Andrew Rambaut, Edward C. Holmes, Verity Hill, Áine O’Toole, JT McCrone, Chris Ruis, Louis du Plessis, Oliver G. Pybus
This is a companion repository to the paper describing a dynamic lineage nomenclature system for SARS-CoV-2.
A pre-print of the paper can be found here: https://doi.org/10.1101/2020.04.17.046086
This contains the following files:
A table of acknowledgements for the GISAID genome sequences used to develop this paper: https://raw.githubusercontent.com/hCoV-2019/lineages/master/gisaid_acknowledgements.tsv
Phylogenetic Assignment of Named Global Outbreak LINeages
Software to help assign your own SARS-CoV-2 genomes to these lineages is available: http://github.com/hCoV-2019/pangolin
This weeks data release has some substantial changes.
-
We've implemented a system of "putative" lineages. Any lineages that have a recall value of < 95% are given
pflag. E.g.B.1.16becomesB.1.p16. -
A large lineage within B.1 with
28881GA,28882GA,28883GCdefining SNPs has been called as B.1.1. Any lineages that existed within this that would have previously been called B.1.X have been renamed as B.1.1.X, with the count restarted. Details on which lineages have been renamed can be found in the lineage descriptions.
Additional notes on justification and descriptions are available after the following table, and can also be accessed by clicking on the lineage name in the table.
Each week as more data is produced and analysed, new lineages may be called and it may turn out that older lineages are in fact not lineages. We take into account both phylogenetic and epidemiological information and use all available evidence to informed lineage calls weekly.
This report gives summaries of globally circulating lineages as of 2020-05-10. 27763 sequences have been included in this analysis. 98 lineages have been assigned in this dataset.
Sequences which were replicates or too error-prone were removed from this analysis.
30 are pending extinction ie last seen three weeks ago. 34 have not been seen for more than one month, and so are viewed as extinct, but will continue to be monitored. 21 lineages have gone quiet, ie haven't been seen this week. 13 lineages have been continuously circulating.
Note that the status of a lineage is highly likely to be due to heterogeneity in sampling, and not necessarily indicative of the real decline of lineages.
The table below shows summary information of each lineage.
The "most common countries" column shows the three countries with the most sequences from each lineage, and the percentages by the country represent the percentage of sequences in that lineage taken from that location.
Again, please interpret this with caution. Some countries are sequencing much more than others, and so locations of lineages may be at least partially due to this. It does not imply direction of transmission from one country to another. Sometimes we have been able to examine lineages which we know are circulating in one country by looking at sequences from another country due to associated epidemiological information.
