Lineage links

  • 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 (BS=16)
  • A.1.1
    Iceland lineage (BS=94)
  • A.1.3
    Low support, has been reassigned to parent lineage. Previously Australian lineage, structure has split up into the diverity of A.1, so all reassigned A.1
  • A.2
    Majoritively Spanish lineage now with a variety of other locations represented, including 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.3
    USA and Australian lineage
  • A.4
    USA lineage nested in A diveristy
  • 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
  • A.6
    Lineage from an introduction event into Thailand, now including a couple of exports
  • A.7
    Indian lineage, including Saudi Arabian & Turkish sequences. A.7, A.8 and A.9 are all lineages with diversity from India, however are difficult to resolve confidently, potentially due to ambiguities or homoplasies in the sequences. All are nested within the diversity of A.
  • A.8
    Low support, has been reassigned to parent lineage. Merged with sister Indian lineage A.7. A.7, A.8 and A.9 are all lineages with diversity from India, however are difficult to resolve confidently, potentially due to ambiguities or homoplasies in the sequences. All are nested within the diversity of A.
  • A.9
    Indian lineage. A.7, A.8 and A.9 are all lineages with diversity from India, however are difficult to resolve confidently, potentially due to ambiguities or homoplasies in the sequences. All are nested within the diversity of A.
  • 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
    European lineage that's been assigned due to high support and 3 clear SNPs `28881GA`,`28882GA`,`28883GC`
  • B.1.1.1
    UK/ Europe
  • B.1.1.2
    Welsh lineage
  • B.1.1.3
    English lineage
  • B.1.1.4
    UK lineage
  • B.1.1.5
    Iceland/ Belgium/ UK
  • B.1.1.6
    Austrian lineage
  • B.1.1.7
    UK lineage
  • B.1.1.8
    Indian lineage
  • B.1.1.9
    Low support, has been reassigned to parent lineage. Reassigned B.1.1, split into three this week, unstable lineage
  • B.1.1.10
    Formerly UK/ Iceland, a lot of diversity in this lineage, now has a Turkish sequence.
  • B.1.1.p11
    Low support, has been reassigned to parent lineage. Reassigned B.1.1, previously Portugal/ Wales/ England/ Ecuador
  • B.1.1.12
    Scottish lineage
  • B.1.1.13
    UK lineage (CAMB)
  • B.1.1.14
    Scottish lineage
  • B.1.1.15
    Luxembourgh/ UK/ Portugal lineage
  • B.1.1.16
    Wales lineage (some reassigned to B.1.1 as split up in most recent phylogeny)
  • B.1.1.17
    Iceland lineage
  • B.1.1.19
    Low support, has been reassigned to parent lineage. Reassigned to B.1.1 as split up in most recent phylogeny. Australian lineage
  • B.1.1.20
    Scottish lineage
  • B.1.1.21
    Low support, has been reassigned to parent lineage. Australian lineage reassigned to B.1.1 in most recent phylogeny
  • B.1.1.22
    South African lineage
  • B.1.1.23
    Low support, has been reassigned to parent lineage. Bangladesh lineage, merged into B.1.1.25 in most recent phylogeny
  • B.1.1.24
    Portuguese lineage
  • B.1.1.25
    Bangladesh lineage
  • B.1.1.26
    US lineage (WA)
  • B.1.1.27
    Lineage in Oman
  • B.1.1.28
    Brazil lineage, some sister sequences from parent node are also from Brazil, however there's sequences from a variety of other locations on that node.
  • B.1.1.29
    Wales lineage
  • B.1.1.30
    UK lineage (Wales & England)
  • B.1.1.31
    Netherlands lineage
  • B.1.1.32
    Indian lineage
  • B.1.1.33
    Majoritively South American lineage, lots of Brazil sequences represented
  • B.1.1.34
    South African lineage
  • B.1.1.35
    Previously a large part of B.1.1.1, however in the most recent phylogeny, this has become a sister lineage to B.1.1.1. UK sequences represented in this lineage.
