Possibly measles or "remittent fever".....see quote below describing camp conditions.

Following the organization of the Regiment, the Georgia 16th was transferred to Richmond, Virginia via railroad. When the unit arrived in Richmond, their quarters were affectionately named "Camp Cobb" in honor of their Colonel. Below is an excerpt from the September 25, 1861 "Richmond Dispatch" describing the morale, shape and discipline of the Regiment:

Camp Cobb--16th Regiment Georgia Volunteers.

"--We were much gratified by a visit yesterday to the camp, at the old Fair Ground, of the 16th Regiment of Georgia Volunteers, commanded by the Hon. Howell Cobb, President of Congress. A finer body of men, or a cleaner or better regulated camp, we have rarely seen. Although a few weeks ago a considerable number of this regiment were sick with the measles and remittent fever, we are happy to say that now, with very few exceptions, the entire strength of the regiment is fit for duty. The rapid improvement in the health of this corps is, we believe, mainly attributable to the rigid enforcement, by the Colonel and his officers, of the wise rule providing for the sick in camp, and only removing to the hospitals and private houses such cases as could not properly be attended to in the camp hospital, and to the extreme attention paid to the cooking of the soldiers' food, and the cleanliness of all parts of the camp.

During a somewhat protracted visit, we did not hear a single profane expression, nor a word which could offend the cars of the most sensitive. We found the men cheerful and happy, the officers courteous and obliging; the tents airy, scrupulously near, and well pitched, and the general arrangements for the comfort and good order of the regiment worthy of all commendation.
We understand that the stand of colors voted by Congress at its last session to the corps commanded by its President, is now ready, and will shortly be formally presented by the President of the Confederate States. From what we have seen of this fine body of Georgians, and from what we have heard of their moral and physical discipline, we can predict that they will prove themselves worthy of the proud distinction which the Congress has conferred upon them in the person of their able and popular Colonel."