| Lineage name | Most common countries | Date range | Number of taxa | Days since last sampling | Known Travel | Recall value |
|---|---|---|---|---|---|---|
| A | China (57%), South_Korea (9%), USA (8%) | January 05 to April 23 | 223 | 17 | China to Belgium, India, Taiwan, Vietnam, Australia (6) USA to New_Zealand (1) Saudia_Arabia to Turkey (1) |
87.76 |
| A.1 | USA (87%), Australia (7%), Canada (4%) | February 22 to April 30 | 1116 | 10 | USA to Iceland (1) |
100 |
| A.1.1 | Iceland (100%) | March 11 to March 20 | 14 | 51 | USA to Iceland (10) |
100 |
| A.1.3 | Australia (90%), Taiwan (10%) | March 19 to April 02 | 10 | 38 | 100 | |
| A.2 | UK (34%), Spain (28%), Australia (28%) | February 26 to April 27 | 295 | 13 | Spain to Brazil (1) Italy to Chile, Spain (2) |
100 |
| A.3 | USA (71%), Australia (21%), UK (7%) | January 28 to April 21 | 191 | 19 | USA to Taiwan, New_Zealand (2) |
99.48 |
| A.4 | USA (100%) | March 13 to April 10 | 25 | 30 | 100 | |
| A.5 | Spain (39%), UK (35%), Uruguay (6%) | February 23 to April 26 | 118 | 14 | 95.93 | |
| A.6 | Thailand (100%) | January 23 to March 28 | 31 | 43 | 100 | |
| A.p7 | Saudi_Arabia (70%), USA (7%), Russia (7%) | March 06 to April 27 | 27 | 13 | Saudia_Arabia to Turkey (1) |
100 |
| B | UK (43%), USA (16%), China (13%) | December 24 to May 03 | 1713 | 7 | China to Thailand, Italy, India, Taiwan, Singapore, Canada, Cambodia, France (9) Italy to Iceland, Finland (2) UK to Iceland (4) Netherlands to Iceland, Ecuador (2) Austria to Iceland (1) USA to Iceland, China, Kuwait (3) Switzerland to Iceland (1) Japan to Taiwan (1) Saudia_Arabia to Turkey (1) |
97.99 |
| B.1 | UK (41%), USA (26%), Australia (5%) | January 24 to May 08 | 7438 | 2 | Egypt;United_Arab_Emirates to Taiwan (1) UK to Iceland (16) Iran to Turkey, Finland (2) Netherlands to Iceland (3) Spain to Iceland, Argentina (6) Germany to Iceland (2) Switzerland to Iceland (2) Austria to Iceland, Taiwan (43) USA to Iceland, Taiwan, Costa_Rica (3) Italy to Brazil, Iceland, Czech_Republic, Finland (16) Croatia to Iceland (1) France to Iceland, Taiwan, Turkey (5) Egypt to Taiwan (2) USA;Czech_Republic to Taiwan (1) Czech_Republic to Taiwan (1) Poland to Taiwan (1) Israel to Argentina (1) Brazil to Argentina (1) Saudia_Arabia to Turkey (1) |
98.47 |
| B.1.1 | UK (79%), Australia (2%), USA (2%) | February 15 to May 09 | 6286 | 1 | Italy to Thailand, Mexico, Iceland, Nigeria, Brazil, Chile, New_Zealand (36) Finland to Iceland (1) UK to Iceland, Kuwait (5) Germany to Iceland (1) USA to Brazil (1) Spain to Iceland, Taiwan (3) Germany;Austria;Spain;Italy to Brazil (1) Austria to Iceland (4) Switzerland to Iceland (1) Mexico to Argentina (1) France to Argentina (1) |
99.86 |
| B.1.1.1 | UK (93%), DRC (1%), Iceland (1%) | March 02 to May 08 | 952 | 2 | Austria to Iceland (5) UK to Iceland, Argentina (3) Peru;Argentina to Costa_Rica (1) |
100 |
| B.1.1.2 | UK (100%) | March 20 to April 20 | 107 | 20 | 99.07 | |
