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---

Branch 51

Transferred to main repo

transferred to cov-lineages/pango-designation#2365

Defining Mutations: EG.5.1.1 > C10015T > G22927T(S:L455F)
Query: C6541T, C10015T, G22927T, -C4586T
Earliest seq: 2023-07-31 (EPI_ISL_18246153, Heilongjiang)
Latest seq: 2023-10-31 (EPI_ISL_18473950, Spain)
Sampled Countries: China (20: SH/6; HL/5; LN/3; AH/1; BJ/1; GS/1; HB/1; SC/1; SX/1; XJ/1), Canada (10: ON/9; NS/1), Australia (5: NSW/4; QLD/1), Singapore (5), Spain (5), Croatia (4), USA (3: NY/2; HI/1), Denmark (2), Japan (2), Belgium (1), France (1), Italy (1), Switzerland (1)

Genomes:

EPI_ISL_18246153, EPI_ISL_18268220, EPI_ISL_18284760, EPI_ISL_18289806, EPI_ISL_18304238, EPI_ISL_18307185, EPI_ISL_18309728, EPI_ISL_18320892, EPI_ISL_18333882, EPI_ISL_18354453, EPI_ISL_18356455, EPI_ISL_18362071, EPI_ISL_18382338, EPI_ISL_18384364, EPI_ISL_18388937, EPI_ISL_18388943, EPI_ISL_18392626, EPI_ISL_18392641, EPI_ISL_18395616, EPI_ISL_18398918, EPI_ISL_18401900, EPI_ISL_18422863, EPI_ISL_18425076, EPI_ISL_18433557, EPI_ISL_18438020, EPI_ISL_18438314, EPI_ISL_18438838, EPI_ISL_18445101, EPI_ISL_18445501, EPI_ISL_18446144, EPI_ISL_18448315, EPI_ISL_18448907-18448908, EPI_ISL_18448913-18448914, EPI_ISL_18461557, EPI_ISL_18461608, EPI_ISL_18461684, EPI_ISL_18461722, EPI_ISL_18464481, EPI_ISL_18464633, EPI_ISL_18465094, EPI_ISL_18465113, EPI_ISL_18465171, EPI_ISL_18465395, EPI_ISL_18465403, EPI_ISL_18466062, EPI_ISL_18466326-18466327, EPI_ISL_18466420, EPI_ISL_18466590, EPI_ISL_18470572, EPI_ISL_18471609, EPI_ISL_18471611, EPI_ISL_18473319, EPI_ISL_18473421, EPI_ISL_18473950, EPI_ISL_18475156, EPI_ISL_18475172, EPI_ISL_18475181, EPI_ISL_18475190, EPI_ISL_18475453

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_25e8a_b47430.json?label=id:node_3494261

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---

Branch 52, now pulled under HK.3.2

Now part of HK.3.2

Defining Mutations: EG.5.1.1 > C26029A(ORF3a:Q213K) > G22927T(S:L455F)
Query: C6541T, G22927T, C26029A, -G24944T, -A26901G
Earliest seq: 2023-08-16 (EPI_ISL_18146001, Hubei, China)
Latest seq: 2023-09-20 (EPI_ISL_18340137, Illinois, USA)
Sampled Countries: China (5: HB/3; SC; YN) USA (3: IL; NY; WA), Oman (1)

Genomes:

EPI_ISL_18146001, EPI_ISL_18246341, EPI_ISL_18290983, EPI_ISL_18292780, EPI_ISL_18313122, EPI_ISL_18322921, EPI_ISL_18330205, EPI_ISL_18333620, EPI_ISL_18340137

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_36145_d6af90.json?f_userOrOld=uploaded%20sample&label=id:node_3648445

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Branch 53

Transferred to main repo

transferred to cov-lineages/pango-designation#2366

Defining Mutations: EG.5.1.1 > C27741T > C1912T, C1968T(ORF1a:T568I), T7111C, A20010T(ORF1b:Q2181H), T20592C, G22927C(S:L455F), C28093T(ORF8:S67F)
Query: C6541T, G22927C, C27741T
Earliest seq: 2023-08-28 (EPI_ISL_18345224, Cork, Ireland)
Latest seq: 2023-10-23 (EPI_ISL_18471085, Connecticut, USA)
Sampled Countries: UK (17: EN/16; WS/1), USA (14: NY/3; NJ/2; TX/2; UT/2; AZ/1; CA/1; CT/1; MN/1; OH/1), Ireland (9), Canada (4: ON/3; BC/1), Denmark (2), France (2), China (2: SC/1; ex. Spain/1), Belgium (1), South Korea (1), Netherlands (1)

Genomes:

EPI_ISL_18250090, EPI_ISL_18284832, EPI_ISL_18290882, EPI_ISL_18290915, EPI_ISL_18308328, EPI_ISL_18308339, EPI_ISL_18315360, EPI_ISL_18321565, EPI_ISL_18332107, EPI_ISL_18332505, EPI_ISL_18345224, EPI_ISL_18354139, EPI_ISL_18362839, EPI_ISL_18362880-18362881, EPI_ISL_18362951, EPI_ISL_18375850, EPI_ISL_18377642, EPI_ISL_18385706, EPI_ISL_18385720, EPI_ISL_18385728, EPI_ISL_18385734, EPI_ISL_18388184, EPI_ISL_18388760-18388761, EPI_ISL_18389241, EPI_ISL_18398829, EPI_ISL_18399988, EPI_ISL_18400877, EPI_ISL_18403587, EPI_ISL_18403998, EPI_ISL_18407932, EPI_ISL_18416430, EPI_ISL_18416450, EPI_ISL_18420893, EPI_ISL_18420911, EPI_ISL_18422267, EPI_ISL_18427521, EPI_ISL_18429173, EPI_ISL_18429518, EPI_ISL_18430506, EPI_ISL_18433870, EPI_ISL_18438642, EPI_ISL_18442008, EPI_ISL_18443922, EPI_ISL_18448322, EPI_ISL_18452961, EPI_ISL_18456955, EPI_ISL_18467439, EPI_ISL_18467445, EPI_ISL_18467479, EPI_ISL_18471085, EPI_ISL_18475314

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2eee6_b4b600.json?label=id:node_3484946

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---

Branch 54:

Defining Mutations: EG.5.1.1 > G24368T(S:D936Y) > G22927T(S:L455F)
Query: G13627A, G22927T, G24368T, -G3567A, -C4012T, -C5031T, -T13234C, -C17976T
Earliest seq: 2023-09-11 (EPI_ISL_18312655, South Korea)
Latest seq: 2023-11-24 (EPI_ISL_18567787, Veneto, Italy)
Sampled Countries: Finland (15), South Korea (15), USA (9: NY/7; UT/2), Italy (2), Singapore (2), Australia (1: QLD), Germany (1)

Genomes:

EPI_ISL_18312655, EPI_ISL_18343453, EPI_ISL_18347772, EPI_ISL_18347778, EPI_ISL_18347783, EPI_ISL_18347794, EPI_ISL_18347862, EPI_ISL_18354114, EPI_ISL_18394470, EPI_ISL_18408694, EPI_ISL_18411981, EPI_ISL_18411986, EPI_ISL_18412002, EPI_ISL_18412024, EPI_ISL_18412052, EPI_ISL_18412131, EPI_ISL_18439287, EPI_ISL_18439475, EPI_ISL_18445086, EPI_ISL_18445161, EPI_ISL_18449963, EPI_ISL_18458264, EPI_ISL_18458329, EPI_ISL_18460569, EPI_ISL_18502041, EPI_ISL_18503589, EPI_ISL_18511443, EPI_ISL_18533418, EPI_ISL_18533465, EPI_ISL_18533560, EPI_ISL_18533727, EPI_ISL_18534149, EPI_ISL_18539237, EPI_ISL_18539435, EPI_ISL_18539679, EPI_ISL_18539701, EPI_ISL_18539776, EPI_ISL_18541395, EPI_ISL_18541532, EPI_ISL_18544389, EPI_ISL_18547900, EPI_ISL_18554927, EPI_ISL_18555070, EPI_ISL_18564736, EPI_ISL_18567787

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_28b3b_c482d0.json?label=id:node_3526683

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---

Branch 55

Designated with 2 levesl: HK.24 and HK.24.1

Designated as HK.24 and HK.24.1

Defining Mutations: EG.5.1.1 > G23522A(S:E654K) > G22927T(S:L455F)
Query: C6541T, G22927T, G23522A
Earliest seq: 2023-08-26 (EPI_ISL_18284795, Shanghai, China)
Latest seq: 2023-09-24 (EPI_ISL_18346833, South Australia, Australia)
Sampled Countries: Australia (6: QLD/2; WA/2; NSW; SA), China (3: SH), New Zealand (1)

Genomes:

EPI_ISL_18284795, EPI_ISL_18284982, EPI_ISL_18324864, EPI_ISL_18346833, EPI_ISL_18347678, EPI_ISL_18352382, EPI_ISL_18352389, EPI_ISL_18352581, EPI_ISL_18354460, EPI_ISL_18360253

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_222ea_2ee540.json?f_userOrOld=uploaded%20sample&label=id:node_3445909

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---

Branch 56

Defining Mutations: EG.5.1.1 > A22582G(S:E340) > G22927T(S:L455F)
Query: G13627A, A22582G, G22927T, -G3153A
Earliest seq: 2023-08-30 (EPI_ISL_18303241, Portugal)
Latest seq: 2023-09-25 (EPI_ISL_18355054, Singapore)
Sampled Countries: Portugal (2), Singapore (2), China (1: QH), UK (1: EN)

Genomes:

EPI_ISL_18268272, EPI_ISL_18274005, EPI_ISL_18303241, EPI_ISL_18303432, EPI_ISL_18307200, EPI_ISL_18355054

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_61cc_2ffcf0.json?label=id:node_3450332

