From 87d92a15d5352580bacfe1043859a3d4f219a4dc Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Tue, 16 Jan 2024 02:03:02 +0800 Subject: [PATCH] Update lineage_notes.txt --- lineage_notes.txt | 94 +++++++++++++++++++++++------------------------ 1 file changed, 47 insertions(+), 47 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 57148367..d2edfe99 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -877,7 +877,7 @@ DV.6 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.6, T15591C DV.6.1 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.6.1, S:Q613H, T15591C, Central Europe DV.6.2 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.6.2, S:Q613H, C6628T, Asia, from #2045 DV.7 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.7, S:L858I, ORF1a:A3548V, England, from #2038 -DV.7.1 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.7.1, S:L455F, S:F456L(T22928C), Spain/Austria, from sars-cov-2-variants/lineage-proposals#135 +DV.7.1 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.7.1, S:L455F (G22927T), S:F456L (T22928C), Spain/Austria, from sars-cov-2-variants/lineage-proposals#135 DV.7.1.1 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.7.1.1, S:K679R, on branch ORF1a:K3353R Spain, from sars-cov-2-variants/lineage-proposals#732 DV.7.1.2 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.7.1.2, ORF1a:A4162V, Spain/England, from #2258 JV.1 Alias of B.1.1.529.2.75.3.4.1.1.1.1.1.7.1.2.1, S:G485R, France, from sars-cov-2-variants/lineage-proposals#760 @@ -1535,7 +1535,7 @@ FC.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.72.1 S:478R, Indonesia BQ.1.1.73 Alias of B.1.1.529.5.3.1.1.1.1.1.1.73, found mainly in Canada and Spain, from #1740 BQ.1.1.74 Alias of B.1.1.529.5.3.1.1.1.1.1.1.74, S:182E, found mainly in Botswana and UK, from #1817 FN.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.74.1, S:478R, Botswana/England, from #1817 -BQ.1.1.75 Alias of B.1.1.529.5.3.1.1.1.1.1.1.75, S:K182N, S:F456L(T22928C), Reunion +BQ.1.1.75 Alias of B.1.1.529.5.3.1.1.1.1.1.1.75, S:K182N, S:F456L (T22928C), Reunion BQ.1.1.76 Alias of B.1.1.529.5.3.1.1.1.1.1.1.76, C15180T, Slovenia/Austria BQ.1.1.77 Alias of B.1.1.529.5.3.1.1.1.1.1.1.77, C12853T, ORF1b:A1428V, USA/France BQ.1.1.78 Alias of B.1.1.529.5.3.1.1.1.1.1.1.78, ORF1a:M315I, ORF1b:P1953L, Japan @@ -2863,7 +2863,7 @@ HZ.1 Alias of XBB.1.5.68.1, S:K478R, 23266T, USA, from sars-cov-2-variants/linea HZ.2 Alias of XBB.1.5.68.2, ORF1a:H3580Y, USA HZ.3 Alias of XBB.1.5.68.3, ORF1a:I3693T, USA XBB.1.5.69 ORF1a:V2943I,C22513T, USA -XBB.1.5.70 S:L455F, S:F456L (T22928C), ORF1a:A4068S, Brazil, from #1982 +XBB.1.5.70 S:L455F (G22927T), S:F456L (T22928C), ORF1a:A4068S, Brazil, from #1982 GK.1 Alias of XBB.1.5.70.1, S:S704L, Brazil, from #2025 GK.1.1 Alias of XBB.1.5.70.1.1, S:T573I, Brazil GK.1.1.1 Alias of XBB.1.5.70.1.1.1, C28432T @@ -2904,7 +2904,7 @@ GK.12 Alias of XBB.1.5.70.12, S:T76I, S:N450D, Brazil 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 -GN.1 Alias of XBB.1.5.73.1, S:F456L (22928C), Peru/Costa Rica +GN.1 Alias of XBB.1.5.73.1, S:F456L (T22928C), Peru/Costa Rica GN.1.1 Alias of XBB.1.5.73.1.1, ORF1b:A1643V, Peru GN.1.2 Alias of XBB.1.5.73.1.2, S:Q321L GN.1.3 