| B.1.1.3 | UK (100%) | March 18 to May 06 | 53 | 4 | 100 | |
| B.1.1.4 | UK (100%) | March 26 to May 08 | 50 | 2 | 100 | |
| B.1.1.5 | UK (59%), Iceland (17%), Belgium (17%) | March 16 to April 09 | 29 | 31 | 100 | |
| B.1.1.6 | Austria (100%) | February 26 to March 25 | 45 | 46 | 100 | |
| B.1.1.7 | UK (94%), Iceland (3%), Australia (2%) | March 07 to April 28 | 108 | 12 | USA to Iceland (1) |
100 |
| B.1.1.8 | UK (89%), Australia (8%), Gambia (2%) | March 17 to April 28 | 65 | 12 | 100 | |
| B.1.1.9 | UK (84%), USA (13%), France (1%) | March 11 to April 18 | 67 | 22 | 100 | |
| B.1.1.10 | UK (92%), Iceland (3%), Australia (2%) | March 06 to May 01 | 171 | 9 | UK to Iceland (1) USA to Iceland (1) Saudia_Arabia to Turkey (1) |
99.42 |
| B.1.1.p11 | UK (89%), Portugal (11%) | March 17 to April 16 | 28 | 24 | 80 | |
| B.1.1.p12 | UK (100%) | March 21 to April 22 | 16 | 18 | 80 | |
| B.1.1.13 | UK (100%) | March 28 to April 15 | 16 | 25 | 100 | |
| B.1.1.14 | UK (100%) | April 16 to May 08 | 15 | 2 | 100 | |
| B.1.1.p15 | Luxembourg (75%), UK (17%), Australia (8%) | March 19 to April 17 | 12 | 23 | 52.17 | |
| B.1.1.p16 | UK (100%) | April 06 to April 16 | 11 | 24 | 91.67 | |
| B.1.1.17 | Iceland (100%) | March 06 to March 28 | 29 | 43 | Italy to Iceland (1) |
100 |
| B.1.1.18 | Austria (100%) | March 22 to April 07 | 8 | 33 | 100 | |
| B.1.1.p19 | Australia (100%) | March 23 to March 26 | 5 | 45 | 71.43 | |
| B.1.p2 | USA (96%), Australia (3%), Canada (1%) | March 08 to April 25 | 364 | 15 | 94.04 | |
| B.1.3 | USA (94%), Argentina (2%), Australia (1%) | March 05 to April 30 | 174 | 10 | 99.42 | |
| B.1.5 | UK (75%), Spain (8%), Australia (5%) | February 26 to May 10 | 710 | 0 | Spain to Iceland (2) Switzerland to Iceland (3) Portugal to Taiwan (1) Saudia_Arabia to Turkey (1) |
71.41 |
| B.1.5.1 | Iceland (100%) | March 12 to March 28 | 93 | 43 | Argentina to Iceland (1) |
100 |
| B.1.5.2 | Netherlands (86%), Belgium (7%), UK (7%) | March 24 to April 06 | 14 | 34 | 100 | |
| B.1.5.3 | UK (94%), Australia (3%), Sweden (3%) | March 18 to April 16 | 33 | 24 | 100 | |
| B.1.5.4 | Spain (75%), Mexico (6%), USA (6%) | March 11 to April 06 | 16 | 34 | 100 | |
| B.1.5.5 | UK (100%) | April 08 to May 06 | 33 | 4 | 100 | |
| B.1.5.6 | UK (100%) | March 19 to May 01 | 32 | 9 | 100 | |
| B.1.6 | Belgium (68%), DRC (18%), UK (9%) | March 11 to April 13 | 22 | 27 | 100 | |
| B.1.8 | Netherlands (63%), Iceland (12%), Austria (6%) | March 04 to April 11 | 83 | 29 | Austria to Iceland (10) |
98.81 |
| B.1.p9 | Belgium (56%), Turkey (13%), Netherlands (13%) | March 14 to April 17 | 39 | 23 | Saudia_Arabia to Turkey (1) |
94.44 |
| B.1.p11 | UK (98%), USA (2%), Australia (0%) | March 02 to May 08 | 584 | 2 | 64.82 | |
| B.1.12 | Luxembourg (59%), Belgium (37%), Switzerland (2%) | March 04 to April 14 | 46 | 26 | 100 | |
| B.1.13 | UK (95%), Australia (4%), Poland (0%) | March 09 to May 07 | 248 | 3 | 100 | |
| B.1.p16 | Belgium (100%) | March 01 to March 20 | 18 | 51 | Italy to Belgium (1) |
