B.1.351 2022-01-22



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 118
Sequence count 30536
Countries South Africa 5401, Philippines 2970, United States of America 2770, Sweden 2559, Germany 2205, France 2063, Finland 1142, Belgium 1073, Reunion 1037, Luxembourg 839, Canada 740, United Kingdom 698, Netherlands 679, Turkey 492, Qatar 440, Norway 409, Spain 345, Malawi 318, Malaysia 278, Zimbabwe 260, Mozambique 258, Austria 255, Switzerland 231, Zambia 220, India 216, Israel 207, Botswana 204, Kenya 171, Angola 129, Djibouti 124, Denmark 116, Singapore 98, Italy 97, Japan 89, Portugal 89, Thailand 79, Hong Kong 79, Czech Republic 72, Ireland 69, Australia 63, Pakistan 57, Madagascar 53, Bangladesh 50, Rwanda 50, Namibia 46, Poland 44, United Arab Emirates 40, Estonia 35, Mayotte 34, Equatorial Guinea 33, Slovenia 31, Slovakia 30, New Zealand 29, Russia 27, Eswatini 25, Croatia 23, South Korea 23, Seychelles 21, Greece 20, Mexico 19, Ghana 18, Indonesia 17, Uganda 15, Costa Rica 14, Latvia 13, Brazil 10, Lithuania 10, Sudan 10, Cameroon 8, Romania 8, Oman 7, Saudi Arabia 7, Democratic Republic of the Congo 6, Liberia 6, Lesotho 6, Suriname 5, China 5, Burundi 5, Gabon 5, Guadeloupe 4, Aruba 4, Benin 4, Somalia 4, Mauritius 4, Sri Lanka 4, Chile 4, Guam 4, Cote d'Ivoire 4, Jordan 3, Iran 3, Bahrain 3, Malta 3, South Sudan 3, Togo 3, Bulgaria 3, Taiwan 3, Ethiopia 2, Senegal 2, Martinique 2, Canary Islands 2, French Guiana 2, Iraq 1, Brunei 1, Guatemala 1, Niger 1, Nigeria 1, Guinea-Bissau 1, Panama 1, Sint Maarten 1, Morocco 1, Central African Republic 1, Argentina 1, Georgia 1, Iceland 1, North Macedonia 1, Kuwait 1, Puerto Rico 1, Tunisia 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
Poland 2021-02-08 44 43656
Belgium 2020-12-20 1073 74956
Czech Republic 2021-02-16 72 22191
United States Of America 2021-01-01 2770 1981273
Switzerland 2020-12-14 231 95409
France 2020-12-22 2063 143273
Singapore 2021-02-07 98 10321
Slovakia 2021-02-08 30 17536
Germany 2020-12-21 2205 339208
Zambia 2020-12-01 220 617
Mozambique 2020-12-14 258 719
United Kingdom 2020-12-10 698 1540354
Malaysia 2020-12-01 278 7728
Netherlands 2020-12-22 679 83112
Turkey 2021-01-21 492 80473
India 2020-12-30 216 70403
Spain 2020-12-24 345 78986
Sweden 2020-11-08 2559 136284
Finland 2020-12-19 1142 23028
Suriname 2021-03-19 5 709
Norway 2020-12-27 409 38741
Brazil 2021-03-07 10 83938
Philippines 2021-01-31 2970 9710
South Africa 2020-09-02 5401 20281
Reunion 2021-01-08 1037 5110
Indonesia 2021-01-25 17 11311
Angola 2020-09-25 129 717
Mayotte 2021-01-11 34 798
Canada 2020-12-19 740 179527
Ireland 2020-12-22 69 43166
Denmark 2021-01-04 116 269999
Botswana 2020-11-21 204 1963
Costa Rica 2021-02-10 14 2125
Guadeloupe 2021-02-23 4 473
Italy 2021-01-29 97 75300
Kenya 2020-12-25 171 2621
Australia 2020-12-26 63 35187
Thailand 2021-02-05 79 9979
Russia 2021-01-19 27 7696
Ghana 2021-01-06 18 1598
Luxembourg 2021-01-15 839 17313
Mexico 2021-04-03 19 36362
New Zealand 2021-01-06 29 5142
Qatar 2020-12-29 440 2444
Iraq 2021-02-26 1 87
Pakistan 2021-03-15 57 1159
Austria 2021-01-12 255 8991
Slovenia 2021-02-09 31 39290
Brunei 2021-01-20 1 479
Japan 2020-12-19 89 162367
Israel 2020-12-17 207 30508
Oman 2021-01-27 7 272
Malawi 2020-11-25 318 658
Bangladesh 2020-11-01 50 2994
Namibia 2021-03-17 46 97
Latvia 2021-03-08 13 5874
China 2020-12-31 5 424
Djibouti 2021-03-15 124 197
Equatorial Guinea 2021-01-12 33 44
Aruba 2021-02-25 4 2781
Rwanda 2020-12-28 50 422
Jordan 2021-03-07 3 528
Cameroon 2021-01-05 8 359
Iran 2021-04-03 3 138
Portugal 2021-01-02 89 22027
Romania 2021-03-24 8 7198
Zimbabwe 2020-09-01 260 615
Guatemala 2021-04-19 1 979
Hong Kong 2020-12-27 79 1108
Democratic Republic Of The Congo 2021-01-22 6 37
Madagascar 2021-02-15 53 321
Croatia 2021-02-09 23 16773
Ethiopia 2021-02-22 2 415
Senegal 2021-01-09 2 1296
Niger 2021-05-03 1 14
Estonia 2021-02-17 35 7767
Greece 2021-01-14 20 11472
Benin 2021-03-23 4 428
South Korea 2020-12-26 23 20652
Bahrain 2021-04-09 3 2052
Somalia 2021-02-28 4 10
Saudi Arabia 2021-04-15 7 64
Lithuania 2021-03-02 10 25208
Malta 2021-04-09 3 617
Burundi 2021-05-27 5 63
South Sudan 2021-03-31 3 41
Sri Lanka 2021-03-02 4 2039
Togo 2021-02-05 3 271
Chile 2021-04-06 4 15370
United Arab Emirates 2020-12-20 40 741
Gabon 2021-02-01 5 323
Nigeria 2021-07-26 1 1885
Bulgaria 2021-06-09 3 8862
Panama 2021-01-12 1 491
Liberia 2021-03-31 6 75
Eswatini 2020-11-23 25 90
Guam 2021-04-05 4 358
Morocco 2021-06-17 1 215
Lesotho 2020-12-16 6 11
Taiwan 2021-03-24 3 71
Central African Republic 2021-02-11 1 40
Sudan 2021-03-27 10 33
Argentina 2021-04-24 1 6645
Ivory Coast 2021-03-06 4 79
Georgia 2021-05-23 1 926
Iceland 2021-02-28 1 4208
North Macedonia 2021-03-10 1 316
Kuwait 2021-06-21 1 110
Uganda 2021-02-13 15 478
Puerto Rico 2021-03-30 1 4891
Tunisia 2021-04-24 1 172

Data source and processing

The data on this page is recent as of 2022-01-22, 20:37 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 3.1.3, pangoLEARN version 2021-06-15.

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.