B.1.351 2022-09-13



Description

A lineage first identified in South Africa and defined by new variant of concern 501Y.V2 - A more detailed description of the lineage is here and a preprint describing the variant is here.
This webpage is generated using publically available sequence data from GISAID, shared by international sequencing efforts.

Table 1 | Summary of B.1.351 data

Statistic Information
Countries with sequences 121
Sequence count 32108
Countries South Africa 6016, Philippines 3007, United States of America 2789, Sweden 2543, Germany 2205, France 2119, Reunion 1247, Finland 1183, Belgium 1053, Luxembourg 841, Turkey 813, Canada 772, United Kingdom 700, Netherlands 681, Norway 440, Qatar 440, Malawi 359, Malaysia 337, Spain 320, Austria 270, Zimbabwe 262, Mozambique 261, Zambia 239, Switzerland 230, India 227, Botswana 219, Israel 208, Angola 189, Kenya 179, Denmark 116, Singapore 95, Italy 93, Portugal 90, Japan 86, Hong Kong 81, Thailand 81, Czech Republic 72, Eswatini 70, Ireland 70, Australia 63, Pakistan 63, Canary Islands 60, Bangladesh 54, Rwanda 49, Namibia 47, Poland 44, United Arab Emirates 39, Estonia 35, Lesotho 34, Croatia 34, Mayotte 34, Slovakia 31, Slovenia 31, Russia 30, New Zealand 29, South Korea 25, Cote d'Ivoire 21, Seychelles 21, Mexico 19, Ghana 19, Kyrgyzstan 18, Sudan 18, Indonesia 17, Greece 17, Equatorial Guinea 16, Uganda 15, Costa Rica 14, Latvia 14, Cameroon 12, Democratic Republic of the Congo 12, Brazil 11, Gabon 11, Mauritius 10, Lithuania 10, Romania 7, Oman 7, Saudi Arabia 7, China 6, Suriname 5, Djibouti 5, Burundi 5, Sri Lanka 5, Guam 4, Aruba 4, Somalia 4, Taiwan 4, Chile 4, Guadeloupe 4, Iran 4, Jordan 3, Malta 3, Togo 3, South Sudan 3, Senegal 3, Bulgaria 3, Bahrain 3, French Guiana 2, Martinique 2, Madagascar 2, Ethiopia 2, Benin 2, Tunisia 2, Central African Republic 2, Cambodia 1, Kuwait 1, Argentina 1, Niger 1, Iceland 1, Sint Maarten 1, Morocco 1, Panama 1, Guinea-Bissau 1, Antigua and Barbuda 1, Brunei 1, North Macedonia 1, Puerto Rico 1, Georgia 1, Iraq 1, Guatemala 1, Nicaragua 1, Nigeria 1
First detected South Africa
Earliest sample date 2020-09-01
Defining SNPs aa:E:P71L
aa:N:T205I
aa:orf1a:K1655N
aa:S:D80A
aa:S:D215G
aa:S:K417N
aa:S:A701V
aa:S:N501Y
aa:S:E484K

Figure 1 | Cumulative sequence count over time B.1.351

Bars show the number of new sequences on GISAID over time, binned by epi-week. The line shows the cumulative number of sequences over time.


Figure 2 | Date of earliest_B.1.351 detected

Schematic map showing the date of the first sequence sample date in each country containing the lineage. Darker countries have earlier first sample dates.


Figure 3 | Map of B.1.351 sequence counts

Map showing the logged number of sequences of the variant in each country. Countries with more sequences are shown in darker colours.


Figure 4 | Sequence count per country B.1.351

The number of sequences of the lineage recorded in each country. The height of the bar is the logged number and the numbers above the bar are the raw counts.


Figure 5 | Frequency B.1.351 in sequences produced since first new variant reported per country

The overall frequency of the lineage, defined as the number of sequences assigned the lineage divided by the total number of sequences from that country in the time since the variant was first sequenced in that country.


Figure 6 | B.1.351 count per continent

Seven day rolling average of sequence counts per continent. Please note that recent declines may be due to delay in reporting rather than reflecting a change in the underlying virus population.


