What virus / flu diseases can affect the joints?

Many. Some viruses commonly associated with joint inflammation are parvovirus b19, hiv, enterovirus, adenovirus, dengue, mumps, herpes. But any virus can stimulate your immune system and produce joint pain / stiffness / inflammation. Non viral organisms associated with post infectious arthritis are yersinia, shigella, campylobacter, salmonella and chlamydia.