My baby's voice is changing. When he whines etc it is much deeper than normal. Could he be getting sick?

Change of Cry. Anything that might change the thickness of th evocal cords might affect the timber of the cry. Illness, allergic drainage or reflux come to mind at the top of my list. Babies also will change their cry in order to open the eustachian tubes and equalize the pressure in the middle ear if they are getting an ear infection. I can usually tell by the change in cry, ( at least in my children ).