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Young Flagstaff researchers adapt to COVID-19
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Young Flagstaff researchers adapt to COVID-19

Since COVID-19 made its way to Flagstaff, work hasn’t been the same for 21-year-old researchers Kaitlyn Parra and Allen Clarke.

But that’s not a bad thing.

Days may be longer and the tasks more complicated to achieve, but the two agreed their work supporting local laboratories has been as worthwhile — if not more — during the pandemic as it was before.

“I think the best part of all of this is probably knowing that this is something that will make a difference,” Parra said of her research on Valley Fever. “It’s not just me doing one small project and it’s the end of it, it’s something that will build on the knowledge we currently have in any scientific discipline.”

Parra, a Flagstaff local and senior microbiology major at Northern Arizona University, is a student researcher at the Pathogen and Microbiome Institute, a role Clarke also held until he graduated last week. Clarke, who now has degrees in computer science and mathematics, is currently a research assistant at TGen North.

PMI has about 40 paid student researchers like Parra and Clarke who work year-round in 10 research areas ranging from viruses to biohazardous materials and software development, according to an NAU report on the undergraduate research program.

Dawn Birdsell, the associate director for PMI’s Training and Education Core, said PMI and TGen are together prioritizing work on new COVID-19 research, including new detection systems and therapeutics, with PMI focusing on treatment options, while TGen is tackling more active virus work.

She explained that student researchers are contributing primarily to COVID-19 research through supportive laboratory work and data analysis. Only PMI’s certified, highly trained researchers work with the virus directly.

“Right now all our resources at PMI are dedicated to COVID work first priority and then whenever resources are not being utilized for COVID, other existing active projects are permitted,” Birdsell said.

Clarke’s schedule has been packed since COVID-19 cases spiked as he worked to revise a database he had created to better track the many samples TGen has been receiving for testing. This software allows scientists to digitally track samples of any kind, including how they are handled or altered throughout testing and genomic sequencing. Since PMI implemented the database about a year ago, Clarke estimated there are about 30,000 samples now in this system. TGen is also using its own version of the database.

Prior to COVID-19, samples arrived without identifying information, Clarke said, but now each sample submitted for testing includes patient information that must be securely recorded and tracked.

“We basically had to take the system we built over a year and a half and rebuild it secure to handle this patient information in two weeks,” Clarke said. “We had a pretty busy stretch there trying to develop all that stuff.”

Among other characteristics new to the software, Clarke has helped create a reporting system that will send the final report on a sample’s positivity back to the agency that ordered the test.

With the database updated, Clarke is now helping to maintain it and help with other technical support at TGen North, which he said has seen some significant changes in climate since the pandemic began.

“People in the lab are so busy in there, they have a hard time communicating out what they need in a timely manner ... Usually, as soon as the developers get the information we need to build something, it was needed 20 minutes ago,” Clarke said.

In addition, he said TGen employees have their temperatures prior to entering the facility and have also been offered routine screening. Clarke has opted for the nasal swab three times so far, a process he described with a laugh as a “free brain scratch.” It was his first swab that made the severity of the pandemic — as well as his role in it — clear.

“The code I’m writing in some sense is helping scientists run these faster,” Clarke said. “At first, not a lot, but over time it’s going to slowly improve the process.”

For Parra, who has been able to continue her existing research on Valley Fever, the impacts of COVID have been felt in the lab itself. She visits the lab less frequently now, she said, and has even been sent images from a microscope as PMI works to maintain social distancing protocols.

“It took me a lot to get the samples from growing to actually on the slide, so I was really excited to process them myself, but now I can’t do that. I have to have someone else process them for me,” she said.

Parra is currently studying a new fungal species to see if they are pathogenic. It is her second project on Valley Fever, following a survey of dogs to search for trends. From nearly 3,000 responses, it was determined boxers, golden retrievers and Yorkshire terriers had high infection rates, while chihuahuas had lower infection rates.

In her regular work at PMI, Parra also helps prepare lab projects for graduate students, from creating spreadsheets for data to preparing lab materials.

Nowadays, when Parra is able to do her work in-person, she voluntarily wears a mask and spends much more time sanitizing surfaces and walking the long way around the lab to avoid being too close to fellow researchers.

She hopes to use this experience in her long-term goal of earning a more prominent research role through a doctoral program.

“I really want to be able to be a principal investigator, one of the people top in the research world, and help with future pandemics — hopefully not anytime soon,” she added quickly. “Maybe epidemics.”

She remembers the quick progression from back in January when one of her professors, who studies coronaviruses, first shared news of how the virus was spreading through China to soon after, when friends studying abroad were sent home as countries locked down and a family member was laid off from his job.

“It’s something that I realized we should have cared about more in the beginning,” Parra said of the virus. “And it’s not going away anytime soon.”

Kaitlin Olson can be reached at the office at or by phone at (928) 556-2253.

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