CH.1.1* Lineage Tracker

[NkRMnZr]

CH.1.1* Lineage Tracker

F486P

478X

• DV.7.1.4 > A11438T(ORF1a:N3725Y) > C27503T(ORF7a:S37F) > C560T(ORF1a:R99C), G6461A(ORF1a:V2066M), C10989T(ORF1a:T3575I), C27476T(ORF7a:T28I), A29342G(N:I357V) > A22504G(S:Q314Q), C22995G(S:T478R) [Query: G6461A, C10989T, C22995G, Dec1] Australia/NSW-ICPMR-51349/2023|EPI_ISL_18566432|2023-11-12

Q613H

• CH.1.1 > C21811T > C193T > T27504C > C2197T > C449T(ORF1a:P62S) > G9652T(ORF1a:M3129I) > G23401T(S:Q613H) [C449T, G9652T, G23401T, 7, Aug25]

RBD Levels

Known Potential Growth Booster

• DV.1.1 > T25695A > C8664T(ORF1a:T2800I), C17076T > C3634A(ORF1a:N1123K), T9475G, C23673T(S:S704L) [Query: C8664T, T9475G, C23673T, 44, Aug17]

FCS & Flanking

• DV.7.1 > A10323G(ORF1a:K3353R) > C2113T > C25919T(ORF3a:T176I) > G16959A, C23997G(S:P812R), C25350T(S:P1263L) [Query: C2113T, C23997G, C25919T, 3, Oct13]
• FK.1.1.2 with S:A684V (32 seqs, Australia) sars-cov-2-variants/lineage-proposals#459 FK.1.1 > C9223T, T23071G > A28154T > C23613T (S:A684V) [Query: T23071G, C23613T, A28154T, 33, Aug17]
• FK.1.1.2 > A28154T > T18657C_reversion > T9223C_reversion > G27156A_reversion(M:G212S_reversion) > C9223T > G1958T(ORF1a:A565S), T13060A > C13115T > C22624T, A23598G(S:K679R), A27156G(M:S212G) [Query: G1958T, C13115T, A23598G, 12, Sep20]

Others

• DV.6.2 > C28791T(N:A173V) > C15588T > G3187A, C15126T, A22215G(S:Q218R) [Query: G3187A, C15588T, A22215G, 44, Sep27]
• DV.7.1.5 > C26907T > G564A(ORF1a:S100N), T5356A(ORF1a:D1697E) > C10336T > C21707T(S:H49Y), C22353A(S:A264D), G23015C(S:G485R), T27285C [Query: T5356A, C10336T, G23015C, 6, Nov14]
• FS.1 (CH.1.1.12.1) > C18029T(ORF1b:A1521V), G25249A(S:M1229I) > A25023G(S:K1154R) [Query: C18029T, A25023G, G25249A, 32, Sep5]
• FK.1.1.2 > A28154T > C1102T, C6258T(ORF1a:T1998I), C6336T(ORF1a:S2024L), C20148T > C23202A
  (S:T547K), C24378T(S:S939F) [Query: C1102T, C6258T, C23202A, 10, Oct12]
• FK.1.2.1 with S:T286I (70 seqs, mainly in Finland, 9 countries) sars-cov-2-variants/lineage-proposals#491 FK.1.2.1 > C22419T(S:T286I) [Query: C2937T, C22419T, 73, Sep4]

Large Undesignated Cluster

Local Prevalence

Recombinant

Designated

• DV.7 with ORF1b:A520V (nsp12_A529V), ORF3a:A72T (120 seqs, 10 countries) sars-cov-2-variants/lineage-proposals#130 CH.1.1.1 > T4402A > C10908T(ORF1a:A3548V) > C24134A(S:L858I), Designated as DV.7, furhter T4036A > C2227T, T25959C > C15026T(ORF1b:A520V) > G25606A(ORF3a:A72T) partial of branches leading to DV.7.1
• FK.1.1 + S:V445A (19 Australia, NZL) sars-cov-2-variants/lineage-proposals#368 FK.1.1 > C4320T(ORF1a:A1352V) > T22896C(S:V445A), Designated as FK.1.1.1
• FK.1.3.2 with S:E1111Q (56 seqs, mainly in Japan, 3 countries) sars-cov-2-variants/lineage-proposals#533 FK.1.3.2 > T25812C > C17352T, G24893C(S:E1111Q), Designated as JL.1 via cov-lineages/pango-designation@3a66166

Inactive

• FS.1 (CH.1.1.12) got S:F486P in Denmark (2 seqs) sars-cov-2-variants/lineage-proposals#518 FS.1 (CH.1.1.12.1) > G12521A(ORF1a:G4086S) > T4608C(ORF1a:M1448T), T10687A, A16408G(ORF1b:T981A), T23018C(S:F486P) [Query: T10687A, A16408G, T23018C, 2, July31]
• CH.1.1.14 > T16593C > C29296T > G14622A > T2107C, C3318T(ORF1a:P1018L), C24134A(S:L858I) [Query: C3318T, G14622A, C24134A, 25, July31]