From 4401ad493c0be700b615a6f4c8a5cf2f1e944ac7 Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Mon, 20 May 2024 17:47:39 +0800 Subject: [PATCH 1/3] Update lineage_notes.txt --- lineage_notes.txt | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index f6147c7b..85cac1ee 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1126,7 +1126,7 @@ KP.2.13 Alias of B.1.1.529.2.86.1.1.11.1.2.13, S:K478E, N:P6T, C9565T, C24553T, KP.3 Alias of B.1.1.529.2.86.1.1.11.1.3, S:Q493E, from sars-cov-2-variants/lineage-proposals#1410 KP.3.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1, G15372T, A19722G KP.3.2 Alias of B.1.1.529.2.86.1.1.11.1.3.2, A2611C, C22858T -KP.3.3 Alias of B.1.1.529.2.86.1.1.11.1.3.3, S:R204P +KP.3.3 Alias of B.1.1.529.2.86.1.1.11.1.3.3, N:R204P KP.4 Alias of B.1.1.529.2.86.1.1.11.1.4, C6070T, India KP.4.1 Alias of B.1.1.529.2.86.1.1.11.1.4.1, S:R346T, C19884T KP.4.2 Alias of B.1.1.529.2.86.1.1.11.1.4.2, S:R346T, S:K187R @@ -1183,8 +1183,8 @@ JN.1.37 Alias of B.1.1.529.2.86.1.1.37, S:S680F JN.1.38 Alias of B.1.1.529.2.86.1.1.38, ORF1b:R1736K, USA JN.1.39 Alias of B.1.1.529.2.86.1.1.39, G2782T JN.1.39.1 Alias of B.1.1.529.2.86.1.1.39.1, S:R346T, S:F456L, C21034T, T25631C, A16011G, T6913C -JN.1.39.2 Alias of B.1.1.529.2.86.1.1.39.2, S:R346T, T111C -JN.1.39.3 Alias of B.1.1.529.2.86.1.1.39.3, S:A67V, T111C, C5512T, China from #2498 (originally known as JN.1.33) +JN.1.39.2 Alias of B.1.1.529.2.86.1.1.39.2, S:R346T, after T111C +JN.1.39.3 Alias of B.1.1.529.2.86.1.1.39.3, S:A67V, C5512T, after T111C, China from #2498 (originally known as JN.1.33) JN.1.40 Alias of B.1.1.529.2.86.1.1.40, S:S31P, Mexico, from sars-cov-2-variants/lineage-proposals#1451 JN.1.41 Alias of B.1.1.529.2.86.1.1.41, S:S1252F, on A29086T, USA, from sars-cov-2-variants/lineage-proposals#1256 JN.1.42 Alias of B.1.1.529.2.86.1.1.42, C5581A, South America @@ -3945,9 +3945,9 @@ XDG Recombinant lineage of FL.37 and EG.5.2.4 (breakpoint at 6729-9693), from #2 XDH Recombinant lineage of BN.1.2.8 and XBB.1.9.1 (or XBB.1.22) (breakpoint between 22630-22663), Lithuania/Belarus, from sars-cov-2-variants/lineage-proposals#128 XDJ Recombinant lineage of XBB.1.16.6 and HK.3.1 (breakpoint between 14857 and 16877), France, from sars-cov-2-variants/lineage-proposals#997 XDK Recombinant lineage of XBB.1.16.11 (likely) and JN.1.1.1 (breakpoint between 5315 and 6182), France, from #2415 -XDK.1 S:R346T, G11596A, from sars-cov-2-variants/lineage-proposals#1407 -XDK.1.1 S:K182R, S:E213G, India -XDK.1.2 S:F456L +XDK.1 S:R346T, G11596A, most with S:E213G, from sars-cov-2-variants/lineage-proposals#1407 +XDK.1.1 