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Update lineage_notes.txt
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@Over-There-Is
Over-There-Is committed Apr 5, 2024
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Expand Up @@ -1072,7 +1072,7 @@ JN.1.4.3 Alias of B.1.1.529.2.86.1.1.4.3, S:T572I, USA, from #2487
KQ.1 Alias of B.1.1.529.2.86.1.1.4.3.1, S:R346T, USA from #2487
JN.1.4.4 Alias of B.1.1.529.2.86.1.1.4.4, S:R346T,from sars-cov-2-variants/lineage-proposals#1089
JN.1.4.5 Alias of B.1.1.529.2.86.1.1.4.5, ORF8:S103L, after T18453C, from #2426
KV.1 Alias of B.1.1.529.2.86.1.1.4.5.1, S:S680F
KV.1 Alias of B.1.1.529.2.86.1.1.4.5.1, S:S680F, after C28948T then A2356T
KV.2 Alias of B.1.1.529.2.86.1.1.4.5.2, S:T572I, ORF1a:P971L, C11956T, USA
JN.1.4.6 Alias of B.1.1.529.2.86.1.1.4.6, S:T572I, after T18453C
JN.1.4.7 Alias of B.1.1.529.2.86.1.1.4.7, ORF3a:G18D
Expand Down Expand Up @@ -1133,7 +1133,7 @@ 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
JN.1.31 Alias of B.1.1.529.2.86.1.1.31, ORF3a:V13L, C19186T
JN.1.32 Alias of B.1.1.529.2.86.1.1.32, S:T572I, directly on JN.1 polytomy
JN.1.33 Alias of B.1.1.529.2.86.1.1.33, S:A67V, G2782T, C5512T, China from https://github.com/cov-lineages/pango-designation/issues/2498
JN.1.33 Alias of B.1.1.529.2.86.1.1.33, S:A67V, G2782T, C5512T, China from #2498
JN.1.34 Alias of B.1.1.529.2.86.1.1.34, S:S704L
JN.1.35 Alias of B.1.1.529.2.86.1.1.35, S:S680Y, after T18471C, Australia/New Zealand
JN.1.36 Alias of B.1.1.529.2.86.1.1.36, S:Q677H, after A29086T
Expand Down Expand Up @@ -1588,7 +1588,7 @@ FQ.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.39.1, found mainly in Sweden, France and
BQ.1.1.40 Alias of B.1.1.529.5.3.1.1.1.1.1.1.40 Canada, defined by N:T24I
BQ.1.1.41 Alias of B.1.1.529.5.3.1.1.1.1.1.1.41 USA, defined by S:K182I, from #1291
BQ.1.1.42 Alias of B.1.1.529.5.3.1.1.1.1.1.1.42 France, defined by S:S704L
BQ.1.1.43 Alias of B.1.1.529.5.3.1.1.1.1.1.1.43 USA, S:Q613H (C26292T)
BQ.1.1.43 Alias of B.1.1.529.5.3.1.1.1.1.1.1.43 USA, S:Q613H (G23401C), C26292T
EZ.1 Alias of B.1.1.529.5.3.1.1.1.1.1.1.43.1 Portugal, S:S247N, S:Y248S, from #1673
BQ.1.1.44 Alias of B.1.1.529.5.3.1.1.1.1.1.1.44 S:D253G
BQ.1.1.45 Alias of B.1.1.529.5.3.1.1.1.1.1.1.45 Europe, S:Y248D, from #1512
Expand Down Expand Up @@ -3082,7 +3082,7 @@ XBB.1.5.110 ORF1aT4129I, Mexico
XBB.1.6 USA, S:L216F, S:H146K, from #1428
XBB.1.7 USA-NY, S:V608I
XBB.1.8 Denmark, S:186insSGG, C3241T, from #1455
XBB.1.9 ORF1a:G1819S, ORF1a:T4175I
XBB.1.9 ORF1a:G1819S, ORF1a:T4175I, on ORF9b:I5T branch
XBB.1.9.1 S:F486P (after C11956T), Indonesia/Singapore/Malaysia/England
FL.1 Alias of XBB.1.9.1.1, S:701V, ORF1a:G993S, from #1808
FL.1.1 Alias of XBB.1.9.1.1.1, ORF1b:Q2635P, USA/Australia
Expand Down Expand Up @@ -3215,8 +3215,8 @@ FL.38 Alias of XBB.1.9.1.38, S:K478R, S:Q613H, C25482T, Russia, from sars-cov-2-
FL.39 Alias of XBB.1.9.1.39, ORF1a:E633K, Russia
FL.39.1 Alias of XBB.1.9.1.39.1, S:K478R, S:P521S, Russia
FL.40 Alias of XBB.1.9.1.40, ORF1a:I3758V, Russia
XBB.1.9.2 S:F486P (after 27507C, 16878T), Indonesia/Singapore, from #1602
