My apologies if this is not a sufficient answer, first time commenter here, hopefully this can be a placeholder for someone more knowledgeable on the topic :)
Hepatitis was a major issue for both Axis and Allied troops, and we were largely unprepared for it. Although we cannot definitively say if it was or was not a deciding factor in military victory or loss in the African theatre, there are some clues we can pick up on to make an educated guess based off the number of infected prisoners of war that the Allies captured and the incidence rate amongst Allied troops in that locality (bolded text below). For American troops, the hepatitis epidemic started in North Africa, while for the British it started in the Middle East. The German population, however, was suffering from it for a longer period of time: in Germany itself there were one to two million cases in 1941, with estimates of 60% of German units being infected.^3
My background is clinical research in hepatology (study of the liver), specifically treatment of Hepatitis C. Some basic information, so others may know, is that Hepatitis A thrives in areas of poor sanitation, typically involving water and feces which would, logically, be major factors to consider for mass military operations. Symptoms are pretty much the same between Hepatitis A, B, and C, where you will see flu like symptoms: fever, fatigue, nausea/vomiting, body aches, and later jaundice due to the beginnings of liver dysfunction. Although war will give you that adrenaline rush, if your body is decompensated enough you will be operating at a much lower level of performance - sure, hepatitis didn't kill you (very low mortality rate of 0.2%), but it put you out of action for long periods of time.
Relatively small numbers of U.S. troops went into Egypt in the early autumn before the subsequent major landings in North Africa in November 1942. It became known very shortly that French, British Commonwealth, and Axis troops had had a bitter experience with epidemic hepatitis at various times during the period from 1939 to 1942 in the North African desert. The French stationed large bodies of troops in southern Tunisia during the spring and summer of 1939 to handle any threat the Italians might make from Libya. Hepatitis appeared among them in September 1939, reaching its peak in December, and declining in January 1940.^1 Jaundice first developed among the German troops near Sirte and Benghazi during the fall of 1940, rapidly became a serious problem among them, and later spread to the Italian ground troops and air force. Thousands of cases occurred but the Germans appeared more vulnerable than the Italians, with a ratio of three to one cases. **In May 1943, the closing of the Tunisian campaign revealed that large numbers of German and Italian prisoners were jaundiced.**^2 Australian troops were involved late in 1941 while attempting to hold Tobruk, and in the following year they, the New Zealanders, and the British Eighth Army were caught up in a great epidemic during and after the campaign for El Alamein.
In 1942, the epidemic was well on its way in August and reached a peak in November. In U.S. troops in Egypt during that autumn and winter, the disease first occurred in the fliers and ground troops of the Ninth Air Force, as these men operated between Alexandria, Benghazi, and Tobruk. Despite the fact the U.S. troops in Egypt had an appreciable amount of hepatitis among the small numbers of men there, the incidence among U.S. forces in North Africa (Algeria and Tunisia) was low during the autumn and winter of 1942-43 and remained so into the summer of 1943.
This security was not to last for long, however, and in the late summer of 1943 began the volcanic experience that was to erupt into the most expensive and devastating problem that we were to encounter in relation to infectious hepatitis. It came to be, during 1943-45, the most important cause of man-days lost due to illness among U.S. forces in the Mediterranean-North African theater. As a cause of death due to medical disease it ranked high, although the case fatality was low (about 1.8 per 1,000). That this should have occurred coincident with the invasion of Sicily and should involve British Commonwealth and American troops in Egypt, in North Africa, and subsequently in Sicily and Italy was a hindrance of inestimable magnitude to military activity and strained the medical facilities almost beyond their capabilities. It is no exaggeration to say that the hospitals from Cairo to Palermo were filled with patients with hepatitis, with beds occupying the corridors and every other available space. The task of caring for all these patients in addition to the mounting numbers of battle casualties was indeed a formidable one.
References:
Essential Technical Medical Data, North African Theater of Operations, U.S. Army, for September 1944, 1 Oct. 1944.
Final Report on Infectious Hepatitis in MTOUSA, Col. Marion H. Barker, MC, to Surgeon, Mediterranean Theater of Operations, APO 512, 23 July 1945.
Baudot, Marcel. The Historical Encyclopedia of World War II. London: Macmillan, 1981. Print.
Most of the information was taken from here which contains a great wealth of information with proper references.