S:K182R, India +XDK.1.2 S:F456L, pre S:E213G XDK.2 S:K679R, T4996A, C11173T, A23598G, C27297T XDK.3 S:F456L, ORF1a:F3397L XDL Recombinant lineage of EG.5.1.1 and non-EG.5 (breakpoint between 25573-29624) with S:I1114T, most with S:L455F(G22927T), China, from #2351 From 9fb59167f169b01664c82a7ce3a9f38d7806242c Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Tue, 21 May 2024 23:18:03 +0800 Subject: [PATCH 2/3] Update lineage_notes.txt --- lineage_notes.txt | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 85cac1ee..bb3eb4d7 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1056,14 +1056,14 @@ JN.1.1.2 Alias of B.1.1.529.2.86.1.1.1.2, S:G181E, France, from sars-cov-2-varia JN.1.1.3 Alias of B.1.1.529.2.86.1.1.1.3, S:R346T JN.1.1.4 Alias of B.1.1.529.2.86.1.1.1.4, S:V1264L on C9142T branch, from #2476 JN.1.1.5 Alias of B.1.1.529.2.86.1.1.1.5, S:R346T on C9142T branch, from #2492 -KR.1 Alias of B.1.1.529.2.86.1.1.1.5.1, S:F456L, after C28498T, from sars-cov-2-variants/lineage-proposals#1253 -JN.1.1.6 Alias of B.1.1.529.2.86.1.1.1.6, S:F456L, from sars-cov-2-variants/lineage-proposals#1253 +KR.1 Alias of B.1.1.529.2.86.1.1.1.5.1, S:F456L (T22928C), after C28498T, from sars-cov-2-variants/lineage-proposals#1253 +JN.1.1.6 Alias of B.1.1.529.2.86.1.1.1.6, S:F456L (T22928C), from sars-cov-2-variants/lineage-proposals#1253 KZ.1 Alias of B.1.1.529.2.86.1.1.1.6.1, ORF1b:V1092F KZ.1.1 Alias of B.1.1.529.2.86.1.1.1.6.1.1, S:R346T from #2548 KZ.1.1.1 Alias of B.1.1.529.2.86.1.1.1.6.1.1.1, S:T572I from #2548 JN.1.1.7 Alias of B.1.1.529.2.86.1.1.1.7, S:S31F, from sars-cov-2-variants/lineage-proposals#1157 LC.1 Alias of B.1.1.529.2.86.1.1.1.7.1, S:R346T -JN.1.1.8 Alias of B.1.1.529.2.86.1.1.1.8, S:F456L (22930A), S:H445P, ORF1a:S2083I, C850T +JN.1.1.8 Alias of B.1.1.529.2.86.1.1.1.8, S:F456L (T22930A), S:H445P, ORF1a:S2083I, C850T JN.1.2 Alias of B.1.1.529.2.86.1.1.2, S:M1229I, USA/Canada, from sars-cov-2-variants/lineage-proposals#1087 JN.1.2.1 Alias of B.1.1.529.2.86.1.1.2.1, S:H1101Y, Ireland, from sars-cov-2-variants/lineage-proposals#1322 JN.1.3 Alias of B.1.1.529.2.86.1.1.3, ORF8:Q18*, Netherlands @@ -1102,7 +1102,7 @@ JN.1.9.2 Alias of B.1.1.529.2.86.1.1.9.2, S:R346T LB.1 Alias of B.1.1.529.2.86.1.1.9.2.1, S:F456L (T22928C) JN.1.10 Alias of B.1.1.529.2.86.1.1.10, S:T95I, USA/Canada, from sars-cov-2-variants/lineage-proposals#1135 JN.1.11 Alias of B.1.1.529.2.86.1.1.11, S:V1104L, G17334T, India, from #2446 -JN.1.11.1 Alias of B.1.1.529.2.86.1.1.11.1, S:F456L, after ORF1a:T2283I, India, from sars-cov-2-variants/lineage-proposals#1253 +JN.1.11.1 Alias of B.1.1.529.2.86.1.1.11.1, S:F456L (T22928C), after ORF1a:T2283I, India, from sars-cov-2-variants/lineage-proposals#1253 KP.1 Alias of B.1.1.529.2.86.1.1.11.1.1, S:K1086R, from sars-cov-2-variants/lineage-proposals#1364 KP.1.