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---

Branch 57

Defining Mutations: EG.5.1.1 > A22582G(S:E340) > G3153A(ORF1a:G963D) > G22927T(S:L455F)
Query: G3153A, A22582G, G22927T
Earliest seq: 2023-08-14 (EPI_ISL_18146012, Hubei, China)
Latest seq: 2023-09-26 (EPI_ISL_18350530, Basque, Spain)
Sampled Countries: China (4: FJ; HB; HK; SH), Japan (2), South Korea (2), USA (2: ex. Greece), Spain (1)

Genomes:

EPI_ISL_18146012, EPI_ISL_18277143, EPI_ISL_18293356, EPI_ISL_18306220, EPI_ISL_18306632, EPI_ISL_18306769, EPI_ISL_18309318, EPI_ISL_18309324, EPI_ISL_18350530, EPI_ISL_18354289, EPI_ISL_18360277

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_61cc_2ffcf0.json?label=id:node_3450116

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---

Branch 58, formerly singlet, thanks to @aviczhl2 for updated info

Defining Mutations: EG.5.1 > T26972C > C28909T > C2106A(ORF1a:T614N), G28423T(ORF9b:R47L) > A21759G(S:H66R), G22927T(S:L455F), G24004A(S:K814), C25572T
Query: A18492G, G22927T, C28909T
Earliest seq: 2023-08-21 (EPI_ISL_18271704, S. Korea)
Latest seq: 2023-09-19 (EPI_ISL_18355498, S. Korea)
Sampled Countries: South Korea (6)

Genomes:

EPI_ISL_18271704, EPI_ISL_18354058, EPI_ISL_18354072, EPI_ISL_18354264, EPI_ISL_18355236, EPI_ISL_18355498

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_26418_30eca0.json?label=id:node_3429102

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---

Branch 59: ⚠️ careful with potential dropout/misplacement.

Defining Mutations: EG.5.1.1 > G20134T(ORF1b:V2223L) > G22927T(S:L455F)
Query: G13627A, G20134T, G22927T
Earliest seq: 2023-09-04 (EPI_ISL_18300595, New South Wales)
Latest seq: 2023-10-03 (EPI_ISL_18361370, NSW)
Sampled Countries: Australia (17: NSW/16; QLD)

Genomes:

EPI_ISL_18300595, EPI_ISL_18300598, EPI_ISL_18300624, EPI_ISL_18300634, EPI_ISL_18300676-18300679, EPI_ISL_18300732, EPI_ISL_18300745-18300746, EPI_ISL_18300790, EPI_ISL_18324806, EPI_ISL_18352578, EPI_ISL_18361360-18361361, EPI_ISL_18361370

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_4fa9_6ad320.json?label=id:node_3451611

Trivia:

• Only one sequence preceding this sub-branch: Heilongjiang/HLJCDC-2004/2023|EPI_ISL_18245889|2023-07-25, please check potential HK.3-dropout/misplacement.

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---

Branch 60: Formerly Y144F artifact branch now masked

Defining Mutations: EG.5.1.1 > T16545G > C1471T, G22927T(S:L455F)
Query: G13627A, T16545G, G22927T
Earliest seq: 2023-08-25 (EPI_ISL_18228384, Finland)
Latest seq: 2023-10-04 (EPI_ISL_18362018, Singapore)
Sampled Countries: Singapore (7), China (3: SH/2; HB), Finland (1)

Genomes:

EPI_ISL_18228384, EPI_ISL_18243407, EPI_ISL_18254180, EPI_ISL_18306951, EPI_ISL_18320869, EPI_ISL_18360325, EPI_ISL_18361717, EPI_ISL_18361964, EPI_ISL_18362005, EPI_ISL_18362018, EPI_ISL_18362077

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_108b5_6b1720.json?f_userOrOld=uploaded%20sample&label=id:node_3457632

Trivia:

• Formerly Y144F artifact sub-branch now seems masked, thanks to @FedeGueli for the quick analysis and query.

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---

Branch 61

⚠️ Please check potential reversion/artifact/misplacement, C26681T is quite homoplastic in HK.3*, no longer tracking

potential HK.3 dropout

Defining Mutations: EG.5.1.1 > C26681T > T5327C, C5986T, T22032C(S:F157S), G22927T(S:L455F)
Query: T22032C, G22927T, C26681T
Earliest seq: 2023-09-03 (EPI_ISL_18376557, Sichuan)
Latest seq: 2023-09-11 (EPI_ISL_18376558, Sichuan, OR EPI_ISL_18277141, Fujian)
Sampled Countries: China (5: SC/4; FJ)

Genomes:

EPI_ISL_18277141, EPI_ISL_18376556-18376559

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice14_genome_f688_7a5e50.json?label=id:node_3447615

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---

Branch 62: With a sub-branch of FLippeR

Defining Mutations: EG.5.1.1 > C18559T(ORF1b:L1698F) > T15927C, G22927T(S:L455F)
Query: C6541T, C18559T, G22927T
Earliest seq: 2023-08-31 (EPI_ISL_18285056, Sichuan, China)
Latest seq: 2023-09-20 (EPI_ISL_18382134, South Korea)
Sampled Countries: China (4: SC/2; SH/2), South Korea (1)

Genomes:

EPI_ISL_18285056-18285057, EPI_ISL_18320863, EPI_ISL_18360320, EPI_ISL_18382134

UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_24de1_9159b0.json?label=id:node_3445922

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---

Branch 63

⚠️ Please check potential misplacement

Transferred to main repo

Transferred to cov-lineages/pango-designation#2400

Defining Mutations: EG.5.1.1 > T14034C > T6556C > G22927T(S:L455F)
Query: T6556C, T14034C, G22927T
Earliest seq: 2023-08-28 (EPI_ISL_18236022, Chiba, Japan)
Latest seq: 2023-11-16 (EPI_ISL_18568493, Ardèche, France)
Sampled Countries: South Korea (66), Japan (11), France (7), China (2: Taiwan), Singapore (2), Germany (1), Ireland (1), UK (1: England)

Genomes:

EPI_ISL_18236022, EPI_ISL_18307101, EPI_ISL_18307183, EPI_ISL_18312967, EPI_ISL_18354179, EPI_ISL_18354386, EPI_ISL_18371409, EPI_ISL_18371437, EPI_ISL_18376385, EPI_ISL_18381917, EPI_ISL_18382077, EPI_ISL_18382170, EPI_ISL_18382306, EPI_ISL_18382313, EPI_ISL_18384744, EPI_ISL_18390972, EPI_ISL_18408733, EPI_ISL_18408999, EPI_ISL_18409046, EPI_ISL_18409110, EPI_ISL_18418096, EPI_ISL_18418099, EPI_ISL_18420466, EPI_ISL_18423347, EPI_ISL_18438958, EPI_ISL_18439063, EPI_ISL_18439157, EPI_ISL_18439221, EPI_ISL_18439371, EPI_ISL_18460530, EPI_ISL_18460541, EPI_ISL_18460589, EPI_ISL_18460966, EPI_ISL_18460978, EPI_ISL_18461033, EPI_ISL_18461094, EPI_ISL_18461485, EPI_ISL_18465933, EPI_ISL_18468665, EPI_ISL_18486472, EPI_ISL_18491815, EPI_ISL_18496187, EPI_ISL_18501996, EPI_ISL_18502046, EPI_ISL_18502053, EPI_ISL_18502059, EPI_ISL_18503696, EPI_ISL_18503846, EPI_ISL_18510036, EPI_ISL_18510038, EPI_ISL_18511034, EPI_ISL_18511095, EPI_ISL_18511104, EPI_ISL_18511108, EPI_ISL_18511172, EPI_ISL_18511241, EPI_ISL_18511380, EPI_ISL_18511416, EPI_ISL_18511461, EPI_ISL_18511469, EPI_ISL_18511480, EPI_ISL_18511508, EPI_ISL_18511521, EPI_ISL_18511532, EPI_ISL_18511557, EPI_ISL_18511580, EPI_ISL_18511661, EPI_ISL_18511670, EPI_ISL_18535606, EPI_ISL_18535663, EPI_ISL_18535697, EPI_ISL_18539307, EPI_ISL_18539369, EPI_ISL_18539422, EPI_ISL_18539428, EPI_ISL_18539447, EPI_ISL_18539483, EPI_ISL_18539547, EPI_ISL_18545014, EPI_ISL_18564392, EPI_ISL_18564436, EPI_ISL_18564462-18564463, EPI_ISL_18564564, EPI_ISL_18564669, EPI_ISL_18564752, EPI_ISL_18564926, EPI_ISL_18565014, EPI_ISL_18565195, EPI_ISL_18568493, EPI_ISL_18570360

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_21541_c2c6a0.json?label=id:node_3526922

Trivia:

• Only 3 seqs preceeding this branch without S:L455F: France/GES-IPP16513/2023|EPI_ISL_18109814|2023-07-241, Australia/QLD0x0138F8/2023|EPI_ISL_18324553|2023-09-12, and SouthKorea/KDCA_270758/2023|EPI_ISL_18503707|2023-10-12` ⚠️ so please check potential dropout/misplacement.

