Wow, that answer takes a bit of work to get to, but it is correct. One way to get to the right answer is to identify the incorrect ones, as follows:

B. Trends in infectious disease data tend to persist for decades, unless there is a major breakthrough in treatment regimens.

Incorrect. We don't know if there has been a major breakthrough in treatment regimens on either malaria or schistosomiasis in the past five years. The passage does not give us any context with respect to what went on before five years ago. It is possible that there were more cases of malaria than schistosomiasis at that time, but some breakthrough in the treatment regimen for malaria led to a decline in its cases.

C. Five years ago, many more people died from schistosomiasis than died from malaria.

Incorrect. The number of people who died is irrelevant to the number of infection cases, since the passage does not address which disease is more likely to cause death, or has a better treatment regimen. It is possible that schistosomiasis had fewer cases five years ago, but is much more likely to cause death because it is a more "nasty" disease.

D. Over the past five years, the percentage of infectious disease cases caused by malaria was not significantly greater than the percentage of cases caused by schistosomiasis.

Incorrect. This answer weakens the argument. It suggests that the percentage of infection cases caused by malaria was slightly ("not significantly") greater than those caused by schistosomiasis.

E. Over the past five years, the percentage of infectious disease cases caused by diseases other than malaria and schistosomiasis did not increase substantially.

Incorrect. This answer does not strengthen the argument. It says that the percentage of infection cases caused by other diseases has essentially remained the same over the past five years, and does not address whether there were more cases of malaria or schistosomiasis five years ago.

Okay, then why is answer A correct? This is really a math question disguised as a Critical Reasoning question - which is by far the hardest type of question on the GMAT).

A. Over the past five years, the percentage of infectious disease cases caused by schistosomiasis has remained unchanged, but the percentage of cases caused by malaria has increased substantially.

Correct. If most of the increase in cases is due to schistosomiasis, but the percentage of schistosomiasis in the total cases has not changed, then most of the cases five years ago were also due to schistosomiasis. This strengthens the argument.