  • B.1.1.36
    USA (CA) lineage
  • B.1.1.37
    UK lineage (England)
  • B.1.1.38
    Wales lineage
  • B.1.1.39
    Swiss lineage
  • B.1.1.40
    South African lineage
  • B.1.1.41
    English lineage
  • B.1.1.42
    Turkish lineage
  • B.1.1.43
    Scottish lineage
  • B.1.1.44
    UK lineage
  • B.1.1.45
    UK lineage
  • B.1.1.46
    Indian lineage
  • B.1.1.47
    Swiss lineage
  • B.1.1.48
    Japanese lineage
  • B.1.1.49
    Wales lineage
  • B.1.1.50
    UK/ Israel lineage
  • B.1.1.51
    UK lineage
  • B.1.1.52
    South African lineage (same parent node as B.1.1.53, but parent node is a large polytomy)
  • B.1.1.53
    South African lineage (same parent node as B.1.1.53, but parent node is a large polytomy)
  • B.1.1.54
    South African lineage
  • B.1.1.55
    England lineage
  • B.1.1.56
    South African lineage
  • B.1.1.57
    South African lineage
  • B.1.1.58
    Swiss lineage
  • B.1.1.59
    Wales lineage
  • B.1.1.60
    Northern Ireland lineage
  • B.1.1.61
    USA lineage (CA)
  • B.1.1.62
    South African lienage
  • B.1.1.63
    Hong Kong lineage
  • B.1.1.64
    UK lineage
  • B.1.1.65
    USA lineage (WA), previously B.1.1.26, however split in most recent phylogeny
  • B.1.1.66
    South African lineage
  • B.1.1.67
    English/ South African lineage
  • B.1.1.68
    Russian lineage
  • B.1.1.69
    Switzerland/ UK/ Italy lineage
  • B.1.1.70
    Northern Ireland lineage
  • B.1.1.71
    Australian/ Belgium/ Netherlands lineage
  • B.1.1.72
    UK/ India lineage
  • B.1.1.73
    USA lineage
  • B.1.1.74
    Northern Ireland/ Belgium lineage
  • B.1.1.75
    Belgium/ South Africa/ DRC lineage
  • B.1.1.76
    USA lineage (WA)
  • B.1.1.77
    USA lineage (WA)
  • B.1.2
    USA lineage
  • B.1.3
    USA lineage
  • B.1.3.1
    South Korean lineage
  • B.1.5
    European lineage/ lots of Spanish sequences towards the basal end of the subtree and exports around the globe. Low support at parent node now, potentially as a result of homoplasies
  • B.1.5.2
    Netherlands lineage
  • B.1.5.3
    Low support, has been reassigned to parent lineage. English lineage (now containing an Australian & Swedish seqeuence), reassigned B.1.5
  • B.1.5.4
    Low support, has been reassigned to parent lineage. Reassigned to B.1.5 as B.1.5 now seems to be European/ Spanish, so B.1.5.4 not a new introduction
  • B.1.5.5
    English lineage
  • B.1.5.6
    UK lineage
  • B.1.5.8
    Low support, has been reassigned to parent lineage. US lineage
  • B.1.5.9
    Low support, has been reassigned to parent lineage. Welsh lineage (reassigned to B.1.142 as it falls outside of B.1.5 in the most recent phylogeny)
  • B.1.5.10
    Low support, has been reassigned to parent lineage. UK lineage
  • B.1.5.11
    USA lineage
  • B.1.5.12
    Senegal lineage
  • B.1.5.13
    Romanian lineage
  • B.1.5.14
    Russian lineage
  • B.1.5.15
    USA lineage (CA)
  • B.1.5.16
    South African lineage
  • B.1.5.17
    USA lineage (OR & AK)
  • B.1.5.18
    Scottish lineage (previously B.1.101)
  • B.1.5.19
    South African lineage
  • B.1.5.20
    Romanian lineage
  • B.1.5.21
    Scottish lineage
  • B.1.5.22
    South Arican lineage
  • B.1.5.23
    Spanish lineage
  • B.1.5.24
    Norwegian lineage
  • B.1.5.25
    UK lineage (previously B.1.99)
  • B.1.5.26
    Scottish lineage (previously B.1.100)
  • B.1.5.27
    USA lineage (CA)
  • B.1.5.28
    English lineage
  • B.1.6
    Belgian lineage
  • B.1.8
    Netherlands/ South African lineage, with sequences from Europe
  • B.1.8.1
    Low support, has been reassigned to parent lineage. South African lineage (sequences reassigned to B.1.8)
  • B.1.8.2
    USA (CA) lineage
  • B.1.9
    Netherlands/ Belgium/ Turkey/ DRC
  • B.1.11
    UK lineage, pruned down relative to previous release. A number of sequences previously assigned B.1.11 reassigned to B.1 and some reassigned to B.1.88.
