From d47f941b799411f48a1ac681fad0dc7abbc22858 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Thu, 11 Feb 2021 13:50:56 +0000 Subject: [PATCH] adding manual notes from pangoLEARN (previous host) with descriptions of lineages in designation repo --- lineage_notes.txt | 1019 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 1019 insertions(+) create mode 100644 lineage_notes.txt diff --git a/lineage_notes.txt b/lineage_notes.txt new file mode 100644 index 00000000..1bcc7e9e --- /dev/null +++ b/lineage_notes.txt @@ -0,0 +1,1019 @@ +Lineage Description +A Root of the pandemic lies within lineage A. Many sequences originating from China and many global exports; including to South East Asia Japan South Korea Australia the USA and Europe represented in this lineage +A.1 A North American lineage +A.2 Mostly Spanish lineage now includes South and Central American sequences, other European countries and Kazakhstan. +A.2.1 Lineage with sequences predominantly from Panama +A.2.2 Australian lineage nested within the diversity of A.2 +A.2.3 Scottish lineage nested within the diversity of A.2 +A.2.4 Panama lineage +A.3 USA lineage +A.4 USA lineage nested in A diversity +A.5 A lineage with a lot of representation from Spanish-speaking countries. A Spanish/ South-American lineage, but now with sequences from an outbreak in Scotland. Also now includes what was previously A.10. +A.6 Lineage from an introduction event into Thailand +A.7 Indian lineage +*A.8 Indian lineage merged with A.9 +A.9 Indian lineage +*A.10 Spanish lineage reassigned to A.5 +A.11 Ghana/ Senegal lineage +A.12 Sierra Leone lineage +A.13 Cote d'Ivoire lineage +A.14 Cote d'Ivoire lineage +A.15 Sweden/ Denmark lineage +A.16 Japanese lineage +A.17 French lineage +A.18 Cote d'Ivoire lineage +A.19 Cote d'Ivoire/ Burkina Faso lineage +A.20 UAE lineage +A.21 West African lineage +A.22 UAE lineage +A.23 Ugandan lineage +A.23.1 International lineage with a number of variants of potential biological concern, including 681R +A.24 South Korean lineage +A.25 Ugandan lineage +A.26 UK lineage +B Base of this lineage also lies in China, with many global exports, two distinct SNPs `8782TC` and `28144CT` define this lineage +B.1 A large European lineage that corresponds to the Italian outbreak. +*B.1.1 Reassigned in the current tree. European lineage with 3 clear SNPs `28881GA`,`28882GA`,`28883GC` +B.1.1.1 UK/ Europe lineage +B.1.1.2 UK and Australia +B.1.1.3 English lineage +B.1.1.4 UK lineage +B.1.1.5 Iceland/ Belgium/ UK +B.1.1.6 USA (TX) +B.1.1.7 UK lineage of concern, associated with the N501Y mutation. More information can be found at cov-lineages.org/global_report.html +B.1.1.8 UK/ Indian lineage +B.1.1.10 European lineage +B.1.1.12 UK lineage +B.1.1.13 English lineage +B.1.1.14 Scottish lineage +B.1.1.15 UK/ Luxembourg lineage +B.1.1.16 Wales lineage +B.1.1.17 Icelandic lineage +B.1.1.20 UK lineage +B.1.1.25 Bangladesh lineage +B.1.1.26 USA (WA) lineage. Contains some of B.1.1.65 +B.1.1.27 Oman lineage +B.1.1.28 Brazilian lineage +B.1.1.29 (expanded a bit) UK and Ireland +B.1.1.30 Lithuanian lineage +B.1.1.31 Russian (a bit upstream) +B.1.1.32 Indian lineage +B.1.1.33 Brazilian lineage +B.1.1.34 South African lineage +B.1.1.35 UK lineage +B.1.1.36 USA +B.1.1.37 UK lineage +B.1.1.38 UK lineage +B.1.1.39 Swiss lineage +B.1.1.40 South African lineage +B.1.1.41 UK +B.1.1.43 Scottish lineage +B.1.1.44 UK/ Spain lineage +B.1.1.45 UK lineage +B.1.1.46 India +B.1.1.47 Swiss lineage +B.1.1.48 Japanese lineage +B.1.1.49 Wales lineage +B.1.1.50 UK/ Israel/ Palestine lineage +B.1.1.51 UK lineage +B.1.1.52 South African +B.1.1.53 South African lineage +B.1.1.54 South African lineage +B.1.1.55 UK lineage +B.1.1.56 South African lineage +B.1.1.57 South African lineage, a few English sequences, one Zimbabwe +B.1.1.58 Denmark/ Switzerland lineage +B.1.1.59 UK lineage +B.1.1.60 Northern Ireland lineage +B.1.1.61 USA lineage +B.1.1.62 South African lineage +B.1.1.63 Hong Kong lineage +B.1.1.64 UK lineage +B.1.1.65 USA lineage +B.1.1.66 South African lineage +B.1.1.67 England and South Africa +B.1.1.71 Netherlands lineage +B.1.1.70 European lineage +B.1.1.72 USA lineage +*B.1.1.73 Reassigned lineage +B.1.1.74 Northern Irish +B.1.1.75 Belgian lineage +B.1.1.76 USA lineage +B.1.1.77 USA lineage +B.1.1.78 Russian lineage +B.1.1.79 Russian lineage +B.1.1.80 Bangladesh lineage +B.1.1.81 Northern Ireland lineage +B.1.1.82 Wales lineage +B.1.1.83 Northern Ireland lineage +B.1.1.84 South African lineage +B.1.1.85 USA lineage +B.1.1.86 English lineage +B.1.1.87 Hungary lineage +B.1.1.88 Portugal lineage +B.1.1.89 UK lineage +B.1.1.90 Swedish lineage +B.1.1.91 Swedish lineage +B.1.1.92 English lineage +B.1.1.93 USA lineage +B.1.1.94 Brazil lineage +B.1.1.95 English lineage +B.1.1.96 Saudi Arabia/ Russia lineage +B.1.1.97 UK lineage +B.1.1.98 USA lineage +B.1.1.99 South African lineage +B.1.1.100 Denmark lineage +B.1.1.101 Indian lineage +B.1.1.102 Latvian lineage +B.1.1.103 Bangladesh lineage +B.1.1.104 Netherlands/ Europe lineage +B.1.1.105 Turkish lineage +B.1.1.106 UK lineage +B.1.1.107 UK lineage +B.1.1.108 UK lineage +B.1.1.109 UK lineage +B.1.1.110 Peru lineage +B.1.1.111 Zimbabwe lineage +B.1.1.112 Netherlands lineage +B.1.1.113 USA lineage +B.1.1.114 Wales lineage +B.1.1.115 UK lineage +B.1.1.116 USA lineage +B.1.1.117 South African lineage, previously B.1.1.66 +B.1.1.118 USA lineage (TX) +B.1.1.119 Northern Ireland lineage +B.1.1.120 UK lineage +B.1.1.121 Canadian lineage +B.1.1.122 Netherlands/ Belgium lineage +B.1.1.123 UK lineage +B.1.1.124 UK/ Switzerland lineage +B.1.1.125 UK lineage +B.1.1.126 USA lineage +B.1.1.127 Russian lineage +B.1.1.128 USA lineage +B.1.1.129 Russian lineage +B.1.1.130 UK/ Swedish lineage +B.1.1.131 UK lineage +B.1.1.132 Gambian lineage +B.1.1.133 UAE lineage +B.1.1.134 USA/UK lineage +B.1.1.135 USA lineage +B.1.1.136 Australian lineage +B.1.1.137 UK lineage +B.1.1.138 UK lineage +B.1.1.139 USA lineage +B.1.1.140 Russian lineage +B.1.1.141 UK/ Russian lineage +B.1.1.142 Australian lineage +B.1.1.143 Brazilian lineage, previously B.1.1.28 +B.1.1.144 Swiss lineage +B.1.1.145 UK lineage +B.1.1.146 UK lineage +B.1.1.147 UK lineage +B.1.1.148 USA lineage +B.1.1.149 UK lineage +B.1.1.150 UK lineage +B.1.1.151 UK lineage +B.1.1.152 Russian lineage +B.1.1.153 UK/Denmark lineage +B.1.1.154 UK lineage +B.1.1.155 UK lineage +B.1.1.156 South African lineage +B.1.1.157 Canadian lineage +B.1.1.158 USA lineage +B.1.1.159 UK/ Denmark lineage +B.1.1.160 Northern Ireland lineage +B.1.1.161 Saudi Arabian lineage +B.1.1.162 Australian/ UK lineage lineage +B.1.1.163 Russian lineage +B.1.1.164 UK lineage +B.1.1.165 UK lineage +B.1.1.166 UK lineage +B.1.1.167 Denmark/ E European lineage +B.1.1.168 UK lineage +B.1.1.169 USA lineage +B.1.1.170 UK/Denmark +B.1.1.171 UK lineage +B.1.1.172 USA (split from B.1.1.36) +B.1.1.173 UK lineage +B.1.1.174 USA (CA) +B.1.1.175 Bangladesh lineage +B.1.1.176 Canada +B.1.1.177 USA (TX) +B.1.1.178 UK lineage +B.1.1.179 Indian (split from B.1.1.32) +B.1.1.180 USA lineage +B.1.1.181 Turkish +B.1.1.182 UAE (Split from B.1.1.72) +B.1.1.183 South Korea +B.1.1.184 Russian lineage +B.1.1.185 Netherlands lineage +B.1.1.186 USA +B.1.1.187 UK lineage +B.1.1.189 European (contains several B.1.1.54) +B.1.1.190 WALES lineage +B.1.1.191 Danish lineage +B.1.1.192 USA lineage +B.1.1.193 UK lineage +B.1.1.194 UK lineage +B.1.1.195 UK lineage +B.1.1.196 UK lineage +B.1.1.197 UK lineage +B.1.1.198 UK/ Portugal lineage (split from B.1.1.15) +B.1.1.199 UK (split from B.1.1.64) +B.1.1.200 UK lineage +B.1.1.201 Indian and Singapore (split from B.1.1.72) +B.1.1.202 Italian lineage +B.1.1.203 UK lineage +B.1.1.204 England (with one czech sequence - party?) +B.1.1.205 USA (CA) +B.1.1.206 South Africa (mostly from B.1.1.54) +B.1.1.207 USA (split from B.1.1.53) +B.1.1.208 Mostly UK, some India, Ireland, Portugal +B.1.1.209 Netherlands +B.1.1.210 USA (TX) +B.1.1.211 French, swiss, UK, Belgian +B.1.1.212 Indian (split from B.1.1.32) +B.1.1.213 England +B.1.1.214 Japan +B.1.1.215 England with a spanish base +B.1.1.216 India mostly, England a bit, two long Singapore seqs with long branches +B.1.1.217 England +B.1.1.218 UK and Switzerland +B.1.1.219 Northern Europe (UK, Denmark, Norway, Sweden) +B.1.1.220 England, one Botswana, one Lithuania (split from B.1.1.44) +B.1.1.221 Belgian (split from B.1.1.74) +B.1.1.222 USA and Mexico +B.1.1.223 USA, NZ, England, one Russia +B.1.1.224 Denmark +B.1.1.225 USA, mostly southern (FL and TX) +B.1.1.226 USA, mostly Texas, A few Canada +B.1.1.227 England +B.1.1.228 USA (WA) +B.1.1.229 Italy and Nigeria +B.1.1.230 USA (TX) +B.1.1.231 USA +B.1.1.232 Northern Europe (UK, Germany, Denmark, Belgium, NL) +B.1.1.233 USA (WA) +B.1.1.234 England and Northern Ireland and Ireland +B.1.1.235 UK lineage +B.1.1.236 UK (split from B.1.1.56) +B.1.1.237 Welsh lineage, previously B.1.1.30 +B.1.1.238 UK and New Zealand (split from B.1.1.7) +B.1.1.239 USA (CA) +B.1.1.240 UK +B.1.1.241 France, Germany, Switzerland lineage- previously B.1.1.55 +B.1.1.242 UK, Gambia and Switzerland +B.1.1.243 UK, Ukraine, Denmark +B.1.1.244 USA and Mexico +B.1.1.245 Northern Ireland lineage, previously B.1.1.60 (split) +B.1.1.246 Russia +B.1.1.247 Northern Europe (UK, NL, Switzerland) and Northern Africa (Egypt and Morocco), Gambia (some B.1.1.55) +*B.1.1.248 Brazilian lineage reassigned B.1.1.28 +B.1.1.249 Wales lineage +B.1.1.250 UK lineage +B.1.1.251 UK and US +B.1.1.252 South Africa (formerly B.1.1.66) +B.1.1.253 UK lineage +B.1.1.254 South Africa and France +B.1.1.255 UK lineage +B.1.1.256 England +B.1.1.257 European/ UK lineage +B.1.1.258 USA (TX) +B.1.1.259 UK (split from B.1.1.64) +B.1.1.260 UK (split from B.1.1.64) +B.1.1.261 Swedish/ Danish lineage +B.1.1.262 UK lineage +B.1.1.263 UAE lineage +B.1.1.264 Wales lineage, previously part of B.1.1.30 +B.1.1.265 USA lineage +B.1.1.266 Czech lineage +B.1.1.267 Irish lineage +B.1.1.268 USA lineage +B.1.1.269 Denmark/ UK lineage +B.1.1.270 UK lineage +B.1.1.271 Austrian lineage +B.1.1.272 Denmark lineage +B.1.1.273 South african lineage, previously part of B.1.1.56 +B.1.1.274 UK lineage +B.1.1.275 DRC lineage +B.1.1.276 Previously part of B.1.1.55, USA lineage +B.1.1.277 Europe/ Denmark lineage +B.1.1.278 UK lineage +B.1.1.279 UK lineage +B.1.1.280 Lithuanian lineage +B.1.1.281 Indian lineage, previously part of B.1.1.32 +B.1.1.282 Netherlands, Denmark lineage +B.1.1.283 Japanese lineage +B.1.1.284 Japanese lineage +B.1.1.285 Japan/ USA lineage +B.1.1.286 UK lineage +B.1.1.287 USA lineage +B.1.1.288 Danish lineage +B.1.1.289 Wales lineage +B.1.1.290 USA lineage, previously part of B.1.1.76 +B.1.1.291 USA lineage (WA), previously part of B.1.1.77 +B.1.1.292 UK lineage +B.1.1.293 Gambian lineage +B.1.1.294 Russain/ UK lineage +B.1.1.295 UK/Australia lineage +B.1.1.296 UK lineage +B.1.1.297 Belgium lineage +B.1.1.298 Danish lineage, contains the origin of the Y453F mutation associated with mink +B.1.1.299 UK lineage +B.1.1.300 UK lineage +B.1.1.301 UK lineage, some previously part of B.1.1.55 +B.1.1.302 Swedish lineage +B.1.1.303 UK lineage +B.1.1.304 UK/USA lineage +B.1.1.305 UK lineage +B.1.1.306 Indian lineage +B.1.1.307 UK lineage +B.1.1.308 UK lineage +B.1.1.309 USA lineage (CA, OR) +B.1.1.310 Northern Ireland lineage +B.1.1.311 UK lineage +B.1.1.312 Jordan lineage +B.1.1.313 English lineage +B.1.1.314 Brazilian lineage, previously part of B.1.1.33 +B.1.1.315 Previously D.1, UK/ UAE lineage +B.1.1.316 International lineage with E484K mutation +B.1.1.317 Russian lineage +B.1.2 USA lineage +B.1.3 USA lineage +*B.1.3.1 South Korean lineage +*B.1.3.2 Argentinian lineage +*B.1.3.3 Israel lineage +*B.1.3.4 Israel/ UK lineage +*B.1.5 Reassigned to B.1 and additional sublineages as this lineage has lost monophyletic status and split into multiple parts of the B.1 tree. Previously had a Spanish base, European lineage/ lots of Spanish sequences towards the basal end of the subtree and exports around the globe. +*B.1.5.2 Reassigned B.1.190, Netherlands lineage +*B.1.5.5 Reassigned B.1.225 +*B.1.5.6 UK lineage reassigned B.1.223 +*B.1.5.11 Reassigned B.1.189, USA/ Mexico lineage +*B.1.5.12 Reassigned to B.1.416, Senegal/ Gambia lineage +*B.1.5.13 Reassigned B.1.180, Romanian lineage +*B.1.5.15 Reassigned B.1.185, USA lineage +*B.1.5.17 Reassigned B.1.181, USA lineage +*B.1.5.16 South African lineage, reassigned to B.1.237 +*B.1.5.18 Reassigned B.1.256 +*B.1.5.19 South African lineage reassigned to B.1.381 +*B.1.5.21 Reassigned B.1.418, Scottish lineage +*B.1.5.25 Reassigned B.1.229 +*B.1.5.26 Reassigned B.1.232 +*B.1.5.27 USA lineage (CA), reassigned to B.1.243 +*B.1.5.28 Reassigned B.1.231 +*B.1.5.29 USA lineage (WI/ IL) reassigned to B.1.415 +*B.1.5.30 UK lineage +*B.1.5.31 South African lineage, reassigned B.1.417 +*B.1.5.32 Colombian lineage, reassigned B.1.420 +*B.1.5.33 Split up in current tree, reassigned to B.1. UK lineage +*B.1.5.34 Reassigned to B.1.222, reassigned Scottish lineage +*B.1.5.35 Indian lineage reassigned B.1, lacks any structure in current tree +*B.1.5.36 Indian lineage reassigned to B.1.136 +*B.1.6 Reassigned lineage +B.1.8 Netherlands/ South African lineage +*B.1.8.2 Reassigned in the current tree. USA lineage (CA) +B.1.9 North European, eastern european, plus Turkey and DRC +B.1.9.1 Scottish lineage +B.1.9.2 USA (VA) +B.1.9.3 Belgium +B.1.9.4 UK, Denmark, Switzerland +B.1.9.5 Denmark, Sweden, Switzerland, England +B.1.9.6 North Macedonia, Switzerland +*B.1.11 UK lineage, reassigned B.1- broken up in current tree +B.1.12 Luxembourg lineage +B.1.13 UK lineage +B.1.14 USA lineage (CA) +*B.1.19 USA lineage (WI), reassigned B.1- broken up in current tree +*B.1.21 Split up Washington (USA), reassigned mostly to B.1.371 +B.1.22 Netherlands lineage +B.1.23 Australian/ New Zealand