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The flu virus enters the body by attacking the cells of mucous tissue. Usually this is the tissue in the upper respiratory tract with influenza viruses. Typically the virus enters via the mouth, nose or eyes. Since the gastrointestinal system is also lined with mucous tissue, the influenza viruses can also enter cells deeper in the GI system and not just in the mouth. When this happens, the symptoms can include gastrointestinal reactions to the virus and to the cells the virus enters being killed, which gives GI symptoms like vomiting, nausea and even diarrhea along with the usual respiratory symptoms.

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