From 1573dd8e69515c0cc795d7d8f88fa2972726cf4a Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Thu, 30 Jan 2025 16:42:22 +0800 Subject: [PATCH 1/9] Update lineage_notes.txt --- lineage_notes.txt | 56 +++++++++++++++++++++++------------------------ 1 file changed, 28 insertions(+), 28 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 3df28b85..1dab0e97 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1144,7 +1144,7 @@ LB.1.3.2 Alias of B.1.1.529.2.86.1.1.9.2.1.3.2, C25413T MH.1 Alias of B.1.1.529.2.86.1.1.9.2.1.3.2.1, S:T572I LB.1.3.3 Alias of B.1.1.529.2.86.1.1.9.2.1.3.3, S:K182R, from #2723 LB.1.3.4 Alias of B.1.1.529.2.86.1.1.9.2.1.3.4, S:A376S, ORF1a:G432S, South Africa, from #2825 -NZ.1 Alias of B.1.1.529.2.86.1.1.9.2.1.3.4.1, S:H445R, South Africa +NZ.1 Alias of B.1.1.529.2.86.1.1.9.2.1.3.4.1, S:H445R, South Africa, from #2825 LB.1.3.5 Alias of B.1.1.529.2.86.1.1.9.2.1.3.5, ORF3a:T64I LB.1.4 Alias of B.1.1.529.2.86.1.1.9.2.1.4, ORF1a:A1473V LB.1.4.1 Alias of B.1.1.529.2.86.1.1.9.2.1.4.1, S:R190S @@ -1184,22 +1184,22 @@ LP.7 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.7, S:R190S, from sars-cov-2-variants LP.8 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8, S:H445R, S:Q493E, S:F186L, ORF3a:P178L, Singapore/Philippines, from #2811 LP.8.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1, S:R190S, from sars-cov-2-variants/lineage-proposals#2199 LP.8.1.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.1, S:K679R, from sars-cov-2-variants/lineage-proposals#2199 -NY.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.1.1.1, S:P85S +NY.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.1.1.1, S:P85S, from #2861 NY.2 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.1.1.2, ORF1a:T2846I -NY.3 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.1.1.3, S:R765L +NY.3 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.1.1.3, S:R765L, from #2874 NY.4 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.1.1.4, ORF1b:V1649I NY.5 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.1.1.5, ORF1a:F843Y -NY.6 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.1.1.6, S:A475V +NY.6 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.1.1.6, S:A475V, on LP.8.1.1 polytomy directly, from #2872 NY.7 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.1.1.7, S:T22N LP.8.1.2 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.2, S:N487D, from sars-cov-2-variants/lineage-proposals#2199 -NW.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.2.1, S:A1174V, ORF3a:L101F +NW.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.2.1, S:A1174V, ORF3a:L101F, from sars-cov-2-variants/lineage-proposals#2199 LP.8.1.3 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.3, S:Q677H, from #2876 LP.8.1.4 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.4, C16308T, Brazil LP.8.1.5 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.5, ORF1a:K3353R -LP.8.1.6 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.6, S:T22N -LP.8.1.7 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.7, ORF1b:V980I +LP.8.1.6 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.6, S:T22N, on LP.8.1 polytomy directly, from #2868 +LP.8.1.7 