94.74 |
| B.1.19 | USA (100%) | March 19 to April 17 | 29 | 23 | 100 | |
| B.1.p21 | USA (100%) | March 08 to April 27 | 265 | 13 | 91.38 | |
| B.1.22 | Netherlands (55%), Australia (29%), Austria (6%) | March 09 to April 17 | 31 | 23 | 100 | |
| B.1.23 | Australia (100%) | March 18 to April 12 | 78 | 28 | 100 | |
| B.1.p25 | Australia (100%) | March 19 to March 27 | 16 | 44 | 75 | |
| B.1.26 | USA (94%), Australia (3%), Taiwan (3%) | March 12 to April 20 | 31 | 20 | 100 | |
| B.1.29 | USA (96%), Australia (4%) | March 15 to May 03 | 27 | 7 | 100 | |
| B.1.30 | UK (100%) | March 17 to May 03 | 60 | 7 | 100 | |
| B.1.31 | Australia (100%) | March 21 to March 27 | 10 | 44 | 100 | |
| B.1.32 | Sweden (100%) | March 04 to March 10 | 17 | 61 | 100 | |
| B.1.33 | Australia (100%) | March 21 to April 11 | 19 | 29 | 100 | |
| B.1.34 | UK (100%) | March 17 to April 26 | 22 | 14 | 100 | |
| B.1.35 | UK (100%) | March 07 to April 22 | 112 | 18 | 100 | |
| B.1.36 | Saudi_Arabia (46%), UK (25%), Turkey (9%) | March 10 to May 07 | 159 | 3 | Saudia_Arabia to Turkey (6) Iran to Turkey (1) |
98.75 |
| B.1.37 | USA (100%) | March 12 to April 04 | 23 | 36 | 100 | |
| B.1.38 | USA (100%) | March 17 to April 09 | 18 | 31 | 100 | |
| B.1.39 | Denmark (89%), UK (8%), Australia (3%) | March 13 to April 07 | 36 | 33 | 97.3 | |
| B.1.40 | UK (100%) | March 18 to May 08 | 22 | 2 | 100 | |
| B.1.41 | USA (100%) | March 19 to April 09 | 31 | 31 | 96.55 | |
| B.1.p42 | Denmark (83%), Iceland (8%), Sweden (8%) | March 03 to April 02 | 63 | 38 | Faroe_Islands to Iceland (1) Denmark to Iceland (2) UK to Iceland (1) |
77.78 |
| B.1.43 | USA (100%) | March 18 to April 02 | 58 | 38 | 100 | |
| B.1.44 | UK (100%) | March 25 to April 21 | 47 | 19 | 97.87 | |
| B.1.66 | UK (100%) | March 29 to April 29 | 30 | 11 | 100 | |
| B.1.67 | UK (100%) | March 25 to April 12 | 14 | 28 | 100 | |
| B.1.p68 | USA (100%) | March 19 to April 15 | 13 | 25 | 92.86 | |
| B.1.69 | UK (100%) | March 06 to March 20 | 16 | 51 | 100 | |
| B.1.70 | UK (100%) | March 13 to April 20 | 19 | 20 | 100 | |
| B.1.71 | UK (100%) | March 18 to April 18 | 22 | 22 | 100 | |
| B.1.72 | UK (100%) | March 16 to April 05 | 29 | 35 | 100 | |
| B.1.p73 | UK (100%) | March 16 to April 28 | 125 | 12 | 96.9 | |
| B.2 | UK (74%), USA (8%), Netherlands (5%) | February 13 to May 01 | 917 | 9 | Germany to Iceland (1) UK to Iceland, China (3) Italy to Brazil (1) |
95.31 |
| B.2.1 | UK (93%), Australia (3%), USA (1%) | February 09 to May 02 | 1568 | 8 | UK to Iceland (1) |
100 |
| B.2.2 | UK (85%), Australia (5%), Iceland (3%) | February 25 to April 22 | 208 | 18 | Spain to Iceland (1) Switzerland to Iceland (1) Ireland to Taiwan (1) |
100 |
| B.2.4 | Australia (83%), UK (12%), Uruguay (4%) | March 11 to April 02 | 24 | 38 | 100 | |
| B.2.5 | UK (86%), Australia (10%), Slovenia (1%) | February 27 to April 27 | 143 | 13 | 99.3 | |
| B.2.6 | UK (77%), Australia (9%), Iceland (6%) | March 05 to May 04 | 47 | 6 | 97.92 | |
