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modified: lineage_notes.txt
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xz-keg committed Jul 21, 2023
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Expand Up @@ -1005,8 +1005,8 @@ BY.1.2 Alias of B.1.1.529.2.75.6.1.2, Europe, 26828T
BY.1.2.1 Alias of B.1.1.529.2.75.6.1.2.1, Austria/England, S:S494P From #1184
BA.2.75.7 Alias of B.1.1.529.2.75.7, mainly found in India, defined by S:F486S on the BA.2.75 polytomy
BA.2.75.8 Alias of B.1.1.529.2.75.8, Singapore/Australia, defined by S:L452Q, issue #1085
BA.2.75.9 Alias of B.1.1.529.2.75.9, India, defined by S:R346T after 17679T
CB.1 Alias of B.1.1.529.2.75.9.1, England, defined by S:486V
BA.2.75.9 Alias of B.1.1.529.2.75.9, India, defined by S:R346T after 17679T From #1098
CB.1 Alias of B.1.1.529.2.75.9.1, England, defined by S:486V From #1098
BA.2.75.10 Alias of B.1.1.529.2.75.10, India, ORF1a:T3959A
BA.2.76 Alias of B.1.1.529.2.76, mainly found in India and USA, from pango-designation issue #787
BA.2.76.1 Alias of B.1.1.529.2.76.1, mainly found in India, from pango-designation issue #899
Expand Down Expand Up @@ -1267,9 +1267,9 @@ CK.1.2 Alias of B.1.1.529.5.2.24.1.2, Pakistan, S:G181V, S:R346T, from issue #14
CK.1.3 Alias of B.1.1.529.5.2.24.1.3, Mexico, S:F157L, S:G181V
CK.1.4 Alias of B.1.1.529.5.2.24.1.4, C10228T, C25824T, C27741T, on C25614T branch
CK.1.5 Alias of B.1.1.529.5.2.24.1.5, C9118T, C15951T, ORF1a:M3733V, on C25614T branch
CK.2 Alias of B.1.1.529.5.2.24.2, Pakistan, defined by E:V62F
CK.2 Alias of B.1.1.529.5.2.24.2, Pakistan, defined by E:V62F From #1190
CK.2.1 Alias of B.1.1.529.5.2.24.2.1, Pakistan, defined by S:N460K From #1125
CK.2.1.1 Alias of B.1.1.529.5.2.24.2.1.1, defined by S:S255F
CK.2.1.1 Alias of B.1.1.529.5.2.24.2.1.1, defined by S:S255F From #1190
CK.3 Alias of B.1.1.529.5.2.24.3, found mainly in Singapore and USA, from pango-designation issue #1121
DG.1 Alias of B.1.1.529.5.2.24.2.1.1.1, defined by S:G252S From #1288
BA.5.2.25 Alias of B.1.1.529.5.2.25, mainly found in France, USA and Canada, from pango-designation issue #1111
Expand All @@ -1291,11 +1291,11 @@ BA.5.2.33 Alias of B.1.1.529.5.2.33, UK lineage, defined by ORF8:P93S
CE.1 Alias of B.1.1.529.5.2.33.1, UK lineage, defined by S:R346I
BA.5.2.34 Alias of B.1.1.529.5.2.34, mainly found in Israel and USA, from pango-designation issue #992
BA.5.2.35 Alias of B.1.1.529.5.2.35, Pakistan lineage, defined by S:R346T after G28423C and C7006T
BA.5.2.36 Alias of B.1.1.529.5.2.36, India/Pakistan lineage, defined by S:K444T
CT.1 Alias of B.1.1.529.5.2.36.1, India/Pakistan lineage, defined by S:K356T
BA.5.2.36 Alias of B.1.1.529.5.2.36, India/Pakistan lineage, defined by S:K444T From #1203
CT.1 Alias of B.1.1.529.5.2.36.1, India/Pakistan lineage, defined by S:K356T From #1203
BA.5.2.37 Alias of B.1.1.529.5.2.37, found mainly in USA and India, from pango-designation issue #1117
BA.5.2.38 Alias of B.1.1.529.5.2.38, S:T430I
