Almost certainly what is causing the joint pain isn't the virus, but rather its the body's response to the infection. Cells that are infected with viruses can release proteins called interferons. Interferons can act on surrounding cells and cause them to become less susceptible to viral infection. Other cells, including your immune cells respond to a virus by releasing other proteins into the blood called cytokines. Cytokines activate other immune cells and can stimulate the body to generate a fever and 'lock up' molecules of iron so they are not available to invading bacteria.
Some cytokines act on the bone marrow and cause the pool of 'reserve' neutrophils (a type of white blood cell) to move into the bloodstream. Other cytokines shut down the lymphatic vessels, causing lymph nodes to swell up. And other molecules such as histamine and prostaglandins are released and also play a role.
SO what you are feeling when you get ill from a virus (or a bacteria or parasite) is the effect of this 'soup' of cytokines, interferons and other 'mediators'. You may have some combination of fever, muscle/joint pain, runny nose, malaise, fatigue etc.
In the US you'll see TV adverts for drugs used to treat Rheumatoid Arthritis. These drugs include synthetic proteins that bind to a cytokine called TNF-alpha and block its role in inflammation.