Nextstrain SARS-CoV-2 resources
Labs from all over the world are sequencing SARS-CoV-2 and sharing genomic data. The Nextstrain team analyzes these data on a global and continental level. More specific analyses are often performed by public health and academic groups from around the world. This page lists a sample of such analyses. In addition to exploring SARS-CoV-2 evolution in finished analyses, you can use Nextclade to compare your sequences to the SARS-CoV-2 reference genome, assign them to clades, and see where they fall on a SARS-CoV-2 phylogeny.
- Latest global SARS-CoV-2 analysis (GISAID data)Jump to our globally-subsampled SARS-CoV-2 dataset which is updated daily using data from GISAID. We also maintain additional analyses to focus subsampling on different geographic regions and different time periods. These include analyses that focus on the previous 6 months for Africa, Asia, Europe, North America, Oceania and South America, as well as analyses that focus on the entire pandemic for Africa, Asia, Europe, North America, Oceania and South America.
- Latest global SARS-CoV-2 analysis (open data)Jump to our globally-subsampled SARS-CoV-2 dataset which is updated daily using open data from GenBank. Additional analyses that focus subsampling on different geographic regions and different time periods include analyses that focus on the previous 6 months for Africa, Asia, Europe, North America, Oceania and South America, as well as analyses that focus on the entire pandemic for Africa, Asia, Europe, North America, Oceania and South America.
- Nextclade (sequence analysis webapp)Drag and drop your sequences to assign them to clades, report potential sequence quality issues and view samples on a phylogenetic tree
- CoVariants (mutations and variants of interest)An overview of SARS-CoV-2 variants, their prevalence around the world and constituent mutations
- SARS-CoV-2 variant growth rates and frequency forecastsHistorical changes in frequency of SARS-CoV-2 variants are used to estimate variant growth rates and forecast changes in frequency
- How to run your own phylogenetic analysis of SARS-CoV-2A tutorial walking through running your own analysis using Nextstrain tools
- Scroll down to all available datasets
- Scroll down to all available interactive situation reports
All SARS-CoV-2 datasets
This section is an index of public Nextstrain datasets for SARS-CoV-2, organized by geography. Some of these datasets are maintained by the Nextstrain team and others are maintained by independent research groups. If you know of a dataset not listed here, please let us know! Please note that inclusion on this list does not indicate an endorsement by the Nextstrain team.
Nextstrain dataset
A dataset maintained by the Nextstrain team.
Regional dataset
A region-level dataset maintained by a group in the scientific community.
Not affiliated with Nextstrain.
More info about these organizations can be found at the links in the dropdown menu below.
National dataset
A country-level dataset maintained by a group in the scientific community.
Not affiliated with Nextstrain.
More info about these organizations can be found at the links in the dropdown menu below.
Divisional dataset
A division-level dataset maintained by a group in the scientific community.
Not affiliated with Nextstrain.
More info about these organizations can be found at the links in the dropdown menu below.
Local dataset
A location-level dataset maintained by a group in the scientific community.
Not affiliated with Nextstrain.
More info about these organizations can be found at the links in the dropdown menu below.