  • B.1.12
    BeNeLux/ UK lineage
  • B.1.13
    UK lineage
  • B.1.14
    USA lineage
  • B.1.p16
    Low support, has been reassigned to parent lineage. Belgium lineage, reassigned to B.1
  • B.1.19
    USA lineage (WI)
  • B.1.21
    Washington (USA)
  • B.1.22
    Netherlands lineage, now with some European sequences and some Australian sequences
  • B.1.23
    Australian lineage with a New Zealand sequence at base
  • B.1.25
    Australian lineage
  • B.1.26
    New Zealand/ USA lineage
  • B.1.29
    Low support, has been reassigned to parent lineage. USA lineage reassigned to B.1 as the structure of this lineage not present in the most recent phylogeny
  • B.1.30
    Low support, has been reassigned to parent lineage. English lineage
  • B.1.31
    Low support, has been reassigned to parent lineage. Australia lineage split up this phylogeny, reassigned to B.1
  • B.1.32
    Swedish lineage
  • B.1.34
    England lineage (NOTT)
  • B.1.35
    UK lineage (Wales & England)
  • B.1.36
    Global lineage with lots of representation of sequences from India and Saudi Arabia. Sequences also from Europe and UK. Now includes sequences that previously had been assigned B.1.113.
  • B.1.36.1
    Indian lineage
  • B.1.36.2
    Bangladesh lineage
  • B.1.37
    USA lineage (VA)
  • B.1.38
    USA lineage
  • B.1.39
    Danish lineage
  • B.1.40
    Scottish lineage
  • B.1.41
    Low support, has been reassigned to parent lineage. USA lineage: Split up in most recent phylogeny, reassigned to B.1
  • B.1.42
    Sweden/ Denmark lineage
  • B.1.43
    USA lineage
  • B.1.44
    Wales lineage
  • B.1.66
    English lineage
  • B.1.67
    Welsh lineage, sequence from Ecuador
  • B.1.68
    USA lineage (UT)
  • B.1.68.1
    USA lineage (TX)
  • B.1.69
    Scottish lineage
  • B.1.70
    Scottish lineage
  • B.1.71
    UK lineage (Scotland and Wales sequences )
  • B.1.72
    UK lineage (BRIS)
  • B.1.74
    Spanish lineage, with sequences from Portugal too
  • B.1.75
    English lineage
  • B.1.76
    English lineage
  • B.1.77
    UK lineage
  • B.1.78
    Netherlands lineage
  • B.1.79
    Low support, has been reassigned to parent lineage. English lineage, now reassigned to B.1.5
  • B.1.80
    Indian lineage with an English sequence
  • B.1.81
    English lineage
  • B.1.82
    English lineage
  • B.1.83
    Belgian lineage
  • B.1.84
    DRC lineage
  • B.1.85
    USA lineage
  • B.1.86
    English lineage (SHEF)
  • B.1.87
    Indian lineage, with some Chinese and South African sequences
  • B.1.88
    UK lineage, previously some of these seqeunces had been assigned B.1.11, but this clade has split in the tree.