lineage +*B.1.25 Australian lineage +*B.1.26 USA/Gambia lineage +*B.1.34 English lineage, reassigned B.1 +B.1.35 UK lineage +B.1.36 Saudi Arabia base, then into UK and Denmark, Australia +*B.1.36.1 UK lineage +*B.1.36.3 Danish lineage +B.1.36.4 Netherlands lineage +*B.1.36.5 Saudi Arabia lineage, reassigned to parent lineage B.1.36 +B.1.36.6 Norway lineage +B.1.36.7 Oman lineage +B.1.36.8 Canadian lineage +B.1.36.9 UK lineage +B.1.36.10 Jordan lineage +*B.1.36.11 Netherlands lineage +B.1.36.12 UK lineage +*B.1.36.13 Irish lineage +*B.1.36.14 Danish lineage +*B.1.36.15 Saudi Arabia lineage +B.1.36.16 SE Asia/ Bangladesh/UK lineage +B.1.36.17 UK lineage +*B.1.36.17.1 Alias F.1 New Zealand lineage +B.1.36.18 Canadian lineage +B.1.36.19 Singapore lineage +B.1.36.20 UK/ Germany lineage +B.1.36.21 Norway lineage +B.1.36.22 Finland lineage +B.1.36.23 UK lineage +B.1.36.24 UK lineage +B.1.36.25 Danish lineage +B.1.36.26 Canadian lineage +B.1.36.27 Hong Kong lineage +B.1.36.28 UK lineage +B.1.37 USA lineage +B.1.38 USA lineage +B.1.39 Danish lineage +B.1.40 Scottish lineage +B.1.44 Wales lineage +B.1.67 Wales lineage +B.1.69 Scottish lineage +B.1.70 Scottish lineage +B.1.74 Spanish lineage +*B.1.75 Reassigned in the current tree. English lineage +B.1.76 English lineage +B.1.77 UK lineage, Some reassigned B.1.5 +B.1.78 Netherlands lineage +B.1.79 UK lineage, some now reassigned to B.1.5 +*B.1.80 Reassigned in the current tree. Indian lineage +B.1.81 English lineage +*B.1.82 Reassigned in the current tree. UK lineage +B.1.83 Belgian lineage +B.1.84 DRC lineage +B.1.88 Scottish lineage +B.1.88.1 Danish lineage +*B.1.89 Reassigned in the current tree. UK lineage +*B.1.90 Reassigned in the current tree. Scottish lineage +B.1.91 Portuguese lineage +B.1.93 UK lineage +B.1.94 Luxembourg lineage +B.1.95 Indian lineage +B.1.96 Netherlands lineage +B.1.97 UK lineage +B.1.98 UK lineage +*B.1.102 Reassigned in the current tree. Iceland lineage +B.1.103 US lineage (MI) +B.1.104 English lineage +B.1.105 UK lineage +B.1.106 South African lineage, some USA sequences +*B.1.107 Reassigned in the current tree. Danish lineage, with USA and UK sequences +B.1.108 USA lineage (NY) +B.1.109 Luxembourg lineage +B.1.110 Chilean/ US and Australia lineage +B.1.110.1 Chilean +B.1.110.2 England and ireland +B.1.110.3 USA (mostly FL) and a few England +B.1.111 South/ Central American lineage (mostly Trinidad and Colombia, an a small cluster from Norwich) +B.1.112 USA lineage (UT) +B.1.113 Indian lineage, some reassigned from B.1.36 +*B.1.114 Reassigned in the current tree. Canadian lineage +B.1.115 Israel lineage +B.1.116 USA lineage +B.1.117 UK lineage +B.1.118 Denmark lineage +B.1.119 US lineage (MI) +B.1.120 Wales lineage +B.1.124 USA lineage (WA) +B.1.126 German lineage +B.1.127 Ukraine lineage +B.1.128 Swiss/ DRC lineage +B.1.131 Ukraine/ European lineage +*B.1.133 Reassigned in the current tree. USA lineage (WA) +B.1.134 USA lineage +*B.1.135 Reassigned in the current tree. Small Portuguese lineage +B.1.137 USA lineage +*B.1.136 Reassigned in the current tree. Indian lineage, split up and reassigned to B.1 +*B.1.138 Reassigned in the current tree. Small Australian lineage +B.1.139 USA lineage +B.1.140 South African lineage +*B.1.141 Reassigned in the current tree. Scottish lineage, first wave of N439K +B.1.142 Welsh lineage +B.1.143 Indian lineage +B.1.144 South African lineage +B.1.145 Indian lineage +B.1.146 Swiss lineage +B.1.147 Canada/ Belgium lineage +B.1.149 DRC lineage +*B.1.150 Reassigned lineage +B.1.151 UK lineage +B.1.152 English lineage +B.1.153 English lineage with some Australian, New Zealand and European sequences +*B.1.154 Reassigned in the current tree. USA lineage +*B.1.156 Reassigned in the current tree. Scottish lineage +B.1.157 Spain/ UK lineage +B.1.158 Finland lineage +B.1.159 French lineage +B.1.160 Large European lineage, sequences from BeNeLuX, Denmark, Switzerland, Hungary and UK. +*B.1.160.1 Reassigned B.1.523 English lineage +*B.1.160.2 Reassigned B.1.523 English lineage +*B.1.160.3 Indonesian lineage (now B.1.470) +*B.1.160.4 English lineage (now B.1.471) +B.1.160.5 Danish lineage +*B.1.160.6 Danish lineage, reassigned B.1.160 lack of resolution in current tree +B.1.160.7 UK lineage +B.1.160.8 Danish lineage +B.1.161 USA lineage (OR) +B.1.162 USA lineage (WI) +B.1.163 USA lineage (CA/OR) +B.1.164 Latvian lineage +B.1.165 UK lineage +B.1.166 USA lineage +B.1.167 UK lineage +B.1.168 Scottish lineage +*B.1.169 USA lineage (WA) Merged with B.1.333/B.1.333.1 +*B.1.173 Reassigned lineage +B.1.177 Spain to Europe +B.1.177.1 Denmark +B.1.177.2 