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Update lineage_notes.txt #2597

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Jul 25, 2024
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Update lineage_notes.txt #2597

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4401ad4
Update lineage_notes.txt
Over-There-Is May 20, 2024
9fb5916
Update lineage_notes.txt
Over-There-Is May 21, 2024
f4ec864
Update lineage_notes.txt
Over-There-Is May 21, 2024
fc744cd
Merge branch 'master' into patch-9
AngieHinrichs Jul 25, 2024
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30 changes: 15 additions & 15 deletions lineage_notes.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -1069,7 +1069,7 @@ 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, from sars-cov-2-variants/lineage-proposals#1521
JN.1.1.8 Alias of B.1.1.529.2.86.1.1.1.8, S:F456L (T22930A), S:H445P, ORF1a:S2083I, C850T, from sars-cov-2-variants/lineage-proposals#1521
JN.1.1.9 Alias of B.1.1.529.2.86.1.1.1.9, G2035A, on C9142T branch, China, from sars-cov-2-variants/lineage-proposals#1525
JN.1.1.10 Alias of B.1.1.529.2.86.1.1.1.10, C23557T, Ukraine
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
Expand Down Expand Up @@ -1138,7 +1138,7 @@ LB.1.7.3 Alias of B.1.1.529.2.86.1.1.9.2.1.7.3, S:R34C
LB.1.8 Alias of B.1.1.529.2.86.1.1.9.2.1.8, ORF1a:I785V
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, after ORF1b:L2213F, from #2510
Expand Down Expand Up @@ -1216,7 +1216,7 @@ KP.5 Alias of B.1.1.529.2.86.1.1.11.1.5, S:T572I, from sars-cov-2-variants/linea
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
KS.1.1 Alias of B.1.1.529.2.86.1.1.13.1.1, S:T22N, Singapore/Taiwan/Canada, from sars-cov-2-variants/lineage-proposals#1565
KS.1.2 Alias of B.1.1.529.2.86.1.1.13.1.2, S:T678I, Russia
KS.1.3 Alias of B.1.1.529.2.86.1.1.13.1.3, S:V642A, Dominican Republic
Expand All @@ -1225,7 +1225,7 @@ JN.1.15 Alias of B.1.1.529.2.86.1.1.15, S:A688V
JN.1.15.1 Alias of B.1.1.529.2.86.1.1.15.1, S:F456L, ORF3a:R122S, Ecuador, from sars-cov-2-variants/lineage-proposals#1253
LU.1 Alias of B.1.1.529.2.86.1.1.15.1.1, S:R346T, after C19269T, from sars-cov-2-variants/lineage-proposals#1089
LU.2 Alias of B.1.1.529.2.86.1.1.15.1.2, S:R346T, after T20865C, from sars-cov-2-variants/lineage-proposals#1652
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, from sars-cov-2-variants/lineage-proposals#1448
Expand Down Expand Up @@ -1279,7 +1279,7 @@ 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, from sars-cov-2-variants/lineage-proposals#1504
LG.1 Alias of B.1.1.529.2.86.1.1.28.1.1.1.1.1, S:R346T, Australia, from sars-cov-2-variants/lineage-proposals#1504
KW.1.2 Alias of B.1.1.529.2.86.1.1.28.1.1.2, S:K529T, Australia
Expand All @@ -1289,7 +1289,7 @@ MJ.1 Alias of B.1.1.529.2.86.1.1.29.1.1.1, S:R346T, S:S31P, ORF1a:E2070K
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, from sars-cov-2-variants/lineage-proposals#1442
Expand All @@ -1300,7 +1300,7 @@ 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, from sars-cov-2-variants/lineage-proposals#1089
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, from sars-cov-2-variants/lineage-proposals#1089
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.1.40 Alias of B.1.1.529.2.86.1.1.40, S:S31P, Mexico, from sars-cov-2-variants/lineage-proposals#1451
Expand All @@ -1318,16 +1318,16 @@ 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, from sars-cov-2-variants/lineage-proposals#1318
JN.1.47.2 Alias of B.1.1.529.2.86.1.1.47.2, S:T572I, S:R683Q, USA, from sars-cov-2-variants/lineage-proposals#1097
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, on T3913A, C8092T branch 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, on T3913A, C8092T branch from #2547
LD.1 Alias of B.1.1.529.2.86.1.1.48.1.1, S:T572I from #2547
JN.1.48.2 Alias of B.1.1.529.2.86.1.1.48.2, S:R346T, ORF1a:A427V, A3829G, India, from sars-cov-2-variants/lineage-proposals#1089
JN.1.48.3 Alias of B.1.1.529.2.86.1.1.48.3, S:60P, S:R346T, S:F456L, ORF3a:S60F, ORF1a:T1761I, on T3913A, C8092T branch, South Africa
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
MB.1 Alias of B.1.1.529.2.86.1.1.49.1.1, S:F456V (T22928G), S:S31F
MB.1.1 Alias of B.1.1.529.2.86.1.1.49.1.1.1, S:T22N, S:K182N, from sars-cov-2-variants/lineage-proposals#1659
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 from #2587
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:A67V, S:L249F, S:H445P, S:F456L (T22930G), Europe from #2587
JN.1.50.1 Alias of B.1.1.529.2.86.1.1.50.1, S:R346T from #2587
JN.1.50.2 Alias of B.1.1.529.2.86.1.1.50.2, ORF1a:N1540S (A4884G, T4885C)
ME.1 Alias of B.1.1.529.2.86.1.1.50.2.1, S:R346K
Expand Down Expand Up @@ -1408,7 +1408,7 @@ 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, from sars-cov-2-variants/lineage-proposals#1089
JQ.2.1.1 Alias of B.1.1.529.2.86.3.2.1.1, S:F456L (T22928C), South Africa, from sars-cov-2-variants/lineage-proposals#1089
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
Expand Down Expand Up @@ -4115,11 +4115,11 @@ 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, from sars-cov-2-variants/lineage-proposals#1490
XDK.1.2 S:F456L, from sars-cov-2-variants/lineage-proposals#1407
XDK.1 S:R346T, S:G213E, G11596A, from sars-cov-2-variants/lineage-proposals#1407
XDK.1.1 S:K182R, S:E213G reversion, India, from sars-cov-2-variants/lineage-proposals#1490
XDK.1.2 S:F456L (T22928C), from sars-cov-2-variants/lineage-proposals#1407
XDK.2 S:K679R, T4996A, C11173T, A23598G, C27297T, from sars-cov-2-variants/lineage-proposals#1385
XDK.3 S:F456L, ORF1a:F3397L, from sars-cov-2-variants/lineage-proposals#1511
XDK.3 S:F456L (T22928C), ORF1a:F3397L, from sars-cov-2-variants/lineage-proposals#1511
XDK.4 C25626T
XDK.4.1 S:F456L, France/Luxembourg, from sars-cov-2-variants/lineage-proposals#1467
XDK.5 S:F456L, C22388T, Spain from #2611
Expand Down
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