Pivoting to pitch in on COVID-19 science

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Spotlight On: Ian Lewis, Assistant Professor University of Calgary Department of Biological Sciences

Ian Lewis has always worked to develop better ways to diagnose infectious diseases. His work always involves leveraging microbial traits and biochemical traits to help determine whether people live or die from infectious diseases and in COVID-19, he’s met a worthy foe. As part of a global effort to combat the virus, he has been working to develop an efficient, effective protein-based COVID-19 test. And he and his team are doing it with high-powered computing.

Using an emerging technology called mass spectrometry, Lewis, an assistant professor and Alberta Innovates Translational Health Chair in the Department of Biological Sciences in the University of Calgary’s Faculty of Science, is trying to detect the unique protein composition of the COVID-19 virus directly in patient samples. This approach is fast and effective, but generates unwieldy amounts of complex data. In order to make sense of this data, he and his team members — with the help of Sergei Noskov, professor and associate head of research in the department of biological sciences at the University of Calgary — have been developing the computational tools that would allow them to convert these complicated mass spectrometry raw files across multiple samples into information that can be automatically interpreted to detect the unique peptide fragments of the virus.

“It requires a huge computational task and we’ve been doing that in partnership with Genome Canada and Compute Canada,” says Lewis.

To accomplish this, a ground-breaking informatics pipeline has been built for automatically processing mass spectrometry proteomics data. This tool is hosted on a public portal accessible through the team’s website, which allows mass spectrometry files from anywhere in the world to be uploaded and interpreted automatically.

“And that’s pretty cool,” Lewis says. “It will allow you to upload your mass spectrometry files and it will convert them into qualitative proteomics data for human or COVID-19 proteomes. This is the first step to automating the COVID-19 epidemiological surveillance effort using our mass spectrometry platform.”

After the algorithms and science was worked out, WestGrid and Compute Canada brought the tool to fruition by helping to roll it over. They also enabled hosting and user access. WestGrid Senior Developer Ikenna Okpala and Compute Canada technical staff worked closely with Noskov’s and Lewis’ team as well as with the resources and personnel from Research Computing Services at the University of Calgary. The project was made possible from funds from Alberta Innovates and Genome Canada, the University of Calgary, and Compute Canada.

“We thought we could leverage and adapt that same infrastructure we’d worked on in the past,” Lewis says. Sergei Noskov’s group and the Compute Canada team have responded really quickly to transform this technology quickly from a microbial to a viral-based application.”

Previous work from the team, also funded by Genome Canada’s Large-Scale Applied Research Project Competition — where similar data-processing pipelines have been built to enable the identification of infections caused by bacteria and fungi — laid the foundation for this new approach to COVID-19 testing.

“One of the things that we were really concerned about is that there were severe supply-chain issues, so it was difficult to get access to the basic testing reagents necessary to do COVID-19 diagnostic tests,” Lewis says.

So far, the testing approaches for COVID-19 use crucial reagents that are in short supply and the province of Alberta was running out and trying to get supplies from non-traditional suppliers.

“We thought ‘Holy smokes, we have a mass spectrometry platform that can do something similar and doesn’t use the same kind of reagents,” Lewis says. “It would be a big win for Canadians if we could find a way of leveraging this technology to provide an alternative testing strategy in the event that we encounter additional supply-chain issues in the future.”

If Drs. Lewis and Noskov are successful, their novel approach to testing and the state-of-the-art data handling tools they’ve built with Compute Canada will enable a high-throughput diagnostic platform that will process as many as a thousand COVID-19 tests per day on a single instrument.

“We’ve made excellent progress,” Lewis says. “We still have a way to go but we have some very exciting things to talk about in the near future.

Creating safer labs

In the meantime, he and his colleagues are also working to increase Canada’s research capacity by creating safer laboratory conditions for researchers working with viruses.

“We’re developing a viral containment device that allows lab workers to handle the virus safely and can measure the impacts of different drugs on viral activity. This allows people to do screens to find new antiviral compounds,” Lewis says.

Currently, a laboratory must have a Biosafety Level-3 designation to concentrate and amplify the COVID-19 virus, but there are only a handful of labs in Canada with such accreditation. The team hopes its device will change that requirement because it effectively traps the virus samples in a sealed lower chamber, allowing it to grow in a way that doesn’t expose the scientists. This would allow hundreds more researchers and small businesses across Canada to conduct urgently needed COVID-19 drug-screening activities.

An entrepreneurial edge and strong partnership

Lewis is part of Alberta Precision Exchange (APEX), a program that connects scientists at the University of Calgary to industry partners and research and development resources such as Compute Canada. One recent example of the success of APEX is another COVID-related project is being done in conjunction with Amir Sanati-Nezhad, assistant professor of mechanical engineering at the Schulich School of Engineering. Sanati-Nezhad saw that pandemic testing needs have vastly outstripped global supplies of the nasopharyngeal swabs needed to retrieve diagnostic test samples from suspected COVID-19 patients. Using APEX resources, he and Lewis decided to team up and produce a locally available supply for southern Alberta diagnostic testing centres. Lewis’ team used its lab’s state-of-the-art 3D printing facilities to design and prototype the swabs.

“Dr. Sanati-Nezhad just launched a new company that’s building these Health Canada-approved swabs to help support testing — it’s called Shapetry,” Lewis says. “I am proud to have played a small role in this and I’m glad that our APEX infrastructure was available to support this important work.”

“Everything that happens in our group involves transforming bacteria or viruses into electrons and then using them in a computational way to find a diagnostic test,” Lewis says. “Compute Canada plays a pivotal role in that interface between electrons and knowledge. It allows us to house and process the data and allows us to transform that info into actionable outcomes. It’s an absolutely critical part of that vision.”

Lewis says none of this work could happen without Compute Canada resources.

“They’re providing data storage and processing capability and, most important, now they’re providing the platform that’s allowing us to scale up and make our technology nationally available. It’s part of the future-looking vision that makes Compute Canada so important.”

Noskov agrees: “We do need a lot of computational power. Compute Canada provides access to cloud computing and large memory computing nodes, which is a central piece in their international rollover. Compute Canada and WestGrid have also provided us with human resources with IT expertise hard to find in academic environment.”

Okpala’s work on the project, through his developer role at WestGrid, is an example of that essential expertise. He has worked closely with the research team, overseeing the technical implementation of the portal’s web-based architecture, managing and maintaining the pipeline’s legacy mass spectrometry packages, and more recently has been contributing to research publications now in progress to share insights from the team’s work in this area.

“It’s been an interesting and challenging project, and I’m proud to have played a role in helping support this important research,” says Okpala. 

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