U of T Researchers Develop Rapid Test to Track Immunity to SARS-CoV-2 Variants

The experts agree — the pandemic is not over. Infections are ticking up again, fueled by new variants for which our immune systems are ill prepared.

That’s according to a University of Toronto study that found antibodies generated in people who were vaccinated against COVID-19 or recovered from the illness before 2022 failed to neutralize the variants circulating today.

The study was led by Igor Stagljar, a professor at the Donnelly Centre for Cellular and Biomolecular Researchin U of T’s Temerty Faculty of Medicine, and Shawn Owen, an associate professor of pharmaceutics and pharmaceutical chemistry at the University of Utah.

The journal Nature Communications published their findings.

The researchers expect the antibody test they developed to measure immunity in the study’s participants will become a valuable tool for deciding who needs a booster and when, which should help save lives and avoid future lockdowns.

“The truth is we don’t yet know how frequent our shots should be to prevent infection,” said Stagljar, who is also a professor of biochemistry and molecular genetics at Temerty Medicine. “To answer these questions, we need rapid, inexpensive and quantitative tests that specifically measure SARS-CoV-2 neutralizing antibodies, which are the ones that prevent infection.”

Researchers have developed many antibody tests over the past two years, but only a few are designed to monitor neutralizing antibodies, which coat the viral spike protein so it can no longer bind its receptor and enter cells.

Only a fraction of all SARS-CoV-2 antibodies generated during infection are neutralizing. And while most vaccines were specifically designed to produce neutralizing antibodies, it’s not clear how much protection they give against variants.

“Our method, which we named Neu-SATiN, is as accurate as, but faster and cheaper than, the gold standard, and it can be quickly adapted for new variants as they emerge,” Stagljar said.

Neu-SATiN stands for Neutralization Serological Assay based on split Tri-part Nanoluciferase, and it’s a newer version of SATiN, which monitors the complete IgG pool the researchers developed last year.

Development of Neu-SATiN was spearheaded by Zhong Yao, a senior research associate in Stagljar’s lab, and Sun Jin Kim, a postdoctoral fellow in Owen’s lab, who are co-first authors on the paper.

The pin prick test is powered by the fluorescent luciferase protein from a deep-water shrimp. It measures the binding between the viral spike protein and its human ACE2 receptor, each of which is attached to a luciferase fragment.

Engagement of the spike protein with ACE2 pulls the fragments close, catalyzing reconstitution of the full-length luciferase, with a concomitant glow of light captured by the luminometer instrument.

When a patient blood sample is added into the mixture, the neutralizing antibodies bind to and mop up all spike protein, while ACE2 remains in an unengaged state. The luciferase remains in pieces and the light signal drops. The researchers say the plug-and-play design of the test means it can be adapted to emerging variants by engineering mutations in the spike protein.

The researchers applied Neu-SATiN to blood samples collected from 63 patients with different histories of COVID-19 and vaccination up to November 2021. They assessed patient neutralizing capacity against the original Wuhan strain, and the variants Alpha, Beta, Gamma, Delta and Omicron.

“We thought it would be important to monitor people that have been vaccinated to see if they still have protection and how long it lasts,” said Owen, who did his postdoctoral training in the Donnelly Centre with bioengineer and University Professor Molly Shoichet. “But we also wanted to see if you were vaccinated against one variant, does it protect you against another variant?”

The neutralizing antibodies were found to last about three to four months, when their levels would drop by about 70 per cent irrespective of infection or vaccination status. Hybrid immunity, acquired through both infection and vaccination, produced higher antibody levels at first, but these too dropped significantly four months later.

Most worryingly, infection and/or vaccination provided good protection against the previous variants, but not Omicron, or its sub-variants, BA.4 and BA.5.

The data match those from a recent UK study. That research showed neutralizing antibodies and cellular immunity (provided by memory T cells) from infection, vaccination or both offered no protection from catching Omicron. In a surprising twist, the UK group also found that infections with Omicron boosted immunity against earlier strains, but not against Omicron itself, for reasons that remain unclear.

"It's important to stress that vaccines still confer significant protection from severe disease and death", said Stagljar. Still, he added that the findings from his team and others call for vigilance in the coming period given the more transmissible BA4 and BA5 sub-variants can escape immunity acquired from earlier infections with Omicron, as indicated by rising reinfections.

“There will be new variants in the near future for sure,” Stagljar said. “Monitoring and boosting immunity with respect to circulating variants will become increasingly important and our method could play a key role in this since it is fast, accurate, quantitative and cheap.”

He is already collaborating with the Canadian vaccine maker Medicago to help determine the efficacy of their candidates against Omicron and its sub-variants. Meanwhile, U of T is negotiating to license Neu-SATiN to a company which will scale it up for real world uses, such as population immunosurveillance and vaccine development.

The research was supported with funding from the Toronto COVID-19 Action Fund, and the Office of the Vice President for Research and the 3i Initiative at the University of Utah.