When COVID-19 (coronavirus) first grabbed big headlines in the US and began to shut down American cities, Chaminade Biology Professor Michael Dohm wanted to give his genomics students an opportunity to put their theoretical knowledge to the test on a very real-world problem. He drew up a series of lessons that would have them studying COVID-19 genome sequences as they became available worldwide.
Dohm’s students had spent the beginning of the term honing their bioinformatics skills, the process of searching and retrieving sequences from databases, looking for similarities, and then building algorithms to represent evolutionary relationships. The point of all that work? To test hypotheses about diseases.
Because his students were studying virus genomes, Dohm decided to have them apply what they’d learned to the novel coronavirus. Peer into the origins of COVID-19, he told them, and try to sleuth out how the virus that triggered a global pandemic is related to other coronaviruses common to humans.
Dohm said the hands-on work wasn’t just relevant to the moment. It was exactly what genomic scientists around the world were doing. “The objective is to provide our students a glimpse into a small part of what Centers for Disease Control and Prevention and other experts are doing right now as the spread of the virus continues,” he said.
He kicked off the project after spring break.
At that point, students were learning fully online and communicating with Dohm regularly remotely to talk through their findings. To unpack COVID-19, his students used bioinformatics software, grabbing sequences from publicly available databases. They also used evolutionary models to estimate rates of mutation in the sequences and then follow the rapid spread of coronavirus worldwide.
COVID-19 genome sequences are being collected around the world, as labs collect patient data, and thousands of samples are now publicly available in databases maintained around the world. “The basic idea of the project,” Dohm said, “is that we are utilizing the rapidly growing number of genetic sequences…to explore how experts can use the sequences to trace the virus’ origins.”
But he also wanted students to consider how the virus was evolving.
Such work has been compared to tracking the travel of COVID-19 as if looking at passport stamps.
While the work is challenging, Dohm was there with his students every step of the way, creating worksheets to help his students get unstuck as they pored over the data. He also had them keep their work for a portfolio to represent not only what they found—but the steps they took to get there.