Primates, Genomics and Ecology Lab takes on COVID-19

Biological anthropologist Dr. Amanda Melin, PhD, is leading a team of six scientists from her Primates, Genomics and Ecology Lab as part of a larger COVID-19 genomics group working to turn back the tides of the global pandemic. 

In partnership with Alberta Precision Laboratories (APL), Alberta Children's Hospital Research Institute (ACHRI) and researchers across University of Calgary and University of Alberta, Melin’s team handles the positive COVID-19 samples from APL’s Public Health Lab, which conducts the initial COVID-19 testing. Once the positive samples are received, Melin and her team reverse transcribe viral RNA to the coding DNA form needed for sequencing at the Centre for Health Genomics and Informatics.

• Photo above: Top row from left: Mareike Janiak, Amanda Melin, Haley Glass. Bottom row from left: Rachel Munds, Gwen Duytschaever, Link Lam. 

This crucial work will allow researchers to track the spread and evolution of the virus and inform vaccine development, and it sets the groundwork for finding new information on virulence and who is most susceptible to COVID-19. 

Melin's lab is uniquely qualified for this work because it's equipped for high containment, designed to deal with potentially infectious biological material from primates. Her lab staff is expertly trained in managing infectious materials. 

“When the world started collapsing into this crisis I reached out to Benedikt Hallgrimsson, a scientific director of ACHRI, who is co-leading the COVID-19 genomics research with Francois Bernier, head of the Department of Medical Genetics in the Cumming School of Medicine (CSM),” says Melin. “We process all the primate samples that come through our lab that are potentially infectious and we have very strict protocols, so we felt we were ideally set up to be handling the positive COVID-19 samples.” 

The genetics of COVID

“Our dynamic provincial collaborations have allowed us to hit the ground running on analyzing the genetics of COVID,” says Dr. Hallgrimsson, PhD, head of the Department of Cell Biology and Anatomy at CSM. “The research team includes virologists, evolutionary biologists, medical geneticists and physicians.” 

All of the initial testing for COVID-19 is handled by Alberta Precision  Laboratories, Melin explains. When the swabs test positive for COVID-19, RNA (ribonucleic acid) is extracted from the samples and sent to Melin’s lab for the necessary treatments prior to genomic sequencing. 

“SARS-CoV-2 exists in RNA form which can’t be sequenced directly,” says Melin. “First we have to reverse transcribe it to DNA form (deoxyribonucleic acid), amplify and purify it so that it’s ready for the genomic sequencing needed for virus epidemiology studies.” 

“Viruses have a very fast mutation rate and there are always different strains floating around. When we’re able to do a virus epidemiology study we can look at transmission patterns, find out which strains are the most virulent, and set the groundwork for understanding which people may have the strongest reactions.”  

This intensive work done in Melin’s lab sets the foundation for these virus epidemiology studies. “This is the background needed for all future downstream analysis and we hope it will inform vaccine development,” Melin says.

Social distancing in the lab

Melin points out that her team is strictly adhering to the conventions of social distancing. Only two members of the group are ever in the lab at one time with Janiak, Munds, Glass and Lam working on a rotating schedule. Lab manager Duytschaever, who is pregnant and therefore at high risk, is co-ordinating the team’s efforts from home. Melin is also able to oversee the project from her home, where she juggles the duties of motherhood caring for and educating her two young daughters. 

“They’re in a Spanish bilingual program so everyday it’s Spanish and math and English literacy, and then we also have their piano lessons,” says Melin. “Yes, it’s overwhelming at times, but a lot of it is also going quite well.” 

The team meets through video conferencing routinely to sort out logistics and co-ordination. “I’m very proud of the fact that there are six of us women who are working on this,” says Melin. 

She adds: “I feel like this is a really difficult time for all us and it’s easy to feel quite powerless. Everybody who’s volunteered to work on this team has told me ‘This gives me a sense of purpose during this crisis. I feel like I’m contributing to finding a solution. To actually be able to help like this, it’s very uplifting.’”

 

UCalgary resources on COVID-19

For the most up-to-date information about the University of Calgary's response to the spread of COVID-19, visit the UCalgary COVID-19 Response website.