I've understood so far that in conventional PCR, the most abundant DNA/genotype present in the speciment at the beginning of the reaction is selected and esponentially amplified. So that cPCR are likely to miss mixed infections.
But I had 1 case in which when I sequenced the PCR product I got in BLAST 100% similarity for 3 different species at the same time. Is this suggestive of a mixed infection?