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---

Branch 64

Defining Mutations: EG.5.1.6 > C28236T(ORF8:R115C) > C16092T > C10969T > G526T(ORF1a:E87D) > C23380T(S:N606) > A12485G(ORF1a:I4074V) > T877C, A15270T(ORF1b:E601D), G22927T(S:L455F)
Query: G526T, A15270T, G22927T
Earliest seq: 2023-10-08 (EPI_ISL_18404805, New Brunswick, Canada)
Latest seq: 2023-10-15 (EPI_ISL_18427247, Ontario, Canada)
Sampled Countries: Canada (4: ON/3; NB)

Genomes:

EPI_ISL_18404805, EPI_ISL_18426514, EPI_ISL_18426586, EPI_ISL_18427247

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_21e1_9e19a0.json?label=id:node_3437762

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---

Branch 65

Defining Mutations: EG.5.1 > A3210G(ORF1a:D982G) > G26888A > G26227T(_TRS of Envelope_), C28720T(_TRS of ORF9c_) > T8909C> G22927T(S:L455F)
Query: A3210G, T8909C, G22927T
Earliest seq: 2023-09-07 (EPI_ISL_18419405, Sicily, Italy)
Latest seq: 2023-09-18 (EPI_ISL_18329969, Denmark)
Sampled Countries: Italy (13), Denmark (1)

Genomes:

EPI_ISL_18258788-18258789, EPI_ISL_18329969, EPI_ISL_18419405, EPI_ISL_18419417, EPI_ISL_18419442, EPI_ISL_18419446, EPI_ISL_18419449, EPI_ISL_18419451, EPI_ISL_18419459, EPI_ISL_18419472, EPI_ISL_18419474, EPI_ISL_18419478, EPI_ISL_18419484

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b9a_9e23b0.json?label=id:node_3428133

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---

Branch 66

Defining Mutations: EG.5.1.1 > C11779T > C12525T(ORF1a:T4087I) > G22927T(S:L455F)
Query: C11779T, C12525T, G22927T
Earliest seq: 2023-08-27 (EPI_ISL_18360191, England)
Latest seq: 2023-10-09 (EPI_ISL_18421921, Belgium)
Sampled Countries: South Korea (4), Canada (3: BC), Belgium (1), China (1: SH), New Zealand (1), Singapore (1), UK (1: EN)

Genomes:

EPI_ISL_18227053, EPI_ISL_18292157, EPI_ISL_18355538, EPI_ISL_18360191, EPI_ISL_18381927, EPI_ISL_18382266, EPI_ISL_18397328, EPI_ISL_18408737, EPI_ISL_18421921, EPI_ISL_18430928, EPI_ISL_18431490, EPI_ISL_18431860

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_34aaf_9ea630.json?label=id:node_3493682

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---

Branch 67

Defining Mutations: EG.5.1.1 > C25613T(ORF3a:S74F) > G22927C(S:L455F)
Query: C6541T, G22927C, C25613T, -C26681T, -G26840A
Earliest seq: 2023-10-12 (EPI_ISL_18428810, Singapore)
Latest seq: 2023-10-16 (EPI_ISL_18428772, Singapore)
Sampled Countries: Singapore (5)

Genomes:

EPI_ISL_18428766, EPI_ISL_18428769, EPI_ISL_18428771-18428772, EPI_ISL_18428810

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_41fd2_a0fe0.json?label=id:node_3487648

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---

Branch 68

Defining Mutations: EG.5.1.1 > G16710A > G22927T(S:L455F)
Query: G16710A, G13627A, G22927T, -G28904T
Earliest seq: 2023-09-25 (EPI_ISL_18355035, Singapore)
Latest seq: 2023-10-18 (EPI_ISL_18428623, Singapore)
Sampled Countries: Singapore (11)

Genomes:

EPI_ISL_18355035, EPI_ISL_18361806, EPI_ISL_18361914, EPI_ISL_18361935, EPI_ISL_18362103, EPI_ISL_18397258, EPI_ISL_18397453, EPI_ISL_18428554, EPI_ISL_18428623, EPI_ISL_18428638, EPI_ISL_18428659

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_c933_9f2590.json?label=id:node_3474466

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---

Branch 69

Defining Mutations: EG.5.1.1 > G1085T(ORF1a:V274L) > G1535A(ORF1a:V424I), G22927T(S:L455F)
Query: G1085T, G13627A, G22927T, -A11000G, -C29375T,
Earliest seq: 2023-10-02 (EPI_ISL_18361916, Singapore)
Latest seq: 2023-10-16 (EPI_ISL_18428661, Singapore)
Sampled Countries: Singapore (5)

Genomes:

EPI_ISL_18361916, EPI_ISL_18397376, EPI_ISL_18397599, EPI_ISL_18428562, EPI_ISL_18428661

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_18f8d_9f5e00.json?label=id:node_3486178

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---

Branch 70

Defining Mutations: EG.5.1.1 > T21748C(S:V62) > A16225G(ORF1b:T920A), T25036C > G22927C(S:L455F)
Query: A16225G, T21748C, G22927C
Earliest seq: 2023-08-10 (EPI_ISL_18438105, Beijing, China)
Latest seq: 2023-10-09 (EPI_ISL_18426675, Montana, USA)
Sampled Countries: China (13: BJ/11; HB/1; HL/1), Netherlands (2), Singapore (1), USA (1: MT)

Genomes:

EPI_ISL_18254239, EPI_ISL_18331365, EPI_ISL_18362093, EPI_ISL_18384410, EPI_ISL_18386767, EPI_ISL_18426675, EPI_ISL_18438074-18438075, EPI_ISL_18438082, EPI_ISL_18438103, EPI_ISL_18438105, EPI_ISL_18438108, EPI_ISL_18438114, EPI_ISL_18438136, EPI_ISL_18438177-18438178, EPI_ISL_18438235

UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4eb1c_b77620.json?label=id:node_3464035

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---

Branch 71

Defining Mutations: EG.5.1.1 > C6638T(ORF1a:H2125Y) > G22927T(S:L455F)
Query: C6638T, G13627A, G22927T, -C14889T
Earliest seq: 2023-09-11 (EPI_ISL_18313157, Hubei, China)
Latest seq: 2023-10-09 (EPI_ISL_18438431, Hubei, China)
Sampled Countries: China (5: HB), South Korea (1)

Genomes:

EPI_ISL_18313157-18313158, EPI_ISL_18382135, EPI_ISL_18438389, EPI_ISL_18438415, EPI_ISL_18438431

UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_b5b8_b7aee0.json?f_userOrOld=uploaded%20sample&label=id:node_3482675

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---

Branch 72

Defining Mutations: EG.5.1.1 > C11779T > G10261A > C9611T(ORF1a:L3116F), C18348T > G22927T(S:L455F)
Query: C9611T, C11779T, G22927T
Earliest seq: 2023-09-06 (EPI_ISL_18313115, Hubei, China)
Latest seq: 2023-10-09 (EPI_ISL_18406324, Vienna, Austria)
Sampled Countries: South Korea (6), Singapore (2), Austria (1), China (1: HB)

Genomes:

EPI_ISL_18313115, EPI_ISL_18355007, EPI_ISL_18355538, EPI_ISL_18376812, EPI_ISL_18381927, EPI_ISL_18382266, EPI_ISL_18406324, EPI_ISL_18408737, EPI_ISL_18435658, EPI_ISL_18439298

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b3db_cbcfb0.json?label=id:node_3497922

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---

Branch 73

Defining Mutations: EG.5.1.1 > C19170T > G22927T(S:L455F)
Query: G13627A, C19170T, G22927T, -C1909T, -C3736T, -C5031T, -C7504T, -A18153G
Earliest seq: 2023-08-31 (EPI_ISL_18438072, Beijing)
Latest seq: 2023-10-14 (EPI_ISL_18442753, Sichuan)
Sampled Countries: China (6: SC/3; BJ/1; HB/1; SC/1), South Korea (1)

Genomes:

EPI_ISL_18320875, EPI_ISL_18360251, EPI_ISL_18360272, EPI_ISL_18438072, EPI_ISL_18438352, EPI_ISL_18439041, EPI_ISL_18442753

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_26c5d_cced10.json?label=id:node_3466266

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---

Branch 74

Defining Mutations: EG.5.1.3 > A28032G(ORF8:I47V) > A1047C(ORF1a:K261T) > C3608A(ORF1a:L1115I), C18261T, G22927T(S:L455F)
Query: A1047C, C1889T, G22927T
Earliest seq: 2023-09-11 (EPI_ISL_18314192, France)
Latest seq: 2023-10-12 (EPI_ISL_18441710, Netherlands)
Sampled Countries: Belgium (2), France (2), Netherlands (1)

Genomes:

EPI_ISL_18314192, EPI_ISL_18337916, EPI_ISL_18338399, EPI_ISL_18399343, EPI_ISL_18441710

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_38cb6_cd6010.json?f_userOrOld=uploaded%20sample&label=id:node_3458506

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---

Branch 75

Defining Mutations: EG.5.1.1 > C29253T(N:S327L) > G22927T(S:L455F)
Query: G13627A, G22927T, C29253T, -G1067T, -C2110T, -A2730C
Earliest seq: 2023-08-17 (EPI_ISL_18389043, Xinjiang, China)
Latest seq: 2023-10-24 (EPI_ISL_18445150, Singapore, travel history: Malaysia)
Sampled Countries: Denmark (3), China (2: XJ), Singapore (2)

Genomes:

EPI_ISL_18320957, EPI_ISL_18377581, EPI_ISL_18377610, EPI_ISL_18389043, EPI_ISL_18397195, EPI_ISL_18442952, EPI_ISL_18445150

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1c2e8_a8650.json?label=id:node_3492354

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---

Branch 76

Defining Mutations: EG.5.1.1 > T26609C > C5907T(ORF1a:T1881I), T17454A > G22927T(S:L455F)
Query: G13627A, T17454A, G22927T
Earliest seq: 2023-09-20 (EPI_ISL_18445852, Castilla y León, Spain)
Latest seq: 2023-10-13 (EPI_ISL_18402965, Donostia-San Sebastián, Spain)
Sampled Countries: Spain (9)

Genomes:

EPI_ISL_18402961, EPI_ISL_18402965, EPI_ISL_18419672, EPI_ISL_18421286, EPI_ISL_18445852, EPI_ISL_18445906, EPI_ISL_18445934, EPI_ISL_18446071-18446072

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b023_af570.json?label=id:node_3474073

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---

Branch 77

Transferred to main repo

Transferred to cov-lineages/pango-designation#2401

Defining Mutations: EG.5.1.6 > C925T, C27161T > C14919A > G14559A > G22927T(S:L455F)
Query: C5835T, G14559A, G22927T
Earliest seq: 2023-09-11 (EPI_ISL_18381025, British Columbia, Canada)
Latest seq: 2023-11-21 (EPI_ISL_18572342, Israel)
Sampled Countries: Canada (59: AB/25; BC/25; SK/7; ON/1; QC/1), Israel (5), USA (3: NY/2; CA), Finland (2), Sweden (2), Austria (1), Ireland (1), UK (1: EN)

Genomes:

