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Genotyping - PCR Typing (Oct/12/2006 )

i would like to know what the rules are to design primers to differnetiate between differnet serotypes, like for hepatitis and rotavirus, they have designed primers that are specific for each serotpyes and hence they are different.
i understand the concept that they do a sequence analysis of the antigenic region that give the specific serotype and the least variable part in all the different serotype and then design the primers, my question is are there any rules set that the primers designed should utilise this many diferences in the serotypes to identify by pcr.
if there are any papers regarding this i would like to get the names of those as well.
also which is the current user friendly software to do this kind of analysis.



I think serotypes, seroconversion => Antibodies

If you find a method for map mutations in the sequece related to disctint serotypes you get what you want.