B.1.351 2022-11-25



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 120
Sequence count 32296
Countries South Africa 6071, Philippines 3017, United States of America 2804, Sweden 2547, Germany 2215, France 2126, Reunion 1254, Finland 1192, Belgium 1056, Turkey 859, Luxembourg 841, Canada 771, United Kingdom 695, Netherlands 682, Norway 440, Qatar 440, Malawi 359, Malaysia 335, Spain 317, Austria 268, Mozambique 262, Zimbabwe 261, Zambia 239, Switzerland 229, Botswana 227, India 225, Israel 209, Angola 202, Kenya 181, Denmark 116, Singapore 97, Italy 94, Portugal 90, Japan 86, Thailand 81, Hong Kong 81, Czech Republic 73, Pakistan 73, Ireland 70, Eswatini 70, Australia 63, Canary Islands 60, Bangladesh 54, Rwanda 49, Namibia 47, Poland 45, United Arab Emirates 39, Estonia 35, Mayotte 34, Lesotho 33, Slovenia 31, Slovakia 31, Russia 30, Croatia 30, New Zealand 29, South Korea 25, Seychelles 21, Cote d'Ivoire 21, Mexico 19, Ghana 19, Sudan 19, Greece 19, Kyrgyzstan 18, Indonesia 17, Uganda 15, Costa Rica 14, Latvia 14, Equatorial Guinea 14, Gabon 13, Democratic Republic of the Congo 12, Brazil 11, Cameroon 11, Lithuania 10, Mauritius 10, Djibouti 8, Romania 7, Oman 7, Saudi Arabia 7, China 6, Burundi 5, Suriname 5, Sri Lanka 5, Guadeloupe 4, Iran 4, Guam 4, Somalia 4, Aruba 4, Taiwan 4, Chile 4, Senegal 3, South Sudan 3, Bulgaria 3, Togo 3, Bahrain 3, Malta 3, Jordan 3, French Guiana 2, Benin 2, Martinique 2, Tunisia 2, Ethiopia 2, Central African Republic 2, Morocco 1, Nigeria 1, Nicaragua 1, North Macedonia 1, Niger 1, Brunei 1, Guatemala 1, Kuwait 1, Iceland 1, Georgia 1, Iraq 1, Antigua and Barbuda 1, Sint Maarten 1, Guinea-Bissau 1, Panama 1, Puerto Rico 1, Cambodia 1, Argentina 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 Kingdom 2020-12-10 916 2620471
Denmark 2021-01-04 126 559875
Czech Republic 2021-02-16 76 51418
Germany 2020-12-21 2290 809347
Bangladesh 2020-11-01 458 5494
United States Of America 2020-09-10 2940 3841165
Madagascar 2020-11-03 271 540
South Africa 2020-09-01 6092 36852
Spain 2020-12-24 1542 161115
Canada 2020-12-19 875 389347
France 2020-12-22 2969 464515
Guadeloupe 2021-02-23 4 2051
Mayotte 2021-01-07 369 1158
Belgium 2020-12-20 1104 157463
Namibia 2021-03-17 47 581
Israel 2020-12-17 211 109430
Ireland 2020-12-22 73 84284
United Arab Emirates 2020-12-20 40 742
Finland 2020-12-19 1198 37594
Malawi 2020-11-25 359 869
Reunion 2021-01-07 3183 16852
Netherlands 2020-12-22 685 138407
Australia 2020-12-26 83 127704
Philippines 2021-01-31 3034 20018
Sweden 2020-11-08 2587 215047
Indonesia 2021-01-25 21 36543
Djibouti 2021-03-15 126 705
Italy 2021-01-29 144 136200
India 2020-12-30 256 172856
Switzerland 2020-12-14 314 135319
Botswana 2020-11-21 240 2632
Poland 2021-02-08 46 84678
Romania 2021-03-24 8 16228
Turkey 2021-01-21 869 97883
Japan 2020-12-19 104 439168
Austria 2021-01-12 273 34773
Thailand 2021-02-05 82 25342
Malaysia 2020-12-01 338 29036
Luxembourg 2021-01-15 841 42957
Pakistan 2021-03-15 74 4124
Senegal 2021-01-09 3 2200
Norway 2020-12-27 441 70661
Angola 2020-09-25 202 869
Mexico 2021-04-03 19 68799
Iran 2021-04-03 4 1733
Guam 2021-04-05 4 838
Oman 2021-01-27 7 350
Burundi 2021-05-27 5 72
South Sudan 2021-03-31 3 123
Lesotho 2020-12-16 33 153
Rwanda 2020-12-28 50 495
Portugal 2020-12-26 107 39610
Qatar 2020-12-29 440 3029
Mozambique 2020-09-28 262 991
Zambia 2020-12-01 239 873
Brazil 2021-03-07 11 167050
Slovenia 2021-02-09 31 67117
New Zealand 2021-01-06 29 21911
Slovakia 2021-02-08 31 42420
Russia 2021-01-19 30 28397
Singapore 2021-02-07 204 24509
Zimbabwe 2020-09-01 261 660
Greece 2021-01-14 57 20330
Kenya 2020-12-25 184 6339
Ghana 2021-01-06 23 2551
Morocco 2021-06-17 1 1141
China 2020-12-31 6 1684
Democratic Republic Of The Congo 2021-01-22 12 470
Costa Rica 2021-02-10 14 7336
Nigeria 2021-07-26 1 3419
Eswatini 2020-11-23 70 805
Estonia 2021-02-17 35 14098
Hong Kong 2020-12-27 83 10915
Uganda 2021-02-13 15 734
Bahrain 2021-04-04 20 9659
Sudan 2021-03-07 19 234
Saudi Arabia 2021-04-15 14 188
Bulgaria 2021-06-09 3 17185
Somalia 2021-02-28 4 12
South Korea 2020-12-26 38 65131
Croatia 2021-02-09 30 38196
Aruba 2021-02-25 4 3419
Kyrgyzstan 2021-05-04 18 230
Ivory Coast 2021-02-10 21 561
Taiwan 2021-03-24 5 2333
Nicaragua 2021-05-02 1 429
North Macedonia 2021-03-10 1 532
Sri Lanka 2021-03-02 7 2575
Equatorial Guinea 2021-01-12 34 49
Latvia 2021-03-08 14 15871
Lithuania 2021-03-02 10 34776
Niger 2021-05-03 1 44
Togo 2021-02-05 4 582
Brunei 2021-01-20 1 4054
Gabon 2021-01-27 13 512
Suriname 2021-03-19 5 831
Jordan 2021-03-07 5 769
Cameroon 2021-01-05 12 938
Guatemala 2021-04-19 1 2197
Kuwait 2021-06-21 1 426
Benin 2021-03-23 4 852
Malta 2021-04-09 3 672
Tunisia 2021-04-20 4 862
Iceland 2021-02-28 2 6264
Liberia 2021-03-31 6 87
Georgia 2021-05-23 1 2195
Ethiopia 2021-02-22 2 497
Iraq 2021-02-26 1 788
Chile 2021-04-06 4 33555
Central African Republic 2021-02-11 2 58
Panama 2021-01-12 1 4941
Puerto Rico 2021-03-30 1 12424
Cambodia 2021-05-31 1 3286
Argentina 2021-04-24 1 13117

Data source and processing

The data on this page is recent as of 2022-11-25, 16:20 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.