  • B.1.89
    Scottish lineage
  • B.1.90
    Scottish lineage
  • B.1.91
    Portuguese lineage, parent node in B.1 also has Portuguese diversity, however is interspersed with sequences from UK and other European countries
  • B.1.93
    UK lineage, majoritively Scottish sequences
  • B.1.94
    Luxembourg lineage
  • B.1.95
    Indian lineage
  • B.1.96
    Netherlands lineage
  • B.1.97
    English lineage
  • B.1.98
    UK lineage with some USA and Australian sequences in
  • B.1.99
    Low support, has been reassigned to parent lineage. Now reassigned to B.1.5.25, English lineage
  • B.1.100
    Low support, has been reassigned to parent lineage. Reassigned to B.1.5.26, Scottish lineage
  • B.1.101
    Low support, has been reassigned to parent lineage. Scottish lineage, reassigned to B.1.5.18
  • B.1.102
    Icelandic lineage
  • B.1.103
    US lineage (MI)
  • B.1.104
    English lineage
  • B.1.105
    English lineage (CAMB)
  • B.1.106
    South African lineage, some USA sequences
  • B.1.107
    Danish lineage, with new USA and UK sequences nested within (previously B.1.5/ B.1.5.8)
  • B.1.108
    US lineage
  • B.1.109
    Luxembourg lineage
  • B.1.110
    Chilean/ US lineage
  • B.1.111
    South American/ English lineage
  • B.1.112
    US lineage (UT & WI)
  • B.1.113
    Indian lineage, some sequences reassigned from B.1.36
  • B.1.114
    Canadian lineage
  • B.1.115
    Israel/ UK lineage
  • B.1.116
    US lineage
  • B.1.117
    UK lineage (BRIS)
  • B.1.118
    Danish lineage
  • B.1.119
    US lineage (MI)
  • B.1.120
    Wales lineage
  • B.1.121
    Australian lineage
  • B.1.122
    Welsh lineage
  • B.1.123
    Low support, has been reassigned to parent lineage. Washington lineage, had previously been part of B.1.21, and has rejoined it in the most recent phylogeny
  • B.1.124
    USA lineage (WA)
  • B.1.125
    South African lineage
  • B.1.126
    German lineage
  • B.1.127
    Ukraine/ Latvian lineage
  • B.1.128
    European/ DRC lineage
  • B.1.129
    Swedish lineage
  • B.1.130
    Saudi Arabian lineage, some sequences had previously been assigned B.1.36. Possible that it may be reassigned B.1.36 again in future due to uncertainty in ML searching.
  • B.1.131
    Ukraine lineage
  • B.1.132
    Indian lineage, some sequences previously assigned B.1.36 & B.1.113. Possible that it may be reassigned B.1.36 again in future due to uncertainty in ML searching.
  • B.1.133
    South African lineage
  • B.1.134
    USA lineage (OR)
  • B.1.135
    Small Portuguese lineage
  • B.1.136
    Indian lineage
  • B.1.137
    USA lineage (UT)
  • B.1.138
    Small Australian lineage
  • B.1.139
    USA lineage
  • B.1.140
    South African/ English lineage
  • B.1.141
    Scottish lineage
  • B.1.142
    Welsh lineage (B.1.5.9 reassigned as it falls outside of B.1.5 in the most recent phylogeny)
  • B.1.143
    Indian lineage
  • B.1.144
    South African lineage
  • B.1.145
    Indian lineage
  • B.1.146
    Swiss lineage
  • B.1.147
    Canadian lineage, with French, Belgian, DRC and English sequences
  • B.1.148
    English lineage
  • B.1.149
    DRC lineage
  • B.1.150
    Indian lineage with very long branch Iran sequence
  • 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
    USA lineage
  • B.1.155
    USA (WA) lineage
  • B.1.156
    Scottish lineage
  • B.1.157
    UK lineage with some European sequences
  • B.1.158
    Finland lineage
  • B.1.159
    France/ Bangladesh lineage
  • B.1.160
    Previously part of B.1.36: Tukey, India Saudi Arabia lineage (split in the most recent phylogeny)
  • B.1.160.1
    English lineage nested in diversity of B.1.160
  • 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
    English lineage
  • B.1.166
    USA lineage (CA)
  • B.1.167
    UK lineage
  • B.1.168
    Scottish lineage
  • B.1.169
    USA lineage (WA & OR)
  • B.1.170
    German lineage
  • B.1.171
    Lineage with sequences from Israel
  • B.1.172
    USA lineage (CA) (also Ireland)
  • B.1.173
    USA lineage (WA) (also Sierra Leone)
  • B.1.174
    English lineage
  • B.1.175
    English lineage (CAMB)
  • B.1.176
    English lineage (SHEF)
  • B.1.177
    Lineage originating in Spain and has become widespread. Three SNPs define this lineage C22227T, C28932T and G29645T. Equates to the 20A.EU1 cluster in Hodcroft et al 2020.