English lineage +B.1.177.3 Welsh/English lineage +B.1.177.4 UK lineage +B.1.177.5 Scottish lineage +B.1.177.6 English lineage +B.1.177.7 Welsh lineage +B.1.177.8 Scottish lineage +B.1.177.9 UK lineage +B.1.177.10 English lineage +B.1.177.11 UK lineage +B.1.177.12 Danish lineage +B.1.177.13 UK lineage +B.1.177.14 Norway/Denmark lineage +B.1.177.15 Welsh/ English lineage +B.1.177.16 English lineage +B.1.177.17 English lineage +B.1.177.18 English lineage +B.1.177.19 UK lineage +B.1.177.20 UK lineage +B.1.177.21 Danish lineage +B.1.177.22 UK lineage +B.1.177.23 UK lineage +B.1.177.24 Danish lineage +B.1.177.25 Gibraltar lineage +B.1.177.26 UK lineage +B.1.177.27 Danish lineage +B.1.178 France/ Switzerland/ Austria/ DRC lineage +B.1.179 Danish lineage +B.1.180 Romanian lineage (previously B.1.5.13) +B.1.181 USA lineage (previously B.1.5.17) +B.1.182 Spanish lineage +*B.1.183 Reassigned in the current tree. Canadian lineage +B.1.184 Indian lineage +*B.1.185 Reassigned in the current tree. USA lineage (previously B.1.5.15) +*B.1.186 Saudi-arabian/ Indian lineage (now B.1.260) +B.1.187 Polish lineage +B.1.188 USA lineage +B.1.189 USA/ Mexico lineage (some previously B.1.5.11) +B.1.190 Previously B.1.5.2, Netherlands lineage +*B.1.191 Reassigned in the current tree. Previously B.1.5.21, Scottish lineage +B.1.192 Equatorial Guinea lineage +*B.1.193 Reassigned in the current tree. USA lineage +B.1.194 USA lineage +B.1.195 Uruguay/ UAE lineage +B.1.196 USA lineage +B.1.197 Australian/ New Zealand lineage +B.1.198 UK lineage +B.1.199 USA lineage +*B.1.200 Reassigned in the current tree. Previously part of B.1.98, reassigned UK lineage +B.1.201 Previously part of B.1.75, reassigned UK lineage +*B.1.202 Reassigned in the current tree. USA lineage +B.1.203 Panama/ Costa Rica lineage +*B.1.204 Reassigned in the current tree. USA lineage +B.1.205 Peru lineage +B.1.206 USA lineage (TX) +B.1.207 USA lineage (TX) +B.1.208 Small French lineage +B.1.209 Small Scottish lineage +B.1.210 Indian lineage, Reassigned from B.1.80, split this assignment +B.1.211 Luxembourg lineage +B.1.212 Brazil lineage +B.1.213 Polish lineage +B.1.214 DRC lineage +B.1.215 Scottish lineage, previously some of B.1.77 +B.1.216 USA lineage +*B.1.217 Reassigned in the current tree. Indian lineage Reassigned from B.1.80, split this assignment +B.1.218 Denmark lineage +B.1.219 Suriname lineage +B.1.220 Netherlands lineage +B.1.221 European/ UK lineage +B.1.221.1 UK lineage +B.1.221.2 German lineage +B.1.221.3 Danish lineage +B.1.222 Scottish lineage, split from B.1.141 +B.1.223 Previously B.1.5.6, Spain/ UK lineage +B.1.224 Austrian lineage +B.1.225 UK lineage (reassigned from B.1.5.5) +*B.1.226 Reassigned in the current tree. Equatorial Guinea lineage +B.1.227 Swedish lineage +*B.1.228 Reassigned in the current tree. USA lineage, reassigned from B.1.5.27 split +B.1.229 UK lineage, reassigned from B.1.5.25 +*B.1.230 Reassigned in the current tree. USA lineage, reassigned from B.1.5.27 split +B.1.231 UK lineage, reassigned from B.1.5.28 +B.1.232 UK and USA lineage, reassigned from B.1.5.26 +B.1.233 USA lineage (OR) +B.1.234 USA lineage +B.1.235 UK lineage +B.1.236 Switzerland/ Denmark lineage +B.1.237 South African lineage +B.1.238 UK lineage +B.1.239 USA lineage +B.1.240 USA lineage +B.1.241 USA/ Mexico lineage +B.1.242 Norway lineage +B.1.243 USA lineage +*B.1.244 Reassigned in the current tree. Saudi Arabian lineage that previously was part of B.1.160 +B.1.245 USA lineage (CA) +*B.1.246 Reassigned in the current tree. Saudi Arabian lineage, previously some assigned B.1.160 +*B.1.247 Indian lineage reassigned to B.1.36 +B.1.248 UK lineage +B.1.249 UK lineage +B.1.250 UK lineage +B.1.251 UK lineage +B.1.252 UK lineage, previously part of B.1.11 +*B.1.253 Reassigned in the current tree. UK lineage +B.1.254 Scottish lineage, previously part of B.1.88 +*B.1.255 North American lineage, with other global diversity (Now all over tree) +B.1.256 Scottish lineage, previously B.1.5.18 +*B.1.257 Reassigned in the current tree. UK lineage +B.1.258 N439K mutation lineage +B.1.258.1 French lineage +B.1.258.2 Irish lineage (has sub-lineage G.1) +B.1.258.3 UK lineage +B.1.258.4 UK lineage, previously B.1.5.23 +B.1.258.5 UK lineage +B.1.258.6 UK lineage +B.1.258.7 UK lineage +B.1.258.8 Danish lineage +B.1.258.9 Danish lineage +B.1.258.10 Scottish lineage +B.1.258.11 Danish lineage +B.1.258.12 UK lineage +*B.1.258.13 Reassigned in the current tree. Danish lineage +B.1.258.14 Italian lineage +B.1.258.15 Danish lineage +B.1.258.16 Danish lineage +B.1.258.17 Danish lineage +B.1.258.18 Danish lineage +B.1.258.19 Danish lineage +B.1.258.20 Luxembourg lineage +B.1.258.21 Netherlands lineage +*B.1.259 Saudi Arabia/ India lineage (now in B.1.260) +B.1.260 Mostly Saudi Arabian, the odd indian sequence, England and Hong Kong at the end lineage (now contains lots of B.1.186, B.1.247, B.1.259) +*B.1.261 Saudi Arabian lineage (now in B.1.260) +*B.1.262 Reassigned in the current tree. Danish lineage +B.1.263 Danish lineage +B.1.264 USA lineage (UT) +B.1.265 USA lineage, cleaned up a lot in release 2021-01-20 +*B.1.266 Reassigned in the current tree. Austrian lineage +B.1.267 USA lineage (CA) +B.1.268 USA lineage +*B.1.269 Reassigned in the current tree. Slovenian lineage +B.1.270 Canadian lineage +*B.1.271 Reassigned in the current tree. USA lineage +*B.1.272 Reassigned in the current tree. France/ Australian lineage +B.1.273 France/ Congo/ Cote d’Ivoire lineage +B.1.274 USA lineage +B.1.275 France lineage +B.1.276 USA lineage +B.1.277 UK/ Portugal lineage +*B.1.278 Reassigned in the current tree. UK/ Australia lineage, previously part of B.1.13 +B.1.279 Canadian lineage +B.1.280 USA lineage +B.1.281 Bahrain lineage +B.1.282 UK lineage +B.1.283 USA lineage +B.1.284 USA lineage +B.1.285 USA lineage +*B.1.286 Reassigned in the current tree. USA lineage +B.1.287 USA lineage +*B.1.288 Reassigned in the current tree. Denmark lineage +B.1.289 USA lineage +*B.1.290 Reassigned in the current tree. USA lineage +B.1.291 Costa Rica lineage +B.1.292 Belgium/ Gambia/ Senegal/ French lineage +B.1.293 USA lineage +B.1.294 USA lineage +*B.1.295 Reassigned in the current tree. Australian lineage +*B.1.296 Reassigned in the current tree. USA/ Australian lineage +*B.1.297 Reassigned in the current tree. USA lineage +*B.1.297.1 Reassigned in the current tree. Canadian lineage +B.1.298 USA lineage +*B.1.299 Reassigned in the current tree. USA lineage +*B.1.300 Reassigned in the current tree. USA lineage +B.1.301 USA lineage +B.1.302 USA/ Denmark lineage +*B.1.303 Reassigned in the current tree. USA lineage +B.1.304 USA lineage +B.1.305 USA lineage +B.1.306 USA lineage +*B.1.307 Reassigned in the current tree. USA lineage +B.1.308 USA lineage +B.1.309 USA lineage +B.1.310 Netherlands lineage +B.1.311 USA lineage +B.1.312 USA lineage +B.1.313 USA lineage +B.1.314 North American lineage +B.1.315 USA lineage +B.1.316 Canadian lineage +*B.1.317 Reassigned in the current tree. USA lineage +B.1.318 USA lineage +B.1.319 USA/ Australia lineage +B.1.320 USA lineage (absorbed some B.1.368) +B.1.321 Belgian lineage +*B.1.322 USA lineage, reassigned B.1 +B.1.323 USA lineage +B.1.324 USA lineage +B.1.325 USA lineage (TX) +B.1.326 USA lineage (TX) +*B.1.327 Reassigned in the current tree. Danish lineage +B.1.328 USA lineage +B.1.329 German lineage +B.1.330 USA lineage +B.1.331 USA lineage +B.1.332 USA lineage +B.1.333 USA lineage, merged with B.1.169 +B.1.333.1 USA lineage (WA) (all B.1.169) +B.1.334 USA lineage +B.1.335 USA lineage +B.1.336 USA lineage, previously part of B.1.2 +B.1.337 USA lineage +B.1.338 Australian lineage +*B.1.339 Reassigned in the current tree. Irish lineage +B.1.340 USA lineage +B.1.341 USA lineage +B.1.342 Swedish lineage +B.1.343 Danish lineage +B.1.344 USA lineage (CO) +*B.1.345 Reassigned in the current tree. Canadian lineage +B.1.346 USA lineage +*B.1.347 Reassigned in the current tree. Canadian lineage, previously part of B.1.114 lineage +B.1.348 USA lineage +B.1.349 USA lineage +B.1.350 Canadian lineage +B.1.351 South African lineage defined by new variant 501Y.V2 - A more detailed description of the lineage is here and a preprint describing the variant is here: https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1. +*B.1.352 Reassigned in the current tree. USA lineage (CA) +*B.1.353 Reassigned in the current tree. European lineage +B.1.354 Danish lineage +B.1.355 USA lineage +B.1.356 Spanish/ Netherlands lineage +B.1.357 USA lineage +B.1.358 Danish lineage +B.1.359 USA lineage +B.1.360 USA lineage +B.1.361 USA lineage +B.1.362 UK/ Israel lineage +B.1.363 USA lineage +*B.1.364 Reassigned in the current tree. USA lineage +*B.1.365 Reassigned in the current tree. USA lineage +B.1.366 USA lineage +B.1.367 French lineage +*B.1.368 Reassigned in the current tree. USA lineage +B.1.369 USA/ New Zealand lineage +B.1.370 USA lineage, cleaned up a lot in release 2021-01-20 +B.1.371 Danish/ USA lineage, previously part of B.1.21 +B.1.372 Danish lineage +*B.1.373 Reassigned in the current tree. Swedish lineage +*B.1.374 Reassigned in the current tree. European lineage +*B.1.374.1 Reassigned in the current tree. Bangladesh lineage +B.1.375 US