"[28] Peter Bogner, a German in his 40s based in the US and who previously had no experience in public health, read an article about Capua's call and helped to found and fund GISAID.

[17] The acronym GISAID was coined in a correspondence letter published in the journal Nature in August 2006,[30] putting forward an initial aspiration of creating a consortium for a new Global Initiative on Sharing Avian Influenza Data (later, "All" would replace "Avian"), whereby its members[17] would release data in publicly available databases up to six months after analysis and validation.

[32] Although no essential ground rules for sharing were established,[33] the correspondence letter was signed by over 70 leading scientists, including seven Nobel laureates, because access to the most current genetic data for the highly pathogenic H5N1 zoonotic virus was often restricted, in part due to the hesitancy of World Health Organization member states to share their virus genomes and put ownership rights at risk.

[34] Towards the end of 2006, Indonesia announced it would not share samples of avian flu with the WHO which led to a global health crisis due to an ongoing epidemic.

[29] 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.

Indonesia's Ministry of Health announced in November 2023 the establishment of GISAID Academy in Bali, to focus on bioinformatics education, advance pathogen genomic surveillance, and increased regional response capacity.

[58] In March 2023, GISAID temporarily suspended database access for some scientists, removing raw data relevant to investigations of the origins of SARS-CoV-2.

[67][68] In June 2023, it was reported in Vanity Fair that Bogner had said that "GISAID will soon launch an independent compliance board 'responsible for addressing a wide range of governance matters'".

[10] The Telegraph similarly reported that GISAID's in-house counsel was developing new governance processes intended to be transparent and allow for the resolution of scientific disputes without the involvement of Bogner.

[50] The creation of the GISAID database was motivated in part by concerns raised by researchers from developing countries,[69] with Scientific American noting in 2009 that "a previous data-sharing system run by WHO forced them to give up intellectual property rights to their virus samples when they sent them to WHO.

The virus samples would then be used by private pharmaceutical companies to make vaccines that are awarded patents and sold at a profit at prices many poor nations cannot afford".

[10][50] 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.

[83] 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.