diff --git a/lineage_notes.txt b/lineage_notes.txt index 2bac5fd8..9447e30b 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -700,7 +700,7 @@ FV.1 Alias of B.1.1.529.2.3.20.8.1.1.1, S:R346T, M:E11Q, Singapore/SouthKorea/Ja CM.8.1.2 Alias of B.1.1.529.2.3.20.8.1.2, Germany/USA, S:K147I CM.8.1.3 Alias of B.1.1.529.2.3.20.8.1.3, USA, S:Y1272H CM.8.1.4 Alias of B.1.1.529.2.3.20.8.1.4, ORF1b:N1790D, Philippines, from #1554 -CM.8.1.5 Alias of B.1.1.529.2.3.20.8.1.5, S:K150E, S:Y248H, N:A155V, Philippines +CM.8.1.5 Alias of B.1.1.529.2.3.20.8.1.5, S:K150E, S:Y248H, N:A155V, Philippines, from sars-cov-2-variants/lineage-proposals#293 CM.9 Alias of B.1.1.529.2.3.20.9, USA/Canada/Israel, S:S256L CM.10 Alias of B.1.1.529.2.3.20.10, USA/South Korea/Singapore, S:K478T reversion, S:V445A CM.11 Alias of B.1.1.529.2.3.20.11, USA/South Korea, S:R346T, S:F486S, from #1509 @@ -842,8 +842,8 @@ CJ.1 Alias of B.1.1.529.2.75.3.1.1.1.1, S:S486P, #1171 CJ.1.1 Alias of B.1.1.529.2.75.3.1.1.1.1.1, S:V445A, Singapore/Malaysia/Japan, from issue #1384 CJ.1.2 Alias of B.1.1.529.2.75.3.1.1.1.1.2, ORF1a:L2609F, Sweden/France/England CJ.1.3 Alias of B.1.1.529.2.75.3.1.1.1.1.3, A261G reversion, G4960A, C14790T, South Korea -CJ.1.3.1 Alias of B.1.1.529.2.75.3.1.1.1.1.3.1, S:R214S, ORF1a:G3578S, South Korea/Japan -CJ.1.3.2 Alias of B.1.1.529.2.75.3.1.1.1.1.3.2, S:D936H, South Korea +CJ.1.3.1 Alias of B.1.1.529.2.75.3.1.1.1.1.3.1, S:R214S, ORF1a:G3578S, South Korea/Japan, sars-cov-2-variants/lineage-proposals#287 +CJ.1.3.2 Alias of B.1.1.529.2.75.3.1.1.1.1.3.2, S:D936H, South Korea, sars-cov-2-variants/lineage-proposals#287 BM.1.1.2 Alias of B.1.1.529.2.75.3.1.1.2, England, S:T883I, S:S939F, S:P1079T BM.1.1.3 Alias of B.1.1.529.2.75.3.1.1.3, India, defined by ORF10:A8V CV.1 Alias of B.1.1.529.2.75.3.1.1.3.1, Ireland, S:L452R @@ -879,7 +879,7 @@ DV.8 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.8, S:Q613H, C8299T, C19602T, Sweden CH.1.1.2 Alias of B.1.1.529.2.75.3.4.1.1.1.1.2, defined by S:T883I, ORF1a:Y1846C, ORF1a:G2294S on T27576C branch CH.1.1.3 Alias of B.1.1.529.2.75.3.4.1.1.1.1.3, S:S255P, New Zealand/Australia/Hong Kong, from #1405 GQ.1 Alias of B.1.1.529.2.75.3.4.1.1.1.1.3.1, S:486P, ORF1a:H1545Q, ORF1b:V1520L, Australia/New Zealand, from #1872 -GQ.1.1 Alias of B.1.1.529.2.75.3.4.1.1.1.1.3.1.1, S:G213E, New Zealand +GQ.1.1 Alias of B.1.1.529.2.75.3.4.1.1.1.1.3.1.1, S:G213E, New Zealand, from sars-cov-2-variants/lineage-proposals#343 