EPI_ISL_18313726, EPI_ISL_18374552, EPI_ISL_18381025, EPI_ISL_18381642, EPI_ISL_18399548, EPI_ISL_18405416, EPI_ISL_18429724, EPI_ISL_18431316, EPI_ISL_18431484, EPI_ISL_18431577, EPI_ISL_18448820, EPI_ISL_18449315, EPI_ISL_18451058, EPI_ISL_18452675, EPI_ISL_18453011, EPI_ISL_18453157, EPI_ISL_18456002, EPI_ISL_18456201, EPI_ISL_18493062, EPI_ISL_18499142, EPI_ISL_18501414, EPI_ISL_18501469, EPI_ISL_18501539, EPI_ISL_18501675, EPI_ISL_18512520, EPI_ISL_18512575, EPI_ISL_18512726, EPI_ISL_18512904, EPI_ISL_18512975, EPI_ISL_18513012, EPI_ISL_18516832, EPI_ISL_18516837, EPI_ISL_18517029, EPI_ISL_18517372, EPI_ISL_18517374-18517375, EPI_ISL_18517477, EPI_ISL_18517505, EPI_ISL_18526773, EPI_ISL_18526937-18526938, EPI_ISL_18526942, EPI_ISL_18526999, EPI_ISL_18527195, EPI_ISL_18532450-18532451, EPI_ISL_18533407, EPI_ISL_18538515, EPI_ISL_18538528, EPI_ISL_18538535, EPI_ISL_18538740, EPI_ISL_18538774, EPI_ISL_18538986, EPI_ISL_18541507-18541508, EPI_ISL_18547665, EPI_ISL_18552699, EPI_ISL_18553923, EPI_ISL_18553948, EPI_ISL_18558921, EPI_ISL_18560813, EPI_ISL_18563933, EPI_ISL_18563975, EPI_ISL_18563992, EPI_ISL_18564064, EPI_ISL_18564086, EPI_ISL_18564088, EPI_ISL_18564119, EPI_ISL_18564154, EPI_ISL_18564182, EPI_ISL_18564194, EPI_ISL_18572342, EPI_ISL_18572380, EPI_ISL_18572384

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2d8f9_c314c0.json?label=id:node_3469419

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---

Branch 78

Defining Mutations: EG.5.1.1 > C18395T(ORF1b:A1643V) > G22927T(S:L455F)
Query: C6541T, C18395T, G22927T
Earliest seq: 2023-08-16 (EPI_ISL_18146006, Hubei, China)
Latest seq: 2023-10-15 (EPI_ISL_18453170, British Columbia, Canada)
Sampled Countries: Canada (7: BC), China (6: FJ/3; HB/2; GS/1), Japan (2)

Genomes:

EPI_ISL_18146006, EPI_ISL_18330196, EPI_ISL_18330296, EPI_ISL_18330311, EPI_ISL_18376315, EPI_ISL_18405472, EPI_ISL_18409239, EPI_ISL_18425055, EPI_ISL_18452695, EPI_ISL_18452923, EPI_ISL_18452979, EPI_ISL_18453059, EPI_ISL_18453168, EPI_ISL_18453170, EPI_ISL_18454186

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3e744_1f9880.json?label=id:node_3476703

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---

Branch 79

Defining Mutations: EG.5.1.1 > T6736C > T23287C(S:A575) > C22075T(S:V171) > C8389T, A16668G, C17474T(ORF1b:T1336I), G22927T(S:L455F), G26416T(E:V58F)
Query: T6736C, G13627A, G22927T
Earliest seq: 2023-08-17 (EPI_ISL_18241549, Yunnan)
Latest seq: 2023-10-14 (EPI_ISL_18454380, Yunnan)
Sampled Countries: China (12: YN)

Genomes:

EPI_ISL_18241549, EPI_ISL_18384462, EPI_ISL_18384468, EPI_ISL_18384485, EPI_ISL_18384488, EPI_ISL_18384501, EPI_ISL_18384510, EPI_ISL_18384514, EPI_ISL_18384522, EPI_ISL_18454363, EPI_ISL_18454380, EPI_ISL_18454383

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6626_1fc330.json?label=id:node_3476751

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---

Branch 80

Defining Mutations: EG.5.1.1 > C8146T > G2035A, G6373T(ORF1a:M2036I), G22927T(S:L455F)
Query: C8146T, G13627A, G22927T, -C27557T
Earliest seq: 2023-08-28 (EPI_ISL_18289791, Anhui, China)
Latest seq: 2023-10-07 (EPI_ISL_18454332, Yunnan, China)
Sampled Countries: South Korea (6), China (3: AH, HB, YN)

Genomes:

EPI_ISL_18289791, EPI_ISL_18376503, EPI_ISL_18382123, EPI_ISL_18454332, EPI_ISL_18460781, EPI_ISL_18460783, EPI_ISL_18460821-18460822, EPI_ISL_18460834

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1d9d0_762270.json?label=id:node_3494057

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---

Branch 81

Defining Mutations: EG.5.1.1 > C2857T > G22927T(S:L455F)
Query: C2857T, G13627A, G22927T, -C5031T, -T17475C
Earliest seq: 2023-09-14 (EPI_ISL_18388886, Hubei, China)
Latest seq: 2023-10-13 (EPI_ISL_18461038, South Korea)
Sampled Countries: China (7: TW/5; HB; SC), Belgium (1), Japan (1), South Korea (1)

Genomes:

EPI_ISL_18388886, EPI_ISL_18399792, EPI_ISL_18427833, EPI_ISL_18432501, EPI_ISL_18438519, EPI_ISL_18440359, EPI_ISL_18440668, EPI_ISL_18461038, EPI_ISL_18461507, EPI_ISL_18461514

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_5f66_766bb0.json?label=id:node_3485431

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---

Branch 82

Defining Mutations: EG.5.1.1 > T16494C, T22307C > G22927C(S:L455F)
Query: G13627A, T16494C, G22927C
Earliest seq: 2023-09-12 (EPI_ISL_18376962, Singapore, Travel History: Malaysia)
Latest seq: 2023-10-09 (EPI_ISL_18461687, New South Wales, Australia)
Sampled Countries: Singapore (7), China (2: HL), Australia (1: NSW)

Genomes:

EPI_ISL_18355070, EPI_ISL_18355078, EPI_ISL_18355084, EPI_ISL_18355119, EPI_ISL_18376962, EPI_ISL_18397262, EPI_ISL_18397335, EPI_ISL_18461687, EPI_ISL_18465032, EPI_ISL_18465036

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice14_genome_1351a_73edc0.json?label=id:node_3508527

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---

Branch 83

Defining Mutations: EG.5.1.1 > C29358T(N:T362I) > T23803C(S:T747T) > C842T(ORF1a:P193S), C15141T, T16743C, C22450T(S:L296L), G22927T(S:L455F), C24442T(S:N960N), C25916T(ORF3a:T175I), C28232T
Query: G22927T, T23803C, C29358T
Earliest seq: 2023-09-11 (EPI_ISL_18384535, Yunnan, China)
Latest seq: 2023-10-31 (EPI_ISL_18473684, Singapore)
Sampled Countries: Singapore (11), France (2), Australia (1: NSW), Canada (1: ON), China (1: YN), Germany (1)

Genomes:

EPI_ISL_18327437, EPI_ISL_18384535, EPI_ISL_18423274, EPI_ISL_18428663, EPI_ISL_18455125, EPI_ISL_18461961, EPI_ISL_18472175, EPI_ISL_18473491, EPI_ISL_18473552, EPI_ISL_18473557, EPI_ISL_18473565, EPI_ISL_18473584, EPI_ISL_18473600, EPI_ISL_18473608, EPI_ISL_18473617, EPI_ISL_18473635, EPI_ISL_18473684

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_33d1_b55240.json?label=id:node_3483621

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---

Branch 84

Defining Mutations: HK.19 > C2455T > G22927T(S:L455F), C23533T(S:N657)
Query: C2455T, C22033A, G22927T, -G25606A
Earliest seq: 2023-09-20 (EPI_ISL_18327665, SEA airport, travel history: China)
Latest seq: 2023-10-06 (EPI_ISL_18454355, Yunnan China)
Sampled Countries: China (7)

Genomes:

EPI_ISL_18327626, EPI_ISL_18327665, EPI_ISL_18454355, EPI_ISL_18475173-18475174, EPI_ISL_18481030, EPI_ISL_18481032

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_14b93_98620.json?label=id:node_3515333

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---

Branch 85: Mostly with ORF6:N34K/C27303A

Defining Mutations: EG.5.1.1 > C7390T > G22927T(S:L455F)
Query: C7390T, G13627A, G22927T
Earliest seq: 2023-08-31 (EPI_ISL_18312335, South Korea)
Latest seq: 2023-10-30 (EPI_ISL_18494555, Denmark)
Sampled Countries: China (7: SC/3; HB/2; XJ/2), South Korea (4), Australia (2), Denmark (1), Spain (1)

Genomes:

EPI_ISL_18284798, EPI_ISL_18312335, EPI_ISL_18312767, EPI_ISL_18313150, EPI_ISL_18330217, EPI_ISL_18355417, EPI_ISL_18361365, EPI_ISL_18376681, EPI_ISL_18402975, EPI_ISL_18447796, EPI_ISL_18461975, EPI_ISL_18475119, EPI_ISL_18481228, EPI_ISL_18494555, EPI_ISL_18495106

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_25e0e_b6750.json?label=id:node_3492892

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---

Branch 86: many with S:N17T/A21612C

Defining Mutations: EG.5.1.1 > G25855T(ORF3a:D155Y) > G22927T(S:L455F)
Query: A21612C, G22927T, G25855T
Earliest seq: 2023-08-31 (EPI_ISL_18284769, Sichuan, China)
Latest seq: 2023-10-24 (EPI_ISL_18458002, Kuala Lumpur, Malaysia)
Sampled Countries: China (9: YN/6; SC/3), Malaysia (3), Japan (1)

Genomes:

