diff --git a/lineage_notes.txt b/lineage_notes.txt index c4feb571..3b609f6d 100644 --- a/lineage_notes.txt +++ b/lineage_notes.txt @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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