Alias of XBB.1.5.73.1.3, S:L455F (G22927T), from sars-cov-2-variants/lineage-proposals#816 @@ -2928,7 +2928,7 @@ XBB.1.5.83 A10624G, South Africa XBB.1.5.84 S:M177I, South Africa XBB.1.5.85 S:L176F, S:478R, Trinidad and Tobago/Hong Kong XBB.1.5.86 ORF1a:G2868S, Brazil -HA.1 Alias of XBB.1.5.86.1, S:F456L (22930A), Brazil/Canada +HA.1 Alias of XBB.1.5.86.1, S:F456L (T22930A), Brazil/Canada HA.2 Alias of XBB.1.5.86.2, S:P521S, Brazil XBB.1.5.87 S:478R, ORF1a:E1633K, ORF1a:M1588K, C9763T, C20946T, pre T17124C, Indonesia XBB.1.5.88 C2299T, South Africa @@ -2943,7 +2943,7 @@ HD.1.1 Alias of XBB.1.5.93.1.1, S:K356T, Dominican Republic, from sars-cov-2-var XBB.1.5.94 S:Q613H, T25461C, France XBB.1.5.95 ORF1a:A1851V HS.1 Alias of XBB.1.5.95.1, S:478R, Mexico -HS.1.1 Alias of XBB.1.5.95.1.1, S:F456L(T22928C), USA, from #2237 +HS.1.1 Alias of XBB.1.5.95.1.1, S:F456L (T22928C), USA, from #2237 XBB.1.5.96 C28603T XBB.1.5.97 S:T941S, C7834T, New Zealand/Australia XBB.1.5.98 S:E554K, ORF8:V32L, Ghana @@ -2952,7 +2952,7 @@ XBB.1.5.100 S:V1122M, USA/Mexico HY.1 Alias of XBB.1.5.100.1, S:478R, USA/Mexico, from sars-cov-2-variants/lineage-proposals#453 XBB.1.5.101 ORF7a:E3Q, C14877T, Scandinavia/Poland/Vietnam XBB.1.5.102 C6896T, C14085T, C19488T, Brazil-Amazonas -JD.1 Alias of XBB.1.5.102.1, S:L455F, S:F456L (T22928C), A14634G, T28282C, Brazil, from #2071 +JD.1 Alias of XBB.1.5.102.1, S:L455F (G22927T), S:F456L (T22928C), A14634G, T28282C, Brazil, from #2071 JD.1.1 Alias of XBB.1.5.102.1.1, S:A475V, Brazil/USA/Spain, from #2174 JD.1.1.1 Alias of XBB.1.5.102.1.1.1, S:Y248H, from sars-cov-2-variants/lineage-proposals#864 JD.1.1.2 Alias of XBB.1.5.102.1.1.2, S:E583D, Ireland/UK, from sars-cov-2-variants/lineage-proposals#754 @@ -2976,8 +2976,8 @@ XBB.1.5.105 S:K304N, USA/Europe XBB.1.5.106 S:A623V, ORF1a:V28I, ORF1a:R3542H, Guatemala, from #2270 XBB.1.5.107 C24130T, Argentina/Uruguay/Bolivia JZ.1 Alias of XBB.1.5.107.1, S:F456L (T22928C), Argentina/Brazil, from sars-cov-2-variants/lineage-proposals#224 -XBB.1.5.108 S:F456L, S:K304N -XBB.1.5.109 S:F456L, ORF1a:T654A +XBB.1.5.108 S:F456L (T22930A), S:K304N +XBB.1.5.109 S:F456L (T22928C), ORF1a:T654A XBB.1.5.110 ORF1aT4129I, Mexico XBB.1.6 USA, S:L216F, S:H146K, from #1428 XBB.1.7 USA-NY, S:V608I @@ -2990,7 +2990,7 @@ FL.1.1.1 Alias of XBB.1.9.1.1.1.1, S:A688S, Australia/Mauritius FL.1.2 Alias of XBB.1.9.1.1.2, ORF1a:T4311I, South Korea/Italy/Spain FL.1.3 Alias of XBB.1.9.1.1.3, ORF1a:T1881I, ORF1b:M606I, South Korea FL.1.4 Alias of XBB.1.9.1.1.4, S:478R, S:Q1208H, Vietnam, from #1985 -FL.1.5 Alias of XBB.1.9.1.1.5, S:456L (T22928C), ORF1b:K2557R, from #2036 +FL.1.5 Alias of XBB.1.9.1.1.5, S:F456L (T22928C), ORF1b:K2557R, from #2036 FL.1.5.1 Alias of XBB.1.9.1.1.5.1, S:478R, from #2036 HN.1 Alias of XBB.1.9.1.1.5.1.1, S:A67S, Dominican Republic, from sars-cov-2-variants/lineage-proposals#408 HN.2 Alias of XBB.1.9.1.1.5.1.2, ORF1b:P223S, from sars-cov-2-variants/lineage-proposals#676 @@ -3063,7 +3063,7 @@ FL.13.4.1 Alias of XBB.1.9.1.13.4.1, S:Q14H, S:A484K, from sars-cov-2-variants/l FL.13.5 Alias of XBB.1.9.1.13.5, S:F456L (T22928C), ORF1a:T1000I, ORF1a:L2527M, Chile/Argentina, from sars-cov-2-variants/lineage-proposals#692 