B.1.351 2024-05-24



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 123
Sequence count 32824
Countries South Africa 6439, Philippines 3018, United States of America 2930, Sweden 2571, Germany 2286, France 2128, Reunion 1219, Finland 1180, Belgium 1056, Luxembourg 841, Canada 781, United Kingdom 700, Netherlands 680, Turkey 553, Qatar 446, Norway 442, Malawi 362, Spain 357, Malaysia 340, Austria 271, Mozambique 268, Zimbabwe 262, Zambia 239, Switzerland 231, India 227, Botswana 221, Israel 208, Angola 201, Kenya 186, Djibouti 126, Denmark 117, Italy 97, Singapore 96, Portugal 90, Japan 89, Pakistan 84, Hong Kong 82, Thailand 81, Czech Republic 73, Ireland 70, Eswatini 70, Russia 66, Australia 64, Canary Islands 60, Rwanda 50, Namibia 47, Poland 44, Bangladesh 41, United Arab Emirates 40, Croatia 36, Estonia 35, Mayotte 34, Lesotho 34, Equatorial Guinea 33, Slovenia 31, Slovakia 30, New Zealand 29, South Korea 25, Cote d'Ivoire 21, Seychelles 21, Sudan 19, Mexico 19, Kyrgyzstan 18, Greece 18, Indonesia 17, Ghana 17, Uganda 15, Costa Rica 14, Latvia 14, Brazil 13, Cameroon 12, Democratic Republic of the Congo 12, Gabon 11, Lithuania 10, Mauritius 10, Tanzania 10, China 9, Oman 7, Saudi Arabia 7, Romania 7, Liberia 6, Suriname 5, Sri Lanka 5, Morocco 5, Burundi 5, Benin 4, Aruba 4, Guam 4, Chile 4, Taiwan 4, Guadeloupe 4, Somalia 4, Iran 4, Bahrain 3, Bulgaria 3, Togo 3, Malta 3, Senegal 3, South Sudan 3, Jordan 3, Tunisia 2, French Guiana 2, Ethiopia 2, Martinique 2, Vietnam 1, Sint Maarten 1, Antigua and Barbuda 1, Iraq 1, North Macedonia 1, Panama 1, Cambodia 1, Kuwait 1, Nigeria 1, Niger 1, Nicaragua 1, Central African Republic 1, Guinea-Bissau 1, Argentina 1, Puerto Rico 1, Brunei 1, Iceland 1, Guatemala 1, Georgia 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 2021-01-01 3017 4467700
Spain 2020-12-24 1561 237683
Germany 2020-12-09 2340 925001
South Korea 2020-12-26 40 154460
Greece 2021-01-14 58 37503
France 2020-12-22 2970 549243
United Kingdom 2020-12-10 915 2792019
Malaysia 2020-12-01 342 40119
Sweden 2020-11-08 2586 266224
Netherlands 2020-12-22 683 166131
Reunion 2021-01-07 3180 20650
South Africa 2020-09-01 6458 44144
Turkey 2021-01-21 566 101102
United Arab Emirates 2020-12-20 40 5341
New Zealand 2021-01-06 29 43873
Canada 2020-12-19 877 545079
Belgium 2020-12-20 1107 172349
Philippines 2021-01-31 3033 23864
India 2020-12-30 258 191561
Israel 2020-12-17 210 122430
Pakistan 2021-03-15 86 5463
Finland 2020-12-19 1188 50253
Norway 2020-12-27 443 77468
Thailand 2021-02-05 82 35579
Madagascar 2020-11-03 271 540
Kenya 2020-12-25 186 7633
Australia 2020-12-26 83 189956
Qatar 2020-12-29 446 4173
Russia 2021-01-19 66 72049
Austria 2021-01-12 276 69827
Switzerland 2020-12-14 313 145854
Denmark 2021-01-04 127 630705
Czech Republic 2021-02-16 77 56403
Rwanda 2020-12-28 50 495
Japan 2020-12-19 104 641748
Botswana 2020-11-21 228 2834
Croatia 2021-02-09 36 44052
Poland 2021-02-08 46 91072
Djibouti 2021-03-15 126 833
Zimbabwe 2020-09-01 262 695
Cameroon 2021-01-05 12 1523
Oman 2021-01-27 7 947
Bangladesh 2020-11-01 469 5938
China 2020-12-31 9 76948
Mayotte 2021-01-07 369 1200
Saudi Arabia 2021-04-15 14 714
Singapore 2021-02-07 204 45977
Italy 2021-01-29 144 172584
Luxembourg 2021-01-15 841 51819
Indonesia 2021-01-25 21 48662
Malawi 2020-11-25 362 974
Portugal 2020-12-26 107 45546
Ireland 2020-12-22 73 100762
Mozambique 2020-09-28 268 1308
Vietnam 2021-05-08 1 8177
Democratic Republic Of The Congo 2021-01-22 12 549
Estonia 2021-02-17 35 14192
Namibia 2021-03-17 47 628
Tunisia 2021-04-20 4 1940
Kyrgyzstan 2021-05-04 18 230
Uganda 2021-02-13 15 1309
Suriname 2021-03-19 5 831
Angola 2020-09-25 201 910
Slovakia 2021-02-08 30 46187
Sri Lanka 2021-03-02 7 2759
Bahrain 2021-04-04 20 10811
Sudan 2021-03-07 19 425
Costa Rica 2021-02-10 14 12143
Ivory Coast 2021-02-11 21 735
Equatorial Guinea 2021-01-12 34 49
Gabon 2021-01-27 11 511
Slovenia 2021-02-09 31 76511
Hong Kong 2020-12-27 84 14992
Brazil 2021-03-07 13 220236
Morocco 2021-05-19 5 1575
Zambia 2020-12-01 239 969
Latvia 2021-03-08 14 25151
Eswatini 2020-11-23 70 1014
Ghana 2021-01-06 21 3250
Benin 2021-03-23 4 891
Mexico 2021-04-03 19 82779
Lithuania 2021-03-02 10 38105
Aruba 2021-02-25 4 3815
Ethiopia 2021-02-22 2 662
Romania 2021-03-24 8 19000
Bulgaria 2021-06-09 3 18319
Togo 2021-02-05 4 767
Guam 2021-04-05 4 902
Chile 2021-04-06 4 44299
Iraq 2021-02-26 1 855
Malta 2021-04-09 3 672
Lesotho 2020-12-16 34 155
Burundi 2021-05-27 5 72
North Macedonia 2021-03-10 1 779
Taiwan 2021-03-24 5 5121
Panama 2021-01-12 1 5794
Cambodia 2021-05-31 1 3643
Liberia 2021-03-31 6 97
Senegal 2021-01-09 3 2378
Kuwait 2021-06-21 1 855
Nigeria 2021-07-26 1 3987
Guadeloupe 2021-02-23 4 2194
Niger 2021-05-03 1 49
Bhutan 2021-03-31 3 135
South Sudan 2021-03-31 3 123
Nicaragua 2021-05-02 1 522
Central African Republic 2021-02-11 1 137
Jordan 2021-03-07 5 872
Argentina 2021-04-24 1 17684
Iceland 2021-02-28 2 17677
Somalia 2021-02-28 4 20
Iran 2021-04-03 4 2166
Puerto Rico 2021-03-30 1 18402
Brunei 2021-01-20 1 7014
Tanzania 2021-01-23 10 13
Guatemala 2021-04-19 1 5053
Georgia 2021-05-23 1 3242

Data source and processing

The data on this page is recent as of 2024-05-24, 18:05 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 4.2, pangoLEARN version 2022-07-09.

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.