CH.1.1.4 Alias of B.1.1.529.2.75.3.4.1.1.1.1.4, S:H681R, Austria, from #1370 CH.1.1.5 Alias of B.1.1.529.2.75.3.4.1.1.1.1.5, ORF3a:P104S, found mainly in Denmark and UK, from pango-designation issue #1539 CH.1.1.6 Alias of B.1.1.529.2.75.3.4.1.1.1.1.6, UK, defined by S:T732I @@ -949,7 +949,7 @@ FR.1 Alias of B.1.1.529.2.75.5.1.2.3.1, S:K187E, N:T366I, Japan/Taiwan/USA, from FR.1.1 Alias of B.1.1.529.2.75.5.1.2.3.1.1, S:P82H, ORF1a:L293F, China FR.1.2 Alias of B.1.1.529.2.75.5.1.2.3.1.2, S:R190M, China FR.1.3 Alias of B.1.1.529.2.75.5.1.2.3.1.3, ORF1a:A206V, ORF1b:A517V, N:G34E, China, from #2039 -FR.1.4 Alias of B.1.1.529.2.75.5.1.2.3.1.4, A3715G, C15960T, on shared T2372C, C7318T, ORF1a:L293F branch with FR.1.1, China +FR.1.4 Alias of B.1.1.529.2.75.5.1.2.3.1.4, A3715G, C15960T, on shared T2372C, C7318T, ORF1a:L293F branch with FR.1.1, China, sars-cov-2-variants/lineage-proposals#256 FR.2 Alias of B.1.1.529.2.75.5.1.2.3.2, ORF1a:Y1920H, ORF1b:I1799S, South Korea BN.1.2.4 Alias of B.1.1.529.2.75.5.1.2.4, ORF1b:D1746H BN.1.2.5 Alias of B.1.1.529.2.75.5.1.2.5, C3241T, C16833T, G22225A, South Korea @@ -2709,7 +2709,7 @@ EU.1 Alias of XBB.1.5.26.1, S:P521S, Germany/Netherlands, from #1688 EU.1.1 Alias of XBB.1.5.26.1.1, S:I410V, Germany/Netherlands, from #1688 EU.1.1.1 Alias of XBB.1.5.26.1.1.1, C21646T, Germany EU.1.1.2 Alias of XBB.1.5.26.1.1.2, S:A1070S, Germany/Finland/Denmark/Sweden -EU.1.1.3 Alias of XBB.1.5.26.1.1.3, S:F157L, Europe +EU.1.1.3 Alias of XBB.1.5.26.1.1.3, S:F157L, Europe, from sars-cov-2-variants/lineage-proposals#312 XBB.1.5.27 S:K478R, on T11431C branch, USA XBB.1.5.28 S:K478R, on 17124C polytomy, USA XBB.1.5.29 S:A348V, USA-NE @@ -2766,7 +2766,7 @@ XBB.1.5.68 S:P521T, ORF3a:L71I, C18501T, USA XBB.1.5.69 ORF1a:V2943I,C22513T, USA XBB.1.5.70 S:L455F, S:F456L (T22928C), ORF1a:A4068S, Brazil, from #1982 GK.1 Alias of XBB.1.5.70.1, S:S704L, Brazil, from #2025 -GK.2 Alias of XBB.1.5.70.2, S:V511I +GK.2 Alias of XBB.1.5.70.2, S:V511I, from sars-cov-2-variants/lineage-proposals#300 XBB.1.5.71 S:V511I, Spain XBB.1.5.72 S:F456L (T22928C), ORF1a:G445S, T9823C, T10204C, South America XBB.1.5.73 T28271C, USA/Peru @@ -2789,7 +2789,7 @@ HA.2 Alias of XBB.1.5.86.2, S:P521S, Brazil XBB.1.5.87 S:478R, ORF1a:E1633K, ORF1a:M1588K, C9763T, C20946T, Indonesia XBB.1.5.88 C2299T, South Africa XBB.1.5.89 S:478R, S:554A, Canada/Italy/France -XBB.1.5.90 S:P621S, ORF1ab:S6713L, Belgium/France +XBB.1.5.90 S:P621S, ORF1ab:S6713L, Belgium/France, from #1849 XBB.1.5.91 S:P621S, USA XBB.1.6 USA, S:L216F, S:H146K, from issue #1428 XBB.1.7 USA-NY, S:V608I @@ -2833,7 +2833,7 @@ FL.7 Alias of XBB.1.9.1.7, S:T51I FL.8 Alias of XBB.1.9.1.8, ORF3a:I62F, Europe FL.9 Alias of XBB.1.9.1.9, C23707T, T29691C, England FL.10 Alias of XBB.1.9.1.10, ORF1a:C657Y -FL.10.1 Alias of XBB.1.9.1.10.1, S:E554K, C4234T, South Korea +FL.10.1 Alias of XBB.1.9.1.10.1, S:E554K, C4234T, South Korea, from #2040 FL.11 Alias of XBB.1.9.1.11, ORF1a:L349F, France/French Guiana, from #1947 FL.12 Alias of XBB.1.9.1.12, ORF1a:C2210F FL.13 Alias of XBB.1.9.1.13, G4354A @@ -2853,8 +2853,8 @@ FL.20 Alias of XBB.1.9.1.20, S:F456L (22928C), S:Q52H, Spain, from #2072 FL.21 Alias of XBB.1.9.1.21, A10564T, South Korea/China FL.22 Alias of XBB.1.9.1.22, ORF1b:I1416V, T24184C FL.23 Alias of XBB.1.9.1.23, ORF1b:V1132I, Philippines -FL.24 Alias of XBB.1.9.1.24, S:Q613H, S:A688V -FL.25 Alias of XBB.1.9.1.25, S:E554K, USA/England +FL.24 Alias of XBB.1.9.1.24, S:Q613H, S:A688V, from sars-cov-2-variants/lineage-proposals#284 +FL.25 Alias of XBB.1.9.1.25, S:E554K, USA/England, from #2040 FL.26 Alias of XBB.1.9.1.26, C22264T FL.26.1 Alias of XBB.1.9.1.26.1, S:493L, Sweden XBB.1.9.2 S:F486P (after 27507C, 16878T), Indonesia/Singapore @@ -2922,7 +2922,7 @@ XBB.1.16.10 N:G25D, from #1984 XBB.1.16.11 S:P521T, India XBB.1.16.12 S:Q52H, South Korea XBB.1.16.13 ORF1a:G519S, ORF1a:G1101D, India -XBB.1.16.14 S:L452Q, after A11782G, India/France/Canada +XBB.1.16.14 S:L452Q, after A11782G, India/France/Canada, from sars-cov-2-variants/lineage-proposals#329 XBB.1.17 Defined by T27995C and ORF1a:L469F, from issue #1712 XBB.1.17.1 Defined by S:215H, S:S486P, from issue #1712 GA.1 Alias of XBB.1.17.1.1, ORF1a:G728C @@ -3124,7 +3124,7 @@ XCC Recombinant lineage of CH.1.1.1 and XBB.1.9.1, predominantly Pakistan, Austr XCD Recombinant lineage of XBB.1* and BQ.1.1.25*, with S:R214H, S:478I, Indonesia, from #2042 XCE Recombinant lineage of BQ.1* and FY.1 (XBB.1.22.1.1), Indonesia, South Korea, France, from lineage-proposals#123 XCF Recombinant lineage of XBB* and FE.1 (XBB.1.18.1.1), possibly South America, from lineage-proposals#2 -XCF.1 S:F157L, USA +XCF.1 S:F157L, USA, from sars-cov-2-variants/lineage-proposals#274 XCF.2 S:S929I, Canada XCG Recombinant lineage of BA.5.2* and XBB.1, Mexico *A.2.1 Withdrawn: Lineage with sequences predominantly from Panama