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.7, ORF1b:V980I, ORF10:Q29*, from #2869 LP.8.1.8 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.8, N:A134V -LP.8.1.9 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.9, S:A475V +LP.8.1.9 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.1.9, S:A475V, on LP.8.1 polytomy directly, #2853 LP.8.2 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.2, S:M153I, S:L176F, on ORF1b:P1452L branch, from sars-cov-2-variants/lineage-proposals#2199 LP.8.2.1 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.8.2.1, S:A475V, ORF1a:T1246I, from sars-cov-2-variants/lineage-proposals#2199 LP.9 Alias of B.1.1.529.2.86.1.1.11.1.1.1.3.9, S:H445P, S:L176F, ORF1a:L1191F @@ -1289,7 +1289,7 @@ KP.3.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1, G15372T, A19722G KP.3.1.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1, ORF1a:S4286C, C12616T, S:S31del, Spain, from sars-cov-2-variants/lineage-proposals#1563 MC.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1, S:T572I, from sars-cov-2-variants/lineage-proposals#1638 MC.1.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.1, S:A942S, C13297T, C14220T, from sars-cov-2-variants/lineage-proposals#1932 -MC.1.1.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.1.1, ORF1a:P1096L, C13264T, Australia-SA +MC.1.1.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.1.1, ORF1a:P1096L, C13264T, C27247T, Australia-SA MC.1.2 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.2, S:A1174V, sibling of MC.1.1, from sars-cov-2-variants/lineage-proposals#2206 MC.1.3 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.3, ORF1a:E977D MC.1.3.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.3.1, S:F4L, from sars-cov-2-variants/lineage-proposals#2192 @@ -1377,7 +1377,7 @@ ML.1 Alias of B.1.1.529.2.86.1.1.11.1.3.3.3.1, S:681H, from sars-cov-2-variants/ ML.2 Alias of B.1.1.529.2.86.1.1.11.1.3.3.3.2, S:Q677H, USA KP.3.3.4 Alias of B.1.1.529.2.86.1.1.11.1.3.3.4, ORF1a:I1367L, from #2707 MR.1 Alias of B.1.1.529.2.86.1.1.11.1.3.3.4.1, S:S31del, ORF1a:V1236I, from #2704 -KP.3.3.5 Alias of B.1.1.529.2.86.1.1.11.1.3.3.5, S:A435S, Chile, from #2844 +KP.3.3.5 Alias of B.1.1.529.2.86.1.1.11.1.3.3.5, S:S31del, A435S, Chile, from #2844 KP.3.4 Alias of B.1.1.529.2.86.1.1.11.1.3.4, ORF3a:L73F, C25521T, Asia KP.3.4.1 Alias of B.1.1.529.2.86.1.1.11.1.3.4.1, S:S31F, N:A134V, ORF1a:E1192K, from sars-cov-2-variants/lineage-proposals#1576 KP.3.5 Alias of B.1.1.529.2.86.1.1.11.1.3.5, S:G213E, most with C1420T, America, from sars-cov-2-variants/lineage-proposals#1630 @@ -4432,11 +4432,11 @@ XDV.1.4 S:I1114T XDV.1.5 S:G184S, S:K478I, China, from sars-cov-2-variants/lineage-proposals#1840 XDV.1.5.1 ORF1a:H1141Y, ORF1a:A1473V, ORF3a:R134H, China NB.1 Alias of XDV.1.5.1.1, S:T22N, S:F59S, ORF1a:I2709V, ORF1a:P4197S, China, from sars-cov-2-variants/lineage-proposals#1840 -NB.1.1 Alias of XDV.1.5.1.1.1, S:I478T (rev), from sars-cov-2-variants/lineage-proposals#2280 -NB.1.2 Alias of XDV.1.5.1.1.2, S:V1264L, China -NB.1.3 Alias of XDV.1.5.1.1.3, G19824A -NB.1.3.1 Alias of XDV.1.5.1.1.3.1, S:T572I -NB.1.4 Alias of XDV.1.5.1.1.4, C26801T +NB.1.1 Alias of XDV.1.5.1.1.1, S:I478T (rev), on ORF1b:D275Y branch, from sars-cov-2-variants/lineage-proposals#2280 +NB.1.2 Alias of XDV.1.5.1.1.2, S:V1264L, China, from sars-cov-2-variants/lineage-proposals#2307 +NB.1.3 Alias of XDV.1.5.1.1.3, G19824A, on ORF1b:D275Y branch +NB.1.3.1 Alias of XDV.1.5.1.1.3.1, S:T572I, from sars-cov-2-variants/lineage-proposals#2299 +NB.1.4 Alias of XDV.1.5.1.1.4, C26801T, on ORF1b:D275Y branch NB.1.5 Alias of XDV.1.5.1.1.5, ORF1a:A117T XDV.1.6 S:K478T, S:A263T, ORF1a:V1783I, ORF1a:E1209D XDV.1.7 ORF1a:D2980N, C8950T, China @@ -4449,9 +4449,9 @@ XDV.1.11 T4057C XDW Recombinant lineage of JN.2 (T1030C branch), XDA (breakpoint between 23424-23603), Japan, from sars-cov-2-variants/lineage-proposals#1471 XDY Recombinant lineage of LB.1.2.1 and KP.3.2 (breakpoint between 22131-22599), Sweden/Spain, from sars-cov-2-variants/lineage-proposals#1559 XDY.1 S:A435S, S:A1174T, N:R36Q, ORF7a:P34L, ORF9b:D33N, France, from sars-cov-2-variants/lineage-proposals#2014 -XDY.1.1 S:T572I -XDY.2 S:Q677H, S:R346T -XDY.3 S:A435S, ORF1a:T4129I +XDY.1.1 S:T572I, from sars-cov-2-variants/lineage-proposals#2014 +XDY.2 S:Q677H, S:R346T, from #2866 +XDY.3 S:A435S, ORF1a:T4129I, from sars-cov-2-variants/lineage-proposals#2281 XDY.4 S:R346T XDY.5 G18756A XDY.5.1 S:T572I, USA @@ -4460,8 +4460,8 @@ XDY.7 C6781T XDZ Recombinant lineage of JG.3 and JN.1.1.10 (breakpoint between 11043-12788), Europe/North America, from sars-cov-2-variants/lineage-proposals#1356 XEA Recombinant lineage of JN.1.63.1 and EG.5 (breakpoint between 27057-27915), East Asia XEB Recombinant lineage of FL.15, JN.1.4+T18453C, FL.15 (breakpoints at 774-896 and 26834-27809), USA, from sars-cov-2-variants/lineage-proposals#1290 -XEC Recombinant lineage of KS.1.1 (JN.1.13.1.1.1) and KP.3.3 (breakpoint 21738-22599), Europe (Germany), from #2717 -XEC.1 S:K182R, ORF1a:L4182F, on ORF1a:A599T branch, France/Ireland/Canada, from sars-cov-2-variants/lineage-proposals#1869 +XEC Recombinant lineage of KS.1.1 (JN.1.13.1.1.1) and KP.3.3 (breakpoint 21738-22599), most with ORF1a:A599T, Europe (Germany), from #2717 +XEC.1 S:K182R, ORF1a:L4182F, France/Ireland/Canada, from sars-cov-2-variants/lineage-proposals#1869 XEC.2 ORF1a:I1367L, lacking ORF1a:A599T, from sars-cov-2-variants/lineage-proposals#1908 XEC.2.1 ORF1a:V3336F, from sars-cov-2-variants/lineage-proposals#2135 XEC.2.2 ORF1a:I280T @@ -4469,7 +4469,7 @@ XEC.2.3 N:T379I, T16476C, from sars-cov-2-variants/lineage-proposals#2104 XEC.2.3.1 S:G181V, from sars-cov-2-variants/lineage-proposals#2104 XEC.3 S:E1202Q, from sars-cov-2-variants/lineage-proposals#2088 XEC.4 S:T572I, from sars-cov-2-variants/lineage-proposals#2087 -XEC.4.1 T23584C, C27294T, C29353T, Australia +XEC.4.1 T23584C, C27294T, C29353T, on C6312T branch, Australia XEC.5 S:G72R, from sars-cov-2-variants/lineage-proposals#2088 XEC.6 S:S680F, from sars-cov-2-variants/lineage-proposals#2088 XEC.7 S:W152R, S:P1263Q, from sars-cov-2-variants/lineage-proposals#2088 @@ -4482,8 +4482,8 @@ XEC.13 S:S98F, from sars-cov-2-variants/lineage-proposals#2088 XEC.14 ORF1a:A138T XEC.15 ORF1b:M2322I, C9803T XEC.16 S:T678I, from sars-cov-2-variants/lineage-proposals#2088 -XEC.17 S:T95I, on ORF1a:A599T branch, Israel, from #2879 -XEC.18 G28378T +XEC.17 S:T95I, Israel, from #2879 +XEC.18 ORF9b:R32L, from #2813 XED Recombinant lineage of JN.1.4 and LF.1.1.1 (breakpoint 19210-21652), from #2691 XEE Recombinant lineage of KP.2.3.7 and JN.1* (breakpoint 24873-25592), from #2721 XEF Recombinant lineage of LB.1.4 and KP.3 (breakpoint 22600-23038), from sars-cov-2-variants/lineage-proposals#1855 @@ -4508,11 +4508,11 @@ XER Recombinant lineage of KS.2, LF.7 (breakpoint: 18349-21626), from sars-cov-2 XES Recombinant lineage of KP.2.3.15, KP.3.3 (breakpoint: 22001-22598), from #2783 XET Recombinant lineage of KP.1.1.1., KP.3.1.1 (breakpoint: 20105-21652), from sars-cov-2-variants/lineage-proposals#2302 XEU Recombinant lineage of XEK, XEC.8 (breakpoint: 3506-7112), from sars-cov-2-variants/lineage-proposals#2298 -XEV Recombinant lineage of KP.3.1.1, XEC.18 (breakpoint: 12617-13120) -XEW Recombinant lineage of KP.3.1.1, XEC.8 (breakpoint: 13122-15371) -XEY Recombinant lineage of MC.29, XEC (breakpoint: 17335-18656) -XEZ Recombinant lineage of MC.6, XEC (breakpoint: 15373-17333) -XFA Recombinant lineage of MC.1.1.1, XEC.4.1 (breakpoint: 13297-15371), from #2878 +XEV Recombinant lineage of KP.3.1.1, XEC.18 (breakpoint: 12617-13120), from #2813 +XEW Recombinant lineage of KP.3.1.1, XEC.8 (breakpoint: 13122-15371), from #2842 +XEY Recombinant lineage of MC.29, XEC (breakpoint: 17746-18656) +XEZ Recombinant lineage of MC.6, XEC (breakpoint: 15373-17333), from sars-cov-2-variants/lineage-proposals#2272 +XFA Recombinant lineage of MC.1.1.1, XEC.4.1 (breakpoint: 13298-14219), from #2878 XFB Recombinant lineage of MC.24, XDY.1.1, MC.24 (breakpoints: 19723-22110,23278-25081), from #2877 XFC Recombinant lineage of LP.8.1.1, LF.7, LP.8.1.1 (breakpoints: 8818-122891,22120-22892), from sars-cov-2-variants/lineage-proposals#2323 *A.2.1 Withdrawn: Lineage with sequences predominantly from Panama From c30a51fe77127ea3143568ed373cd26a3a8d50f8 Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Thu, 30 Jan 2025 19:51:31 +0800 Subject: [PATCH 2/9] 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 1dab0e97..56c770b2 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -4514,7 +4514,7 @@ XEY Recombinant lineage of MC.29, XEC (breakpoint: 17746-18656) XEZ Recombinant lineage of MC.6, XEC (breakpoint: 15373-17333), from sars-cov-2-variants/lineage-proposals#2272 XFA Recombinant lineage of MC.1.1.1, XEC.4.1 (breakpoint: 13298-14219), from #2878 XFB Recombinant lineage of MC.24, XDY.1.1, MC.24 (breakpoints: 19723-22110,23278-25081), from #2877 -XFC Recombinant lineage of LP.8.1.1, LF.7, LP.8.1.1 (breakpoints: 8818-122891,22120-22892), from sars-cov-2-variants/lineage-proposals#2323 +XFC Recombinant lineage of LP.8.1.1, LF.7, LP.8.1.1 (breakpoints: 8818-12891,22120-22892), from sars-cov-2-variants/lineage-proposals#2323 *A.2.1 Withdrawn: Lineage with sequences predominantly from Panama *A.8 Withdrawn: Indian lineage merged with A.9 *A.10 Withdrawn: Spanish lineage reassigned to A.5 From c57d9c602f222aef0c4c90f023305e97da2b8044 Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Sat, 1 Feb 2025 05:36:34 +0800 Subject: [PATCH 3/9] Update lineage_notes.txt --- lineage_notes.