fundamentals of eDNA

I’ve spoken in a few different forums about the difficulties we’ve had developing lobster blockers for my own research. I think that has given me a little perspective into the difficulties there are in designing a primer specific to an organism. That being said it doesn’t really surprise me that early attempts at creating Covid-19 specific primers produced sub-par results. The paper we read I think does a really good job of outlining how these primers were not optimal, and showing how they tested their own primer sets. One thing I find interesting in comparing sources of error between this study and Maine eDNA studies, is that a lot of the off-target or non-specific amplification in Covid-19 research may come from rapid mutation, whereas in Maine eDNA it is likely to come from incomplete reference databases. The resulting errors would likely look similar, but the source of the error is completely different. The former is due to the actual study subject changing, whereas the latter comes from improper primer design due to limited background info. One of the fixes they introduce is the idea of multiplexing, adding multiple primers to one amplification. Again, having struggled to obtain a single working blocker in my own work, I can’t imagine how difficult it would be to design multiple primers that are each specific and won’t interact with each other. It is pretty impressive the work that these researchers did and that other Covid researchers continue doing to produce accurate tests, and now vaccines as well.