B.1.351 2023-08-24



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 32801
Countries South Africa 6393, Philippines 3019, United States of America 2938, Sweden 2570, Germany 2299, France 2129, Reunion 1220, Finland 1181, Belgium 1056, Luxembourg 841, Canada 780, United Kingdom 701, Netherlands 680, Turkey 574, Norway 442, Qatar 442, Malawi 362, Spain 348, Malaysia 337, Austria 270, Mozambique 268, Zimbabwe 262, Zambia 239, Switzerland 231, India 227, Botswana 224, Israel 208, Angola 203, Kenya 186, Djibouti 126, Denmark 116, Italy 97, Singapore 96, Portugal 90, Japan 89, Pakistan 83, Hong Kong 82, Thailand 81, Czech Republic 72, 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, Seychelles 21, Cote d'Ivoire 20, Mexico 19, Sudan 19, Kyrgyzstan 18, Greece 18, Ghana 17, Indonesia 17, Uganda 15, Latvia 14, Costa Rica 14, Brazil 13, Cameroon 12, Democratic Republic of the Congo 12, Gabon 10, Lithuania 10, Mauritius 10, Tanzania 10, Oman 7, China 7, Romania 7, Saudi Arabia 7, Liberia 6, Sri Lanka 5, Burundi 5, Suriname 5, Aruba 4, Benin 4, Taiwan 4, Somalia 4, Iran 4, Chile 4, Guadeloupe 4, Guam 4, Jordan 3, Bahrain 3, Senegal 3, Bulgaria 3, Togo 3, Malta 3, South Sudan 3, Morocco 2, French Guiana 2, Martinique 2, Tunisia 2, Ethiopia 2, Nigeria 1, Iceland 1, Sint Maarten 1, Niger 1, Argentina 1, Vietnam 1, Central African Republic 1, Puerto Rico 1, Iraq 1, Kuwait 1, Antigua and Barbuda 1, Brunei 1, Guatemala 1, Panama 1, Guinea-Bissau 1, North Macedonia 1, Georgia 1, Cambodia 1, Nicaragua 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
Botswana 2020-11-21 231 2813
Latvia 2021-03-08 14 24588
Equatorial Guinea 2021-01-12 34 49
Reunion 2021-01-07 3179 19882
United States Of America 2020-10-12 3025 4333955
Belgium 2020-12-20 1107 167346
Germany 2020-12-21 2353 914137
Finland 2020-12-19 1189 47027
Ghana 2021-01-06 21 3236
South Africa 2020-09-01 6412 42394
Portugal 2020-12-26 107 43924
Canada 2020-12-19 876 476434
United Kingdom 2020-12-10 916 2739208
Sweden 2020-11-08 2585 250142
Philippines 2021-01-31 3034 22974
Malaysia 2020-12-01 339 37246
Mozambique 2020-09-28 268 1295
Norway 2020-12-27 443 76102
France 2020-12-22 2971 518928
Australia 2020-12-26 83 175114
Croatia 2021-02-09 36 42161
Japan 2020-12-19 104 595390
Djibouti 2021-03-15 126 833
Netherlands 2020-12-22 683 157269
Bangladesh 2020-11-01 464 5707
Greece 2021-01-14 58 30508
Russia 2021-01-19 66 65100
Switzerland 2020-12-14 313 141908
Namibia 2021-03-17 47 625
Pakistan 2021-03-15 84 5130
India 2020-12-30 258 187396
Turkey 2021-01-21 587 99388
Austria 2021-01-12 275 66997
Ireland 2020-12-22 73 96580
Hong Kong 2020-12-27 84 14590
Denmark 2021-01-04 126 594780
Oman 2021-01-27 7 587
Luxembourg 2021-01-15 841 49573
Italy 2021-01-29 144 159040
Spain 2020-12-24 1545 209481
Poland 2021-02-08 46 88683
Singapore 2021-02-07 204 36654
Israel 2020-12-17 210 118470
Aruba 2021-02-25 4 3785
Zambia 2020-12-01 239 967
Uganda 2021-02-13 15 1134
Mayotte 2021-01-07 369 1198
Cameroon 2021-01-05 12 1490
Madagascar 2020-11-03 271 540
Czech Republic 2021-02-16 76 54806
Kenya 2020-12-25 186 7082
Sri Lanka 2021-03-02 7 2652
Indonesia 2021-01-25 21 47071
Thailand 2021-02-05 82 33207
Gabon 2021-01-27 10 512
Jordan 2021-03-07 5 820
Burundi 2021-05-27 5 72
Nigeria 2021-07-26 1 3757
Estonia 2021-02-17 35 14098
Mexico 2021-04-03 19 76908
China 2020-12-31 7 53635
Slovenia 2021-02-09 31 74612
Brazil 2021-03-07 13 204768
Malawi 2020-11-25 362 974
Benin 2021-03-23 4 890
Zimbabwe 2020-09-01 262 695
Ivory Coast 2021-02-11 20 658
Kyrgyzstan 2021-05-04 18 230
New Zealand 2021-01-06 29 34196
Lithuania 2021-03-02 10 36198
Suriname 2021-03-19 5 831
Qatar 2020-12-29 442 3981
Lesotho 2020-12-16 34 154
Bahrain 2021-04-04 20 10444
Slovakia 2021-02-08 30 44722
South Korea 2020-12-26 40 122925
Angola 2020-09-25 203 910
Eswatini 2020-11-23 70 925
Rwanda 2020-12-28 50 495
Democratic Republic Of The Congo 2021-01-22 12 511
Saudi Arabia 2021-04-15 14 676
Senegal 2021-01-09 3 2306
Taiwan 2021-03-24 5 3467
Romania 2021-03-24 8 17785
Morocco 2021-05-19 2 1461
Iceland 2021-02-28 2 16702
Sudan 2021-03-07 19 425
Somalia 2021-02-28 4 20
United Arab Emirates 2020-12-20 40 5341
Iran 2021-04-03 4 2074
Chile 2021-04-06 4 40837
Guadeloupe 2021-02-23 4 2160
Niger 2021-05-03 1 49
Bulgaria 2021-06-09 3 17841
Togo 2021-02-05 4 685
Costa Rica 2021-02-10 14 11278
Argentina 2021-04-24 1 16775
Vietnam 2021-05-08 1 7867
Central African Republic 2021-02-11 1 133
Tanzania 2021-01-23 10 13
Guam 2021-04-05 4 882
Tunisia 2021-04-20 4 1603
Puerto Rico 2021-03-30 1 15987
Iraq 2021-02-26 1 832
Kuwait 2021-06-21 1 790
Malta 2021-04-09 3 672
Brunei 2021-01-20 1 6645
Liberia 2021-03-31 6 87
South Sudan 2021-03-31 3 123
Guatemala 2021-04-19 1 4415
Bhutan 2021-03-31 3 127
Panama 2021-01-12 1 5680
Ethiopia 2021-02-22 2 513
North Macedonia 2021-03-10 1 596
Georgia 2021-05-23 1 2923
Cambodia 2021-05-31 1 3561
Nicaragua 2021-05-02 1 522

Data source and processing

The data on this page is recent as of 2023-08-24, 10:12 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.