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 6e588f6b..ed4c98ae 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1291,16 +1291,16 @@ KP.2.27 Alias of B.1.1.529.2.86.1.1.11.1.2.27, S:T572I, C3811T, C9857T, A23080G, 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.3.1.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1, ORF1a:S4286C, C12616T, S:S31del, Spain, from sars-cov-2-variants/lineage-proposals#1563 -MC.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1, S:T572I, from sars-cov-2-variants/lineage-proposals#1638 -MC.1.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.1, S:A942S, C13297T, C14220T, from sars-cov-2-variants/lineage-proposals#1932 +MC.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1, S:T572I, most with C13297T, from sars-cov-2-variants/lineage-proposals#1638 +MC.1.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.1, S:A942S, on C14220T branch, from sars-cov-2-variants/lineage-proposals#1932 MC.1.1.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.1.1, ORF1a:P1096L, C13264T, Australia-SA -MC.1.2 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.2, S:A1174V, sibling of MC.1.1, from sars-cov-2-variants/lineage-proposals#2206 +MC.1.2 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.2, S:A1174V, on C14220T branch, from sars-cov-2-variants/lineage-proposals#2206 MC.1.3 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.3, ORF1a:E977D MC.1.3.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.3.1, S:F4L, from sars-cov-2-variants/lineage-proposals#2192 MC.1.4 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.4, ORF1a:I671V MC.1.5 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.5, T1030C, C19875T MC.1.6 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.6, C589T, C9857T -MC.1.7 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.7, S:A942S, ORF1a:L3806M, A11500G, A20559G +MC.1.7 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.1.7, S:A942S, ORF1a:L3806M, A11500G, A20559G, without C13297T MC.2 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.2, S:A845S, from sars-cov-2-variants/lineage-proposals#1707 MC.2.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.2.1, S:R237K, from sars-cov-2-variants/lineage-proposals#1707 MC.3 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.3, S:G72R, Spain, from sars-cov-2-variants/lineage-proposals#1733 From b8d17682f34552c80c9ee3977e260af7922bee11 Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Sat, 1 Feb 2025 05:44:01 +0800 Subject: [PATCH 4/9] 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 ed4c98ae..3501e9b0 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1354,7 +1354,7 @@ MC.28.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.28.1, S:C1235F, S:A435S, from sar MC.28.1.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.28.1.1, S:R346T MC.29 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.29, ORF1a:N615K MC.30 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.30, C1093T, T15750C -MC.30.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.30.1, ORF1b:P1645S, NA119T, C23896T, C26801T +MC.30.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.30.1, ORF1b:P1645S, N:A119T, C23896T, C26801T MC.30.1.