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I read that opening in our face like nose and eyes are one which get us infected with numerous communicable diseases like cold , flu ebola etc. Both these organs have preventive mechanism like nose hairs, eye lash , etc. Which one of eye and nose does protect human better from airborne virus and bacteria?

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Between the eyes and nose, which offers better immune protection

Neither. Both are mucous membranes lined by epithelial cells. Each is their own niche (and the nose has a number of sub-niches), with particular receptors, environmental factors, and immune factors that interact with pathogen factors. The interaction between the two produces the tissue tropism of a particular pathogen. Each is colonized with many commensal microbes, with some overlap (see Murray Medical Microbiology Ch 7 and this study of the eye). As far as "airborne" transmission, vs. inoculation by physical contact, the nose and nasopharynx are important structures in respiration. The eye is not.

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