lineage circulating in Connecticut with the 69-70del, which leads to SGTF. However, they express 484E and 501N in their spike proteins. +B.1.376 Wales lineage +B.1.377 US lineage +B.1.378 US lineage +B.1.379 UK lineage, previously B.1.5.30 +B.1.380 Ugandan/ Rwandan lineage +B.1.381 South African lineage reassigned from B.1.5.19 +B.1.382 US lineage, reassigned from B.1.5 +B.1.383 Wales lineage +B.1.384 US lineage +*B.1.386 Reassigned in the current tree. US lineage +B.1.387 French lineage +B.1.388 Cote d'Ivoire lineage +B.1.389 UK lineage +B.1.390 US lineage +B.1.391 UK lineage +B.1.392 UK lineage +B.1.393 Ugandan lineage +B.1.394 North Macedonian lineage +B.1.395 Wales lineage +B.1.396 USA lineage +B.1.397 USA lineage +B.1.398 Saudi Arabia/ Denmark lineage +B.1.399 USA lineage +B.1.400 USA lineage +B.1.401 USA lineage +B.1.402 USA lineage +B.1.403 USA lineage +B.1.404 USA/ Mexico lineage +B.1.405 USA lineage +B.1.406 Denmark/ Sweden lineage +B.1.407 UK lineage +B.1.408 UK/ Romania lineage +B.1.409 US (NY) lineage +*B.1.410 Reassigned in the current tree. Danish lineage +B.1.411 Sri_Lanka lineage +B.1.412 Russian lineage +B.1.413 USA lineage +B.1.414 Netherlands lineage +B.1.415 USA lineage, reassigned from B.1.5.29 +B.1.416 Senegal/ Gambian lineage, reassigned from B.1.5.12 +B.1.416.1 European lineage within diversity of B.1.416. Previously assigned E.1 +B.1.417 South African lineage +B.1.418 Scottish lineage, previously B.1.5.21 +B.1.419 Iceland lineage +B.1.420 Colombian lineage, previously B.1.5.32 +B.1.421 USA lineage +B.1.422 Canadian lineage +B.1.423 USA lineage (MI) +B.1.424 USA lineage (LA), reassigned from part of B.1.370 +B.1.425 USA lineage (UT), reassigned from part of B.1.370 +B.1.426 USA lineage (UT), reassigned from part of B.1.2 +B.1.427 USA lineage (CA) +B.1.428 Danish lineage (amalgam of Danish sequences from B.1.358, B.1.288, B.1.262) +B.1.429 A lineage predominantly circulating in California but with exports to other countries. Characterised by the spike L452R mutation but also has spike:W152C orf1ab:D5584Y and N:T205I. +B.1.431 Scottish lineage +B.1.432 USA lineage (TX) +B.1.433 USA lineage (MA) +B.1.434 Australian lineage (previously a couple part of B.1.25, B.1.295) +B.1.435 USA lineage (Previously part of B.1.2) +B.1.436 USA lineage (UT) +B.1.437 USA lineage (FL) +B.1.438 Northern Europe, Australia and New Zealand (mostly B.1.255) +B.1.439 USA lineage (VA) +B.1.440 USA lineage (All NM, one AZ) +B.1.441 UK/Denmark, India, UAE, Turkey +B.1.442 USA (VA) +B.1.443 USA (UT, OR, CA, AZ, VA) Some B.1.9 +B.1.444 USA lineage (UT) +B.1.445 USA lineage (AZ) +B.1.446 USA lineage (WA) +B.1.447 Saudi Arabian lineage +B.1.448 USA lineage +B.1.449 Saudi Arabia (mixture of B.1.260 and B.1.160) +B.1.450 USA lineage (TX) +B.1.451 USA lineage (VA), previously B.1.328 and B.1.317 +B.1.452 USA lineage (CA), previously B.1.229 and B.1.346 +B.1.453 USA lineage (CA) +B.1.454 India (was part of B.1.160) +B.1.455 Saudi Arabia (was part of B.1.247) +B.1.456 Saudi Arabia (was part of B.1.160, B.1.246, B.1.247) +B.1.457 UK, Norway, South Korea, Denmark (mostly B.1.160) +B.1.457.1 USA (MI) plus England (was B.1.247, B.1.160) +B.1.458 India (split from B.1.247) +B.1.459 South East Asia (mostly Indonesia) (split from B.1.160, B.1.247) +B.1.460 England (from B.1.247, B.1.160) +B.1.461 India (from B.1.247) +B.1.462 Nigeria plus one Italy and england (from B.1.246) +B.1.463 Finland (from B.1.160) +B.1.464 India and Nepal +B.1.465 England (was B.1.160.1) +B.1.466 England (mostly B.1.247) +B.1.467 Nigeria, England, Switzerland (mostly B.1.247) +B.1.468 Saudi Arabia, Indonesia, Singapore, South Korea, UK (B.1.247, B.1.247, B.1.36, B.1.160) +B.1.469 England, Singapore, Denmark, NL, Norway (B.1.247, B1.160) +B.1.470 South East Asia and (Was B.1.160.3) +B.1.471 England (Was B.1.160.4) +B.1.472 England and Denmark (was part of B.1.160) +B.1.473 USA (NM) +B.1.474 Luxembourg, UK, Denmark, Switzerland +B.1.475 German (some B.1.275) +B.1.476 Nigeria and Cote D’Ivoire +B.1.477 England (all were B.1.275) +B.1.478 USA (NY, MA, CT) +B.1.479 USA (MA) +B.1.480 England, Australia, Sweden, Norway (some B.1.275) +B.1.481 DRC and Senegal base, into Switzerland +B.1.482 France and Cote D’Ivoire +B.1.483 USA (WI) +B.1.484 France and USA (MI) +B.1.485 USA (MI, WI and TX) +B.1.486 USA (MA) +B.1.487 USA (TX) +B.1.488 Denmark and Sweden +B.1.489 Wales and Norway +B.1.490 Finland +B.1.491 England +B.1.492 England and USA (CO) +B.1.493 USA (FL) +B.1.494 USA (Split from B.1.3) +B.1.495 USA (Split from B.1.3) +B.1.496 USA (Split from B.1.3) +B.1.497 South Korea (was