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.30.1.1, S:T572I, S:A435S MC.31 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.31, S:R346T, S:A435S, ORF1a:L552F, ORF1a:S1825N MC.32 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.32, ORF1a:T1840I From ad1a40b6ccf39fb82e49511e31e0891403d0d89e Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Sat, 1 Feb 2025 05:50:21 +0800 Subject: [PATCH 5/9] Update lineage_notes.txt --- lineage_notes.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 3501e9b0..e3bf8bf6 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1332,8 +1332,8 @@ MC.13.3 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.13.3, S:Q613E, from sars-cov-2-va MC.14 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.14, S:T259R, from sars-cov-2-variants/lineage-proposals#1815 MC.15 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.15, S:K182R MC.16 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.16, G2890A -MC.17 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.17, S:A575S, C5512T, from sars-cov-2-variants/lineage-proposals#1989 -MC.17.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.17.1, S:R346T +MC.17 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.17, S:A575S, C5512T, from #2782 +MC.17.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.17.1, S:R346T, from #2782 MC.18 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.18, S:N185D, ORF1a:G465S, Spain/Canada, from sars-cov-2-variants/lineage-proposals#2075 MC.19 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.19, S:R346T, from sars-cov-2-variants/lineage-proposals#1809 MC.19.1 Alias of B.1.1.529.2.86.1.1.11.1.3.1.1.19.1, S:H445R From 3b418e4e0b2f87dcde3bcc28de295c6c26c11bf9 Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Sat, 1 Feb 2025 05:59:40 +0800 Subject: [PATCH 6/9] 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 e3bf8bf6..05ca1268 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1441,7 +1441,7 @@ NC.1.1 Alias of B.1.1.529.2.86.1.1.13.1.1.1.1.1.1, ORF1a:D1639N NC.1.2 Alias of B.1.1.529.2.86.1.1.13.1.1.1.1.1.2, S:H445P, C16887T, from sars-cov-2-variants/lineage-proposals#2212 NC.2 Alias of B.1.1.529.2.86.1.1.13.1.1.1.1.2, ORF1a:G112S, from sars-cov-2-variants/lineage-proposals#1764 KS.1.1.2 Alias of B.1.1.529.2.86.1.1.13.1.1.1.2, ORF1a:L2146F, C19716T -KS.1.1.3 Alias of B.1.1.529.2.86.1.1.13.1.1.1.3, S:A575S, ORF1a:H1160Y, Russia +KS.1.1.3 Alias of B.1.1.529.2.86.1.1.13.1.1.1.3, S:A575S, ORF1a:D1160Y, ORF1a:H1610Y, Russia KS.1.2 Alias of B.1.1.529.2.86.1.1.13.1.1.2, S:T678I, Russia KS.1.3 Alias of B.1.1.529.2.86.1.1.13.1.1.3, S:V642A, Dominican Republic, from sars-cov-2-variants/lineage-proposals#1535 KS.1.4 Alias of B.1.1.529.2.86.1.1.13.1.1.4, C22414T, S:R237K, from sars-cov-2-variants/lineage-proposals#1752 From 1e24cd05238f9c3e5aafd77cba4967b8b85f4e97 Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Mon, 3 Feb 2025 04:22:20 +0800 Subject: [PATCH 7/9] 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 c9b5609a..b5ad5596 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1270,11 +1270,11 @@ KP.2.9 Alias of B.1.1.529.2.86.1.1.11.1.2.9, S:T572I, from sars-cov-2-variants/l KP.2.10 Alias of B.1.1.529.2.86.1.1.11.1.2.10, S:F59S, Singapore, from