Figure 7 | Rolling average B.1.351 frequency per continent

Seven day rolling average of frequency of sequences of the lineage of interest. Frequency is calculated by dividing the number of sequences of the lineage of interest by the total sequences for each continent for each day.


Figure 9 | Air traffic by destination B.1.351

The number of ticketed origin-to-destination journeys from South African airports to destinations outside of South Africa during October 2020.

Colours indicate numbers of published genomes of B.1.351 deposited on GISAID. Grey bars indicate countries that have reported the presence of the variant but have not yet published B.1.351 sequences on GISAID. White bars indicate countries with no reports of B.1.351.

Flight data come from the International Air Transportation Association that capture anonymized, passenger-level flight itinerary data, comprising both commercial flights and scheduled charter flights. These data account for ~90% of global air travel volumes, with the remaining volumes modelled using market intelligence. We report data from destinations including >5,000 passengers.

Note that flight data reflects final-destination on a booked journey, we cannot account for instances where two separate tickets were purchased.



Table 2 | Reported B.1.351 imports | Country count: 68




Country Earliest report Date local transmission Local transmission Method of surveillance Source
South Africa 2020-10-08 2020-10-08 1 community_sequencing https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1
United Kingdom 2020-12-12 2020-12-20 1 community_sequencing https://travelhealthpro.org.uk/news/561/covid-19-variant-south-africa-two-cases-reported-in-the-united-kingdom
Switzerland 2020-12-14 0 https://www.swissinfo.ch/eng/south-african-covid-variant-reported-in-southern-switzerland/46257338
Finland 2020-12-19 0 travellers https://news.sky.com/story/covid-19-finland-reports-cases-of-new-variants-first-identified-in-uk-and-south-africa-12173983
Zambia 2020-12-30 2020-12-30 1 https://twitter.com/danieljbridges/status/1344227535870164992
Botswana 2020-12-17 2021-01-04 1 community_sequencing https://www.sabcnews.com/sabcnews/botswana-government-adjusts-national-lockdown-regulations/
France 2020-12-31 0 travellers https://www.france24.com/en/france/20201231-france-detects-first-case-of-south-african-strain-of-covid-19
Japan 2020-12-19 0 travellers https://www.japantimes.co.jp/news/2020/12/29/national/japan-south-africa-variant/
Australia 2020-12-22 0 travellers https://news.sky.com/story/australia-reports-its-first-case-of-south-africa-coronavirus-variant-12174611
Sweden 2021-01-03 0 travellers http://outbreaknewstoday.com/sweden-reports-1st-south-african-covid-19-virus-variant-49394/
Austria 2021-01-04 2021-01-08 1 community_sequencing https://www.sn.at/panorama/wissen/live-corona-mutationen-sind-in-oesterreich-angekommen-97891537; https://www.derstandard.at/story/2000123550006/suedafrika-mutation-bei-mindestens-fuenf-faellen-im-zillertal-nachgewiesen
Norway 2020-12-31 0 travellers https://www.vg.no/nyheter/innenriks/i/rgzer8/mer-smittsom-virusmutasjon-fra-soer-afrika-paavist-i-norge
China 2020-12-08 0 travellers https://news.cgtn.com/news/2021-01-06/Guangdong-detects-first-COVID-19-case-of-variant-found-in-S-Africa-WPW5sbHcju/index.html