B.1.3.1) +B.1.498 USA (Split from B.1.3) +B.1.499 Argentina, Spain, NL, Hong Kong (was B.1.3.2) +B.1.500 USA (split from B.1.3) +B.1.501 USA (Split from B.1.3) +B.1.502 USA (Split from B.1.3) +B.1.503 USA (Split from B.1.3) +B.1.504 Israel and England (was B.1.3.3) +B.1.505 Israel and england (was B.1.3.4) +B.1.506 USA (NY, split from B.1.3) +B.1.507 USA (MI, NY, split from B.1.3) +B.1.508 USA (NY, AZ, split from B.1.3) +B.1.509 USA (split from B.1.3, mostly FL) +B.1.510 Norway, Canada +B.1.511 USA (TX) +B.1.512 UK, Australia, USA +B.1.513 Northern Europe +B.1.514 USA (TX) split from B.1.2 +B.1.515 USA (UT) +B.1.516 USA (mostly AZ) +B.1.517 USA, Australia +B.1.518 USA +B.1.519 England, split from B.1.117 +B.1.520 Germany, Norway, England +B.1.521 USA lineage (TX) +B.1.523 Reassigned from B.1.160, which split in the tree. Turkey, Saudi_Arabia and European lineage. +B.1.524 Malaysian lineage +B.1.525 Nigerian, Ghanaian and international lineage with E484K, del69-70 among other defining mutations. +*B.2.1 Reassigned to B.40 +*B.2.6 Reassigned to B.35 +*B.2.10 Reassigned to B.41 +*B.2.11 Reassigned to B.36 +*B.2.12 Reassigned to B.30 +B.3 A European lineage +B.3.1 Welsh lineage +B.4 Iranian lineage and global exports +B.4.1 Lineage from Kazakhstan within the B.4 diversity +B.4.2 Bahrein lineage +B.4.4 USA lineage +B.4.5 Australian lineage +B.5 Japanese lineage +B.6 Indian lineage +B.6.1 Malaysian lineage +B.6.2 Malaysian lineage +B.6.3 Singapore lineage +B.6.4 Singapore lineage +B.6.5 Australian lineage +B.6.6 Singapore lineage +B.10 Northern Irish lineage/Users/s1680070/repositories/cov-support/cov_support/scripts/update_website.py +B.11 European lineage with sequences from the Netherlands, UK, Austria, Slovakia +B.12 Japanese lineage +B.13 USA lineage +B.14 USA lineage +B.15 USA lineage +B.18 European lineage (Iceland and England) +B.19 USA lineage +B.20 USA lineage +B.23 Lineage with representation from mainly UK sequences, but also sequences from Portugal, Iceland and Brazil +B.26 UK lineage +B.27 UK lineage +B.28 UK lineage +B.29 UK/ Australian lineage +B.30 Reassigned from B.2.12, USA lineage +B.31 Reassigned from B.2.5, UK/ Australia/ New Zealand lineage +B.32 Scottish lineage +B.33 UK lineage +B.34 Scottish lineage +B.35 Previously B.2.6, USA lineage +B.36 Previously B.2.11, Israel lineage +B.37 USA lineage +B.38 Belgium lineage +B.39 Previously B.2.2, USA/ UK/ Australian lineage +B.40 Previously B.2.1. Large lineage majoritively from UK and Australia with representation from Europe, Jordan, USA, India, Ghana +B.41 Previously B.2.10, South Korean lineage +B.42 Hong Kong lineage +B.43 Hong Kong lineage +B.44 Portugal lineage +B.45 Scottish lineage +B.46 USA lineage +B.47 English lineage +B.48 UK lineage +B.49 Danish lineage +B.50 Indonesian lineage +B.51 USA lineage +B.52 UK lineage +B.53 Lithuanian lineage +B.54 UK lineage +C.1 Alias of B.1.1.1.1, South African lineage +C.2 Alias of B.1.1.1.2, South African lineage +C.3 Alias of B.1.1.1.3, English lineage +C.4 Alias of B.1.1.1.4, Peru lineage +C.5 Alias of B.1.1.1.5, Swiss lineage +C.6 Alias of B.1.1.1.6, South African lineage +C.7 Alias of B.1.1.1.7, Denmark lineage +C.8 Alias of B.1.1.1.8, Canada lineage +C.9 Alias of B.1.1.1.9, South African lineage +C.10 Alias of B.1.1.1.10, Poland lineage +C.11 Alias of B.1.1.1.11,Chilean lineage +C.12 Alias of B.1.1.1.12,New Zealand lineage +C.13 Alias of B.1.1.1.13, Peru lineage +C.14 Alias of B.1.1.1.14, Peru lineage +C.15 Alias of B.1.1.1.15, Denmark lineage +C.16 Alias of B.1.1.1.16, Portuguese lineage +D.2 Australian lineage, Alias of B.1.1.25.1 +D.3 Australian lineage, alias of B.1.1.25.3 +*E.1 Reassigned B.1.416.1. French lineage within the diversity of a Senegal/ Gambia lineage +F.1 Alias of B.1.36.17.1, New Zealand lineage +G.1 Alias of B.1.258.2.1, N439K UK lineage +H.1 Alias of B.1.1.67.1, South African lineage, split from B.1.1.10 +I.1 Alias of B.1.1.217.1, Latvian lineage, split from B.1.1.25 +J.1 Alias of B.1.1.250.1, Australian lineage +K.1 Alias of B.1.1.277, South Korean lineage +L.1 Alias of B.1.1.10.1, Canadian lineage +L.2 Alias of B.1.1.10.2, Netherlands lineage +M.1 Alias of B.1.1.294.1, Danish lineage +N.1 Alias of B.1.1.33.1, USA lineage +N.2 Alias of B.1.1.33.2, French lineage +N.3 Alias of B.1.1.33.3, Argentinian lineage +N.4 Alias of B.1.1.33.4, Chilean lineage +P.1 Alias of B.1.1.28.1, Brazilian lineage with a number of spike mutaions with likely functional significance E484K, K417T, and N501Y. Described in https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586. +P.2 Alias of B.1.1.28.2, Brazilian lineage