EG.1 Alias of XBB.1.9.2.1, S:Q613H on N:L219F branch, from #1664 and https://github.com/jmcbroome/auto-pango-designation/pull/193
XBB.1.9.2 S:F486P (after A27507C, A16878T), Indonesia/Singapore, from #1602
EG.1 Alias of XBB.1.9.2.1, S:Q613H on N:L219F branch, from #1664 and jmcbroome/auto-pango-designation#193
EG.1.1 Alias of XBB.1.9.2.1.1, S:V70F and ORF1a:T403I, Luxembourg/Belgium/France
EG.1.2 Alias of XBB.1.9.2.1.2, ORF7b:H42Y, mostly Austria, from #1711
EG.1.3 Alias of XBB.1.9.2.1.3, C3784T, A6613G, Europe
Expand Down Expand Up @@ -3376,7 +3376,7 @@ EG.11 Alias of XBB.1.9.2.11, S:E554K, A26319G, Malaysia, from sars-cov-2-variant
EG.12 Alias of XBB.1.9.2.12, S:E554K, N:R195T, ORF1a:T4159I, Oman/Austria/Brunei/India
EG.13 Alias of XBB.1.9.2.13, ORF1a:K798N
EG.14 Alias of XBB.1.9.2.14, Orf1b:K1383R, from #2274
XBB.1.9.3 ORF1b:G2005S, ORF1b:G1568C, Europe, from https://github.com/jmcbroome/auto-pango-designation/pull/193
XBB.1.9.3 ORF1b:G2005S, ORF1b:G1568C, Europe, from jmcbroome/auto-pango-designation#193
GD.1 Alias of XBB.1.9.3.1, S:Y453F, Mexico/USA, from #1897
GD.2 Alias of XBB.1.9.3.2, S:L212S, Philippines
GD.3 Alias of XBB.1.9.3.3, S:F59L, Russia
Expand Down Expand Up @@ -3503,7 +3503,7 @@ FE.1.1.1 Alias of XBB.1.18.1.1.1.1, ORF1a:T999I, North America
HE.1 Alias of XBB.1.18.1.1.1.1.1, S:V622I, ORF8:A55V, USA/Puerto Rico, from #2067
HE.2 Alias of XBB.1.18.1.1.1.1.2, S:H1058Y, USA
FE.1.1.2 Alias of XBB.1.18.1.1.1.2, S:K1086R, Brazil/USA
FE.1.1.3 Alias of XBB.1.18.1.1.1.3, A24775G, China
FE.1.1.3 Alias of XBB.1.18.1.1.1.3, A24775G, on G28371T (N:G33V, ORF9b:V30L) branch, China
FE.1.1.4 Alias of XBB.1.18.1.1.1.4, A4336G, T24073C, Brazil
FE.1.1.5 Alias of XBB.1.18.1.1.1.5, S:E554K, Brazil, from sars-cov-2-variants/lineage-proposals#556
FE.1.2 Alias of XBB.1.18.1.1.2, A5488G
Expand All @@ -3526,7 +3526,7 @@ GW.5.3.1 Alias of XBB.1.19.1.5.3.1, S:A475V, S:G184A, from sars-cov-2-variants/l
XBB.1.19.2 Defined by S:P521S, Pakistan, from sars-cov-2-variants/lineage-proposals#233
XBB.1.20 Defined by ORF3a:A72V, ORF1a:P4312T on C541T, pre ORF8:8* branch, Malaysia
XBB.1.21 Defined by S:486A, ORF1a:K1247R, Turkey, from #1646
XBB.1.22 Defined by S:486P, on 28297C branch, from #1704
XBB.1.22 Defined by S:486P, on ORF9b:I5T branch, from #1704
XBB.1.22.1 Defined by S:Y200C, from #1704
FY.1 Alias of XBB.1.22.1.1, Defined by ORF1b:D1782N
FY.1.1 Alias of XBB.1.22.1.1.1, S:A83S, Malaysia/Japan
Expand Down Expand Up @@ -3569,13 +3569,13 @@ HU.1 Alias of XBB.1.22.2.1, S:K529N, France, from #2136
HU.1.1 Alias of XBB.1.22.2.1.1, S:E471Q, S:Y28H, France/USA, from #2136
HU.2 Alias of XBB.1.22.2.2, S:T76I, ORF1a:R24H, ORF1b:A1428V, Australia/New Zealand, from sars-cov-2-variants/lineage-proposals#364
XBB.1.22.3 Defined by ORF1a:P3504L, ORF1b:H1838N, Japan
XBB.1.23 Defined by E:S68F, on 28297C branch, South East Asia
XBB.1.23 Defined by E:S68F, on ORF9b:I5T branch, South East Asia
XBB.1.24 Defined by S:F486P, on T13704C branch, South East Asia, from #1654
XBB.1.24.1 S:L518Q, Singapore
XBB.1.24.2 S:R158S, after ORF1a:K261N, N:A35T, Singapore/Malaysia
