Learn by doing — risk-free and from your home: how a genetic test detects Coronavirus

A proposal to bring this unfortunately vibrant topic into an educational opportunity: to guide your students into learning how genetic testing for an infection works, what is the polymerase chain reaction (PCR) and what is the use of gel electrophoresis everyday in laboratories.

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Using a simulation (not real samples, no hazard at all), your students can run their own experiment in their computer or tablet, to detect whether several "patients" are infected with Coronavirus (COVID-19) or with Influenza virus (common flu), or they are free from both.

In this virtual laboratory they will acquire reagents and equipment, use a micropipette to mix samples and reagents into a battery of Eppendorf tubes, and run the PCR. Then they will apply the products onto an agarose gel, run the electrophoresis and check the results.

The virtual lab (http://biomodel.uah.es/en/lab/cybertory2) has been in use for years, available at no cost for anyone using a web browser (see http://bit.ly/2SWOpST for a description and a video demo). The types of experiments that may be performed have been expanding, and this week the new one has been added, allowing to test for Coronavirus.

The simulation uses data from genomic RNA of SARS-CoV-2 and Influenza A (H1N1 variant) viruses, as well as DNA sequence of the human gene for glyceraldehyde-3P dehydrogenase as a control for the PCR. Primers for Coronavirus were designed not to react with Influenza genome, and all other cross-reactions in the virtual assay were checked as negative.

Experiments may be designed openly, with any composition of reaction mixtures, and the results will be consistent with that design, i.e. PCR will work or not. That does not mean the position and intensity of bands in the gel is questionable. You are encouraged to provide minimal instructions to the students and let them play exploring conditions; pipetting takes a little time but each 3-hour PCR takes just 10 seconds of real time!.  A protocol to ensure that the most novice users will achieve successful results is in preparation for this Coronavirus test. (Protocols are already available for the other kinds of assay: paternity testing, forensics, dairy products adulteration, testing for the sickle cell gene, celiac disease, cytochrome P450 polymorphism.)

Depending on the expertise of your students, some previous tutorials will be needed, e.g. on genes, DNA, the PCR, electrophoresis, virus structure, viral genomes, sample collection...

Note: The use of the virtual laboratory needs an access key that you may request by email (instructions are in the Cybertory web page), but it is free and may be used by all your students. Files that make the simulation are under the GNU General Public Licence and the associated documents under Creative Commons Attribution – NonComercial – ShareAlike Licence.

** Poster image: left part from Pixabay, free and no recognition needed; right part is own artwork after screen capture.

Angel Herráez

Associate professor, University of Alcalá

biochemistry, molecular biology, bioinformatics, molecular visualisation, technology for teaching and learning

2 Comments

Go to the profile of Fiona Veira-McTiernan
Fiona Veira-McTiernan 6 months ago

Nature article: “Simulated labs are booming. Blowing up your lab is usually discouraged, but it’s part of the experience when you’re learning online.”

https://www.nature.com/articles/d41586-018-06831-1

Go to the profile of Angel Herráez
Angel Herráez 6 months ago

Thank you for sharing that, Fiona!

In this particular lab there is absolutely no risk of explosion. At the most, maybe a splash if you are really not careful at all. ;-)