Gisaid Download Sequences UPDATED

GISAID (/sed/), the Global Initiative on Sharing All Influenza Data,[9] previously the Global Initiative on Sharing Avian Influenza Data,[10][11] is a global science initiative established in 2008 to provide access to genomic data of influenza viruses. The database was expanded to include the coronavirus responsible for the COVID-19 pandemic,[12][13] as well as other pathogens. The database has been described as "the world's largest repository of COVID-19 sequences".[14] GISAID facilitates genomic epidemiology and real-time surveillance to monitor the emergence of new COVID-19 viral strains across the planet.[15]

Some of the earliest SARS-CoV-2 genetic sequences were released by the Chinese Center for Disease Control and Prevention and shared through GISAID in mid January 2020.[44] Since 2020, millions of SARS-CoV-2 genome sequences have been uploaded to the GISAID database.[45]

Gisaid Download Sequences

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GISAID maintains what has been described as "the world's largest repository of COVID-19 sequences",[14] and "by far the world's largest database of SARS-CoV-2 sequences".[7] By mid-April 2021, GISAID's SARS-CoV-2 database reached over 1,200,000 submissions, a testament to the hard work of researchers in over 170 different countries.[50] Only three months later, the number of uploaded SARS-CoV-2 sequences had doubled again, to over 2.4 million.[51] By late 2021, the database contained over 5 million genome sequences;[52] as of December 2021, over 6 million sequences had been submitted;[53] by April 2022, there were 10 million sequences accumulated; and in January 2023 the number had reached 14.4 million.[54]

In January 2020, the SARS-CoV-2 genetic sequence data was shared through GISAID.[55] Throughout the first year of the COVID-19 pandemic, most of the SARS-CoV-2 whole-genome sequences that were generated and shared globally were submitted through GISAID.[56] When the SARS-CoV-2 Omicron variant was detected in South Africa, by quickly uploading the sequence to GISAID, the National Institute for Communicable Diseases there was able to learn that Botswana and Hong Kong had also reported cases possessing the same gene sequence.[57]

A difficulty that GISAID's Data Access Agreement attempts to address is that many researchers fear sharing of influenza sequence data could facilitate its misappropriation through intellectual property claims by the vaccine industry and others, hindering access to vaccines and other items in developing countries, either through high costs or by preventing technology transfer. While most public interest experts agree with GISAID that influenza sequence data should be made public, and this is the subject of agreement by many researchers, some provide the information only after filing patent claims while others have said that access to it should be only on the condition that no patents or other intellectual property claims are filed, as was controversial with the Human Genome Project.[70] GISAID's Data Access Agreement addresses this directly to promote sharing data. GISAID's procedures additionally suggest that those who access the EpiFlu database consult the countries of origin of genetic sequences and the researchers who discovered the sequences. As a result, the GISAID license has been important in rapid pandemic preparedness.[71] However, these restrictions evidence common criticisms to an open data model.[72][73]

In 2017, GISAID's editorial board stated that "re3data.org and DataCite, the world's leading provider of digital object identifiers (DOI) for research data, affirmed the designation of access to GISAID's database and data as Open Access".[79] However, after several researchers had their accounts suspended in March 2023 as reported by the journal Science[80] and other news outlets,[81] its open access status was revoked by the Registry of Research Data Repositories (re3data), which now classifies it as a "restricted access repository".[82] In 2020 the World Health Organization chief scientist Soumya Swaminathan called the initiative "a game changer",[12] while the co-director of the European Bioinformatics Institute (EBI) Rolf Apweiler has argued that because it does not allow sequences to be reshared publicly, it hampers efforts to understand the coronavirus and the rapid rise of new variants.[77]

GISAID's restrictions on access have led to conflict with "labs and institutions whose priorities are academic rather than driven by the immediate priorities of public health protection".[49] In January 2021, GISAID's restricted access led a group of scientists to write an open letter asking for SARS-CoV-2 sequences to be deposited in open databases,[83] which was replicated in the journals Nature[72][84] and Science.[7] Furthermore, the article from Science points out that the lack of transparency in access to the database also prevents many scientists from even criticising the platform.[7] A paper from 2017 describing the success of GISAID mentions that revoking researchers' credentials was rare, but it did happen.[85] The same publication described a "perceived merit in GISAID's formula for balancing the need for control and openness". In April 2023, Science and The Economist reported these issues continue as well as the lack of transparency of its governance.[67][66] An investigation by The Telegraph into claims made by Science noted the incentives of various potential competitors in the field, for whom GISAID is an obstacle to consolidation of control over the field, and also noted that GISAID's position inevitably places it at the center of disputes between groups of scientists, which will tend to result in the losing side blaming GISAID for that outcome.[49]

We use these data in our official Nextstrain builds. If you have sufficient computing resources, you can use these files as inputs for the workflow in a the workflow config file like the one described above. However, the workflow starts by aligning all input sequences to a reference and this alignment can take hours to complete even with multiple cores. As an alternative, we show how to select specific data from these large files prior to starting the workflow.

First, prepare the sequence data. This step strips prefixes from strain ids in sequence records, removes whitespace from the strain ids, removes additional metadata in the FASTA defline, and removes duplicate sequences present for the same strain id.

On 12 March 2023, WHO was made aware of new SARS-CoV-2 sequences and metagenomics data associated with samples collected in the Huanan Seafood Wholesale Market, Wuhan, China, from January 2020, that became available on GISAID for a short period of time. The data had subsequently been downloaded by a number of researchers from several countries. Access was restricted shortly after, apparently to allow further data updates by China CDC. WHO then immediately reached out to China CDC and to the Chair and Vice-Chair of SAGO. Upon discussions between WHO and Chinese colleagues, it was explained that the genomic data are the basis for an expected update to the existing Liu et al. 2022 preprint (1), which is in the process of being re-submitted for publication to Nature by China CDC.

After discussions with the WHO secretariat and the SAGO Chair and Vice-Chair, a call was arranged on 12 March with the scientists involved from China CDC, and some of those who had accessed the data from GISAID, to gauge the significance of this data and the analyses of this data. WHO subsequently organized a meeting on 14 March 2023 with all SAGO members, and invited researchers from China CDC to present the updated analysis of their data. WHO and SAGO also invited the researchers who had informed WHO that they had accessed data from GISAID, to present their analysis of the temporarily released sequences.

The presentations from China CDC and invited international researchers indicated that there were newly available data from the Huanan Seafood Wholesale Market. This included metagenomic data of environmental samples from various stalls and wastewater collection sites collected as early as January 2020. Analyses of these data suggest that apart from SARS-CoV-2 sequences, some samples also contained human DNA, as well as mitochondrial DNA of several animal species, including some that are known to be susceptible to SARS-CoV-2. This included DNA from wild raccoon dogs, Malaysian porcupine, and bamboo rats among others, in SARS-CoV-2 positive environmental samples.