XBB.1.24.3 S:S256L, after ORF1a:K261N, Malaysia/Japan
XBB.1.25 Defined by C673T, G487T, on 28297C branch
XBB.1.26 Defined by T10663C on 28297C branch, Canada
XBB.1.25 Defined by C673T, G487T, on ORF9b:I5T branch
XBB.1.26 Defined by T10663C, on ORF9b:I5T branch, Canada
XBB.1.27 Defined by S:478R, S:A890V, Mexico/USA/India, from #1654
XBB.1.28 Defined by S:403K, Europe, from #1757
XBB.1.28.1 Defined by S:356T, Indonesia, global
Expand Down Expand Up @@ -3731,7 +3731,7 @@ XBB.2.3.20 N:A267S, S:210del, Bangladesh, from sars-cov-2-variants/lineage-propo
XBB.2.3.21 S:T883I, ORF1a:D3042N, 670T reversion, Japan, from sars-cov-2-variants/lineage-proposals#281
XBB.2.3.22 S:S937T, ORF8:K94T, Romania/Bulgaria
XBB.2.4 Defined by S:S486P, Spain/Denmark/Germany, from #1603 and #1518
XBB.2.5 S:Q613H, from https://github.com/jmcbroome/auto-pango-designation/pull/193
XBB.2.5 S:Q613H, from jmcbroome/auto-pango-designation#193
XBB.2.6 Mostly Peru, C5144T, T5731A
XBB.2.6.1 S:P521S, Peru, from #1869
GH.1 Alias of XBB.2.6.1.1, ORF9b:P51Q, T6895C, T9148C, A15192C, Peru, from #1869
Expand All @@ -3745,23 +3745,23 @@ XBB.2.10 S:Q52H, Latvia/Poland
XBB.2.11 C18129T
XBB.2.11.1 C4084T, C9559T, T16521C, USA
XBB.2.12 S:Q613H (G23401C), C4090T, T24194C, India
XBB.3 Defined by ORF1b:I1988V on ORF1a:D82G branch
XBB.3.1 Defined by S:Q677R, India-TN/Singapore, from #1241
XBB.3.2 Defined by S:M177T
XBB.3.3 Defined by S:V1122L, USA
XBB.3.4 Defined by S:E990D
XBB.3 ORF1b:I1988V, on ORF1a:D82G branch
XBB.3.1 S:Q677R, after T1993C, India-TN/Singapore, from #1241
XBB.3.2 S:M177T
XBB.3.3 S:V1122L, after T1993C, USA
XBB.3.4 S:E990D
XBB.3.5 ORF1a:T4083M, Mozambique, from #1778
XBB.4 Defined by S:K444R on ORF1a:D82G branch, from #1239
XBB.4 S:K444R, on ORF1a:D82G branch, from #1239
XBB.4.1 England/Austria, S:L5F, S:T470N
XBB.5 Defined by S:A653V on ORF1a:D82G branch, India-TN, Singapore, Australia
XBB.6 Defined by C14178T, USA/India/England
XBB.6.1 Defined by S:F486P, USA, from #1459
XBB.7 Defined by S:Q613H, Malaysia
XBB.8 T14574C after ORF1a:D82G, India/Malaysia/Brunei
XBB.8.1 S:486P, Malaysia
XBB.5 S:A653V, after G5518A, on ORF1a:D82G branch, India-TN, Singapore, Australia
XBB.6 C14178T, on ORF1a:D82G branch, USA/India/England
XBB.6.1 S:F486P, USA, from #1459
XBB.7 S:Q613H, after G5518A, on ORF1a:D82G branch, Malaysia
XBB.8 T14574C, on ORF1a:D82G branch, India/Malaysia/Brunei
XBB.8.1 S:486P, ORF1a:K634N, ORF1a:K3353R, Malaysia
XBB.8.2 S:486P, ORF1a:A2529V, Reunion/Mayotte/Mauritius, from #1995
XBB.9 N:T49I after ORF1a:D82G, Philippines
XBC Recombinant lineage of BA.2 and B.1.617.2*, predominantly in Philippines, from #1100
XBB.9 N:T49I, on ORF1a:D82G branch, Philippines
XBC Recombinant lineage of BA.2 and B.1.617.2(21I), predominantly in Philippines, from #1100
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
Expand Down Expand Up @@ -3796,12 +3796,12 @@ XBC.2 Mostly Philippines, defined by S:K97R
XBC.2.1 S:K444T, Australia, from #1538
XBD Recombinant lineage of BA.2.75.2 and BF.5, India and world, from #1137
XBE Recombinant lineage of BA.5.2 and BE.4.1, predominantly in USA and England, from #1246