EPI_ISL_18284769, EPI_ISL_18324153, EPI_ISL_18324208, EPI_ISL_18324235, EPI_ISL_18384546, EPI_ISL_18419659, EPI_ISL_18419662, EPI_ISL_18454181, EPI_ISL_18458002, EPI_ISL_18475350, EPI_ISL_18481259, EPI_ISL_18488097, EPI_ISL_18488110

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_372c6_bbb70.json?label=id:node_3488769

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---

Branch 87

Defining Mutations: EG.5.1 > C15960T > C16260T > G22927T(S:L455F), C24771T(S:A1070V), C25658T(ORF3a:T89I)
Query: C15960T, C16260T, A18492G, G22927T
Earliest seq: 2023-09-01 (EPI_ISL_18384575, Yunnan, China)
Latest seq: 2023-10-27 (EPI_ISL_18493260, Alberta, Canada)
Sampled Countries: China (5: SH/3; SX; YN), Canada (3: AB), South Korea (2)

Genomes:

EPI_ISL_18384575, EPI_ISL_18426071, EPI_ISL_18436785, EPI_ISL_18460945-18460946, EPI_ISL_18475132, EPI_ISL_18481223, EPI_ISL_18493260, EPI_ISL_18495087, EPI_ISL_18495466

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice95_genome_43bfd_a83e0.json?label=id:node_3517572

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---

Branch 88

⚠️ sibling to Branch 32 please check potential misplacement

Defining Mutations: EG.5.1.1 > T4579A > A4576T > G22927T(S:L455F)
Query: A4576T, G13627A, G22927T
Earliest seq: 2023-08-18 (EPI_ISL_18239385, South Korea)
Latest seq: 2023-10-30 (EPI_ISL_18520721, Saitama, Japan)
Sampled Countries: South Korea (39), Japan (2), USA (2, ex. Japan), China (1, ex. S. Korea)

Genomes:

EPI_ISL_18239385, EPI_ISL_18313064, EPI_ISL_18320761, EPI_ISL_18354110, EPI_ISL_18355244, EPI_ISL_18355256, EPI_ISL_18355270, EPI_ISL_18355539, EPI_ISL_18368435, EPI_ISL_18368571, EPI_ISL_18382929, EPI_ISL_18408987, EPI_ISL_18411143, EPI_ISL_18432570, EPI_ISL_18439431, EPI_ISL_18460891, EPI_ISL_18460981, EPI_ISL_18461196, EPI_ISL_18503870, EPI_ISL_18510989, EPI_ISL_18511173, EPI_ISL_18511218, EPI_ISL_18511236, EPI_ISL_18511259, EPI_ISL_18511379, EPI_ISL_18511388, EPI_ISL_18511531, EPI_ISL_18511534, EPI_ISL_18511636, EPI_ISL_18511644, EPI_ISL_18511659, EPI_ISL_18511666, EPI_ISL_18511675, EPI_ISL_18511683, EPI_ISL_18520721, EPI_ISL_18535535, EPI_ISL_18539100, EPI_ISL_18539189, EPI_ISL_18539430, EPI_ISL_18539531, EPI_ISL_18539554, EPI_ISL_18539681, EPI_ISL_18539751, EPI_ISL_18539824

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2459b_3b16b0.json?f_userOrOld=uploaded%20sample&label=id:node_3488766

view from EG.5.1.1 > T4579A branch, sibling to Branch 32?

details

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---

Branch 89

Defining Mutations: EG.5.1.1 > C27406T(ORF7a:L5F) > G22927T(S:L455F)
Query: C6541T, G13627A , G22927T, C27406T
Earliest seq: 2023-08-11 (EPI_ISL_18145981, Hubei, China)
Latest seq: 2023-10-18 (EPI_ISL_18487967, Henan, China)
Sampled Countries: China (6: HA/2; HB/2; SC/2; BJ), South Korea (1)

Genomes:

EPI_ISL_18145981, EPI_ISL_18320871, EPI_ISL_18360327, EPI_ISL_18382216, EPI_ISL_18438321, EPI_ISL_18485262, EPI_ISL_18487967

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice16_genome_15d09_3ad150.json?label=id:node_3506957

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---

Branch 90

Defining Mutations: EG.5.1.1 > C13724T(ORF1a:A4487V), A25636T(ORF3a:N82Y) > T10750C, G22927T(S:L455F)
Query: G13627A, C13724T, G22927T, -C5031T
Earliest seq: 2023-08-22 (EPI_ISL_18272130, South Korea)
Latest seq: 2023-10-19 (EPI_ISL_18451971, SEA airport, travel history: South Korea)
Sampled Countries: South Korea (6), USA (2: ex. South Korea)

Genomes:

EPI_ISL_18272130, EPI_ISL_18376686, EPI_ISL_18376765, EPI_ISL_18451971, EPI_ISL_18460748, EPI_ISL_18488908-18488909, EPI_ISL_18492194

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_42b73_3bb260.json?label=id:node_3520099

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---

Branch 91

Defining Mutations: EG.5.1.1 > C22987T(S:A475A) > G22927T(S:L455F) > G19419A, G21974C(S:D138H)
Query: G13627A, G19419A, G21974C
Earliest seq: 2023-08-24 (EPI_ISL_18284675, Beijing, China)
Latest seq: 2023-11-04 (EPI_ISL_18486471, Dublin, Ireland)
Sampled Countries: China (6: SC/4; BJ; YN), Ireland (2), Greece (1)

Genomes:

EPI_ISL_18284675, EPI_ISL_18409255, EPI_ISL_18409302, EPI_ISL_18429520, EPI_ISL_18438109, EPI_ISL_18442759, EPI_ISL_18454352, EPI_ISL_18486471, EPI_ISL_18490986

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_6555_3bdc60.json?label=id:node_3502929

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---

Branch 92

Defining Mutations: EG.5.1.1 > C629T(ORF1a:L122F) > A1168G > C22987T(S:A475A) > T595C, C20148T, G22927T(S:L455F)
Query: A1168G, G22927T, C22987T
Earliest seq: 2023-09-08 (EPI_ISL_18330247, Hubei, China)
Latest seq: 2023-10-30 (EPI_ISL_18539359, South Korea)
Sampled Countries: South Korea (5), Japan (2), China (1, HB), USA (1: CA)

Genomes:

EPI_ISL_18330247, EPI_ISL_18435755, EPI_ISL_18443954, EPI_ISL_18446528, EPI_ISL_18502023, EPI_ISL_18503555, EPI_ISL_18511230, EPI_ISL_18520709, EPI_ISL_18539359

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6555_3bdc50.json?label=id:node_3498262

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---

Branch 93

Defining Mutations: EG.5.1 > G26051T(ORF3a:S220I) > G9269A(ORF1a:G3002S) > T1216C, A9034G, A12121T, A12519G(ORF1a:D4085G), G22927T(S:L455F)
Query: G9269A, G22927T, G26051T
Earliest seq: 2023-10-21 (EPI_ISL_18453659, South Australia)
Latest seq: 2023-11-05 (EPI_ISL_18524643, Queensland)
Sampled Countries: Australia (7: QLD/6; SA)

Genomes:

EPI_ISL_18453659, EPI_ISL_18489126, EPI_ISL_18501702, EPI_ISL_18501758, EPI_ISL_18524643, EPI_ISL_18524655, EPI_ISL_18524668

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice52_genome_199a5_39a640.json?label=id:node_3459700

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---

Branch 94

a sub-branch of #1074 proposed by @aviczhl2

Defining Mutations: EG.5.1.13 > G670T_rev(ORF1a:R135S_rev) > T28861C > G8889A(ORF1a:R2875H) > C13381T > G22424T(S:A288S) > C25047T(S:P1162L) > G25855T(ORF3a:D155Y) > G22927T(S:L455F)
Query: G8889A, C13381T, G22927T
Earliest seq: 2023-10-10 (EPI_ISL_18486858, Temuco, Chile)
Latest seq: 2023-11-26 (EPI_ISL_18582164, Ontario, Canada)
Sampled Countries: Canada (14: ON/13; NS), Chile (3), USA (3: NY/2; PA)

Genomes:

EPI_ISL_18483588, EPI_ISL_18483657, EPI_ISL_18486858, EPI_ISL_18523437, EPI_ISL_18534577, EPI_ISL_18548162, EPI_ISL_18581551-18581554, EPI_ISL_18581688, EPI_ISL_18581705, EPI_ISL_18582159, EPI_ISL_18582162, EPI_ISL_18582164, EPI_ISL_18582914, EPI_ISL_18582921-18582922, EPI_ISL_18582983, EPI_ISL_18602138

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_7d45_55cdd0.json?label=id:node_3474267

