There are loads of things that might trigger deep cleaning of a GPs' surgery. For example a patient attending the surgery with food poisoning (which is notifiable disease but which which does not normally present a high health risk to other patients) who then throws up all over the floor in one of the surgery's toilets (or, possibly worse, all over the receptionist's counter) might be deemed sufficient reason to require deep cleaning of some, or all, of the premises. Anyone presenting themselves to the surgery with a norovirus (even if they manage to contain their bodily fluids whilst there) might also 'set alarm bells ringing' as far as cleaning is concerned.
Deep cleaning might also be just a periodic routine procedure. After all, hospital wards are given the full 'deep cleaning' treatment, where (for example) every horizontal surface including the tops of doors, noticeboards, window frames and curtain rails are all thoroughly cleaned, on a daily basis.