Ireland 2021-01-08 2021-01-26 1 community_sequencing https://www.gov.ie/en/press-release/463de-statement-from-the-national-public-health-emergency-team-tuesday-26-january/; https://www.reuters.com/article/health-coronavirus-ireland/south-african-covid-19-variant-present-in-ireland-health-chief-idINS8N2II031
Canada 2021-01-08 2021-02-01 1 community_sequencing https://www.cbc.ca/news/canada/toronto/ontario-covid-omnibus-february-1-1.5895875; https://www.sylvanlakenews.com/news/south-african-covid-19-found-in-alberta-as-provinces-tighten-restrictions/
Taiwan 2020-12-24 0 travellers https://www.reuters.com/article/healthcoronavirus-taiwan/taiwan-confirms-first-case-of-safrican-covid-19-variant-idUSL1N2JO0K9
Germany 2020-12-21 2021-01-26 1 community_sequencing https://www.stadt-koeln.de/politik-und-verwaltung/presse/fluechtlingsunterkunft-herkulesstrasse; https://www.dw.com/en/south-african-covid-variant-found-in-germany/a-56205752
Belgium 2021-01-13 2021-01-13 1 https://www.standaard.be/cnt/dmf20210114_94148148
South Korea 2020-12-26 0 travellers https://www.donga.com/news/Society/article/all/20210102/104736108/1
Netherlands 2020-12-22 2021-01-26 1 community_sequencing https://www.ad.nl/dossier-coronavirus-in-de-drechtsteden/eerste-uitbraak-zuid-afrikaanse-coronavariant-in-nederland-fysiopraktijk-gorinchem-dicht~a0c8248b/?utm_source=twitter&utm_medium=social&utm_campaign=socialsharing_web&referrer=https%3A%2F%2Ft.co%2F; https://www.rivm.nl/en/news/south-african-coronavirus-variant-found-in-netherlands
Israel 2021-01-10 2021-01-27 1 community_sequencing https://twitter.com/Nadav_Eyal/status/1354374717193519105?s=20; https://www.ynetnews.com/health_science/article/rkwq3XuCP
New Zealand 2021-01-10 0 travellers https://www.stuff.co.nz/national/health/coronavirus/300201729/covid19-health-officials-confirm-31-new-cases-of-coronavirus-first-case-of-south-african-variant-found
Ghana 2021-01-18 0 travellers https://twitter.com/gordon_awandare/status/1351235484085846019
Kenya 2020-12-15 0 travellers GISAID
United Arab Emirates 2020-12-26 0 travellers https://www.reuters.com/article/us-health-coronavirus-emirates/uae-reports-limited-number-of-cases-of-new-coronavirus-variant-idUKKBN2931RJ?edition-redirect=uk
Tanzania 2021-01-19 2021-01-19 1 community_sequencing https://files.ssi.dk/covid19/status-b117/status-b117-24012021-2lys
Mozambique 2020-11-01 2020-11-01 1 community_sequencing http://www.xinhuanet.com/english/2021-01/28/c_139702375.htm
Gambia 2021-01-14 2021-01-14 1 community_sequencing https://www.afro.who.int/regional-director/speeches-messages/opening-statement-covid-19-press-conference-14-january-2021
Mayotte 2021-01-07 2021-01-07 1 community_sequencing GISAID
Panama 2021-01-23 0 travellers https://www.reuters.com/article/us-health-coronavirus-panama-idUSKBN29R2R1
United States of America 2021-01-27 2021-01-27 1 community_sequencing https://www.live5news.com/2021/01/28/health-department-nations-first-cases-south-african-covid-variant-found-sc/
Turkey 2021-02-03 0 community_sequencing https://www.aa.com.tr/en/health/turkey-2-s-africa-1-brazil-variant-detected/2133077
Malawi 2021-02-08 2021-02-08 1 community_sequencing https://www.voanews.com/covid-19-pandemic/malawi-sticks-astrazeneca-despite-concerns-over-efficacy
Thailand 2021-02-09 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---09-january-2021