| B.2.7 | Iceland (100%) | March 12 to March 29 | 46 | 42 | 97.87 | |
| B.3 | UK (84%), Germany (3%), Denmark (3%) | February 23 to April 23 | 752 | 17 | UK to Brazil, Iceland (2) Austria to Iceland (1) |
100 |
| B.4 | Australia (35%), UK (18%), Turkey (8%) | January 18 to April 14 | 258 | 26 | Iran to Kuwait, Australia, Germany, Canada, Pakistan, New_Zealand, Turkey (12) Turkey to Taiwan (1) |
99.61 |
| B.5 | Japan (94%), Australia (6%) | February 10 to February 24 | 18 | 76 | 100 | |
| B.6 | India (36%), Singapore (27%), Australia (19%) | March 04 to April 30 | 221 | 10 | Philippines to Taiwan (1) |
100 |
| B.7 | Hong_Kong (97%), Canada (3%) | January 30 to March 04 | 37 | 67 | 100 | |
| B.9 | UK (80%), Australia (20%) | March 12 to May 01 | 35 | 9 | 100 | |
| B.10 | UK (100%) | March 13 to April 22 | 66 | 18 | 100 | |
| B.p11 | Netherlands (100%) | March 02 to March 24 | 14 | 47 | 93.33 | |
| B.p12 | Japan (100%) | March 25 to March 27 | 4 | 44 | 100 | |
| B.13 | USA (100%) | April 03 to April 17 | 19 | 23 | 100 | |
| B.14 | USA (100%) | March 16 to May 01 | 38 | 9 | 97.44 | |
| B.15 | UK (100%) | March 11 to April 14 | 37 | 26 | 100 | |
| B.16 | UK (100%) | March 13 to April 28 | 86 | 12 | 100 |
BS = bootstrap
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 North American lineage, with some sequences from Australia in (BS=95)
Iceland lineage (BS:100->79)
Reassigned to A.1 (low BS two weeks running)
Australian lineage (BS=100)
Spain/ Chile/ Australia/ Europe (BS=93)
USA and Australian lineage (BS: 100 -> 44). Low BS likely due to India/NCDC-3279/2020, which was misassigned and likely jumps around the tree.
Lineage circulating in USA (all sequences Wisconsin) (BS=100)
A lineage with a lot of representation from Spanish-speaking countries. A majoritively Spain/ South-American lineage, lower bootstrap this week BS 87->20.
Lineage in Thailand (BS=87)
Potential lineage: Saudi Arabia, Russia, Turkey, India (BS=50)
Base of this lineage also lies in China, with many global exports, two distinct SNPs 8782TC and 28144CT define this lineage
A large European lineage that corresponds to the Italian outbreak.
Australian lineage (more support this week BS=91), all Australian sequences within a background of European and Asian
Scotland (BS=92)
New European lineage that's been assigned due to high support and 3 clear SNPs 28881GA,28882GA,28883GC. Note: Sub-lineages that previously existed within this lineage have been reassigned a new lineage name.
Formerly B.1.1, UK/ Europe (BS=80)
Formerly B.1.24, Welsh lineage (BS=100->47 this week)
Formerly B.1.65, English lineage (BS=100)
Formerly B.1.55, UK (BS=100)
Formerly B.1.54, Iceland/ Belgium/ UK (BS=100)
Formerly B.1.62, Austrian lineage (BS=100)
Formerly B.1.1.56, UK/ Australia/ Iceland (BS=100)
Formerly B.1.63, UK/ USA/ Australia (BS=100)
Formerly B.1.53, England / USA (BS=83)
Formerly B.1.10, UK/ Iceland (BS lower this week 70 -> 11), a lot of diversity in this lineage, now has a Turkish sequence.
