NEW YORK – As the Omicron variant puts the world on edge, researchers from Duke University have unveiled a variant-specific test to assess a person's level of protection from antibodies against SARS-CoV-2.
Notably, the point-of-care test could tell clinicians if, and how well, a patient's neutralizing antibodies, obtained from vaccination or natural infection, can fight against each specific variant of the virus, indicating if a vaccine is effective against a certain variant.
In a paper published in Science Advances earlier this month, the researchers laid out how their CoVariant-SCAN test works and how it can determine the ability of someone's antibodies to neutralize spike proteins from different variants. Jake Heggestad, a graduate student in the department of biomedical engineering at Duke's Pratt School of Engineering and a member of Ashutosh Chilkoti's lab, noted that the team designed the test to mimic more common antibody assays that use live viruses.
Rather than using live virus, the test uses recombinant proteins, which makes it easier to see the differences between variants by using different proteins, and lessens the turnaround time, according to Heggestad. Live virus assays are also labor-intensive and expensive, the researchers wrote in the paper.
The test uses part of the virus's spike protein and fluorescently labeled human ACE2 proteins to measure the ability of a patient's neutralizing antibodies to block interactions between the virus and ACE2 proteins. A drop of a patient's plasma sample is put onto a slide that also has spike proteins specific to each variant of SARS-CoV-2 at different locations. The slide has 24 wells that can run 24 separate samples in parallel, and after 15 to 60 minutes of incubation time, the plasma is washed with a buffer solution. The slide is then put into a fluorescent scanner to determine if fluorescence is present.
If the ACE2 proteins are caught by the spike proteins, a bright fluorescent spot is left behind, meaning the patient's antibodies do not protect against that spike protein.
Heggestad put it this way: If a person has never been exposed to the virus, the binding of the ACE2 protein and spike protein should be unhindered and the fluorescence would glow. However, if a person has antibodies to the spike protein, whether through vaccination or previous infection, the binding of the proteins will be inhibited and the fluorescence will not appear or will be less bright.
The research team quantified the number of fluorescent spots on each slide to determine a patient's ability to protect against the variant. By looking at the average fluorescence on a slide and comparing it to a negative control, the researchers were able to get a number indicating the level of antibody neutralization.
However, Heggestad said that the interpretation of the number from each test is not set in stone, meaning the team couldn't say that a specific percent of neutralizing antibodies meant that a patient was fully protected. Instead, the test provided a "spectrum of the possibility of protection," he said. Because it's generally believed that the more neutralizing antibodies a patient has, the more protected they are against the virus, that is the assumption the research team worked with.
The assay has been tested with different variants, including Alpha, Beta, and Gamma, although the team hasn't yet applied it to the Omicron variant because it is still trying to get the right proteins. For the other variants, the researchers have used commercially available recombinant proteins to lessen the workload, but since none are available for Omicron yet, the lab is working to manufacture the proteins itself, Heggestad said.
The Delta variant appeared while the researchers were conducting the study, and they were able to detect it as well without reengineering the test, he said, so the team is confident it can adapt the test to detect Omicron, too.
Clinically, the CoVariant-SCAN test can be used to guide treatment, Heggestad said. For example, if a person has a low neutralizing antibody level against the Delta variant, and they were exposed to the virus, a physician may decide to treat them with a monoclonal antibody therapy early in the disease to avoid more serious disease, he said.
While the test could potentially be used as a surveillance tool to tell how widespread a variant is, the team hasn't yet validated it for that purpose, Heggestad said. "It could potentially be deployed as an epidemiological tool to assess the efficacy of vaccines against circulating or emerging variants in specific regions," he said.
Although in the Science Advances paper the team used a tabletop scanner, Heggestad said the team is trying to move toward a more portable platform to allow the test to be run at the point of care. They are also working to use the test with whole blood instead of plasma, to make it easier to use in a POC setting, by adding microfluidic components to the slide.
In this paper's iteration, the team also looked at the slides and hand drew circles around each fluorescent spot, but Heggestad said this process could all be automated.
Once the test is more automated and easier to use at the point of care, the team is interested in commercializing it, Heggestad said. The researchers must "make more progress" before commercialization steps are taken, but it's "on our radar," he said, adding the team has formed a startup company that could partner with another firm to produce and distribute the test.
Cameron Wolfe, an associate professor at the Duke University School of Medicine and infectious disease physician, said that although the test is "early days technology," it could be useful in determining treatments for patients affected by the virus. He noted that he helped the team by providing samples and reviewing its manuscript but was not involved in the development of the test.
Wolfe said current COVID-19 testing is lacking "a couple of elements," namely that there is no timely and mobile way to see what variants are present on a day-to-day basis. Sequencing can't be done at a patient's bedside or in real time, so there's no ability to understand what variant a patient may be infected with, he said. In addition, a clinician can assume a vaccinated patient has a defense against the virus, but tests to confirm the defense are "drawn out" and hard to interpret, he said.
Right now, any treatment decision is "a very broad and blunt clinical decision," he said.
While different variants currently don't impact which treatment a physician gives to a patient, with Omicron "we are starting to see limits with some of our monoclonal therapies, for example, that weren't there with Delta," Wolfe said. Knowing the variant up front "could allow you to tinker with which drug you give, thereby rationing supply better," he added.
The idea of having an "adaptable platform" to answer these questions in real time is compelling, especially in smaller labs that don't have access to high-tech sequencing instruments, Wolfe said. It would provide "a far more colored-in picture," he added.
The key issues that must be addressed before the test can be used clinically are the classics for any test, he said: cost and reproducibility. The test would need to be available at a price point that works for physicians, and it must be shown to work in different settings, he said. The team must also show clinicians would use the information, and how it would benefit them, he said. In addition, it needs to be easy to use.
Wolfe said he can see it being used as a way to rapidly verify protection, such as before traveling or before a patient undergoes chemotherapy. There's a "quite wide scope" of how it could be used, he said.
The utility of the test, however, also depends on "what happens with the pandemic," he said. With the spread of the Delta variant — which currently makes up the vast majority of COVID-19 cases in the US, according to the US Centers for Disease Control and Prevention — clinical decisions are less difficult, since a physician can assume a patient has the Delta variant and proceed with treatment accordingly.
If the pandemic continues in this vein, with one dominant variant, the test will not necessarily be in demand, he said. But if there are many circulating variants that ebb and flow throughout the world, the test could "be more helpful" in narrowing treatment options, he added.