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1, S:R346T, from sars-cov-2-variants/lineage-proposals#1089 KP.1.1.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1.1, S:K182N from #2510 @@ -1135,10 +1135,10 @@ KP.5 Alias of B.1.1.529.2.86.1.1.11.1.5, S:T572I JN.1.12 Alias of B.1.1.529.2.86.1.1.12, S:F456V, ORF7a:A8T, from sars-cov-2-variants/lineage-proposals#1253 JN.1.13 Alias of B.1.1.529.2.86.1.1.13, S:A1087S, after C26894T, C25680T, USA, from #2464 JN.1.13.1 Alias of B.1.1.529.2.86.1.1.13.1, S:R346T, S:F59S, USA, from sars-cov-2-variants/lineage-proposals/issues/1386 -KS.1 Alias of B.1.1.529.2.86.1.1.13.1.1, S:F456L, from sars-cov-2-variants/lineage-proposals#1253 +KS.1 Alias of B.1.1.529.2.86.1.1.13.1.1, S:F456L (T22928C), from sars-cov-2-variants/lineage-proposals#1253 JN.1.14 Alias of B.1.1.529.2.86.1.1.14, S:R346S, after C26894T, C25680T, USA JN.1.15 Alias of B.1.1.529.2.86.1.1.15, S:A688V -JN.1.16 Alias of B.1.1.529.2.86.1.1.16, S:F456L, from sars-cov-2-variants/lineage-proposals#1253 +JN.1.16 Alias of B.1.1.529.2.86.1.1.16, S:F456L (T22928C), from sars-cov-2-variants/lineage-proposals#1253 JN.1.16.1 Alias of B.1.1.529.2.86.1.1.16.1, S:R346T, from sars-cov-2-variants/lineage-proposals#1089 LF.1 Alias of B.1.1.529.2.86.1.1.16.1.1, ORF1a:A1268T, ORF1a:S2103F LF.1.1 Alias of B.1.1.529.2.86.1.1.16.1.1.1, S:P1263L @@ -1163,7 +1163,7 @@ JN.1.27 Alias of B.1.1.529.2.86.1.1.27, S:M153I, after C26894T, C25680T, USA, fr JN.1.28 Alias of B.1.1.529.2.86.1.1.28, C24034T, A29700G, East Asia/Oceania JN.1.28.1 Alias of B.1.1.529.2.86.1.1.28.1, ORF1a:P1640L, C19545T, C24370T, from sars-cov-2-variants/lineage-proposals#1244 KW.1 Alias of B.1.1.529.2.86.1.1.28.1.1, S:T572I, Australia, from sars-cov-2-variants/lineage-proposals#1244 -KW.1.1 Alias of B.1.1.529.2.86.1.1.28.1.1.1, S:F456L, ORF1b:R2009K, Australia/Japan, from sars-cov-2-variants/lineage-proposals#1244 +KW.1.1 Alias of B.1.1.529.2.86.1.1.28.1.1.1, S:F456L (T22928C), ORF1b:R2009K, Australia/Japan, from sars-cov-2-variants/lineage-proposals#1244 KW.1.1.1 Alias of B.1.1.529.2.86.1.1.28.1.1.1.1, S:T95S, Australia LG.1 Alias of B.1.1.529.2.86.1.1.28.1.1.1.1.1, S:R346T, Australia KW.1.2 Alias of B.1.1.529.2.86.1.1.28.1.1.2, S:K529T, Australia @@ -1171,7 +1171,7 @@ JN.1.29 Alias of B.1.1.529.2.86.1.1.29, ORF1a:T3224A, after C2644T, Brazil JN.1.30 Alias of B.1.1.529.2.86.1.1.30, G21255T JN.1.30.1 Alias of B.1.1.529.2.86.1.1.30.1, S:R346T, after