FL.14 Alias of XBB.1.9.1.14, S:V1122M, C29311T, C22978T, Russia/Finland FL.15 Alias of XBB.1.9.1.15, S:F456L (T22928C), ORF1a:E637K, Vietnam/China/South Korea, from #1994 -FL.15.1 Alias of XBB.1.9.1.15.1, S:L455F, ORF1a:T2007I, on ORF1a:S2185N branch, from #2293 +FL.15.1 Alias of XBB.1.9.1.15.1, S:L455F (G22927T), ORF1a:T2007I, on ORF1a:S2185N branch, from #2293 FL.15.1.1 Alias of XBB.1.9.1.15.1.1, S:A475V, Canada/Romania/Belgium, from sars-cov-2-variants/lineage-proposals#646 KF.1 Alias of XBB.1.9.1.15.1.1.1, S:P251H, Australia/Canada, from sars-cov-2-variants/lineage-proposals#890 KF.2 Alias of XBB.1.9.1.15.1.1.2, S:E183D, England/Australia/New Zealand, from sars-cov-2-variants/lineage-proposals#1111 @@ -3078,8 +3078,8 @@ FL.18 Alias of XBB.1.9.1.18, ORF1a:T2007I FL.18.1 Alias of XBB.1.9.1.18.1, N:T166I, A27507C, from #2019 FL.18.1.1 Alias of XBB.1.9.1.18.1.1, S:Y200C, S:478R, Australia/Indonesia, from #2019 FL.19 Alias of XBB.1.9.1.19, T2377C, C17502T, T24505G, South Korea -FL.19.1 Alias of XBB.1.9.1.19.1, S:F456L (22928C), ORF1b:A1877V, Spain/Italy/Puerto Rico, from #2138 -FL.20 Alias of XBB.1.9.1.20, S:F456L (22928C), S:Q52H, Spain, from #2072 +FL.19.1 Alias of XBB.1.9.1.19.1, S:F456L (T22928C), ORF1b:A1877V, Spain/Italy/Puerto Rico, from #2138 +FL.20 Alias of XBB.1.9.1.20, S:F456L (T22928C), S:Q52H, Spain, from #2072 FL.20.1 Alias of XBB.1.9.1.20.1, S:L455W, Northern Ireland/England, from #2145 FL.20.2 Alias of XBB.1.9.1.20.2, S:478R, from sars-cov-2-variants/lineage-proposals#571 FL.21 Alias of XBB.1.9.1.21, A10564T @@ -3103,7 +3103,7 @@ FL.30.1 Alias of XBB.1.9.1.30.1, S:A852S, Greece FL.31 Alias of XBB.1.9.1.31, ORF1b:M657I FL.31.1 Alias of XBB.1.9.1.31.1, S:478R, S:D80H, S:Q613H, Morocco/Europe/US/Canada, from sars-cov-2-variants/lineage-proposals#836 FL.32 Alias of XBB.1.9.1.32, S:E554Q, S:V6L, from sars-cov-2-variants/lineage-proposals#719 -FL.32.1 Alias of XBB.1.9.1.32.1, S:F456L, USA, from sars-cov-2-variants/lineage-proposals#719 +FL.32.1 Alias of XBB.1.9.1.32.1, S:F456L (T22928C), USA, from sars-cov-2-variants/lineage-proposals#719 FL.33 Alias of XBB.1.9.1.33, ORF1b:A1377V FL.33.1 Alias of XBB.1.9.1.33.1, S:478R, Georgia, from sars-cov-2-variants/lineage-proposals#828 FL.34 Alias of XBB.1.9.1.34, S:D1118Y @@ -3143,14 +3143,14 @@ EG.5 Alias of XBB.1.9.2.5, S:F456L (T22930A), ORF1a:A690V, ORF1a:A3143V, Indones EG.5.1 Alias of XBB.1.9.2.5.1, S:Q52H EG.5.1.1 Alias of XBB.1.9.2.5.1.1, China, from #2020 HK.1 Alias of XBB.1.9.2.5.1.1.1, S:G257V, China, from sars-cov-2-variants/lineage-proposals#359 -HK.1.2 Alias of XBB.1.9.2.5.1.1.1.2, S:455F (G22927C), S:T307I, China/New Zealand , from sars-cov-2-variants/lineage-proposals#631 +HK.1.2 Alias of XBB.1.9.2.5.1.1.1.2, S:L455F (G22927C), S:T307I, China/New Zealand , from sars-cov-2-variants/lineage-proposals#631 HK.2 Alias of XBB.1.9.2.5.1.1.2, S:Q14H, China, from sars-cov-2-variants/lineage-proposals#432 -HK.2.1 Alias of XBB.1.9.2.5.1.1.2.1, S:L455F, Singapore, from sars-cov-2-variants/lineage-proposals#537 -HK.3 Alias of XBB.1.9.2.5.1.1.3, S:L455F, China, from sars-cov-2-variants/lineage-proposals#414 +HK.2.1 Alias of XBB.1.9.2.5.1.1.2.1, S:L455F (G22927T), Singapore, from