It’s because of how the immune response works. Respiratory illnesses often enter the body via the nasal passages, either infecting the cells there or alerting the immune system. One of the first responses the immune cells cause is inflammation. Immune cells secrete chemical messengers to recruit more immune cells and to cause an increase in local blood supply. The capillaries in the nasal passage become engorged and the tissue swells in response. Mucous cells in the nasal passages are working overtime to trap and contain other infectious particles as well. Hence the swelling and excess mucous production leads to stuffy runny noses. It’s not the virus that does it, it’s your immune system making your nose less comfortable for viruses.
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