DA.1 Alias of B.1.1.529.5.2.38.1, Indonesia, S:R346T
BA.5.2.38 Alias of B.1.1.529.5.2.38, S:T430I From #1254
DA.1 Alias of B.1.1.529.5.2.38.1, Indonesia, S:R346T From #1254
BA.5.2.39 Alias of B.1.1.529.5.2.39, USA, S:R346T From #1279
BA.5.2.40 Alias of B.1.1.529.5.2.40, Sweden, S:N450D
BA.5.2.41 Alias of B.1.1.529.5.2.41, found mainly in Sweden, from pango-designation issue #1328
Expand Down Expand Up @@ -2301,18 +2301,18 @@ AY.9.2.1 Alias of B.1.617.2.9.2.1, Canada lineage
AY.9.2.2 Alias of B.1.617.2.9.2.2, Sweden lineage, from pango-designation issue #284
AY.10 Alias of B.1.617.2.10, UK lineage, from pango-designation issue #180
AY.11 Alias of B.1.617.2.11, UK lineage, from pango-designation issue #142
AY.13 Alias of B.1.617.2.13, USA lineage
AY.14 Alias of B.1.617.2.14, USA lineage
AY.15 Alias of B.1.617.2.15, Canada lineage
AY.16 Alias of B.1.617.2.16, lineage in Kenya and multiple other countries
AY.13 Alias of B.1.617.2.13, USA lineage From #198
AY.14 Alias of B.1.617.2.14, USA lineage From #198
AY.15 Alias of B.1.617.2.15, Canada lineage From #198
AY.16 Alias of B.1.617.2.16, lineage in Kenya and multiple other countries From #198
AY.16.1 Alias of B.1.617.2.16.1, France lineage
AY.17 Alias of B.1.617.2.17, Ireland and Northern Ireland lineage
AY.18 Alias of B.1.617.2.18, Canada lineage
AY.19 Alias of B.1.617.2.19, South Africa lineage
AY.20 Alias of B.1.617.2.20, USA and Mexico lineage
AY.17 Alias of B.1.617.2.17, Ireland and Northern Ireland lineage From #198
AY.18 Alias of B.1.617.2.18, Canada lineage From #198
AY.19 Alias of B.1.617.2.19, South Africa lineage From #198
AY.20 Alias of B.1.617.2.20, USA and Mexico lineage From #198
AY.20.1 Alias of B.1.617.2.20.1, Czech Republic lineage From #318
AY.21 Alias of B.1.617.2.21, lineage predominantly in Italy and Switzerland
AY.22 Alias of B.1.617.2.22, predominantly Portugal lineage
AY.21 Alias of B.1.617.2.21, lineage predominantly in Italy and Switzerland From #198
AY.22 Alias of B.1.617.2.22, predominantly Portugal lineage From #198
AY.23 Alias of B.1.617.2.23, predominantly Singapore and Indonesia lineage, from pango-designation issue #175
AY.23.1 Alias of B.1.617.2.23.1, Singapore lineage, from pango-designation issue #237
AY.23.2 Alias of B.1.617.2.23.2, European lineage, from pango-designation issue #265
Expand All @@ -2339,7 +2339,7 @@ AY.33.1 Alias of B.1.617.2.33.1, Reunion and France lineage, from pango-designat
AY.33.2 Alias of B.1.617.2.33.2, mainly found in Germany, Poland, Gibraltar and Spain, from pango-designation issue #403
AY.34 Alias of B.1.617.2.34, lineage with spike Q677H circulating in multiple countries, from pango-designation issue #217
AY.34.1 Alias of B.1.617.2.34.1, lineage in multiple countries including Gambia, Senegal, Benin and Mali, from pango-designation issue #255
AY.34.1.1 Alias of B.1.617.2.34.1.1, Brazil and Chile lineage
AY.34.1.1 Alias of B.1.617.2.34.1.1, Brazil and Chile lineage From #255
