Flue and Muscle ache

If I remember correctly, it is due in part to the immune responce

 

Flu is more virulent than the common cold. The flu migth also have genes that mislead the immune responce toward something else.

 

almost any virus can cause myalgias (muscle aches)

Parvoviru B-19 (fifth's disease in kids), adenovirus, Hepatitis C, Mononucleosis from either cytomegolovirus or epstein barr, and Hiv; the latter can present with severe flu like illness and myalgias during the acute infection (before you seroconvert and can detect the HIV antibody.) The list is endless. It is due to the immune response and inflammatory mediators that are relesed during the acute infection. (although hep c can give you chronic clinical course with regards to myalgias and arthritis.)

 

The general census among clinicians is that we don't know the exact etiology... Possibilities include direct invasion of muscle tissue by the virus, release of myotoxic cytokines or other immunologic processes. a cell biologist would probably know more of the details, but once again, I think it is still speculative how these viruses cause myalgias.