Africa (Nextstrain Team)
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Asia (Nextstrain Team)
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Europe (Nextstrain Team)
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North America (Nextstrain Team)
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Oceania (Nextstrain Team)
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South America (Nextstrain Team)
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Algeria (Africa CDC PGI)
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Angola (Africa CDC PGI)
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Benin (Africa CDC PGI)
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Botswana (Africa CDC PGI)
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Burkina Faso (Africa CDC PGI)
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Burundi (Africa CDC PGI)
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Cabo Verde (Africa CDC PGI)
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Cameroon (Africa CDC PGI)
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Central Africa (Africa CDC PGI)
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Central African Republic (Africa CDC PGI)
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Chad (Africa CDC PGI)
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Comoros (Africa CDC PGI)
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Cote d'Ivoire (Africa CDC PGI)
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Democratic Republic of the Congo (Africa CDC PGI)
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Djibouti (Africa CDC PGI)
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Eastern Africa (Africa CDC PGI)
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Egypt (Africa CDC PGI)
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Equatorial Guinea (Africa CDC PGI)
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Eswatini (Africa CDC PGI)
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Ethiopia (Africa CDC PGI)
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Gabon (Africa CDC PGI)
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Gambia (Africa CDC PGI)
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Ghana (Africa CDC PGI)
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Guinea (Africa CDC PGI)
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Guinea-Bissau (Africa CDC PGI)
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Kenya (Africa CDC PGI)
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Lesotho (Africa CDC PGI)
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Liberia (Africa CDC PGI)
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Libya (Africa CDC PGI)
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Madagascar (Africa CDC PGI)
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Malawi (Africa CDC PGI)
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Mali (Africa CDC PGI)
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Mauritius (Africa CDC PGI)
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Morocco (Africa CDC PGI)
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Mozambique (Africa CDC PGI)
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Namibia (Africa CDC PGI)
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Niger (Africa CDC PGI)
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Nigeria (Africa CDC PGI)
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Northern Africa (Africa CDC PGI)
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Republic of the Congo (Africa CDC PGI)
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Rwanda (Africa CDC PGI)
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Senegal (Africa CDC PGI)
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Seychelles (Africa CDC PGI)
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Sierra Leone (Africa CDC PGI)
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Somalia (Africa CDC PGI)
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South Africa (Africa CDC PGI)
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South Sudan (Africa CDC PGI)
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Southern Africa (Africa CDC PGI)
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Sudan (Africa CDC PGI)
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Togo (Africa CDC PGI)
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Tunisia (Africa CDC PGI)
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Uganda (Africa CDC PGI)
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Western Africa (Africa CDC PGI)
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Zambia (Africa CDC PGI)
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Zimbabwe (Africa CDC PGI)
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Sri Lanka (AICBU at University of Sri Jayewardenepura)
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Pakistan (CITRIC Center for Bioinformatics Aga Khan University Pakistan)
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Gulf Cooperation Council (Alghoribi Lab (MNGHA - KAIMRC))
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California (SEARCH, San Diego)
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San Diego (SEARCH, San Diego)
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Puerto Rico (Puerto Rico Public Health Laboratory)
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India (Vinod Scaria Lab)
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Middle East (Vinod Scaria Lab)
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Austria (Bergthaler Lab)
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Washington (Bedford Lab)
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Nebraska Last Four EpiWeeks (Bryan Tegomoh (CDCF/NDHHS))
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Cameroon (Bryan Tegomoh (CDCF/NDHHS))
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Bangladesh (Child Health Research Foundation)
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Portugal (INSA / NIH Portugal)
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CoVSeQ (CoVSeQ Partnership)
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California (CZ BioHub)
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Louisiana (LCSC)
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South-Central Region (Hodcroft et al.)
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Texas (Hodcroft et al.)
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Thailand (COVID-19 Network Investigations (CONI) Alliance)
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Connecticut (Grubaugh Lab)
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Belgium (Baele Lab)
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Nebraska (Joseph Fauver)
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Japan (Center for Medical Genetics, Keio University School of Medicine)
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Re-emergence of community transmission in Aotearoa New Zealand - Genomic overview of the Auckland Outbreak (Hadfield, Douglas et al)
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Real-time genomics to track COVID-19 post-elimination border incursions in Aotearoa New Zealand (Douglas et al)
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Canada (Maguire et. al., for work with ONCoV/CanCOGeN)
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Ontario, Canada (Maguire et. al., for work with ONCoV/CanCOGeN)
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Nebraska (Nebraska Department of Health and Human Services (DHHS))
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Austria (neherlab)
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Belarus (neherlab)
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Belgium (neherlab)
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Bosnia and Herzegovina (neherlab)
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Bulgaria (neherlab)
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Croatia (neherlab)
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Czech Republic (neherlab)
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Denmark (neherlab)
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Estonia (neherlab)
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Europe (neherlab)
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Finland (neherlab)