XBF Recombinant lineage of BA.5.2.3 and CJ.1, Australia, from #1259
XBF Recombinant lineage of BA.5.2* and CJ.1, Australia, from #1259
XBF.1 Australia/England, S:S939F
XBF.1.1 England, S:P621S, from #1651
XBF.2 Australia, ORF8:V62A
XBF.3 Australia, ORF1a:V274I
XBF.4 Europe, ORF1a:H417Y, from https://github.com/jmcbroome/auto-pango-designation/pull/193
XBF.4 Europe, ORF1a:H417Y, from jmcbroome/auto-pango-designation#193
XBF.5 Australia, C2455T
XBF.6 Australia, ORF1a:V3986A
XBF.7 Global, N:T379I (not on ORF1a:K120N branch)
Expand All @@ -3819,7 +3819,7 @@ XBJ.2 C22006T, Europe
XBJ.3 ORF1a:K2928N, Europe
XBJ.4 S:G485D, Japan/Thailand
XBK Recombinant lineage of BA.5.2 and CJ.1, Denmark/Europe, from #1418
XBK.1 S:P1162S, from #1551 and https://github.com/jmcbroome/auto-pango-designation/pull/193
XBK.1 S:P1162S, from #1551 and jmcbroome/auto-pango-designation#193
XBL Recombinant lineage of XBB.1.5.57-BA.2.75* (short segment from ~1k-~5k)-XBB.1.5.57, Malaysia, from #1532
XBL.1 S:V635I, T2461C
XBL.2 A1393G
Expand Down Expand Up @@ -3881,19 +3881,19 @@ XDH Recombinant lineage of BN.1.2.8 and XBB.1.9.1 (or XBB.1.22) (breakpoint betw
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
XDL Recombinant lineage of EG.5.1.1 and non-EG.5 (breakpoint between 25573-29624) with S:L455F and S:I1114T, China, from #2351
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
XDP Recombinant lineage of JN.1.4 and FL.15 (breakpoint between 26834 and 27809), from #2451
XDP.1 S:E1092D, after ORF1a:L397P, ORF1a:H388Y
XDQ Recombinant lineage of BA.2.86.1 and FL.15.1.1 (breakpoint between 223605 and 24377), from #2481
XDQ.1 S:A475V, Japan
XDQ Recombinant lineage of BA.2.86.1 and FL.15.1.1 (breakpoint between 223605 and 24377), most with T22846C, Vietnam/Japan/South Korea, from #2481
XDQ.1 S:A475V, Japan/South Korea, from #2497
XDR Recombinant lineage of JD.1.1.1 and JN.1.1 (breakpoint between 11043 and 11726), Brazil, from #2477
XDS Recombinant lineage of EG.5.1.3, JN.3.2.1, EG.5.1.3 (breakpoints at 8294-8392 and 26834-27506), from sars-cov-2-variants/lineage-proposals#1267
XDT Recombinant lineage of BA.2.86.4, GK.1 (breakpoint between 23673-24378), Ireland/UK, from #2485
XDU Recombinant lineage of BA.2.86.1, XBB.1.16 (breakpoint between 11957-12729), Japan, from #2502
XDV Recombinant lineage of XDE, JN.1, XDE, JN.1 (breakpoints between 19326-21608, 27915-28297, 28958-29535), from #2402
XDV.1 S:F456L (T22930A), on C11572T branch
XDV Recombinant lineage of XDE, JN.1, XDE, JN.1 (breakpoints between 19327-21608, 27916-28296, 28959-29534), USA/China, from #2402
XDV.1 S:F456L (T22930A), on C11572T branch, Hong Kong
*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
Expand Down Expand Up @@ -4176,7 +4176,7 @@ XDV.1 S:F456L (T22930A), on C11572T branch
*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:L455F (G22927T), 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 (now considered as an HK.3+S:G257D branch being misplaced with HK.1+S:L455F)
*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)

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