AY.34.2 Alias of B.1.617.2.34.2, lineage in multiple countries including Martinique, from pango-designation issue #269
AY.35 Alias of B.1.617.2.35, lineage with spike E484Q circulating in USA, from pango-designation issue #217
AY.36 Alias of B.1.617.2.36, lineage predominantly in Nigeria, UK and USA, from pango-designation issue #225
Expand Down Expand Up @@ -2389,12 +2389,12 @@ AY.54 Alias of B.1.617.2.54, USA lineage
AY.55 Alias of B.1.617.2.55, lineage in Rwanda and other countries
AY.56 Alias of B.1.617.2.56, USA lineage
AY.57 Alias of B.1.617.2.57, Vietnam lineage
AY.58 Alias of B.1.617.2.58, European lineage
AY.58 Alias of B.1.617.2.58, European lineage From #286
AY.59 Alias of B.1.617.2.59, Malaysia lineage
AY.60 Alias of B.1.617.2.60, European lineage
AY.61 Alias of B.1.617.2.61, Italy lineage
AY.62 Alias of B.1.617.2.62, USA and Mexico lineage
AY.63 Alias of B.1.617.2.63, Norway lineage
AY.63 Alias of B.1.617.2.63, Norway lineage From #286
AY.64 Alias of B.1.617.2.64, USA lineage
AY.65 Alias of B.1.617.2.65, lineage in Bahrain and other countries
AY.66 Alias of B.1.617.2.66, European lineage From #271
Expand Down Expand Up @@ -2432,9 +2432,9 @@ AY.95 Alias of B.1.617.2.95, Maldives and European lineage
AY.98 Alias of B.1.617.2.98, UK lineage
AY.98.1 Alias of B.1.617.2.98.1, European lineage
AY.98.1.1 Alias of B.1.617.2.98.1.1, mainly found in Germany and Denmark, from pango-designation issue #604
AY.99 Alias of B.1.617.2.99, South Africa and Nigeria lineage
AY.99.1 Alias of B.1.617.2.99.1, Brazil lineage
AY.99.2 Alias of B.1.617.2.99.2, Brazil lineage
AY.99 Alias of B.1.617.2.99, South Africa and Nigeria lineage From #258
AY.99.1 Alias of B.1.617.2.99.1, Brazil lineage From #258
AY.99.2 Alias of B.1.617.2.99.2, Brazil lineage From #258
AY.100 Alias of B.1.617.2.100, USA lineage
AY.101 Alias of B.1.617.2.101, Brazil and Chile lineage
AY.102 Alias of B.1.617.2.102, Peru and Chile lineage, from pango-designation issue #272
Expand All @@ -2452,7 +2452,7 @@ AY.109 Alias of B.1.617.2.109, lineage in Nigeria and other countries
AY.110 Alias of B.1.617.2.110, USA lineage
AY.111 Alias of B.1.617.2.111, UK lineage
AY.112 Alias of B.1.617.2.112, lineage in India and other countries, from pango-designation issue #283
AY.112.1 Alias of B.1.617.2.112.1, Bahrain lineage
AY.112.1 Alias of B.1.617.2.112.1, Bahrain lineage From #283
AY.112.2 Alias of B.1.617.2.112.2, mainly found in India, from pango-designation issue #385
AY.112.3 Alias of B.1.617.2.112.3, mainly found in Israel, from pango-designation issue #388
AY.113 Alias of B.1.617.2.113, USA and Mexico lineage
Expand All @@ -2469,8 +2469,8 @@ AY.120.1 Alias of B.1.617.2.120.1, USA lineage
AY.120.2 Alias of B.1.617.2.120.2, South Africa lineage
AY.120.2.1 Alias of B.1.617.2.120.2.1, European lineage
AY.121 Alias of B.1.617.2.121, European lineage From #301
AY.121.1 Alias of B.1.617.2.121.1, Poland and Germany lineage
AY.122 Alias of B.1.617.2.122, European lineage
AY.121.1 Alias of B.1.617.2.121.1, Poland and Germany lineage From #344
