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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?

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If you had a 100% BLAST hit for 3 species from a single amplicon sequence then it only means that region of DNA is conserved in the three species so you have at least one of those species present not necessarily all three.

If you had three different amplicon sequences and each one matched one species to a total of three, then you have all three species present.

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  • $\begingroup$ I see. Is it correct to say that: 1) it is possible that one PCR product contains more than 1 organism's DNA, for example if your primers are quite generic and you got several unspecific bands. 2) the readable sequence corresponds to only one organism, even if this sequence is equally conserved in more species ?Thanks $\endgroup$
    – Azzurra
    Mar 24, 2017 at 13:38
  • $\begingroup$ You have have more then one species PCR product in the same band. If you get multiple bands then they by definition have differing sequences. That doesn't mean it's two species, it could be one species with two different amplicons in it's genome. And 2) No, if the sequence is equally conserved in more species you can't say which or how many species are present. $\endgroup$
    – Artem
    Mar 24, 2017 at 17:29

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