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---

Singlets

• Guangdong/GDCDC_GZ_0568/2023|EPI_ISL_18033894|2023-06-28
  EG.5.1 > G1069A > C12005T > C9803T, A13707G, C14809T(ORF1b:R448C), C18348T, G22927C(S:L455F) [Query: C14809T, C18348T, G22927C, 07/24]
• Japan/PG-568093/2023|EPI_ISL_18279075|2023-09-05
  EG.5.1 > T15198A > C1191A(ORF1a:P309Q), A24999C(S:D1146A), A27642G > A21137G(ORF1a:K2557R) > T25851C > C6120T(ORF1a:S1952L), T13030C, G22927T(S:L455F) [Query: C1191A, T15198A, G22927T, 09/19]
• Canada/QC-L00671579001/2023|EPI_ISL_18478213|2023-10-30
  EG.5.1 > T15198A > G22317C(S:G252A) > C3267T(ORF1a:T1001I), T8421C(ORF1a:M2719T), G22927T(S:L455F), C22949T(S:P463S) [Query: T15198A, G22317C, G22927T, 11/08]
• Sichuan/NJCDC-0906-7/2023|EPI_ISL_18261486|2023-08-30
  EG.5.1.1 > A3069G(ORF1a:D935G) > C367T, A1197C(ORF1a:E311A), A6925G, G22927T(S:L455F), T27212C(ORF6:L4P) [Query: A3069G, C6541T, G22927T, 09/14]
• Shanghai/SCDC-HP-XG-0731-1/2023|EPI_ISL_18138078|2023-07-31
  EG.5.1.1 > G3242A(ORF1a:G993S) > G1595A(ORF1a:E444K), C6628T, G22927T(S:L455F), A27721G(ORF7a:I110V) [Query:G3242A, C6541T, G22927T, 08/25]
• Shanghai/SCDC-XG09-13670/2023|EPI_ISL_18285000|2023-09-07
  EG.5.1.1 > C3653T(ORF1a:L1130F) > G410T(ORF1a:G49C), C1498T, C2227A, C6395T, C11563T, G22927C(S:L455F), G27604T(ORF7a:V71L) [Query: C3653T, C6541T, G22927C, 09/19]
• South_Korea/KDCA262399/2023|EPI_ISL_18271956|2023-08-22
  EG.5.1.1 > C7764T(ORF1a:S2500F) > T5448C(ORF1a:V1728A), G22927T(S:L455F), C25539T [Query: C7764T, G13627A, G22927T, 09/18]
• Japan/TKYnat15208/2023|EPI_ISL_18285185|2023-09-01
  EG.5.1.1 > C13730T(ORF1b:A88V) > T12727C, G22927T(S:L455F) [Query: C6541T, C13730T, G22927T, -C11779T, 09/20]
• Australia/QLD0x01374B/2023|EPI_ISL_18122559|2023-08-09 FLIP+346I+478R
  EG.5.1.1 > C16830T, C18348T, G22599T(S:R346I), G22927T(S:L455F), C22995G(S:T478R), T23176C [Query: C18348T, G22599T, G22927T, 08/22]
• South_Korea/KDCA262306/2023|EPI_ISL_18271874|2023-08-15
  EG.5.1.1 > C21588T(S:P9L) > G22927T(S:L455F), C28770T(N:T166I) [Query: G13627A, C21588T, G22927T, 09/18]
• Anhui/HCDC-176/2023|EPI_ISL_18289771|2023-09-04
  EG.5.1.1 > C24130T > G9177T(ORF1a:G2971V), T28705C > A10863C(ORF1a:E3533A), G22927T(S:L455F), G25522A(ORF3a:G44R), G27933A(ORF8:A14T) [Query: G9177T, G22927T, C24130T, 09/20]
• GZSCDC-GY07-14/2023|EPI_ISL_18074217|2023-07-18
  EG.5.1.1 > G24926T(S:V1122L) > C1960T, C12076T, T22926C(S:L455S), T27428A(ORF7a:L12H) [Query: G13627A, T22926C, G24926T, 08/07]
• England/CLIMB-CM7YRMOM/2023|EPI_ISL_18227115|2023-08-22
  EG.5.1.3 > A4340G(ORF1a:I1359V) > A2163G(ORF1a:E633G) > C23185T > T11932G, T14022C, T22926C(S:L455S) [Query: A2163G, A4340G, T22926C, 09/06]
• Sweden/W-49492298L6/2023|EPI_ISL_18249322|2023-08-23
  EG.5.1.3 > A10703C > C1314T(ORF1a:T350I), C9118T > G4907A(ORF1a:G1548S) > C6936G(ORF1a:S2224C), C18959T(ORF1b:A1831V), G22094T(S:D178Y), T22926C(S:L455S), G27160A(M:S213N) [Query: G4907A, C9118T, T22926C, 09/12]
• Spain/CT-HUGTiP-B1R154/2023|EPI_ISL_18281164|2023-09-13
  EG.5.1.3 > T14568C > T7651C, G27962T(ORF8:Q23H) > T4579A, C19017T, G22927T(S:L455F) [Query: C1889T, T7651C, G22927T, 09/19]
• Canada/ON-PHL-23-30576/2023|EPI_ISL_18277805|2023-09-11
  EG.5.1.4 > C26111T(ORF3a:P240L) > C21622A > C9430T > C20133T > G22927T(S:L455F) [Query: C9430T, C20133T, G22927T, 09/18]
• USA/NY-URMC-N6S1J239-1/2023|EPI_ISL_18247548|2023-08-27
  EG.5.1.4 > C26111T(ORF3:P240L) > G25563T(ORF3a:Q57H) > C1427T(ORF1a:H388Y) > G25494A > A21759G(S:H66R), G22927T(S:L455F) [Query: G22927T, G25494A, G25563T, 09/11]
• USA/MD-HP49490-PIDPVKAURD/2023|EPI_ISL_18432449|2023
  HV.1 (EG.5.1.6.1) > C2695T > C26964T(M:H148Y) > C27600T > C14376T > A5424G(ORF1a:K1720R) > C4752T(ORF1a:T1496I), G22927T(S:L455F) [Query: A5424G, C14376T, G22927T, 10/24]
• USA/OH-ODH-SC3032871/2023|EPI_ISL_18422243|2023-09-29
  HV.1 > A5021G(ORF1a:M1586V) > C6117T(ORF1a:A1951V), G22927T(S:L455F), C29028T(N:A252V) [Query: A5021G, C5835T, G22927T, 10/23]

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Doublets

• USA/NY-NYULH-16857/2023|EPI_ISL_18440726|2023-10-19 and USA/NY-CDC-VSX-A357619/2023|EPI_ISL_18534359|2023-10-26
  EG.5.1 > C2147T(ORF1a:L628F), T6115C > G18498T(ORF1b:M1677I) > C21811T, A22911T(S:N450I), G22927T(S:L455F) [Query: C2147T, G18498T, G22927T, 2 seqs, 11/22] (Another 3 seqs not on GISAID yet
• Shanghai/SCDC-MH200506/2023|EPI_ISL_18114819|2023-07-30 and Liaoning/LNCDC-360-1/2023|EPI_ISL_18330279|2023-09-12
  EG.5.1 > C6706T > C7482T(ORF1a:S2406L) > C2507T(ORF1a:P748S), C4543T, C8251T, G22927T(S:L455F) [Query: C6706T, C7482T, G22927T, 2 seqs, 09/30]
• Shanghai/SCDC-804/2023|EPI_ISL_18268355|2023-09-02 and Shanghai/SCDC-831/2023|EPI_ISL_18284896|2023-09-09
  EG.5.1.1 > A3021G(ORF1a:H919R), A21493C > C1913T(ORF1a:R550C), C4965T(ORF1a:T1567I), C17977T(ORF1b:L1504F), A19237C, G22927T(S:L455F), C27393T, C28791T(N:A173V) [Query: A3021G, A21493C, G22927T, 2 seqs, 09/19]
• Taiwan/CDC-W30906/2023|EPI_ISL_18164789|2023-07-29 and USA/HI-H2324424/2023|EPI_ISL_18283168|2023-08-29
  EG.5.1.1 > C6317T(ORF1a:P2018S) > C1567T, C8152T, C16192T(ORF1b:P909S), G22927C(S:L455F), G25606A(ORF3a:A72T) [Query: C6317T, C6541T, G22927C, 2 seqs, 09/19]
• Sichuan/YACDC-XGcx133/2023|EPI_ISL_18232742|2023-08-14 and Sichuan/YACDC-XGCX151/2023|EPI_ISL_18304270|2023-09-18
  EG.5.1.1 > C6327T(ORF1a:T2021I) > C1684A, A17008G(ORF1b:I1181V), G22927C(S:L455F), G27217T(ORF6:D6Y) [Query: C6327T, C6541T, G22927C, 2 seqs, 09/25]
• Hubei/HCDC-ES2799/2023|EPI_ISL_18254184|2023-08-30 and England/CLIMB-CM7YEDUX/2023|EPI_ISL_18274069|2023-09-08
  EG.5.1.1 > C9142T > G22927T(S:L455F) [Query: C9142T, G13627A, G22927T, 2 seqs, 09/18]
• Shanghai/SCDC-XG08-12942/2023|EPI_ISL_18268428|2023-08-27 and Shanghai/SCDC-836/2023|EPI_ISL_18284901|2023-09-10
  EG.5.1.1 > C9996T(ORF1a:S3244L) > G22927T(S:L455F) [Query: C6541T, C9996T, G22927T, 2 seqs, 09/19]
• Sichuan/CDCDC-3-LZJ/2023|EPI_ISL_18166147|2023-07-29 and Sichuan/CDCDC-19-CX2806/2023|EPI_ISL_18246264|2023-08-20
  EG.5.1.1 > C11779T > C7420T > A12644G(ORF1a:I4127V), G16662A, G22927T(S:L455F), A27736T(ORF7a:T115S), C28585T [Query: C7420T, C11779T, G22927T, 2 seqs, 09/11]
• USA/OR-OSPHL08951/2023|EPI_ISL_18285283|2023-09-07 and USA/OR-OSPHL08953/2023|EPI_ISL_18285285|2023-09-10
  EG.5.1.1 > C11956T > C17746T(ORF1b:P1427S), T20252C(ORF1b:I2262T), G22927T(S:L455F) [Query: C11956T, G13627A, G22927T, 2 seqs, 09/20]
• Shanghai/SCDC-XG09-13443/2023|EPI_ISL_18284954|2023-08-30 and Sichuan/MYCDC-XGCX312/2023|EPI_ISL_18284766|2023-09-03
  EG.5.1.1 > C14571T > T16340C(ORF1b:I958T), T17736C, G22927T(S:L455F) [Query: C6541T, C14571T, G22927T, -A1051G, 2 seqs, 09/19]
• Germany/NW-RKI-I-1137155/2023|EPI_ISL_18131003|2023-08-02 and Ukraine/81521/2023|EPI_ISL_18539909|2023-10-12
  EG.5.1.3 > C1059T(ORF1a:T265I) > G22927C(S:L455F) [Query: C1059T, C1889T, G22927C, 2 seqs, 11/23]
• Canada/QC-L00650653001/2023|EPI_ISL_18252385|2023-08-28 and Canada/QC-L00650647001/2023|EPI_ISL_18252388|2023-08-29
  EG.5.1.3 > C17718T > A17066G(ORF1b:Y1200C), A17622G, G22927T(S:L455F) [Query: C1889T, C17718T, G22927T, 2 seqs, 09/12]
• Canada/ON-PHL-23-36533/2023|EPI_ISL_18448204|2023-10-18 and Canada/ON-PHL-23-36753/2023|EPI_ISL_18448385|2023-10-20
  HV.1 (EG.5.1.6.1) > C12513T(ORF1a:T4083M) > T17343C > G22918T(S:R452) > T22926C(S:L455S), C29784T [Query: C12513T, T17343C, T22926C, 2 seqs, 10/30]
• USA/HI-H2325918/2023|EPI_ISL_18487957|2023-10-26 and USA/HI-H2325960/2023|EPI_ISL_18535129|2023-11-03
  HV.1 > T23198C(S:L546L) > C29466T > T28417C(ORF9b:I45T) > C875T(ORF1a:L204F), G22927T(S:L455F) [Query: G22927T, T23198C, T28417C, 2 seqs, 11/22]