Formerly B.1.50, Portugal/ Wales (BS=55 this week)
Formerly B.1.49, Scottish lineage (BS=48)
Formerly B.1.61, UK lineage (BS=95)
Formerly B.1.60, Scottish lineage (BS=89)
Formerly B.1.46, Luxembourg (BS=11, but internal nodes all 100 and all Luxembourg)
Formerly B.1.59, Wales lineage (BS=70)
Formerly B.1.58, Iceland lineage (BS=100)
Formerly B.1.57, Austrian lineage (BS=97)
Formerly B.1.45, Australian lineage (BS=91)
USA (low BS=9)
USA(BS=39)
England/ Spain/ Turkey/ Australia/ USA/ Brasil. Low support at parent node now, potentially as a result of homoplasies (BS=5)
Iceland (BS=27), but all sequences suggest an Icelandic lineage
Netherlands (BS=100)
England (now containing an Australian & Swedish seqeuence) (BS=96)
Spain (BS=100)
England (BS=100)
UK (BS=100)
Belgian lineage (BS=55)
Low support (BS=9), reassigned B.1
Netherlands/ Europe (BS=47)
Netherlands/ Belgium/ Turkey/ DRC (BS=9)
UK lineage but low support and splitting up, pruned down quite a lot, but may need to be removed next time (BS=31)
BeNeLux (BS=18 this week, lots of internal 100)
England/ Australia, may need refining parent node BS=59, internal node of 100
Belgium, low support (BS=19), keep an eye on this with new data
USA (BS=100)
Low support (BS=5), reassigned B.1
Washington (USA) (Low BS=9)
Netherlands (BS=100)
Australia (BS=68)
Australian lineage, some low internal bootstrap values and parent node BS=16. However all sequences within it are Australian and that's with quite a lot of diversity as well.
USA lineage (BS=83)
USA/ Argentina (BS=74)
Denmark/ USA new parent node BS=9, reassigned B.1
USA (BS=86)
England (BS=100)
Australia (BS=100)
Swedish lineage (BS=95)
Australian lineage (BS=100)
England (BS=100)
Wales (BS=9)
Turkey/ Saudi Arabia/ Egypt / Finland & England (BS=100)
USA lineage (BS=93)
USA (BS=100)
Denmark (BS=100)
Scotland (BS=90)
USA lineage (BS=100)
Sweden/ Denmark lineage, split up in the tree this week
USA (BS=100)
Wales (BS=100)
England, caused a lot of problems last release and many misassignments (BS=100)
England (BS=39)
UK (BS=11, got split in half)
England (BS=30)
English lineage (BS=100)
English lineage (BS=100)
Wales lineage (BS=96)
USA lineage (UT) (BS=100)
Scottish lineage (BS=100)
Scottish lineage (BS=70)
UK lineage (BS=100)
UK lineage (BRIS) (BS=100)
Scotland lineage (BS=5, so very low)
A previously defined large European/ Australian lineage that with new data has low support (BS=13). This lineage and its sublineage will need to be re-examined and perhaps refined quite significantly in next weeks data
Large lineage with representation from UK, Europe, Jordan, Australia, USA, India, Ghana (BS=11)
BeNeLux/ UK/ Singapore /Australia /USA (BS=85)
Reassigned B.2 (No good internal BS, misassignments)
Australian lineage, took a subset of previously defined B.2.4 and reassigning them B.2
Spain/ England / Australia (BS=17) *flagged because of low bootstrap
UK/ Singapore/ Jordan/ Iceland, previously just UK & Australia (BS=11, low support)
Iceland lineage (BS=60)
A European lineage, including a large set of sequences from Wales, low parent node support (BS=14)
Iran lineage, many sequences we have of this lineage are associated with travel histories from Iran (BS=43)
Japanese lineage (BS=75)
India/ Philippines/ UK/ North America/ Australia/ Singapore (BS=100)
Hong Kong lineage (BS 73 -> 27)
Reassigned to B (BS 27 -> 14, got split into two clades with low support in this weeks tree)
Australian/ England lineage (BS=100)
Northern Ireland/ England/ Scotland (BS=89)
Netherlands lineage (BS=100)
Japan lineage (BS=99, but only a few sequences)
USA (WI) lineage (BS=100)
USA (CA) lineage (BS=100)
UK lineage (BS=100)
Mostly Scottish lineage (BS=95)