B.1.351 2022-05-19



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 31774
Countries South Africa 5900, Philippines 3016, United States of America 2763, Sweden 2548, Germany 2206, France 2104, Reunion 1213, Finland 1189, Belgium 1042, Turkey 869, Luxembourg 840, Canada 761, United Kingdom 697, Netherlands 682, Qatar 444, Norway 440, Malawi 359, Spain 299, Malaysia 282, Austria 270, Mozambique 262, Zimbabwe 262, Zambia 233, India 232, Switzerland 230, Israel 209, Angola 198, Botswana 193, Kenya 178, Denmark 116, Singapore 96, Italy 90, Portugal 90, Japan 86, Thailand 81, Hong Kong 80, Czech Republic 72, Eswatini 70, Ireland 70, Bangladesh 68, Pakistan 63, Australia 63, Rwanda 49, Namibia 47, Poland 44, Croatia 41, United Arab Emirates 39, Estonia 35, Mayotte 34, Slovenia 31, Slovakia 31, Russia 30, New Zealand 29, South Korea 25, Cote d'Ivoire 21, Seychelles 21, Mexico 19, Ghana 19, Indonesia 17, Greece 17, Uganda 15, Costa Rica 14, Latvia 14, Equatorial Guinea 13, Democratic Republic of the Congo 12, Gabon 12, Cameroon 11, Lithuania 10, Sudan 10, Brazil 10, Oman 7, Saudi Arabia 7, Romania 7, Madagascar 6, Lesotho 6, Sri Lanka 5, China 5, Suriname 5, Burundi 5, Iran 4, Guam 4, Aruba 4, Somalia 4, Mauritius 4, Guadeloupe 4, Chile 4, Taiwan 4, Bulgaria 3, Togo 3, Malta 3, South Sudan 3, Jordan 3, Martinique 2, Djibouti 2, Ethiopia 2, Senegal 2, Benin 2, Canary Islands 2, Central African Republic 2, French Guiana 2, Tunisia 2, Brunei 1, Guinea-Bissau 1, Niger 1, Panama 1, Iceland 1, Guatemala 1, Antigua and Barbuda 1, Puerto Rico 1, Cambodia 1, Nigeria 1, Nicaragua 1, Bahrain 1, Kyrgyzstan 1, Kuwait 1, Sint Maarten 1, Iraq 1, North Macedonia 1, Georgia 1, Argentina 1, Morocco 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 2898 2822459
Germany 2020-12-21 2285 593874
Finland 2020-12-19 1195 30466
Denmark 2021-01-04 126 461606
Canada 2020-12-19 864 281455
Belgium 2020-12-20 1090 105642
United Kingdom 2020-12-10 912 2441639
Netherlands 2020-12-22 685 111115
Sweden 2020-11-08 2589 182727
Singapore 2021-02-07 204 14739
France 2020-12-22 2928 256735
Israel 2020-12-17 211 55211
South Africa 2020-09-01 6013 29887
Reunion 2021-01-07 3045 10932
Lithuania 2021-03-02 10 34431
Italy 2021-01-29 137 102017
Malawi 2020-11-25 359 833
Thailand 2021-02-05 82 18388
Eswatini 2020-11-23 70 425
Philippines 2021-01-31 3033 11312
Hong Kong 2020-12-27 82 4728
India 2020-12-30 255 129347
Switzerland 2020-12-14 313 121794
Austria 2021-01-12 275 18864
Mayotte 2021-01-07 369 923
Bangladesh 2020-11-01 451 4852
Czech Republic 2021-02-16 76 38396
Qatar 2020-12-29 444 2863
Kenya 2020-12-25 181 5143
Turkey 2021-01-21 877 89329
Pakistan 2021-03-15 64 1881
Malaysia 2020-12-01 285 15294
Taiwan 2021-03-24 5 141
Norway 2020-12-27 441 59612
Brunei 2021-01-20 1 1860
Croatia 2021-02-09 41 30297
Spain 2020-12-24 1471 111046
Ireland 2020-12-22 73 59466
Australia 2020-12-26 83 71042
Japan 2020-12-19 104 240216
Estonia 2021-02-17 35 10462
Poland 2021-02-08 46 78742
Slovenia 2021-02-09 31 56669
Niger 2021-05-03 1 14
Zambia 2020-12-01 233 760
Iran 2021-04-03 4 810
Guam 2021-04-05 4 672
Luxembourg 2021-01-15 840 26713
New Zealand 2021-01-06 29 9564
Costa Rica 2021-02-10 14 3667
Jordan 2021-03-07 5 693
Panama 2021-01-12 1 3219
Rwanda 2020-12-28 50 495
Sri Lanka 2021-03-02 7 2495
Botswana 2020-11-21 218 2272
Mozambique 2020-09-28 262 895
Madagascar 2020-11-03 271 454
Democratic Republic Of The Congo 2021-01-22 12 328
Iceland 2021-02-28 2 4213
Latvia 2021-03-08 14 11164
Angola 2020-09-25 199 823
Mexico 2021-04-03 19 49650
Gabon 2021-01-27 12 500
Guatemala 2021-04-19 1 1379
Aruba 2021-02-25 4 2856
Lesotho 2020-12-16 6 11
Ghana 2021-01-06 23 2373
Djibouti 2021-03-15 126 508
Somalia 2021-02-28 4 10
Cameroon 2021-01-05 12 526
Portugal 2020-12-26 107 30613
Uganda 2021-02-13 15 479
Ivory Coast 2021-02-10 21 518
Slovakia 2021-02-08 31 34319
Greece 2021-01-14 57 14912
Zimbabwe 2020-09-01 262 631
China 2020-12-31 5 626
Sudan 2021-03-27 10 34
Brazil 2021-03-07 10 121337
Oman 2021-01-27 7 334
Guadeloupe 2021-02-23 4 754
Bulgaria 2021-06-09 3 12470
Namibia 2021-03-17 47 223
Togo 2021-02-05 4 584
United Arab Emirates 2020-12-20 40 741
Puerto Rico 2021-03-30 1 7895
Cambodia 2021-05-31 1 2757
Ethiopia 2021-02-22 2 497
Malta 2021-04-09 3 672
South Korea 2020-12-26 38 32819
Equatorial Guinea 2021-01-12 34 47
Saudi Arabia 2021-04-15 14 96
Bahrain 2021-04-04 12 2070
Senegal 2021-01-09 2 1320
Chile 2021-04-06 4 21209
Russia 2021-01-19 30 10206
Indonesia 2021-01-25 21 21408
Suriname 2021-03-19 5 780
Benin 2021-03-23 4 463
Nigeria 2021-07-26 1 2886
Burundi 2021-05-27 5 63
South Sudan 2021-03-31 3 123
Romania 2021-03-24 8 11978
Nicaragua 2021-05-02 1 315
Liberia 2021-03-31 6 87
Kyrgyzstan 2021-07-07 1 84
Central African Republic 2021-02-11 2 58
Kuwait 2021-06-21 1 167
Iraq 2021-02-26 1 707
North Macedonia 2021-03-10 1 401
Tunisia 2021-04-20 4 679
Georgia 2021-05-23 1 1552
Argentina 2021-04-24 1 10533
Morocco 2021-06-17 1 392

Data source and processing

The data on this page is recent as of 2022-05-19, 11:47 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.