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Mapping disease: medical students create tool to track COVID-19 through antibody testing

The Joule Innovation grant program offered funding, professional support and mentorship to physicians and medical learners making a difference in health care. This is part of a series of stories about the 2020 recipients and their innovations.

Looking back to the start of the pandemic, medical student Tingting Yan remembers a feeling of helplessness.

“We were sitting idle doing Zoom university at U of T when our preceptors were out there fighting COVID.”

Dr. David Naylor, medical researcher and former University of Toronto president, had just been named co-chair of the COVID-19 Immunity Task Force (CITF), a newly created body charged with tracking the spread of the virus. Looking for an opportunity to help, Ms. Yan and some of her peers reached out to him for direction. He connected them with Dr. Tim Evans, executive director of the CITF, and shortly after, the idea for SeroTracker was born.

“We realized there was a way for us to contribute to figuring out how this pandemic was evolving.” – Ms. Tingting Yan, team co-lead for SeroTracker

A home for serological data

The goal of the CITF was to fund seroprevalence studies — to determine how many people in Canada had SARS-CoV-2 antibodies, an indicator that suggests a previous infection. But in order for the results of these studies to be useful to public health officials and other medical professionals, they needed to be accessible and searchable.

With the support of the CITF, Ms. Yan quickly got to work, employing a vast network of friends and peers — 22 students across eight time zones — with a diverse skill set: engineers, data scientists, statisticians, public health experts and fellow med students, like Niklas Bobrovitz. He too had been itching to help public health efforts for a COVID recovery plan.

“The problem we tried to solve was, how do we get this vast amount of evidence coming out every day to stakeholders?” says Mr. Bobrovitz. “How do we synthesize it and put it in their hands in real time, so they can make evidence-informed decisions?” was the result — a custom-built dashboard that monitors and synthesizes findings from hundreds of global serological studies, allowing users to visualize antibody estimates on a world map and compare results by regions, demographics and test types.

Watch Ms. Yan explain how the SeroTracker dashboard works

Providing a complete picture of COVID-19

While swab-based diagnostic tests for COVID-19 can confirm the number of people diagnosed with the virus, serology tests can provide a much broader picture of how many people have been exposed.

“Some of the data we’ve analyzed show serology tests indicating 20 times more people than we thought originally had been infected,” says Mr. Bobrovitz, referring to data from several countries with the largest gaps between reported cases and estimated infection prevalence.

In Canada, the proportion of undetected infections appears much lower due to increasingly efficient testing and ongoing public health measures. But serology does illustrate that spread of COVID-19 has been wider than confirmed case counts suggest. 

In October and November 2020, Canadian Blood Services, with CITF support, tested nearly 34,000 blood samples collected from donors during the second wave of the pandemic for SARS-CoV-2 antibodies. The tests revealed that overall, 1.5% of healthy Canadians had been infected with the virus — double the number confirmed by swabs for the population as a whole.

In November, in particular:

  • seroprevalence increased dramatically in Manitoba (8.56%) and Saskatchewan (4.2%);
  • donors between 17 and 24 years of age had the highest seroprevalence (2.97%); and
  • racialized Canadians had higher seroprevalence (2.08%) than donors who self-identified as white (1.35%).

By collecting and analyzing this kind of population immunity data, SeroTracker can help public health officials better target their messaging to specific communities, increase diagnostic testing in specific regions, track immunity and develop plans for vaccine rollout.

In addition to public health agencies, government research organizations, non-profits and the private sector are also using SeroTracker estimates to calculate the infection fatality rate (vs. the case fatality rate), gauge the pandemic’s impact globally and evaluate country responses to COVID-19 by mapping its early spread.

Adapting to the “vaccine era”

With COVID vaccines now rolling out in many countries, Ms. Yan and her team plan to use their $50,000 Joule Innovation grant to adapt the SeroTracker’s utility. Before vaccines were available, a positive serology test meant a person had had a natural infection. Now, a positive test could be the result of infection or vaccination. With this in mind, the dashboard is being tweaked to capture information on vaccine deployment and integrate it with serology data, paying special attention to tests that distinguish between the two possible causes for the presence of antibodies. This can help gauge how well vaccination programs have induced immune responses in a population.

The Joule funding will also help the team develop natural language processing tools to help speed up data extraction. To date, the team has scanned more than 20,000 abstracts and collected information from more than 750 studies, resulting in half-a-million data points — all manually.

“This is about making sure we maximize value from the data infrastructure and pipelines we’ve created,” says Ms. Yan. “With SeroTracker, we aim to bring this pandemic to a faster end and cut short future disease outbreaks.”

The 2020 Joule Innovation grant program provided $500,000 to support physician-led innovations in the areas of sustainable health care, physician health and wellness, health care solutions and access to care.

Read about the other innovations:

Pandemic pivot: Winnipeg psychiatrist launches virtual mental health ward in face of COVID-19 restrictions


About the author(s)

CMA Joule supports physicians and medical learners in the pursuit of clinical excellence. As a subsidiary of the Canadian Medical Association (CMA), we support the profession with continuing education and other learning opportunities as well as leading evidence-based clinical products and research.