  • B.2
    European lineage
  • B.2.1
    Large lineage majoritively from UK and Australia with representation from Europe, Jordan, USA, India, Ghana (BS=21)
  • B.2.2
    Lineage with representation from UK/ USA/ Australia
  • B.2.4
    England/ Australia/ New Zealand lineage (BS=94)
  • B.2.5
    Low support, has been reassigned to parent lineage. Reassigned to B.2 this week, consistently low support with similar metadata now present in parent lineage.
  • B.2.6
    UK lineage
  • B.2.7
    Iceland lineage
  • B.2.8
    Hong Kong lineage nested within B.2, B.2 also contains diversity from Hong Kong along with sequences from around the globe.
  • B.2.9
    Low support, has been reassigned to parent lineage. Reassigned B.2 as similiar diversity to parent nodes
  • B.2.10
    South Korean lineage
  • B.2.11
    Lineage with sequences from Israel
  • B.2.12
    USA lineage
  • B.3
    A European lineage with a lot of Welsh sequences
  • B.4
    Iran lineage, many sequences we have of this lineage are associated with travel histories from Iran. Significant number of sequences from the UAE, Kenya and Australia
  • B.4.1
    A small lineage from Kazakhstan within the B.4 diversity
  • B.4.2
    A lineage with mostly sequences from Bahrein
  • B.4.3
    Australian lineage nested within the diversity of B.4
  • B.5
    Japanese lineage
  • B.6
    Indian and Singapore lineage with global diversity. Within this lineage, Indian sequences are the majority of the sequences present at the base of the lineage. Towards the tips, there is a greater representation of sequences derived from Singapore. There is also representation from South East Asia/ North America/ Europe/ Israel/ Gambia/ Timor-leste
  • B.6.1
    Malaysian lineage
  • B.7
    Low support, has been reassigned to parent lineage. Hong Kong lineage reassigned to B.2.8 (BS=75)
  • B.9
    Lineage with sequences from the UK, Australia and New Zealand
  • B.10
    Lineage with a lot of representation from sequences in the UK, including Northern Ireland, England and Scotland
  • B.11
    European lineage with sequences from the Netherlands, UK, Austria, Slovakia
  • B.12
    Japan lineage (BS=100)
  • B.13
    USA (WI) lineage located off the polytomy at the base of the B lineage
  • B.14
    USA (CA) lineage
  • B.15
    UK lineage (England and Wales)
  • B.16
    Scottish lineage
  • B.17
    US lineage (WI)
  • B.18
    European lineage (Iceland and England)
  • B.19
    US lineage (CA)
  • B.20
    US lineage (CA)
  • B.21
    UK lineage
  • B.22
    Denmark lineage (BS=100)
  • B.23
    Lineage with representation from mainly UK sequences, but also sequences from Portugal, Iceland and Brazil
  • B.24
    Scottish lineage
  • B.25
    English lineage
  • B.26
    Scottish lineage
  • B.27
    English lineage
  • C.1
    South African lineage (Alias of B.1.1.1.1)
  • C.2
    South African lineage (Alias of B.1.1.1.2)
  • C.3
    English lineage (Alias of B.1.1.1.3)
  • D.1
    UK lineage (Alias of B.1.1.25.2)
  • D.2
    Australian lineage (Alias of B.1.1.25.1)