T7789C, India, from sars-cov-2-variants/lineage-proposals#1089 KU.1 Alias of B.1.1.529.2.86.1.1.30.1.1, S:K182Q -KU.2 Alias of B.1.1.529.2.86.1.1.30.1.2, S:F456L, from sars-cov-2-variants/lineage-proposals#1089 +KU.2 Alias of B.1.1.529.2.86.1.1.30.1.2, S:F456L (T22928C), from sars-cov-2-variants/lineage-proposals#1089 JN.1.31 Alias of B.1.1.529.2.86.1.1.31, ORF3a:V13L, C19186T, from sars-cov-2-variants/lineage-proposals#1319 JN.1.32 Alias of B.1.1.529.2.86.1.1.32, S:T572I, directly on JN.1 polytomy JN.1.32.1 Alias of B.1.1.529.2.86.1.1.32.1, S:Q183H @@ -1182,7 +1182,7 @@ JN.1.36.1 Alias of B.1.1.529.2.86.1.1.36.1, S:S680F, South Korea, from sars-cov- JN.1.37 Alias of B.1.1.529.2.86.1.1.37, S:S680F JN.1.38 Alias of B.1.1.529.2.86.1.1.38, ORF1b:R1736K, USA JN.1.39 Alias of B.1.1.529.2.86.1.1.39, G2782T -JN.1.39.1 Alias of B.1.1.529.2.86.1.1.39.1, S:R346T, S:F456L, C21034T, T25631C, A16011G, T6913C +JN.1.39.1 Alias of B.1.1.529.2.86.1.1.39.1, S:R346T, S:F456L (T22928C), C21034T, T25631C, A16011G, T6913C JN.1.39.2 Alias of B.1.1.529.2.86.1.1.39.2, S:R346T, after T111C JN.1.39.3 Alias of B.1.1.529.2.86.1.1.39.3, S:A67V, C5512T, after T111C, China from #2498 (originally known as JN.1.33) JN.1.40 Alias of B.1.1.529.2.86.1.1.40, S:S31P, Mexico, from sars-cov-2-variants/lineage-proposals#1451 @@ -1199,13 +1199,13 @@ JN.1.47 Alias of B.1.1.529.2.86.1.1.47, C8074T, C7594T JN.1.47.1 Alias of B.1.1.529.2.86.1.1.47.1, S:S221L, USA/Mexico JN.1.47.2 Alias of B.1.1.529.2.86.1.1.47.2, S:T572I, S:R683Q, USA JN.1.48 Alias of B.1.1.529.2.86.1.1.48, G29134T, after T18471C, India -JN.1.48.1 Alias of B.1.1.529.2.86.1.1.48.1, S:S60P, S:R346T, S:F456L, after ORF3a:A99V from #2547 +JN.1.48.1 Alias of B.1.1.529.2.86.1.1.48.1, S:S60P, S:R346T, S:F456L (T22928C), after ORF3a:A99V from #2547 LD.1 Alias of B.1.1.529.2.86.1.1.48.1.1, S:T572I JN.1.48.2 Alias of B.1.1.529.2.86.1.1.48.2, S:R346T, ORF1a:A427V, A3829G, India JN.1.49 Alias of B.1.1.529.2.86.1.1.49, ORF3a:T89I, India JN.1.49.1 Alias of B.1.1.529.2.86.1.1.49.1, S:R346T -JN.1.49.2 Alias of B.1.1.529.2.86.1.1.49.2, S:F456L -JN.1.50 Alias of B.1.1.529.2.86.1.1.50, S:H445P,S:F456L, S:A67V, S:L249F, Europe +JN.1.49.2 Alias of B.1.1.529.2.86.1.1.49.2, S:F456L (T22930A) +JN.1.50 Alias of B.1.1.529.2.86.1.1.50, S:H445P,S:F456L (T22930G), S:A67V, S:L249F, Europe JN.2 Alias of B.1.1.529.2.86.1.2, ORF1a:Y621C, Europe/North America, from #2284 JN.2.1 Alias of B.1.1.529.2.86.1.2.1, S:S31F, Sweden/Australia JN.2.2 Alias of B.1.1.529.2.86.1.2.2, S:T572I, N:G25C, ORF1a:L3644F, Netherlands, from #2433 @@ -1242,7 +1242,7 @@ BA.2.86.3 Alias of