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France (neherlab)
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Germany (neherlab)
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Greece (neherlab)
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Hungary (neherlab)
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Iceland (neherlab)
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Ireland (neherlab)
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Israel (neherlab)
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Italy (neherlab)
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Latvia (neherlab)
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Lithuania (neherlab)
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Luxembourg (neherlab)
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Netherlands (neherlab)
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Norway (neherlab)
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Poland (neherlab)
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Portugal (neherlab)
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Romania (neherlab)
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Russia (neherlab)
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Serbia (neherlab)
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Slovakia (neherlab)
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Slovenia (neherlab)
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Spain (neherlab)
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Sweden (neherlab)
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United Kingdom (neherlab)
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Spain (FISABIO Sequencing and Bioinformatics Service)
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South Africa (Network for Genomics Surveillance in South Africa (NGS-SA))
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Pakistan (NIH BIGVI BioInformatics Group of VIrology - Pakistan)
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Peru (Laboratorio de Genómica Microbiana - Universidad Peruana Cayetano Heredia)
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Wisconsin (WISC)
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Boston GenBank (Broad Institute)
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Boston GISAID (4k) (Broad Institute)
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Zambia (Zambia Genomic Sequencing Consortium)
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Florida (FL-BPHL)
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South-East Region (FL-BPHL)
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Alabama (CDC/AMD)
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Alaska (CDC/AMD)
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Arizona (CDC/AMD)
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Arkansas (CDC/AMD)
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California (CDC/AMD)
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Colorado (CDC/AMD)
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Connecticut (CDC/AMD)
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Delaware (CDC/AMD)
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Florida (CDC/AMD)
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Georgia (CDC/AMD)
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Hawaii (CDC/AMD)
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Idaho (CDC/AMD)
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Illinois (CDC/AMD)
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Indiana (CDC/AMD)
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Iowa (CDC/AMD)
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Kansas (CDC/AMD)
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Kentucky (CDC/AMD)
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Louisiana (CDC/AMD)
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Maine (CDC/AMD)
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Maryland (CDC/AMD)
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Massachusetts (CDC/AMD)
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Michigan (CDC/AMD)
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Minnesota (CDC/AMD)
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Mississippi (CDC/AMD)
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Missouri (CDC/AMD)
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Montana (CDC/AMD)
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Nebraska (CDC/AMD)
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Nevada (CDC/AMD)
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New Hampshire (CDC/AMD)
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New Jersey (CDC/AMD)
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New Mexico (CDC/AMD)
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New York (CDC/AMD)
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North Carolina (CDC/AMD)
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North Dakota (CDC/AMD)
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Ohio (CDC/AMD)
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Oklahoma (CDC/AMD)
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Oregon (CDC/AMD)
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Pennsylvania (CDC/AMD)
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Puerto Rico (CDC/AMD)
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Rhode Island (CDC/AMD)
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South Carolina (CDC/AMD)
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South Dakota (CDC/AMD)
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Tennessee (CDC/AMD)
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Texas (CDC/AMD)
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Utah (CDC/AMD)
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Vermont (CDC/AMD)
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Virginia (CDC/AMD)
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Washington (CDC/AMD)
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Washington DC (CDC/AMD)
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West Virginia (CDC/AMD)
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Wisconsin (CDC/AMD)
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Wyoming (CDC/AMD)
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Switzerland (nextstrain.org/groups/swiss)
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Maine (Tewhey Lab)
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Arizona (TGen North)
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Washington (Washington State Public Health Laboratories)
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Data is filtered by forming a union of selected values within each category, and then taking the intersection between categories (if more than one category is selected).
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Contributor
Hadfield, Douglas et al
Nextstrain TeamNextstrain TeamNextstrain TeamNextstrain TeamNextstrain TeamNextstrain TeamNextstrain TeamAll SARS-CoV-2 situation reports
We have been writing interactive situation reports using Nextstrain Narratives to communicate how COVID-19 is moving around the world and spreading locally. These are kindly translated into a number of different languages by volunteers and Google-provided translators — click on any language below to see the list of situation reports available.
Support
Hadfield et al., Nextstrain: real-time tracking of pathogen evolution, Bioinformatics (2018)The core Nextstrain team is
Please see the team page for more details.
All source code is freely available under the terms of the GNU Affero General Public License. Screenshots may be used under a CC-BY-4.0 license and attribution to nextstrain.org must be provided.
This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions. Special thanks to Kristian Andersen, Josh Batson, David Blazes, Jesse Bloom, Peter Bogner, Anderson Brito, Matt Cotten, Ana Crisan, Tulio de Oliveira, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Nate Grubaugh, Becky Kondor, Dylan George, Ian Goodfellow, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Duncan MacCannell, Erick Matsen, Sebastian Maurer-Stroh, Placide Mbala, Danny Park, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Cecile Viboud for comments, suggestions and data sharing.