sars-cov-2-variants/lineage-proposals#537 +HK.3 Alias of XBB.1.9.2.5.1.1.3, S:L455F (G22927T), China, from sars-cov-2-variants/lineage-proposals#414 HK.3.1 Alias of XBB.1.9.2.5.1.1.3.1, S:F157L, China, from #2193 HK.3.2 Alias of XBB.1.9.2.5.1.1.3.2, S:Q14K, C853T, Chinaļ¼Œfrom sars-cov-2-variants/lineage-proposals#730 HK.3.2.1 Alias of XBB.1.9.2.5.1.1.3.2.1, S:Q677H, Canada, from #2362 -HK.3.2.2 Alias of XBB.1.9.2.5.1.1.3.2.2, S:N185D, Australia, from sars-cov-2-variants/lineage-proposals#867 +HK.3.2.2 Alias of XBB.1.9.2.5.1.1.3.2.2, ORF8:M1L, S:N185D, China/Australia, from sars-cov-2-variants/lineage-proposals#867 HK.3.3 Alias of XBB.1.9.2.5.1.1.3.3, S:S256L, N:P364L, China/Singapore, from sars-cov-2-variants/lineage-proposals#744 HK.3.4 Alias of XBB.1.9.2.5.1.1.3.4, S:P809S, from sars-cov-2-variants/lineage-proposals#764 HK.3.5 Alias of XBB.1.9.2.5.1.1.3.5, S:P174S, Singapore, from sars-cov-2-variants/lineage-proposals#865 @@ -3167,7 +3167,7 @@ HK.4 Alias of XBB.1.9.2.5.1.1.4, S:T883I, China HK.5 Alias of XBB.1.9.2.5.1.1.5, S:Q677H, China HK.6 Alias of XBB.1.9.2.5.1.1.6, S:D253G, ORF1a:A1923T, on T14988C branch UK/USA, from #2184 HK.7 Alias of XBB.1.9.2.5.1.1.7, S:N148T, China -HK.8 Alias of XBB.1.9.2.5.1.1.8, S:L455F, on C11779T branch, China, from #2230 +HK.8 Alias of XBB.1.9.2.5.1.1.8, S:L455F (G22927T), on C11779T branch, China, from #2230 HK.8.1 Alias of XBB.1.9.2.5.1.1.8.1, S:D1153Y, China, from #2356 HK.9 Alias of XBB.1.9.2.5.1.1.9, S:R190K, on C11779T branch, England, from sars-cov-2-variants/lineage-proposals#564 HK.11 Alias of XBB.1.9.2.5.1.1.11, S:G184S, China/England/SouthKorea, from #2255 @@ -3182,41 +3182,41 @@ HK.16 Alias of XBB.1.9.2.5.1.1.16, N:P67S, S:A684V, S:V1264L, from sars-cov-2-va HK.17 Alias of XBB.1.9.2.5.1.1.17, S:S494P, China HK.18 Alias of XBB.1.9.2.5.1.1.18, S:L452R, from sars-cov-2-variants/lineage-proposals#800 HK.19 Alias of XBB.1.9.2.5.1.1.19, S:F157L -HK.20 Alias of XBB.1.9.2.5.1.1.20, S:L455F, on ORF1a:P2144S branch, China, from sars-cov-2-variants/lineage-proposals#537 +HK.20 Alias of XBB.1.9.2.5.1.1.20, S:L455F (G22927T), on ORF1a:P2144S branch, China, from sars-cov-2-variants/lineage-proposals#537 HK.20.1 Alias of XBB.1.9.2.5.1.1.20.1, S:G482R, from sars-cov-2-variants/lineage-proposals#537 HK.21 Alias of XBB.1.9.2.5.1.1.21, S:T470N, S:796H, from #2367 -HK.22 Alias of XBB.1.9.2.5.1.1.22, S:L455F, S:L452Q, Australia/China, from #2357 +HK.22 Alias of XBB.1.9.2.5.1.1.22, S:L452Q, S:L455F (G22927T), Australia/China, from #2357 HK.23 Alias of XBB.1.9.2.5.1.1.23, ORF8:A65V -HK.23.1 Alias of XBB.1.9.2.5.1.1.23.1, S:L455F, ORF1a:T2906N, from sars-cov-2-variants/lineage-proposals#537 +HK.23.1 Alias of XBB.1.9.2.5.1.1.23.1, S:L455F (G22927T), ORF1a:T2906N, from sars-cov-2-variants/lineage-proposals#537 HK.23.1.1 Alias of XBB.1.9.2.5.1.1.23.1.1, S:A348S, China/Canada, from sars-cov-2-variants/lineage-proposals#537 HK.24 Alias of XBB.1.9.2.5.1.1.24, S:E654K -HK.24.1 Alias of XBB.1.9.2.5.1.1.24.1, S:L455F, Australia, from sars-cov-2-variants/lineage-proposals#537 +HK.24.1 Alias of XBB.1.9.2.5.1.1.24.1, S:L455F (G22927T), Australia, from sars-cov-2-variants/lineage-proposals#537 HK.25 Alias of XBB.1.9.2.5.1.1.25, S:K356T, S:H681R, N:P365L, and 