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Triplets

• Shanghai/SCDC-770/2023|EPI_ISL_18232641|2023-08-20; Shanghai/SCDC-802/2023|EPI_ISL_18268353|2023-08-31 and Germany/NW-RKI-I-1138223/2023|EPI_ISL_18343384|2023-09-19
  EG.5.1.1 > G347A(ORF1a:V28I) > T27956C > G3091A > C13959T, T22020G(S:M153R), G22927T(S:L455F) [Query: G347A, G3091A, G22927T, 3 seqs, 10/04]
• Shanghai/SCDC-0823-3241/2023|EPI_ISL_18208400|2023-08-21; France/BRE-IPP21293/2023|EPI_ISL_18350826|2023-09-18 and USA/CA-GBW-H20-334-1265/2023|EPI_ISL_18357649|2023-09-26
  EG.5.1.1 > G347A(ORF1a:V28I) > T27956C > G22927T(S:L455F), A26117G(ORF3a:E242G) [Query: G347A, G22927T, T27956C, -G3091A, 3 seqs, 10/06]
• Yunnan/YNCDC-2364/2023|EPI_ISL_18166234|2023-08-02; Yunnan/YNCDC-2493/2023|EPI_ISL_18241493|2023-08-28 and Yunnan/YNCDC-2972/2023|EPI_ISL_18384579|2023-09-22
  EG.5.1.1 > C629T(ORF1a:L122F) > A1168G > T6640C > C18864T, G22927T(S:L455F), A25506G [Query: C629T, T6640C, G22927T, 3 seqs, 10/12]
• Xinjiang/XJCDCWLMQ-412/2023|EPI_ISL_18161044|2023-07-29; South_Korea/KDCA271622/2023|EPI_ISL_18511017|2023-10-20; Shanghai/SCDC-JD1024_1/2023|EPI_ISL_18495067|2023-10-21 and Denmark/DCGC-663353/2023|EPI_ISL_18518786|2023-11-06
  EG.5.1.1 > C4832T > G22927T(S:L455F) [Query: C4832T, G13627A, G22927T, C27874T, 3 seqs, 11/18]
• Shanghai/SCDC-FX0906-018/2023|EPI_ISL_18284805|2023-09-03; Hubei/HCDC-JZ3118/2023|EPI_ISL_18376469|2023-09-25 and Hubei/HCDC-YC3307/2023|EPI_ISL_18438465|2023-09-27
  EG.5.1.1 > C26151T > C19524G, C20235T, G22927T(S:L455F), G29044A [Query: C19524G, G22927T, C26151T, 3 seqs, 10/26]
• Australia/SA708969/2023|EPI_ISL_18453685|2023-10-23; Australia/SA832208/2023|EPI_ISL_18536619|2023-11-14 and Australia/SA832209/2023|EPI_ISL_18536620|2023-11-14
  EG.5.1.3 > C1057T > G18462A > C6578T(ORF1a:L2105F) > G22927T(S:L455F), C26058T, T27210C [Query: C1057T, C6578T, G22927T, 3 seqs, 11/23] thanks to @FedeGueli
• Spain/CU-19903/2023|EPI_ISL_18294739|2023-08-22; Denmark/DCGC-661638/2023|EPI_ISL_18442881|2023-10-16 and Italy/LOM_Unimi-3611-23/2023|EPI_ISL_18443629|2023-10-19
  EG.5.1.6 > C12513T(ORF1a:T4083M) > G22927T(S:L455F) [Query: C5835T, C12513T, G22927T, 3 seqs, 10/28]

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Quadruplets

• Shanghai/SCDC-826/2023|EPI_ISL_18284891|2023-09-07; Yunnan/YNCDC-3103/2023|EPI_ISL_18454372|2023-10-13; Sichuan/CDCDC-19-CX3446/2023|EPI_ISL_18457460|2023-10-22 and Hubei/HCDC-WH3507/2023|EPI_ISL_18485337|2023-10-25
  EG.5.1.1 > A2483G(ORF1a:I740V) > T15996C, G22927C(S:L455F) [Query: A2483G, G13627A, G22927C, 4, 11/08], many with S:R158K/G22035A and S:E554K/G23222A
• South_Korea/KDCA267746/2023|EPI_ISL_18408949|2023-09-18; South_Korea/KDCA268248/2023|EPI_ISL_18411258|2023-09-19; South_Korea/KDCA269573/2023|EPI_ISL_18460793|2023-10-04; and South_Korea/KDCA269703/2023|EPI_ISL_18460915|2023-10-09
  EG.5.1.1 > C3695T > G22927T(S:L455F) [Query: C3695T, G13627A, G22927T, -T2959C, 4 seq, 11/03]
• France/COR-HCL-723001296701/2023|EPI_ISL_18387770|2023-09-25; France/NAQ-HCL723001378601/2023|EPI_ISL_18423405|2023-10-09; Austria/AGES-1141981/2023|EPI_ISL_18485506|2023-10-18 and Germany/BY-MVP-000022265/2023|EPI_ISL_18525885|2023-10-30
  EG.5.1.3 > C6151T > G2468A(ORF1a:A735T), T22926G(S:L455W) [Query: C6151T, T22926G, 4 seqs, 11/21]

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Quintuplets

Fujian/FCDC-QZ08S024/2023|EPI_ISL_18145964|2023-08-18; England/CLIMB-CM7YJZ4C/2023|EPI_ISL_18392773|2023-10-05; Yunnan/YNCDC-3090/2023|EPI_ISL_18454344|2023-10-12; Yunnan/YNCDC-3139/2023|EPI_ISL_18488099|2023-10-12; Singapore/R78MR69/2023|EPI_ISL_18444918|2023-10-25; South_Korea/KDCA273761/2023|EPI_ISL_18535687|2023-10-31 and USA/MN-MDH-37408/2023|EPI_ISL_18510684|2023-11-01
EG.5.1.1 > C25578T > G22927T(S:L455F) [Query: C8320T, G22927T, C25578T, 5 seqs, 11/23]

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[FedeGueli]

Thank you for this one @NkRMnZr great work, please credit @BorisUitham who was the first to notice the high homoplasy of L455F in EG.5.1 backbone.

[BorisUitham]

I dont have a lot of problems with credits or axknowledgements, we all find these separately :)

[NkRMnZr]

Tracking updates:

08-08, 1 sequence from Ontario, Canada on Branch 1: EPI_ISL_18076513; Adding Branch 3 from previously singlet Shanghai/SCDC-XG07-10066/2023|EPI_ISL_17994488|2023-07-04; Adding a few doublets.

08-11, Adding Branch 4 from former doublets: Shanghai/SCDC-MH071302/2023|EPI_ISL_18060822|2023-07-09(local case) and Shanghai/SCDC-HG0724-2748_2-2/2023|EPI_ISL_18075026|2023-07-22 (travel history: Thailand), 2 additional seqs from Ginkgo BioWorks with travel history to Japan, spotted by @FedeGueli

08-15, Branch 3, +14 (Shanghai, China); Adding Branch 5 & 6 from previously doublets and singlet

08-17, Branch 1, +2 (China); Branch 4, +1 (China); Branch 5, +1 (China); Adding Branch 7

08-18, Branch 4, +2 (China); Branch 5, +1 (South Korea); Adding Branch 8, 9, 10 from former doublets

08-21, Branch 9, +2 (China); Branch 10, +1 (China)

08-22, Branch 1, +2 (China); Branch 2, +3 (USA); Branch 4, +1 (USA)

08-24, Branch 2 +1 (Japan); Adding Branch 11 (3 seqs, Japan)

08-25, Branch 1 +5 (China); Branch 4 +1 (China); Branch 10 +2 (China)

08-26, Branch 4, +3 (China); Branch 9, +3 (England; Denmark); Branch 10, +1 (China); Adding Branch 12 from Singlets

08-28, Branch 2, +1 (Japan); Branch 7, +1 (China); Branch 8, +1 (Singapore); Branch 4 Transferred to main repo

08-29, Branch 1, +2 (China); Branch 2, +1 (Austria); Branch 5, +1 (China); Branch 7, +1 (China); Branch 9, +1 (China); Branch 10, +1 (China); Adding Branch 13

08-30, Branch 1 & 2 transferred to main repo; Branch 5, +1 (USA)

08-31, Branch 10, +1 (China); Branch 11, +2 (Japan); Adding Branch 14

09-01, Branch 7, +3 (China); Branch 10, +1 (China); Adding Branch 15

09-05, Branch 7, +1 (Malaysia); Branch 8 & 11, +1 (Japan); Branch 13, +2 (China); Adding Branch 16~19 from former doublets

09-06, Branch 17, +1 (Japan); Branch 18, +2 (USA); Adding Branch 20; Removing former singlets now merged into designated branches.

