B.1.351 2024-02-22



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 122
Sequence count 32837
Countries South Africa 6435, Philippines 3018, United States of America 2932, Sweden 2570, Germany 2284, France 2129, Reunion 1219, Finland 1177, Belgium 1056, Luxembourg 841, Canada 781, United Kingdom 700, Netherlands 680, Turkey 582, Qatar 446, Norway 442, Malawi 362, Spain 357, Malaysia 340, Austria 271, Mozambique 268, Zimbabwe 262, Zambia 239, Switzerland 231, India 226, Botswana 221, Israel 208, Angola 201, Kenya 186, Djibouti 126, Denmark 116, Singapore 96, Italy 93, Portugal 90, Japan 89, Pakistan 85, 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 40, United Arab Emirates 40, Croatia 36, Estonia 35, Lesotho 34, Mayotte 34, Equatorial Guinea 33, Slovenia 31, Slovakia 30, New Zealand 29, South Korea 25, Seychelles 21, Cote d'Ivoire 20, Mexico 19, Sudan 19, Greece 18, Ghana 18, Kyrgyzstan 18, Indonesia 17, Uganda 15, Latvia 14, Costa Rica 14, Brazil 13, Democratic Republic of the Congo 12, Cameroon 12, Gabon 11, Lithuania 10, Tanzania 10, Mauritius 10, China 7, Romania 7, Oman 7, Saudi Arabia 7, Liberia 6, Burundi 5, Suriname 5, Sri Lanka 5, Morocco 5, Iran 4, Benin 4, Chile 4, Aruba 4, Taiwan 4, Guam 4, Guadeloupe 4, Somalia 4, South Sudan 3, Bulgaria 3, Malta 3, Bahrain 3, Togo 3, Senegal 3, Jordan 3, Tunisia 2, French Guiana 2, Martinique 2, Ethiopia 2, Guinea-Bissau 1, Panama 1, Nicaragua 1, Iceland 1, Sint Maarten 1, Guatemala 1, Nigeria 1, Niger 1, Kuwait 1, Antigua and Barbuda 1, Puerto Rico 1, Central African Republic 1, Cambodia 1, North Macedonia 1, Argentina 1, Georgia 1, Iraq 1, Brunei 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
Philippines 2021-01-31 3033 23774
United States Of America 2020-10-12 3019 4514236
Germany 2020-12-09 2338 923811
Australia 2020-12-26 83 185796
France 2020-12-22 2971 547897
Madagascar 2020-11-03 271 540
Switzerland 2020-12-14 313 145671
Portugal 2020-12-26 107 45459
Reunion 2021-01-07 3180 20650
United Kingdom 2020-12-10 915 2782747
Netherlands 2020-12-22 683 165370
Ireland 2020-12-22 73 100005
New Zealand 2021-01-06 29 41994
Russia 2021-01-19 66 70612
South Africa 2020-09-01 6454 43767
Malaysia 2020-12-01 342 39557
Bangladesh 2020-11-01 469 5938
Finland 2020-12-19 1185 49939
Sweden 2020-11-08 2585 265545
Italy 2021-01-29 144 171786
Turkey 2021-01-21 595 100425
Canada 2020-12-19 877 533512
Luxembourg 2021-01-15 841 51410
Norway 2020-12-27 443 77101
Panama 2021-01-12 1 5785
Spain 2020-12-24 1560 233439
South Sudan 2021-03-31 3 123
Burundi 2021-05-27 5 72
Qatar 2020-12-29 446 4147
Belgium 2020-12-20 1107 172237
Mayotte 2021-01-07 369 1200
Lesotho 2020-12-16 34 155
Israel 2020-12-17 210 121946
Thailand 2021-02-05 82 34830
Mozambique 2020-09-28 268 1307
India 2020-12-30 258 189921
Croatia 2021-02-09 36 43875
Liberia 2021-03-31 6 87
Latvia 2021-03-08 14 25151
Mexico 2021-04-03 19 81105
Greece 2021-01-14 58 36778
Uganda 2021-02-13 15 1150
Rwanda 2020-12-28 50 495
Zambia 2020-12-01 239 967
Japan 2020-12-19 104 626628
Bulgaria 2021-06-09 3 18249
Costa Rica 2021-02-10 14 11819
Slovakia 2021-02-08 30 46099
Czech Republic 2021-02-16 77 56237
Namibia 2021-03-17 47 628
Kenya 2020-12-25 186 7463
China 2020-12-31 7 67513
Austria 2021-01-12 276 69751
Eswatini 2020-11-23 70 925
Romania 2021-03-24 8 18875
Botswana 2020-11-21 228 2834
Angola 2020-09-25 201 910
Estonia 2021-02-17 35 14098
Malawi 2020-11-25 362 974
Ivory Coast 2021-02-11 20 687
Brazil 2021-03-07 13 215636
Singapore 2021-02-07 204 45185
Denmark 2021-01-04 126 616247
South Korea 2020-12-26 40 147167
Slovenia 2021-02-09 31 76443
Poland 2021-02-08 46 90877
Hong Kong 2020-12-27 84 14871
Iran 2021-04-03 4 2152
Tunisia 2021-04-20 4 2043
Benin 2021-03-23 4 891
Zimbabwe 2020-09-01 262 695
Nicaragua 2021-05-02 1 522
Iceland 2021-02-28 2 17508
United Arab Emirates 2020-12-20 40 5341
Pakistan 2021-03-15 87 5360
Equatorial Guinea 2021-01-12 34 49
Chile 2021-04-06 4 42873
Djibouti 2021-03-15 126 833
Lithuania 2021-03-02 10 37480
Democratic Republic Of The Congo 2021-01-22 12 524
Gabon 2021-01-27 11 511
Aruba 2021-02-25 4 3815
Suriname 2021-03-19 5 831
Indonesia 2021-01-25 21 48281
Guatemala 2021-04-19 1 4743
Malta 2021-04-09 3 672
Bahrain 2021-04-04 20 10811
Oman 2021-01-27 7 776
Sri Lanka 2021-03-02 7 2759
Nigeria 2021-07-26 1 3779
Niger 2021-05-03 1 49
Ghana 2021-01-06 22 3243
Kuwait 2021-06-21 1 855
Morocco 2021-05-19 5 1570
Tanzania 2021-01-23 10 13
Saudi Arabia 2021-04-15 14 714
Taiwan 2021-03-24 5 4633
Togo 2021-02-05 4 748
Senegal 2021-01-09 3 2371
Jordan 2021-03-07 5 837
Puerto Rico 2021-03-30 1 17137
Guam 2021-04-05 4 899
Guadeloupe 2021-02-23 4 2192
Sudan 2021-03-07 19 425
Cameroon 2021-01-05 12 1523
Central African Republic 2021-02-11 1 135
Cambodia 2021-05-31 1 3623
Somalia 2021-02-28 4 20
North Macedonia 2021-03-10 1 753
Argentina 2021-04-24 1 17354
Kyrgyzstan 2021-05-04 18 230
Georgia 2021-05-23 1 3227
Ethiopia 2021-02-22 2 582
Iraq 2021-02-26 1 855
Bhutan 2021-03-31 3 135
Brunei 2021-01-20 1 6908

Data source and processing

The data on this page is recent as of 2024-02-22, 22:41 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.