Your answer will depend on what you call a prefix. I would call the following letters prefixes: un-, mulit-, pre-, post-, and dis-. In my opnion, 'agri-food' is a word formed by combining two words, 'agriculture' and 'food'.
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HellenVareBut if I search in the Internet, most of the texts I find use "Agri-food", which makes me think that "Agri-food" is the most common use.The question is a little cloudy, as "Agrifood" seems to appear as part of various company names (e.g. AgriFood).