B.1.1.529.2.86.3, C222T, C1960T, T12775C, South Africa JQ.1 Alias of B.1.1.529.2.86.3.1, S:T95I, Denmark/France/South Africa, from sars-cov-2-variants/lineage-proposals#906 JQ.2 Alias of B.1.1.529.2.86.3.2, S:R346T, G2944A, South Africa, from #2505 JQ.2.1 Alias of B.1.1.529.2.86.3.2.1, S:L455S, South Africa, from sars-cov-2-variants/lineage-proposals#1373 -JQ.2.1.1 Alias of B.1.1.529.2.86.3.2.1.1, S:F456L, South Africa +JQ.2.1.1 Alias of B.1.1.529.2.86.3.2.1.1, S:F456L (T22928C), South Africa BA.2.86.4 Alias of B.1.1.529.2.86.4, S:A222V, ORF1a:V3892A, from sars-cov-2-variants/lineage-proposals#1032 BA.2.86.5 Alias of B.1.1.529.2.86.5, S:I197V, C5575T, T6085C, T23278C BA.2.86.6 Alias of B.1.1.529.2.86.6, C9226T @@ -3947,9 +3947,9 @@ XDJ Recombinant lineage of XBB.1.16.6 and HK.3.1 (breakpoint between 14857 and 1 XDK Recombinant lineage of XBB.1.16.11 (likely) and JN.1.1.1 (breakpoint between 5315 and 6182), France, from #2415 XDK.1 S:R346T, G11596A, most with S:E213G, from sars-cov-2-variants/lineage-proposals#1407 XDK.1.1 S:K182R, India -XDK.1.2 S:F456L, pre S:E213G +XDK.1.2 S:F456L (T22928C), pre S:E213G XDK.2 S:K679R, T4996A, C11173T, A23598G, C27297T -XDK.3 S:F456L, ORF1a:F3397L +XDK.3 S:F456L (T22928C), ORF1a:F3397L XDL Recombinant lineage of EG.5.1.1 and non-EG.5 (breakpoint between 25573-29624) with S:I1114T, most with S:L455F(G22927T), China, from #2351 XDM Recombinant lineage of XDA, GW.5, XDA (breakpoints between 22107-22926 and 24047-25838), from sars-cov-2-variants/lineage-proposals#1163 XDN Recombinant lineage of JN.1.1 and JD.1 (breakpoint between 24379 and 24989), from #2448 From f4ec864ed002247106514c6f513acd615a8ef3b3 Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Tue, 21 May 2024 23:19:39 +0800 Subject: [PATCH 3/3] Update lineage_notes.txt --- lineage_notes.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index bb3eb4d7..747a3a23 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1205,7 +1205,7 @@ JN.1.48.2 Alias of B.1.1.529.2.86.1.1.48.2, S:R346T, ORF1a:A427V, A3829G, India JN.1.49 Alias of B.1.1.529.2.86.1.1.49, ORF3a:T89I, India JN.1.49.1 Alias of B.1.1.529.2.86.1.1.49.1, S:R346T JN.1.49.2 Alias of B.1.1.529.2.86.1.1.49.2, S:F456L (T22930A) -JN.1.50 Alias of B.1.1.529.2.86.1.1.50, S:H445P,S:F456L (T22930G), S:A67V, S:L249F, Europe +JN.1.50 Alias of B.1.1.529.2.86.1.1.50, S:A67V, S:L249F, S:H445P, S:F456L (T22930G), Europe JN.2 Alias of B.1.1.529.2.86.1.2, ORF1a:Y621C, Europe/North America, from #2284 JN.2.1 Alias of B.1.1.529.2.86.1.2.1, S:S31F, Sweden/Australia JN.2.2 Alias of B.1.1.529.2.86.1.2.2, S:T572I, N:G25C, ORF1a:L3644F, Netherlands, from #2433