Leading metabolomics researcher in Faculty of Science mobilizes lab to help with COVID-19 relief

Dr. Ian Lewis, PhD, has devoted his career to developing faster, more efficient ways to diagnose infections. Now, during the COVID-19 global pandemic, he and his collaborators are ready to face an unprecedented challenge as his field of research is being thrust into the spotlight.

Lewis, an assistant professor and Alberta Innovates Translational Health Chair in the Department of Biological Sciences in the Faculty of Science, and member of the Snyder Institute for Chronic Diseases at the Cumming School of Medicine, is a leader in the emerging field of metabolomics — the science of measurement and analysis of metabolites. His laboratory, the Lewis Research Group, specializes in analyzing the host-pathogen metabolic dynamics that happen in infections.

• Photo above: Research associate Tom Rydzak optimizes new diagnostic tests for real-world clinical tools. Photo by Troy Feener

Through a series of partnerships across universities, the public sector, and industry, Lewis and his team have been able to quickly adapt their efforts and lab facilities to aid the pandemic research response.

Novel detection and manufacturing approaches may help ramp up testing capabilities

Alberta has been a national, and international, leader in COVID-19 testing. Several initiatives out of UCalgary aim to help ensure testing levels are consistent, if not expanded. Along the way, shortages of reagents used in the current COVID-19 testing methods have proven to be a hurdle.

Lewis’s lab is working on a rapid diagnostic test that uses protein-based screening and mass spectrometry to detect the virus directly from swabs.

“We’re developing a protein-based detection system using proteomics and mass spectrometry technology that allows us to test up to 750 or maybe 1000 samples per day per instrument, and it doesn’t use any of the reagents that are currently in short supply,” Lewis explains. “We’re now trying to find out more about its performance and sensitivity.”

One factor in reagent shortages, Lewis says, has been that nearly all the testing methods use polymerase chain reaction (PCR) reagents to detect the virus. PCR-based testing involves rapidly “amplifying” – making millions to billions of copies – of a specific DNA sample, which gives scientists a large enough amount to study in detail. Amplifying requires enzymes and reagents, which are difficult to come by under the current crisis. Lewis’ lab’s new detection method, however, does not use those reagents, and the device should be able to rapidly diagnose COVID-19 infections at a significantly increased rate.

“All of the strategies currently being used in diagnostic laboratories detects the virus' genomic material. Our diagnostic approach doesn’t require these same reagents, since we don’t detect the virus’ genetic information. Rather, we use mass spectrometry to detect the virus proteins directly, without having to amplify them.”

The project is being developed in collaboration with Drs. Daniel Gregson, MD, and Bryan Yipp, MD, clinicians at the Cumming School of Medicine.

Thermo Fisher Scientific provided instrumentation to help support the project.

Viral containment device to increase research lab capacity

Further work by Lewis’s lab aims to increase Canada’s research capacity by helping create safer laboratory conditions for researchers working with viruses.

Currently, a laboratory must possess a Biosafety Level 3 designation to concentrate or amplify viruses. This ensures that lab workers are not put at risk during the course of their research work. Lewis says there are “only a handful” of these laboratories across Canada, and they are all working at capacity, preventing researchers from across the country from being involved in the response.

“Some critical COVID-19 research, like screening for new drugs, or finding out if different products can contain or kill the virus, requires a Biosafety Level 3 lab,” Lewis explains. “Most of Canada’s scientific capacity has been sidelined because of not having access to these labs.”

To help bolster COVID-19 research efforts, the Lewis lab teamed up with collaborators at the University of Alberta to develop a new way of securely containing the virus that will allow research activities, such as drug screening, to be carried out safely without exposing workers to virus.

Says Lewis, “We’ve developed a viral containment device. It securely traps the virus samples in a lower chamber, allowing the virus to grow, but in a way that doesn’t expose the lab workers. Samples can be taken from the upper chamber, which doesn’t allow viruses through.”

The device, which is in the process of safety testing, is currently being reviewed by the Public Health Agency of Canada. Lewis hopes rolling out the device will quickly have a major impact on the number of labs able to participate in COVID-19 research.

“It’s a method to allow Canadian researchers and small businesses to be able to participate in COVID activities,” he says. “If it’s approved, we’re prepared to manufacture 10,000 devices in partnership with Alta Injection Molding in Airdrie.”

UCalgary scientists pulling together to meet health-care system needs

Lewis’s lab is also lending expertise and equipment to help support COVID-19 response research by Dr. Amir Sanati-Nezhad, PhD, assistant professor of mechanical and manufacturing engineering at the Schulich School of Engineering.

“Dr. Sanati-Nezhad is making nasopharyngeal swabs that are in short supply, as there are supply chain issues in getting access to them. He’s manufacturing prototypes that could potentially help contribute to that. Those are being manufactured in our lab using our 3D printers,” Lewis says.

Lewis is also working on another new project — creating a fully automated bioinformatics tool for decoding COVID-19 proteins out of samples — with Compute Canada and Dr. Sergei Noskov, PhD, professor in the Department of Biological Sciences.

Collaboration and partnerships key to helping response

While Lewis is pleased at how quickly researchers across campus and beyond have been able to re-purpose their labs to join in the COVID-19 response, he is not surprised at his network’s adaptability.

Their existing connections have allowed for rapid re-tooling of labs to help meet needs in the city, province, and country.

“Our group have re-diverted all of our resources to COVID-19-related activities,” he says.

One of the few labs still open on campus, Lewis’s team is supporting clinical research around the province, with a small full-time staff contingent running samples for clinicians and their patients in support of COVID response.

The lab is also part of the Alberta Precision Exchange (APEX), a program that connects the scientific resources at UCalgary with small businesses and large industry partners in health care.

“This program is really successful because our partnerships and networks are already in place to address problems when they come up,” Lewis explains. “To get to work right away, we just need to put new things in the pipeline rather than starting from scratch. The nasopharyngeal swab project is a great example — we’re helping meet a provincial need with an engineering team and a small business partner, Alta Injection Molding, which was part of our network.

"We have a really unique infrastructure of a microbiology team, an engineering team, a mass spectrometry team, and an informatics team that are all integrated with the health-care system, so we’re able to pivot and respond quickly when necessary to new crises. We developed it with the intention of responding to epidemics. APEX has provided the framework to very rapidly bring these projects into reality.

"We’re doing exactly what we had intended to do, which is deploy our resources when needed, so we’re very pleased to see that happened. This is a multi-pronged, collaborative effort that wouldn’t really be possible outside the university.”

 

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.