10 more nucs, Germany/Austria/France/US, from #2327 and sars-cov-2-variants/lineage-proposals#986 -HK.26 Alias of XBB.1.9.2.5.1.1.26, S:L455F, ORF3a:L52I, on 14988C branch, Finland, from sars-cov-2-variants/lineage-proposals#763 +HK.26 Alias of XBB.1.9.2.5.1.1.26, S:L455F (G22927T), ORF3a:L52I, on 14988C branch, Finland, from sars-cov-2-variants/lineage-proposals#763 HK.26.1 Alias of XBB.1.9.2.5.1.1.26.1, S:A475V, Finland, formerly HK.3.11, from sars-cov-2-variants/lineage-proposals#763 HK.27 Alias of XBB.1.9.2.5.1.1.27, ORF1a:T1589I, China -HK.27.1 Alias of XBB.1.9.2.5.1.1.27.1, S:L455F, China, from sars-cov-2-variants/lineage-proposals#525 +HK.27.1 Alias of XBB.1.9.2.5.1.1.27.1, S:L455F (G22927T), China, from sars-cov-2-variants/lineage-proposals#525 HK.27.1.1 Alias of XBB.1.9.2.5.1.1.27.1.1, S:Q14H, China HK.28 Alias of XBB.1.9.2.5.1.1.28, C19170T, China HK.29 Alias of XBB.1.9.2.5.1.1.29, ORF1a:G2509D, North America HK.30 Alias of XBB.1.9.2.5.1.1.30, T26609C, China HK.31 Alias of XBB.1.9.2.5.1.1.31, ORF1a:G604S HK.32 Alias of XBB.1.9.2.5.1.1.32, S:Q14R, ORF1a:S2193F, China, from sars-cov-2-variants/lineage-proposals#601 -HK.33 Alias of XBB.1.9.2.5.1.1.33, S:L455F on C2644T branch, North America, from sars-cov-2-variants/lineage-proposals#537 +HK.33 Alias of XBB.1.9.2.5.1.1.33, S:L455F (G22927T) on C2644T branch, North America, from sars-cov-2-variants/lineage-proposals#537 HK.34 Alias of XBB.1.9.2.5.1.1.34, S:F186S, ORF1a:V3660M, on C2644T branch, Singapore, from sars-cov-2-variants/lineage-proposals#905 HK.34.1 Alias of XBB.1.9.2.5.1.1.34.1, S:K356T, Singapore, from sars-cov-2-variants/lineage-proposals#1048 EG.5.1.2 Alias of XBB.1.9.2.5.1.2, Japan, ORF1b:V1644I, from sars-cov-2-variants/lineage-proposals#301 EG.5.1.3 Alias of XBB.1.9.2.5.1.3, ORF1a:R542C, C22570T, from sars-cov-2-variants/lineage-proposals#222 JG.1 Alias of XBB.1.9.2.5.1.3.1, S:T732I, France, from #2218 JG.2 Alias of XBB.1.9.2.5.1.3.2, S:G75V, Europe, from #2249 -JG.3 Alias of XBB.1.9.2.5.1.3.3, S:L455F, S:S704L, Europe, from #2231 +JG.3 Alias of XBB.1.9.2.5.1.3.3, S:L455F (G22927T), S:S704L, Europe, from #2231 JG.3.1 Alias of XBB.1.9.2.5.1.3.3.1, S:T307I, from sars-cov-2-variants/lineage-proposals#829 JG.3.2 Alias of XBB.1.9.2.5.1.3.3.2, S:N450D, Canada, from #2376 JG.3.3 Alias of XBB.1.9.2.5.1.3.3.3, S:A83S, Belgium, from #2363 JG.3.4 Alias of XBB.1.9.2.5.1.3.3.4, S:478R, USA JG.4 Alias of XBB.1.9.2.5.1.3.4, C1684T, Europe EG.5.1.4 Alias of XBB.1.9.2.5.1.4, ORF1b:K2557R, from #2117 -JJ.1 Alias of XBB.1.9.2.5.1.4.1, S:L455F, ORF3a:I47V, China/Japan, from #2208 +JJ.1 Alias of XBB.1.9.2.5.1.4.1, S:L455F (G22927T), ORF3a:I47V, China/Japan, from #2208 EG.5.1.5 Alias of XBB.1.9.2.5.1.5, ORF1a:L3293I, ORF1b:T1274I, ORF1b:L2349V, Portugal EG.5.1.6 Alias of XBB.1.9.2.5.1.6, S:F157L, ORF1a:S1857L, USA, from sars-cov-2-variants/lineage-proposals#394 HV.1 Alias of XBB.1.9.2.5.1.6.1, S:L452R, USA @@ -3234,9 +3234,9 @@ HV.1.8 Alias of XBB.1.9.2.5.1.6.1.8, S:T208M, USA HV.1.9 Alias of XBB.1.9.2.5.1.6.1.9, S:N211I, S:T1117I, New Zealand HV.1.10 Alias of XBB.1.9.2.5.1.6.1.10, S:R452W, USA HV.1.11 Alias of XBB.1.9.2.5.1.6.1.11, S:N450D, USA -HV.2 Alias of XBB.1.9.2.5.1.6.2, S:L455F, Canada +HV.2 Alias of XBB.1.9.2.5.1.6.2, S:L455F (G22927T), Canada EG.5.1.7 Alias of XBB.1.9.2.5.1.7, S:K278N -EG.5.1.8 Alias of XBB.1.9.2.5.1.8, S:L455F, China, on C29762T branch, from sars-cov-2-variants/lineage-proposals#537 +EG.5.1.8 Alias of XBB.1.9.2.5.1.8, S:L455F (G22927T), China, on C29762T branch, from sars-cov-2-variants/lineage-proposals#537 KB.1 Alias of XBB.1.9.2.5.1.8.1, S:E654V, China, from #2347 KB.2 Alias of XBB.1.9.2.5.1.8.2, S:R214H KB.3 Alias of XBB.1.9.2.5.1.8.2, S:A83T, from sars-cov-2-variants/lineage-proposals#1052 @@ -3254,14 +3254,14 @@ EG.5.1.15 Alias of XBB.1.9.2.5.1.15, ORF1a:T753I EG.5.1.16 Alias of XBB.1.9.2.5.1.16, ORF1b:A2431V, from sars-cov-2-variants/lineage-proposals#899 EG.5.1.17 Alias of XBB.1.9.2.5.1.17, S:L455F (G22927C), China, from sars-cov-2-variants/lineage-proposals#537 EG.5.1.18 Alias of XBB.1.9.2.5.1.18, ORF1a:G3002S, ORF3a:S220I -EG.5.1.19 Alias of XBB.1.9.2.5.1.19, S:L455F, ORF1b:K1383R, ORF3a:M260K, from sars-cov-2-variants/lineage-proposals#537 +EG.5.1.19 Alias of XBB.1.9.2.5.1.19, S:L455F (G22927T), ORF1b:K1383R, ORF3a:M260K, from sars-cov-2-variants/lineage-proposals#537 EG.5.2 Alias of XBB.1.9.2.5.2, N:L161F EG.5.2.1 Alias of XBB.1.9.2.5.2.1, S:S704L, USA, from sars-cov-2-variants/lineage-proposals#189 EG.5.2.2 Alias of XBB.1.9.2.5.2.2, ORF1b:T239I, China EG.5.2.3 Alias of XBB.1.9.2.5.2.3, S:S704L, S:N1178D, Austria/USA, from sars-cov-2-variants/lineage-proposals#353 EG.5.2.4 Alias of XBB.1.9.2.5.2.4, S:K679R, on ORF3a:I118V branch, from sars-cov-2-variants/lineage-proposals#770 EG.6 Alias of XBB.1.9.2.6, C1684T, Israel -EG.6.1 Alias of XBB.1.9.2.6.1, S:456L (T22928C), Israel/Japan/Canada, from #1950 +EG.6.1 Alias of XBB.1.9.2.6.1, S:F456L (T22928C), Israel/Japan/Canada, from #1950 EG.6.1.1 Alias of XBB.1.9.2.6.1.1, S:484K, S:L242I, from sars-cov-2-variants/lineage-proposals#546 EG.6.1.2 Alias of XBB.1.9.2.6.1.2, S:V705I, Israel, from sars-cov-2-variants/lineage-proposals#826 EG.7 Alias of XBB.1.9.2.7, S:R403K, S:L513F, ORF1a:N2531S, Germany/England @@ -3314,7 +3314,7 @@ FU.4 Alias of XBB.1.16.1.4, S:Y453F, T29410C, from #1832 FU.5 Alias of XBB.1.16.1.5, S:K97E, ORF1a:R542C, Bangladesh, from #2137 XBB.1.16.2 Defined by ORF3a:V13L, ORF1a:P926H, India, from #1802 GY.1 Alias of XBB.1.16.2.1, S:L84I, ORF1a:A4068S, China, from #2066 -GY.1.1 Alias of XBB.1.16.2.1.1, S:F456L, S:L455F, China, from sars-cov-2-variants/lineage-proposals#804 +GY.1.1 Alias of XBB.1.16.2.1.1, S:L455F (G22927T), S:F456L (T22928C), China, from sars-cov-2-variants/lineage-proposals#804 GY.1.1.1 Alias of XBB.1.16.2.1.1.1, S:A475V, Thailand, from sars-cov-2-variants/lineage-proposals#804 GY.2 Alias of XBB.1.16.2.2, S:T883I GY.2.1 Alias of XBB.1.16.2.2.1, S:S255F, South Korea @@ -3323,18 +3323,18 @@ GY.4 Alias of XBB.1.16.2.4, S:N450K, C29095T, Laos, from sars-cov-2-variants/lin GY.5 Alias of XBB.1.16.2.5, G9190C GY.6 Alias of XBB.1.16.2.6, ORF1a:V1765I, from sars-cov-2-variants/lineage-proposals#308 GY.7 Alias of XBB.1.16.2.7, ORF1a:G3617C, G5515T, Thailand/Laos -GY.8 Alias of XBB.1.16.2.8, S:F456L(T22928C), C25452T, Japan, from #2148 +GY.8 Alias of XBB.1.16.2.8, S:F456L (T22928C), C25452T, Japan, from #2148 GY.9 Alias of