hi
well iam working on rotavirus . i do RT-PCR and nested PCR. for the purpose of surviallance studeis.

i alawys have a problem with genotyping my positves samples. on RT-PCR maybe 30-40% of the samples show the ampification product. either VP4 or VP7 but when i genotype using DAS primers i somtimes have 50% and most time 40% or less of the samples show thier genotype.

so what do u think this could be due to?
and how will i able to optimize my results .

What are your CT values?