Denmark 2021-01-04 0 community_sequencing https://www.reuters.com/article/health-coronavirus-denmark-idUSC7N2DT01O
Spain 2020-12-24 2020-12-24 1 community_sequencing https://english.elpais.com/spanish_news/2021-02-04/coronavirus-variant-detected-in-south-africa-is-already-circulating-in-spain.html
Luxembourg 2021-01-16 2021-01-16 0 community_sequencing https://lns.lu/departement/microbiologie/revilux/
Portugal 2021-01-06 2021-01-06 1 community_sequencing https://www.portugalresident.com/south-african-variant-already-circulating-in-portugal/
Democratic Republic Of The Congo 2021-01-22 community_sequencing GISAID
Bangladesh 2021-01-24 2021-01-24 1 community_sequencing https://www.dhakatribune.com/health/coronavirus/2021/02/01/experts-south-african-coronavirus-variant-detected-in-bangladesh
India 2021-01-31 0 travellers https://timesofindia.indiatimes.com/india/south-africa-brazil-mutated-covid-strains-have-reached-india/articleshow/81014842.cms
Malta 2021-02-16 0 travellers https://timesofmalta.com/articles/view/malta-records-first-case-of-south-africa-covid-19-variant.851942
Greece 2021-02-17 2021-02-17 1 community_sequencing https://www.capital.gr/epikairotita/3526406/eodu-oi-arithmoi-gia-ta-krousmata-tis-bretanikis-kai-tis-notioafrikanikis-metallaxis
Vietnam 2021-02-16 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---16-february-2021
Singapore 2021-02-07 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---16-february-2021
Poland 2021-02-19 0 travellers https://www.reuters.com/article/us-health-coronavirus-poland/poland-entering-third-wave-of-covid-19-health-ministry-says-idUSKBN2AJ15Y
Slovenia 2021-02-26 0 travellers http://www.xinhuanet.com/english/europe/2021-02/27/c_139770452.htm
Czech Republic 2021-02-25 1 community_sequencing https://news.trust.org/item/20210225133818-xxafw/
Angola 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Aruba 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Brunei 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Cameroon 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Costa Rica 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Cuba 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Eswatini 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Guadeloupe 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Lesotho 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Mauritania 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Namibia 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Philippines 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Reunion 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Romania 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Rwanda 2021-03-23 1 community_sequencing GISAID
Saint Martin 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Slovakia 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Sri Lanka 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Zimbabwe 2021-03-23 community_sequencing https://www.who.int/publications/m/item/weekly-epidemiological-update---23-march-2021
Lithuania 2021-03-24 2021-03-24 1 community_sequencing https://www.lrt.lt/naujienos/lietuvoje/2/1372161/lietuvoje-siuo-metu-tiriama-dar-keliolika-atveju-del-koronaviruso-par-mutacijos-isplitus-savivaldybems-grestu-karantino-draudimai