XBB.1.16.2.9, S:F186S, Europe XBB.1.16.3 Defined by A2893C, India XBB.1.16.4 Defined by S:T678I, India, from #1903 XBB.1.16.5 Defined by T9991C,C16332T, India, from #1983 -XBB.1.16.6 S:F456L (T22930A), A12397G, USA/Canada/China -JF.1 Alias of XBB.1.16.6.1, S:L455F, USA, from #2207 +XBB.1.16.6 S:F456L (T22930A), A12397G, USA/Canada/China/Malaysia +JF.1 Alias of XBB.1.16.6.1, S:L455F (G22927T), USA, from #2207 JF.1.1 Alias of XBB.1.16.6.1.1, ORF1a:S2030L JF.1.1.1 Alias of XBB.1.16.6.1.1.1, S:A475V, ORF1a:P2005S, Canada JF.1.1.2 Alias of XBB.1.16.6.1.1.2, S:V1264L JF.2 Alias of XBB.1.16.6.2, S:Q675H, USA/Wales, from sars-cov-2-variants/lineage-proposals#457 -JF.3 Alias of XBB.1.16.6.3, S:L455F, S:Q14H, S:S810L, USA/Australia +JF.3 Alias of XBB.1.16.6.3, S:Q14H, S:L455F (G22927T), S:S810L, USA/Australia JF.4 Alias of XBB.1.16.6.4, ORF1a:S212L, ORF8:A15V XBB.1.16.7 S:T732I after T12214C, Singapore/Japan/SouthKorea XBB.1.16.8 S:T732I after C28531T, India/USA/China/Australia @@ -3360,8 +3360,8 @@ XBB.1.16.22 ORF3a:E242Q, from #1893 XBB.1.16.23 S:K304Q, India/USA/Japan/Singapore, from #2187 XBB.1.16.24 S:K182E, S:V551I, S:E554K, on A25410G branch, India, from #2223 XBB.1.16.25 ORF1a:K510E, C16611T, A29221G -XBB.1.16.26 S:L455F, S:F456L, China, from sars-cov-2-variants/lineage-proposals#685 -XBB.1.16.27 S:F456L, S:E554K, ORF1a:A3889T, France, from #2345 +XBB.1.16.26 S:L455F (G22927T), S:F456L (T22928C), China, from sars-cov-2-variants/lineage-proposals#685 +XBB.1.16.27 S:F456L (T22928C), S:E554K, ORF1a:A3889T, France, from #2345 XBB.1.16.28 S:V1230A, S:Q613H, S:Q675K, Russia XBB.1.16.29 S:T883I, on C7765T branch, TrinidadTobago XBB.1.16.30 S:E554Q, on C7765T branch, USA/Germany @@ -3392,7 +3392,7 @@ GA.8 Alias of XBB.1.17.1.8, C3619T, C27389T, Congo GA.8.1 Alias of XBB.1.17.1.8.1, S:K182E, S:S494P, S:E554K, France/Belgium GA.9 Alias of XBB.1.17.1.9, ORF3a:K67N,T7534C,C29719A GA.10 Alias of XBB.1.17.1.10, ORF1a:V4520I, Mali -GA.10.1 Alias of XBB.1.17.1.10.1, S:L455F, S:F456L, S:K478R, ORF1a:A776V, ORF1a:F1214S, ORF1b:K1947R, from sars-cov-2-variants/lineage-proposals#919 +GA.10.1 Alias of XBB.1.17.1.10.1, S:L455F (G22927T), S:F456L (T22928C), S:K478R, ORF1a:A776V, ORF1a:F1214S, ORF1b:K1947R, from sars-cov-2-variants/lineage-proposals#919 XBB.1.17.2 Defined by ORF1a:A698S, Russia, from #1712 XBB.1.18 Defined by A8001G, Brazil XBB.1.18.1 Defined by S:F486P, Brazil @@ -3409,11 +3409,11 @@ FE.1.2 Alias of XBB.1.18.1.1.2, A5488G XBB.1.19 Defined by S:486P, A10042G, T21363C, on C541T, pre ORF8:8* branch, Pakistan, from #1680 XBB.1.19.1 Defined by S:E554K, Pakistan, from #1765 GW.1 Alias of XBB.1.19.1.1, ORF1a:D264N, N:M322V, China, from sars-cov-2-variants/lineage-proposals#157 -GW.1.1 Alias of XBB.1.19.1.1.1, S:F456L(T22928C), China/Japan/Singapore, from sars-cov-2-variants/lineage-proposals#355 +GW.1.1 Alias of XBB.1.19.1.1.1, S:F456L (T22928C), China/Japan/Singapore, from sars-cov-2-variants/lineage-proposals#355 GW.2 Alias of XBB.1.19.1.2, S:D936G, USA GW.3 Alias of XBB.1.19.1.3, ORF1a:S100N, ORF1a:N3537S GW.4 Alias of XBB.1.19.1.4, ORF1a:M3280I -GW.5 Alias of XBB.1.19.1.5, S:K478I, S:L455F, S:F456L(T22928C), Pakistan, from #2142 +GW.5 Alias of XBB.1.19.1.5, S:L455F (G22927T), S:F456L (T22928C), S:K478I, Pakistan, from #2142 GW.5.1 Alias of XBB.1.19.1.5.1, ORF3a:W149C, Pakistan GW.5.1.1 Alias of XBB.1.19.1.5.1.1, S:A475V, S:F79S, Pakistan, from #2277 KE.1 Alias of XBB.1.19.1.5.1.1.1, S:F186S, England/Wales @@ -3494,7 +3494,7 @@ XBB.1.33 Defined by S:A376Trev, on ORF1b:L1061I, A27965G, pre ORF8:8* branch, fo XBB.1.34 S:486P, S:681R, N:A50V, Uganda/Sudan, from #1621 XBB.1.34.1 S:E554K, ORF1b:P970L XBB.1.34.2 S:K182I, ORF8:C90F, ORF1a:G989C -HB.1 Alias of XBB.1.34.2.1, S:F456L (22928C), USA/China/Canada, from sars-cov-2-variants/lineage-proposals#217 +HB.1 Alias of XBB.1.34.2.1, S:F456L (T22928C), USA/China/Canada, from sars-cov-2-variants/lineage-proposals#217 XBB.1.35 ORF1a:V89A, Indonesia XBB.1.36 Defined by S:S490P, found mainly in Malaysia, Indonesia and Singapore, from #1781 XBB.1.37 Defined by A5371G, Indonesia/Russia, from #1929 @@ -3530,7 +3530,7 @@ XBB.1.45.1 S:486P, A3139G, A19137G, C28291T, USA/Portugal, from #1937 XBB.1.46 ORF1a:C1114F, Singapore/Malaysia XBB.1.47 ORF1a:T1761I, ORF1a:C2180Y, ORF1a:I2854V, Philippines/Singapore/Japan XBB.1.47.1 S:486P, S:A260V, S:V1122G, Japan/USA/Australia/Germany -XBB.1.48 S:L455F, S:F456L (22928C), C2509T, on C541T, pre ORF8:8* branch, Pakistan, from #1681 +XBB.1.48 S:L455F (G22927T), S:F456L (T22928C), C2509T, on C541T, pre ORF8:8* branch, Pakistan, from #1681 XBB.1.49 S:346S, S:486P, on ORF1b:L1061I, A27965G, pre ORF8:8* branch with XBB.1.33, Somalia, from sars-cov-2-variants/lineage-proposals#208 XBB.2 Defined by S:D253G, from #1173 XBB.2.1 Defined by S:N764R (C23853G), two step mutation on top of C23854A (S:N764K defining of all Omicrons) @@ -3660,7 +3660,7 @@ XBC Recombinant lineage of BA.2 and B.1.617.2*, predominantly in Philippines, fr XBC.1 Mostly Philippines, South Korea, USA, Singapore, defined by S:L452M, from #1130 XBC.1.1 Mostly Australia, ORF1a:I3619T, ORF8:V114L XBC.1.1.1 Australia, S:G476S -XBC.1.1.2 S:L244F, ORF7b:L32F, Australia +XBC.1.1.2 ORF7b:L32F, Australia XBC.1.2 Philippines/Netherlands/Denmark, T11269C XBC.1.2.1 Denmark, ORF1b:T132I XBC.1.3 Philippines/Australia, C25614T @@ -4058,8 +4058,8 @@ XDM Recombinant lineage of XDA, GW.5, XDA (breakpoints between 22107-22926 and 2 *H.1 Withdrawn: Alias of B.1.1.67.1, South African lineage, split from B.1.1.10 *I.1 Withdrawn: Alias of B.1.1.217.1, Latvian lineage, split from B.1.1.25 *J.1 Withdrawn: Alias of B.1.1.250.1, Australian lineage -*HK.1.1 Withdrawn as smaller than thought (only 6 sequences have 257V and G22927T): Alias of XBB.1.9.2.5.1.1.1.1, S:455F (G22927T), China -*HK.10 Withdrawn unless lineage grows: Alias of XBB.1.9.2.5.1.1.10, S:L455F, on C19983T branch, China +*HK.1.1 Withdrawn as smaller than thought (only 6 sequences have 257V and G22927T): Alias of XBB.1.9.2.5.1.1.1.1, S:L455F (G22927T), China +*HK.10 Withdrawn unless lineage grows: Alias of XBB.1.9.2.5.1.1.10, S:L455F (G22927T), on C19983T branch, China (now considered as HK.3 with homoplastic C19983T) *HK.3.11 Withdrawn, as part of 14988C sublineage of EG.5.1.1, not HK.3: Alias of XBB.1.9.2.5.1.1.3.11, S:A475V, Finland/Denmark/Sweden *KD.5 Withdrawn: Alias of XBC.1.3.1.5, S:L244F, Australia, indel artefact caused false S:L244F (#2405)