B.1.351 2021-09-23



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 110
Sequence count 27588
Countries South Africa 5003, Sweden 2429, United States of America 2264, Germany 2190, France 2020, Spain 1377, Finland 1146, Philippines 1113, Belgium 1041, Luxembourg 838, Reunion 826, United Kingdom 693, Netherlands 674, Canada 511, Turkey 492, Qatar 437, Norway 409, Zimbabwe 260, Malawi 258, Austria 256, Malaysia 239, Mozambique 232, Switzerland 227, Israel 205, Botswana 200, India 160, Kenya 160, Zambia 153, Djibouti 126, Angola 119, Denmark 118, Singapore 98, Portugal 89, Japan 89, Hong Kong 77, Czech Republic 72, Ireland 69, Thailand 63, Australia 61, Italy 57, Pakistan 54, Poland 45, Rwanda 45, Bangladesh 41, Estonia 35, Mayotte 34, Equatorial Guinea 32, Slovenia 31, Slovakia 30, New Zealand 29, Russia 25, Eswatini 25, Croatia 23, South Korea 23, Greece 20, Mexico 19, Indonesia 17, Ghana 15, Uganda 15, Costa Rica 13, Lithuania 10, Latvia 9, Romania 8, Oman 7, Lesotho 6, Democratic Republic of the Congo 6, Cameroon 6, Liberia 6, United Arab Emirates 6, Brazil 6, Suriname 5, Gabon 5, Burundi 5, Sri Lanka 4, Aruba 4, Mauritius 4, Chile 4, Guam 4, Guadeloupe 4, Somalia 4, Cote d'Ivoire 4, Madagascar 4, Togo 3, Bulgaria 3, Malta 3, South Sudan 3, China 3, Jordan 3, Iran 2, Iceland 2, Taiwan 2, French Guiana 2, Martinique 2, Brunei 1, Iraq 1, Argentina 1, Central African Republic 1, Puerto Rico 1, Guinea-Bissau 1, North Macedonia 1, Kuwait 1, Guatemala 1, Saudi Arabia 1, Tunisia 1, Nigeria 1, Morocco 1, Sint Maarten 1, Bahrain 1, Panama 1, Georgia 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
South Africa 2020-09-02 5003 12706
United Kingdom 2020-12-10 693 717951
Switzerland 2020-12-14 227 50849
Angola 2020-09-25 119 567
United States Of America 2021-01-01 2264 813089
Norway 2020-12-27 409 22308
Mayotte 2021-01-11 34 661
Belgium 2020-12-20 1041 41495
Turkey 2021-01-21 492 61306
France 2020-12-22 2020 74197
Germany 2020-12-21 2190 176324
Malaysia 2021-02-01 239 1694
New Zealand 2021-01-06 29 1253
Estonia 2021-02-17 35 4884
Spain 2020-12-24 1377 50961
Canada 2020-12-19 511 74402
Reunion 2021-01-08 826 3145
Sweden 2020-11-08 2429 100025
India 2020-12-30 160 32721
Austria 2021-01-12 256 6583
Finland 2020-12-19 1146 16324
Portugal 2021-01-02 89 13239
Ireland 2020-12-22 69 27083
Slovenia 2021-02-09 31 16818
Italy 2021-01-29 57 43989
Brunei 2021-01-20 1 31
Slovakia 2021-02-08 30 6067
Iraq 2021-02-26 1 17
Botswana 2020-11-21 200 712
Bangladesh 2020-11-01 41 1601
Sri Lanka 2021-03-02 4 827
Japan 2020-12-19 89 75469
Luxembourg 2021-01-15 838 8404
Netherlands 2020-12-22 674 53396
Lesotho 2020-12-16 6 6
Thailand 2021-02-05 63 2270
Israel 2020-12-17 205 13172
Australia 2020-12-26 61 10784
Croatia 2021-02-09 23 6111
Togo 2021-02-05 3 266
Aruba 2021-02-25 4 2166
Poland 2021-02-08 45 17888
Denmark 2021-01-04 118 128071
Democratic Republic Of The Congo 2021-01-22 6 36
Mexico 2021-04-03 19 18959
Singapore 2021-02-07 98 5514
Czech Republic 2021-02-16 72 6229
Iran 2021-04-03 2 27
Kenya 2021-01-22 160 1427
Bulgaria 2021-06-09 3 958
Ghana 2021-01-06 15 869
Russia 2021-01-19 25 3977
Zambia 2020-12-01 153 249
Pakistan 2021-03-15 54 638
Iceland 2021-02-28 2 4208
Hong Kong 2020-12-27 77 777
Indonesia 2021-01-25 17 4860
Cameroon 2021-01-05 6 91
Equatorial Guinea 2021-01-12 32 34
Qatar 2020-12-29 437 998
Liberia 2021-03-31 6 75
Taiwan 2021-04-25 2 47
Zimbabwe 2020-09-01 260 394
Malawi 2020-11-25 258 336
Suriname 2021-03-19 5 412
United Arab Emirates 2020-12-26 6 88
Gabon 2021-02-01 5 118
Argentina 2021-04-24 1 1621
Latvia 2021-03-08 9 3719
Chile 2021-04-06 4 5717
Guam 2021-04-05 4 119
Rwanda 2021-01-04 45 265
Guadeloupe 2021-02-23 4 299
Malta 2021-04-09 3 175
South Korea 2020-12-26 23 7500
Burundi 2021-05-27 5 9
South Sudan 2021-03-31 3 41
China 2020-12-31 3 140
Brazil 2021-03-07 6 27097
Romania 2021-03-24 8 1530
Central African Republic 2021-02-11 1 39
Uganda 2021-02-13 15 261
Mozambique 2020-12-14 232 356
Puerto Rico 2021-03-30 1 2045
Costa Rica 2021-02-10 13 833
Philippines 2021-02-03 1113 2565
Lithuania 2021-03-02 10 14397
North Macedonia 2021-03-10 1 268
Kuwait 2021-06-21 1 99
Oman 2021-01-27 7 262
Guatemala 2021-04-19 1 315
Greece 2021-01-14 20 7448
Djibouti 2021-03-15 126 138
Somalia 2021-02-28 4 10
Saudi Arabia 2021-04-15 1 8
Tunisia 2021-04-24 1 2
Ivory Coast 2021-03-06 4 73
Nigeria 2021-07-26 1 368
Morocco 2021-06-17 1 15
Jordan 2021-03-07 3 78
Madagascar 2021-02-15 4 241
Eswatini 2020-11-23 25 90
Bahrain 2021-04-09 1 677
Panama 2021-01-12 1 124
Georgia 2021-05-23 1 102

Data source and processing

The data on this page is recent as of 2021-09-23, 10:46 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 pre-print up on virological here describing this web tracker.