Molecular diagnosis can be divided into biochemical, antibody and DNA based analysis. In other words, isoenzyme patterns are genetically controlled and parasites with different banding patterns are genetically distinct. For example, enzyme based assays have been useful in diagnosis of Leishmaniasis, Sleeping sickness and Chagas disease. The advantages of enzyme analysis is that it is a relatively simple technique, it is possible to type many samples in parallel as large numbers of typing enzymes are available and it is sometimes the only available strategy to distinguish morphologically similar parasites. The disadvantage is the inability to distinguish between past and current infections or between morphologically similar parasites.
Assay development can also be expensive.
However, antibody based analysis is routinely incorporated into Sleeping sickness surveillance. PCR based tests can also fail because of uncharacterised inhibitors in samples of the key PCR enzyme, Taq polymerase, non-parasite nucleic acid contamination and false positives. Moreover, PCR, at the present time, can only at best be considered as semi-quantitative. For the reasons discussed above, it is unclear if PCR will eventually fully replace conventional diagnosis in developing countries. However, examples of developments in DNA based diagnosis in veterinary parasitology include Eimeria detection.