Table 3 | Raw data for figures




Country Earliest sequence Number of variant sequences Total sequences since first variant sequence
United States Of America 2020-09-10 2932 3576528
Sweden 2020-11-08 2584 203484
Guam 2021-04-05 4 745
Belgium 2020-12-20 1105 148507
Jordan 2021-03-07 5 760
Bangladesh 2020-11-01 452 5286
France 2020-12-22 2964 428737
Germany 2020-12-21 2279 753036
India 2020-12-30 255 161102
South Africa 2020-09-01 6034 35032
Reunion 2021-01-07 3179 15236
Malaysia 2020-12-01 339 23838
Malawi 2020-11-25 359 834
Kenya 2020-12-25 182 6088
China 2020-12-31 6 1163
Canada 2020-12-19 875 349445
Netherlands 2020-12-22 684 128296
Indonesia 2021-01-25 21 30754
Cambodia 2021-05-31 1 3143
Suriname 2021-03-19 5 831
Mayotte 2021-01-07 369 1140
Norway 2020-12-27 441 68365
Finland 2020-12-19 1191 35893
Russia 2021-01-19 30 15010
Cameroon 2021-01-05 12 893
Switzerland 2020-12-14 313 129598
Spain 2020-12-24 1469 137551
Hong Kong 2020-12-27 83 7297
Philippines 2021-01-31 3025 17527
Eswatini 2020-11-23 70 805
Zambia 2020-12-01 239 870
Mexico 2021-04-03 19 64392
Italy 2021-01-29 143 125708
United Kingdom 2020-12-10 916 2576428
Singapore 2021-02-07 204 20920
Poland 2021-02-08 46 82311
Equatorial Guinea 2021-01-12 34 49
Ireland 2020-12-22 73 78475
Australia 2020-12-26 83 108553
Czech Republic 2021-02-16 76 46174
Mozambique 2020-09-28 261 964
Uganda 2021-02-13 15 626
Turkey 2021-01-21 826 94022
Japan 2020-12-19 104 368228
Ghana 2021-01-06 23 2499
Luxembourg 2021-01-15 841 38462
Rwanda 2020-12-28 50 495
Denmark 2021-01-04 126 523495
Kuwait 2021-06-21 1 353
Qatar 2020-12-29 440 3005
Thailand 2021-02-05 82 23539
Israel 2020-12-17 210 99655
Madagascar 2020-11-03 271 540
Argentina 2021-04-24 1 12030
Lesotho 2020-12-16 34 127
Portugal 2020-12-26 107 37505
Brazil 2021-03-07 11 155856
Greece 2021-01-14 57 18306
Slovakia 2021-02-08 31 40092
Romania 2021-03-24 8 14226
Pakistan 2021-03-15 65 3000
Malta 2021-04-09 3 672
Estonia 2021-02-17 35 12385
Lithuania 2021-03-02 10 34776
Kyrgyzstan 2021-05-04 18 230
Botswana 2020-11-21 235 2536
Angola 2020-09-25 196 869
Namibia 2021-03-17 47 581
Zimbabwe 2020-09-01 262 631
South Korea 2020-12-26 38 51288
Austria 2021-01-12 275 30544
Djibouti 2021-03-15 126 537
Costa Rica 2021-02-10 14 6319
Ivory Coast 2021-02-10 21 518
Tunisia 2021-04-20 4 679
Latvia 2021-03-08 14 15871
Democratic Republic Of The Congo 2021-01-22 12 393
Niger 2021-05-03 1 44
New Zealand 2021-01-06 29 18935
Iceland 2021-02-28 2 5393
Oman 2021-01-27 7 350
Aruba 2021-02-25 4 3229
Somalia 2021-02-28 4 12
Liberia 2021-03-31 6 87
Gabon 2021-01-27 11 512
Saudi Arabia 2021-04-15 14 97
Taiwan 2021-03-24 5 2308
Croatia 2021-02-09 34 35262
Togo 2021-02-05 4 583
Slovenia 2021-02-09 31 62667
United Arab Emirates 2020-12-20 40 742
Bahrain 2021-04-04 20 7349
Burundi 2021-05-27 5 72
South Sudan 2021-03-31 3 123
Chile 2021-04-06 4 30951
Morocco 2021-06-17 1 627
Sri Lanka 2021-03-02 7 2564
Panama 2021-01-12 1 4563
Senegal 2021-01-09 3 2167
Guadeloupe 2021-02-23 4 2019
Brunei 2021-01-20 1 3092
Iran 2021-04-03 4 1290
Bulgaria 2021-06-09 3 15448
Sudan 2021-03-07 18 234
North Macedonia 2021-03-10 1 492
Benin 2021-03-23 4 852
Ethiopia 2021-02-22 2 497
Puerto Rico 2021-03-30 1 9800
Georgia 2021-05-23 1 1967
Iraq 2021-02-26 1 786
Guatemala 2021-04-19 1 1944
Nicaragua 2021-05-02 1 320
Central African Republic 2021-02-11 2 58
Nigeria 2021-07-26 1 3302

Data source and processing

The data on this page is recent as of 2022-09-13, 04:50 GMT. All SARS-CoV-2 sequences were downloaded from GISAID and genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here. The sequences were then assigned lineages with pangolin 3.1.20, pangoLEARN version 2022-02-02.

Pangolin assigns B.1.351 to sequences with at least 5 of the 9 defining B.1.351 SNPs – defined here.

Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.

Acknowledgements

Created by: Áine O'Toole and Verity Hill, Rambaut Group, University of Edinburgh. Flight volume data from Kamran Khan, Isaac Bogoch, Alexander Watts, Oliver Pybus, Moritz Kraemer. Sequences sourced from GISAID, full acknowledgements table here.

We have a publication in Wellcome Open Research here describing this web tracker.