sars-cov-2-variants/lineage-proposals#1553 KP.2.11 Alias of B.1.1.529.2.86.1.1.11.1.2.11, S:F56V, ORF1a:T2093I, England, from sars-cov-2-variants/lineage-proposals#1520 KP.2.12 Alias of B.1.1.529.2.86.1.1.11.1.2.12, S:V1176F, G25088T, Australia, from sars-cov-2-variants/lineage-proposals#1550 -KP.2.13 Alias of B.1.1.529.2.86.1.1.11.1.2.13, S:K478E, N:P6T, C9565T, C24553T, USA/Canada +KP.2.13 Alias of B.1.1.529.2.86.1.1.11.1.2.13, S:K478E, N:P6T, ORF9b:D2E, C9565T, C24553T, USA/Canada KP.2.14 Alias of B.1.1.529.2.86.1.1.11.1.2.14, S:T22N, S:S31F, S:G184V, from sars-cov-2-variants/lineage-proposals#1578 KP.2.14.1 Alias of B.1.1.529.2.86.1.1.11.1.2.14.1, S:T572I -KP.2.14.2 Alias of B.1.1.529.2.86.1.1.11.1.2.14.2, S:A435S -KP.2.15 Alias of B.1.1.529.2.86.1.1.11.1.2.15, A10861G, S:31del, USA/Canada +KP.2.14.2 Alias of B.1.1.529.2.86.1.1.11.1.2.14.2, S:A435S, ORF1a:S443T, ORF1a:T2183I +KP.2.15 Alias of B.1.1.529.2.86.1.1.11.1.2.15, A10861G, S:S31del, USA/Canada KP.2.15.1 Alias of B.1.1.529.2.86.1.1.11.1.2.15.1, S:T572I, from #2711 KP.2.16 Alias of B.1.1.529.2.86.1.1.11.1.2.16, ORF8:F6S KP.2.17 Alias of B.1.1.529.2.86.1.1.11.1.2.17, S:G35R, C23758T, C7765T, T14418C, Singapore @@ -1418,7 +1418,7 @@ KP.3.3.4 Alias of B.1.1.529.2.86.1.1.11.1.3.3.4, ORF1a:I1367L, from #2707 MR.1 Alias of B.1.1.529.2.86.1.1.11.1.3.3.4.1, S:S31del, ORF1a:V1236I, from #2704 KP.3.3.5 Alias of B.1.1.529.2.86.1.1.11.1.3.3.5, S:A435S, Chile, from #2844 KP.3.3.6 Alias of B.1.1.529.2.86.1.1.11.1.3.3.6, S:S31del, S:D138H, Oceania -KP.3.3.7 Alias of B.1.1.529.2.86.1.1.11.1.3.3.7, ORF1a:T2093I, ORF1a:L642F +KP.3.3.7 Alias of B.1.1.529.2.86.1.1.11.1.3.3.7, ORF1a:T2093I, ORF1a:L642F, Japan KP.3.3.8 Alias of B.1.1.529.2.86.1.1.11.1.3.3.8, ORF1b:A1603S, S:F59S PB.1 Alias of B.1.1.529.2.86.1.1.11.1.3.3.8.1, S:T22N, ORF1a:L3201P, Japan PB.2 Alias of B.1.1.529.2.86.1.1.11.1.3.3.8.2, S:T22N, S:I794T @@ -4545,7 +4545,7 @@ XEC.15 ORF1b:M2322I, C9803T XEC.16 S:T678I, from sars-cov-2-variants/lineage-proposals#2088 XEC.17 S:T95I, on ORF1a:A599T branch, Israel, from #2879 XEC.18 G28378T -XEC.19 4423T +XEC.19 C4423T XED Recombinant lineage of JN.1.4 and LF.1.1.1 (breakpoint 19210-21652), from #2691 XEE Recombinant lineage of KP.2.3.7 and JN.1* (breakpoint 24873-25592), from #2721 XEF Recombinant lineage of LB.1.4 and KP.3 (breakpoint 22600-23038), from sars-cov-2-variants/lineage-proposals#1855 @@ -4565,7 +4565,7 @@ XEK.5 C478T XEK.6 S:Y1155F XEL Recombinant lineage of KS.1.1.2, JN.1 (breakpoint: 22929-24820), South Korea, from #2751 XEL.1 S:V1264L -XEL.2 S:V159I +XEL.2 S:V159I, Russia XEL.3 ORF1a:P971L XEL.4 S:R190S, S:S680F XEL.5 S:M177T, ORF1a:F586S From fdfdb5ec7441d871eb5099c270573b174c484785 Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Mon, 3 Feb 2025 04:30:08 +0800 Subject: [PATCH 8/9] Update lineage_notes.txt --- lineage_notes.