AY.122 Alias of B.1.617.2.122, European lineage From #320
AY.122.1 Alias of B.1.617.2.122.1, Israel lineage, formally AY.12 but renamed as descends from AY.122 which was designated after AY.12, from pango-designation issue #170
AY.122.2 Alias of B.1.617.2.122.2, Finland and Estonia lineage, from pango-designation issue #273
AY.122.3 Alias of B.1.617.2.122.3, Denmark and Sweden lineage, from pango-designation issue #371
Expand Down Expand Up @@ -2886,7 +2886,7 @@ EG.2.1 Alias of XBB.1.9.2.2.1, S:F456L (T22930A), S:V327I, Indonesia
EG.3 Alias of XBB.1.9.2.3, ORF1a:L2778F on N:L219F branch
EG.4 Alias of XBB.1.9.2.4, C28651T
EG.4.1 Alias of XBB.1.9.2.4.1, S:I870V, N:A119S
EG.4.2 Alias of XBB.1.9.2.4.2, S:A623V, T14652C, China
EG.4.2 Alias of XBB.1.9.2.4.2, S:A623V, T14652C, China From sars-cov-2-variants/lineage-proposals/#46
EG.4.3 Alias of XBB.1.9.2.4.3, S:Q613H
EG.5 Alias of XBB.1.9.2.5, S:F456L (T22930A), ORF1a:A690V, ORF1a:A3143V, Indonesia From #1918
EG.5.1 Alias of XBB.1.9.2.5.1, S:Q52H
Expand Down Expand Up @@ -2935,7 +2935,7 @@ GY.2.1 Alias of XBB.1.16.2.2.1, S:S255F, South Korea
GY.3 Alias of XBB.1.16.2.3, S:M177I, Thailand
GY.4 Alias of XBB.1.16.2.4, S:N450K, C29095T, Laos
GY.5 Alias of XBB.1.16.2.5, G9190C
GY.6 Alias of XBB.1.16.2.6, ORF1a:V1765I
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
XBB.1.16.3 Defined by A2893C, India
XBB.1.16.4 Defined by S:T678I, India, from #1903
Expand Down Expand Up @@ -3007,7 +3007,7 @@ XBB.1.30 Defined by ORF1b:K2557R, South East Asia
XBB.1.31 Defined by S:453F and S:478R, Indonesia/Singapore From #1837
XBB.1.31.1 S:E554K, Indonesia
XBB.1.31.2 ORF1a:A1049V, Indonesia
XBB.1.32 Defined by ORF1a:E148D, Philippines
XBB.1.32 Defined by ORF1a:E148D, Philippines From #1827
XBB.1.32.1 S:Y453F, ORF1a:L642F, ORF1b:L2497I, Philippines/Thailand, from #1908
XBB.1.33 Defined by S:A376T, found mainly in Italy, from pango-designation issue #1879
XBB.1.34 S:486P,S:681R, N:A50V, Uganda/Sudan, from pango-designation issue #1621
Expand All @@ -3016,7 +3016,7 @@ XBB.1.34.2 S:K182I, ORF8:C90F, ORF1a:G989C
HB.1 Alias of XBB.1.34.2.1, S:F456L (22928C), US/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 pango-designation issue #1781
XBB.1.37 Defined by A5371G, Indonesia/Russia
XBB.1.37 Defined by A5371G, Indonesia/Russia From #1929
XBB.1.37.1 Defined by S:486P, A1846G, G7459T, T27285C, Russia/South Korea, from #1929
XBB.1.38 Defined by S:T732I, Russia
XBB.1.38.1 S:T883I, Russia
Expand Down Expand Up @@ -3123,7 +3123,7 @@ XBD Recombinant lineage of BA.2.75.2 and BF.5, India and world, from pango-desig
XBE Recombinant lineage of BA.5.2 and BE.4.1, predominantly in USA and England, from pango-designation issue #1246
XBF Recombinant lineage of BA.5.2.3 and CJ.1, Australia, from pango-designation issue #1259
XBF.1 Australia/England, S:S939F
XBF.1.1 England, S:P621S
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
Expand Down

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