09-07, Branch 5, +1 (Singapore); Branch 8, +2 (China); Adding Branch 21~23

09-08, Branch 17, +2 (Japan)

09-09, Branch 5, +3 (Canada); Branch 9 +1 (US); Branch 17, +2 (Japan); Branch 18, +5 (Canada); Adding Branch 24

09-12, Update on Branch 5, 6, 7, 10, 11, 12, 15, 17, 23, 24; Adding Branch 25~30

09-13, Update on Branch 5, 8, 10, 13, 17, 18; Adding Branch 31~33

09-15, Updates on Branch 10, 11 and 17; Adding Branch 35

09-16, Update on Branch 5-11, 13, 18, 23, 25, 26, 30, 31, 33; adding Branch 36~40

09-18, Branch 17 +1 (S. Korea); Adding Branch 41

09-19, Update on Branch 5, 10-12, 17, 23, 25, 31, 33, 36 and 40; Adding Branch 42-44

09-20, Update on Branch 5, 7-15, 17, 22-24, 27, 30-32, 38. Remove Branch 6. Adding Branch 45-49

09-21 Final update, clean up singlets/doublets, adding Branch 50-51, remove Branch 29

[FedeGueli]

propose in the main page (Pango) each of them when reaching 5

[FedeGueli]

I think two more intercepted by American airports: 18094969-18094946 i m checking

[FedeGueli]

• Shanghai/SCDC-MH071302/2023|EPI_ISL_18060822|2023-07-09 and Shanghai/SCDC-MH071302/2023|EPI_ISL_18060822|2023-07-09
  EG.5.1 > C12100G, G22927T(S:L455F) [Query: C12100G, G22927T, 2 seqs, 08/02]

Two samples imported in Usa from japan cluster with this Shanghai sequence ( i think you double counted it but it is the same!)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_381d3_6b7940.json?c=gt-S_455&label=id:node_6794559

They are four now: EPI_ISL_18060822, EPI_ISL_18075026, EPI_ISL_18094946,
EPI_ISL_18094969

I would propose it in a separate issue.

[xz-keg]

Branch 3 explodes to 17 seqs

[NkRMnZr]

08-15, Branch 3, +14 (Shanghai, China)：

EPI_ISL_18105750, EPI_ISL_18105752, EPI_ISL_18105756-18105765, EPI_ISL_18105768, EPI_ISL_18105818

Transferred Branch 3 to Main Repo cov-lineages/pango-designation#2194

Adding Branch 5 & 6 from previously doublets and singlet.

[FedeGueli]

Thank you @NkRMnZr

[xz-keg]

Branch 1 also reaches 5 now

[NkRMnZr]

08-17, Branch 1, +2 (China); Branch 4, +1 (China); Branch 5, +1 (China); Adding Branch 7
Branch 1, +2 (Fujian, Shanghai): EPI_ISL_18108313, EPI_ISL_18108479
Branch 4, +1 (Shanghai): EPI_ISL_18108375
Branch 5, +1 (Shanghai): EPI_ISL_18108346

Adding Branch 7 from previously singlet
Adding a few singlets and doublets

[FedeGueli]

08-17, Branch 1, +2 (China); Branch 4, +1 (China); Branch 5, +1 (China); Adding Branch 7 Branch 1, +2 (Fujian, Shanghai): EPI_ISL_18108313, EPI_ISL_18108479 Branch 4, +1 (Shanghai): EPI_ISL_18108375 Branch 5, +1 (Shanghai): EPI_ISL_18108346

Adding Branch 7 from previously singlet Adding a few singlets and doublets

Great work thank you,

[xz-keg]

Branch 5 and 6 also reached 5. Shall do a lot of proposals.

[NkRMnZr]

08-18, Branch 4, +2 (China); Branch 5, +1 (South Korea); Adding Branch 8, 9, 10 from former doublets

Branch 4: +2 China (Shanghai) EPI_ISL_18114693, EPI_ISL_18114890
Branch 5: +1 South Korea EPI_ISL_18111663

Adding Branch 8, 9, 10 from former Doublets
A former singlet now became #644

[NkRMnZr]

08-21, Branch 9, +2 (China); Branch 10, +1 (China)
Branch 9 +2 (Liaoning) EPI_ISL_18116287, EPI_ISL_18116314
Branch 10 +1 (Liaoning) EPI_ISL_18116311

[xz-keg]

Branch 2 reaches 5 too.

[NkRMnZr]

08-22, Branch 1, +2 (China); Branch 2, +3 (USA); Branch 4, +1 (USA)

Branch 1, 2 seqs from Fujian: EPI_ISL_18127148, EPI_ISL_18127155
Branch 2, 3 seqs from SFO, California, with travel history to Switzerland: EPI_ISL_18124861, EPI_ISL_18124879, EPI_ISL_18125017
Branch 4, 1 more from New York: EPI_ISL_18126507

[FedeGueli]

What a work @NkRMnZr ! ( and @aviczhl2 too!) really grateful to you. ping @corneliusroemer : this is high level tracking!

[FedeGueli]

• Xinjiang/XJCDCWLMQ_369/2023|EPI_ISL_18108848|2023-07-04 and Xinjiang/XJCDCWLMQ-398/2023|EPI_ISL_18108876|2023-07-18
  HK.1 (EG.5.1.1.1) > G6320A(ORF1a:V2019I) > C11704T, C22482T(S:T307I), G22927C(S:L455F) [Query: G6320A, G22332T, G22927C, 2, 08/16]

this one has been proposed in #631

[FedeGueli]

@NkRMnZr when each of them reaches 10 propose in the main page.

[NkRMnZr]

08-24, Branch 2 +1 (Japan); Adding Branch 11 (3 seqs, Japan)

Branch 2, +1 (Japan): EPI_ISL_18130075
Adding Branch 11 with 3 seqs from Japan

[NkRMnZr]

Branch 28 together with Branch 2 of #978 moved to main repo: cov-lineages/pango-designation#2398
Branch 30 is now pulled under HK.3 so no longer tracking.
Branch 36 transferred to cov-lineages/pango-designation#2399
Branch 63 transferred to cov-lineages/pango-designation#2400
Branch 77 transferred to cov-lineages/pango-designation#2401

[FedeGueli]

Branch 28 together with Branch 2 of #978 moved to main repo: cov-lineages/pango-designation#2398 Branch 30 is now pulled under HK.3 so no longer tracking. Branch 36 transferred to cov-lineages/pango-designation#2399 Branch 63 transferred to cov-lineages/pango-designation#2400 Branch 77 transferred to cov-lineages/pango-designation#2401

thank you great work.

[FedeGueli]

branch 21 seems moving

[FedeGueli]

pls propose branch 88

[FedeGueli]

i think now we can close this one. no one of the branches could compete with JN.1 , thank you great work @NkRMnZr

[FedeGueli]

@NkRMnZr please propose Branch 86 is from Malaysia with 5% prevalence there

[xz-keg]

There seems to be new branch following EG.5.1.1->T14988C, A23014T->C1471T->C12823T->G25459T,G22927T.

GISAID query: G25459T,G22927T,T14988C (54 seqs)

usher

[FedeGueli]

There seems to be new branch following EG.5.1.1->T14988C, A23014T->C1471T->C12823T->G25459T,G22927T.

GISAID query: G25459T,G22927T,T14988C (54 seqs)

usher

Please propose directly

[FedeGueli]

Branch 77 designated HV.2 via cov-lineages/pango-designation@61ef3fc

[FedeGueli]

Branch 90 seems to have had a late spread in pacific countries as SK NZL cc @NkRMnZr

[xz-keg]

USA/NY-NYULH-16857/2023|EPI_ISL_18440726|2023-10-19 and USA/NY-CDC-VSX-A357619/2023|EPI_ISL_18534359|2023-10-26
EG.5.1 > C2147T(ORF1a:L628F), T6115C > G18498T(ORF1b:M1677I) > C21811T, A22911T(S:N450I), G22927T(S:L455F) [Query: C2147T, G18498T, G22927T, 2 seqs, 11/22]

11 on usher now.

[FedeGueli]

USA/NY-NYULH-16857/2023|EPI_ISL_18440726|2023-10-19 and USA/NY-CDC-VSX-A357619/2023|EPI_ISL_18534359|2023-10-26 EG.5.1 > C2147T(ORF1a:L628F), T6115C > G18498T(ORF1b:M1677I) > C21811T, A22911T(S:N450I), G22927T(S:L455F) [Query: C2147T, G18498T, G22927T, 2 seqs, 11/22]

11 on usher now.

Pleas propose it separately in this repo crediting @NkRMnZr

[FedeGueli]

C2147T, G18498T, G22927T

it is 6 not 11, mostly on usher are repeats

[AngieHinrichs]

it is 6 not 11, mostly on usher are repeats

It seems like the USA/NY-PRL and USA-MI-UM sequences are not (yet?) imported into GISAID:

[FedeGueli]

it is 6 not 11, mostly on usher are repeats

It seems like the USA/NY-PRL and USA-MI-UM sequences are not (yet?) imported into GISAID:

thx i have put it under tracking anyway!

[FedeGueli]

@NkRMnZr please propose 86 88 and eventually 73

[FedeGueli]

Branch 86 now 79,
branch 88 now 118

[FedeGueli]

There maybe this EG.5.1.1 branch with Orf1a:K3353R > 455F > S:Q677R in Italy

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_17255_8f44a0.json?label=id:node_3489111

[krosa1910]

There maybe this EG.5.1.1 branch with Orf1a:K3353R > 455F > S:Q677R in Italy

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_17255_8f44a0.json?label=id:node_3489111

K3353R is for some reason very highly convergent, so not sure how valuable this categorization is.

[krosa1910]

There maybe this EG.5.1.1 branch with Orf1a:K3353R > 455F > S:Q677R in Italy

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_17255_8f44a0.json?label=id:node_3489111

K3353R is for some reason very highly convergent, so not sure how valuable this categorization is.

[FedeGueli]

There maybe this EG.5.1.1 branch with Orf1a:K3353R > 455F > S:Q677R in Italy

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_17255_8f44a0.json?label=id:node_3489111

K3353R is for some reason very highly convergent, so not sure how valuable this categorization is.

Yeah for sure .but the italian cluster from Umbria is clearly monophyletic and defined by 677R not sure if 3353 happened first or it has been acquired later, in fact lineages with it has not been tracked here.
Interestingly Umbria has another big cluster of JN.1 with JN.1 S:K147N . That makes me think that they are both just hospital clusters