Great question! Upper airway virus start and do their main business between up until the larynx (not necessarily with same strength on all structures, usually it's more nose/throat/sinus). They do infect our trachea and bronchi, but it's a different kind of cell lining so things are usually not too intense.

From there, we have two things happening at same time:

• the virus is not as efficient getting into your lower airway cells, taking longer (or not! e.g. omicron COVID)

• your immune system is not interested in being kind. The inflammatory response is meant to target infected cells, but it does damage to the surrounding environment and healthy cells.

While your upper airways are meant to be attacked and quickly recover (afterall, it's exposed to the outside world), lower airways are not, they take longer to heal and to return it's inflammatory response back to base levels.

Edit: formatting