The paper by Park et al (2020) on primer optimization for SARS-Cov-2 was very eye opening for me and I enjoyed learning more about the details behind the PCR tests that have become a part of my weekly life. I was shocked to see that some of the primer sets actually in use are quite inefficient and have a high chance of providing false positives. I hope that everyone enjoyed our choice of paper for this week’s discussion even if it was not directly related to eDNA research, and personally I thought it was interesting to make the connection between medical and environmental applications of PCR assays. Each are difficult in their own way. As we discussed, medical research might have better reference sequence databases than environmental research for primer development, however the medical targets most likely mutate and have more variation making it difficult to develop a specific enough primer set. There are also different implications and consequences of false negatives and false positives in medical versus environmental research. Especially in the case of the COVID pandemic the consequences of a false negative could be a lot more extreme than a false negative in a Maine eDNA research project.
I really liked the part of our conversation centered around the variants of COVID and how tests should be adapted to account for the various mutations. I think that multiplexing is a great way to try and handle these variant strains by looking at multiple genes. We also brought up many important questions that relate to this. How quickly does the COVID strain mutate? What regions of the strain mutate? How similar are the strains and are they similar enough to all be detected with the same PCR primer sets? I also started thinking about the extraction process associated with the PCR tests. On a weekly basis I get both saliva tests and nose swab tests done, and I wonder how the extraction process varies based on collection method and if one is more effective and results in higher yield than another. While I do feel that I ended our discussion with more questions than I began with, I really enjoyed our discussion and think that it is important that we ask even more questions and challenge methods associated with PCR testing to ensure that they are adequate.