I've been looking into this quite a lot just lately.
A typical narrowbody probably has the air in three zones: forward, rear, and cockpit. They can be controlled independently, although most times not. Each zone is controllable in terms of the refresh / recirc proportions. Historically recirc is preferred by the airlines as it's more energy efficient to recirculate the air than it is to bleed and cool a lot of HP air. More modern aircraft (I've been working with a 737-400 lately, which isn't at all modern, but it still applies there) have two sets of in-line filters, a HEPA filter which is usually replaced at around 5,000hrs / C-check, and a coarse filter which is basically there to stop the HEPA filter being clogged by everyday dirt and dust. Nominal refresh of the parcel of air in a zone is around 5 minutes but don't get misled by that, there's a lot of mixing so individual molecules and particles could be hanging around all day.
Operating theatres have similar arrangements but actually they tend to replace the filters *less* often than we are - usually at 3-5 years.
However, you are comparing apples with pears if you consider building a/c. Building air conditioning systems are much less capable in filtering out particles than the systems in use in airliners and hospitals. We are working with the state of the art at the moment - your average office building emphatically is not.
This does not mean that I'm saying being in an airliner is safe right now, I'm just saying it's a lot safer than being in an open plan office.
G