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I am going to be running an effective giving event about malaria. For this I need three effective anti-malaria charities that attendees can split a funding pool between (and thereby learn things about what malaria is and how to tackle it, which is the main purpose of the event). I have the Against Malaria Foundation and the Malaria Consortium. I would like a charity that is focused on the roll-out of malaria vaccines, or better malaria vaccine research, that can at least be argued to be near EA's effectiveness threshold (possibly only when downstream effects of research or advocacy is taken into account). Ideally it should have "Malaria" in its name. Anyone have any ideas?

perhaps targetmalaria.org

Perhaps The Global Fund to Fight AIDS, Tuberculosis and Malaria

They accept donations through the United Nations Foundation. One drawback: I did not see an option on the donation page to direct the donation to only malaria work, so the funds will probably get distributed between malaria, and the other health problems they focus on.

Good for having "Malaria" in name, however it seems they mostly distribute to bednets or seasonal chemoprevention. Thus it comes down to a discussion on charity governance.

The aim of the event is to inspire attendees to investigate different mechanisms for tackling malaria, and how they feel about those mechanisms from the stance of a donor. I was hoping to get nets, chemoprevention, and vaccines, as I'm aware that malaria treatment is pretty well known to be less cost-effective than prevention. I know vaccines are currently less headline effective than bednets and chemoprevention... but maybe not, when their downstream effects are accounted for.

(or at least, they're within the threshold of an interesting philosophy discussion)

Here is a list of all malaria-related grants GiveWell has made. 

One organization that GiveWell has made some grants to is PATH, they do work on vaccines (as well as some other things). You might want to look into them.

Open Philanthropy made a grant to PATH for malaria vaccine implementation, maybe you would want to consider that program? There were also malaria vaccine research grants to WHO, Imperial College London, University of Georgia, University of Oxford, Yale University, Hospital for Sick Children, and probably others, however I feel like these grants may not correspond to "programs" per se, especially something that individual donors could give to.

Another one to consider is Target Malaria, which is working on gene drives for mosquito control.

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