fundamentals of eDNA

This week we discussed the study by Park et al. (2020) that aimed to find the best primers and accompanying protocols for detecting SARS-CoV-2, which is the virus responsible for the disease COVID-19 in humans. In the study, the target genes were RdRP, N, E, and S. The authors designed the primers via Primer3 and tested them in-silico via idtdna.com and genome.ucsc.edu. Traditional, real-time, and multiplex PCR were utilized in this study along with gel electrophoresis. The authors developed detection protocols for traditional PCR, real-time PCR, traditional multiplex PCR, and real-time multiplex PCR. Overall, I enjoyed the paper since it was a refreshing change from only reading research related to marine environmental work. I thought that their flow charts were helpful visualizations.

We discussed the following questions:

• Was there sufficient testing for cross reactivity in-silico and/or in-vitro? I do not believe that there was sufficient testing for cross reactivity in-silico nor in-vitro. However, the authors were most likely under a lot of pressure to produce this work as fast as possible.
• If testing an environmental sample, how might you want to validate against cross reactivity differently? I would try to compare with as many other non-target species as I could get my hands on to test for cross reactivity.