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index b5ad5596..c39bd4b0 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1537,15 +1537,15 @@ LQ.1.2 Alias of B.1.1.529.2.86.1.1.18.1.1.2, ORF3a: T221I LQ.2 Alias of B.1.1.529.2.86.1.1.18.1.2, S:N556K, China,from sars-cov-2-variants/lineage-proposals#1414 LQ.3 Alias of B.1.1.529.2.86.1.1.18.1.3, ORF1a:T1761I, Russia JN.1.18.2 Alias of B.1.1.529.2.86.1.1.18.2, S:F59S, after C4331T, T22321C, from sars-cov-2-variants/lineage-proposals#1441 -LZ.1 Alias of B.1.1.529.2.86.1.1.18.2.1, S:F456L (T22930A), N:A152T, ORF1a:I740V from #2654 +LZ.1 Alias of B.1.1.529.2.86.1.1.18.2.1, S:F456L (T22930A), N:A152T, ORF1a:I740V, on T23377C branch, from #2654 LZ.1.1 Alias of B.1.1.529.2.86.1.1.18.2.1.1, S:P217S, S:N1125S from #2654 -LZ.2 Alias of B.1.1.529.2.86.1.1.18.2.2, S:F456L (T22928C), ORF1a:K1226E, China, from sars-cov-2-variants/lineage-proposals#1089 +LZ.2 Alias of B.1.1.529.2.86.1.1.18.2.2, S:F456L (T22928C), on ORF1a:K1226E branch, China, from sars-cov-2-variants/lineage-proposals#1089 LZ.2.1 Alias of B.1.1.529.2.86.1.1.18.2.2.1, ORF10:Q29* LZ.2.1.1 Alias of B.1.1.529.2.86.1.1.18.2.2.1.1, S:K478E, from sars-cov-2-variants/lineage-proposals#2092 LZ.2.1.2 Alias of B.1.1.529.2.86.1.1.18.2.2.1.2, S:K478T (rev), from sars-cov-2-variants/lineage-proposals#1909 LZ.2.2 Alias of B.1.1.529.2.86.1.1.18.2.2.2, T2032C, C19041T, China -LZ.3 Alias of B.1.1.529.2.86.1.1.18.2.3, S:T572I, on ORF1a:K1226E branch with LZ.2 -LZ.4 Alias of B.1.1.529.2.86.1.1.18.2.4, S:R190S, on T23377C branch with LZ.1 +LZ.3 Alias of B.1.1.529.2.86.1.1.18.2.3, S:T572I, on ORF1a:K1226E branch +LZ.4 Alias of B.1.1.529.2.86.1.1.18.2.4, S:R190S, on T23377C branch LZ.5 Alias of B.1.1.529.2.86.1.1.18.2.5, C19185T JN.1.18.3 Alias of B.1.1.529.2.86.1.1.18.3, S:F456V (T22928G), from sars-cov-2-variants/lineage-proposals#1253 MA.1 Alias of B.1.1.529.2.86.1.1.18.3.1, S:R190S, S:31del, from sars-cov-2-variants/lineage-proposals#1635 From 45834dbe67b512f453f3474073f1812ecab97add Mon Sep 17 00:00:00 2001 From: Yat-sing Ng <38100637+Over-There-Is@users.noreply.github.com> Date: Wed, 5 Feb 2025 14:06:03 +0800 Subject: [PATCH 9/9] Update lineage_notes.txt --- lineage_notes.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/lineage_notes.txt b/lineage_notes.txt index 0cdcbf18..7edb8a50 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -1711,12 +1711,12 @@ MF.2 Alias of B.1.1.529.2.86.1.1.65.1.2, S:S60P, S:W64L from #2461 JN.1.66 Alias of B.1.1.529.2.86.1.1.66, S:H445P, S:F456L (T22930A), S:T1117I, ORF1a:L2146F, ORF3a:L106F, Iceland/Sweden JN.1.67 Alias of B.1.1.529.2.86.1.1.67, M:L46F, from #2531 JN.1.67.1 Alias of B.1.1.529.2.86.1.1.67.1, S:F456L, China, from #2531 -MZ.1 Alias of B.1.1.529.2.86.1.1.67.1.1, S:S31F -MZ.2 Alias of B.1.1.529.2.86.1.1.67.1.2, T177C, China -MZ.3 Alias of B.1.1.529.2.86.1.1.67.1.3, S:R346T, S:F59S, China +MZ.1 Alias of B.1.1.529.2.86.1.1.67.1.1, S:S31F, on G1126A branch +MZ.2 Alias of B.1.1.529.2.86.1.1.67.1.2, T177C, on G1126A branch, China +MZ.3 Alias of B.1.1.529.2.86.1.1.67.1.3, S:R346T, S:F59S, on G1126A branch, China MZ.4 Alias of B.1.1.529.2.86.1.1.67.1.4, S:K478T (rev), N:T379A, China MZ.4.1 Alias of B.1.1.529.2.86.1.1.67.1.4.1, S:V1264L -MZ.5 Alias of B.1.1.529.2.86.1.1.67.1.5, S:T572I +MZ.5 Alias of B.1.1.529.2.86.1.1.67.1.5, S:T572I, on G1126A branch JN.1.68 Alias of B.1.1.529.2.86.1.1.68, C19011T JN.1.68.1 Alias of B.1.1.529.2.86.1.1.68.1, S:K679R, C9836T, from sars-cov-2-variants/lineage-proposals#1350 JN.1.69 Alias of B.1.1.529.2.86.1.1.69, C16329T