COVID-19 antibody tests have been the subject of scrutiny since their arrival, but they still represent an important tool in understanding population health. Molecular tests have become the top method of identifying cases of COVID-19. One scientist thinks we should be looking at using a combination of antibody tests, antigen tests, and molecular RNA tests to better understand who has COVID-19 and whether or not they’re actively recovering.
Dr. David Walt is one of the cofounders of genetic sequencing technology giant Illumina and Quanterix, a company that makes technology for detecting biomarkers. He is also co-director of the MGB Center for COVID Innovation at Brigham and Women’s Hospital, in Boston. When COVID-19 struck, he had to close his lab at Harvard University due to the pandemic. He petitioned to reopen, so he and a team could work on a super antibody test that would enable him to better understand immune response in COVID-19 patients. The request was approved.
The test uses a technology that he invented back in 2007 called SIMOA, or single molecule array; he cofounded Quanterix in order to commercialize it, and now sits on the company’s board. The test separates out antibodies and other molecules into microwells: tiny little reservoirs that make them more easy to quantify. The technique also uses immunofluorescence to identify antibodies. Where a more traditional immunofluorescent antibody test reflects how much antibody is in the sample by how brightly the liquid lights up, the SIMOA method illuminates antibodies in a blood sample like stars in the sky.
“When you look at an image of our assay, it will look like a bunch of bright lights in a very dark background,” Walt says. “It allows us to count the number of molecules.”
His test looks for three antibody types and their interactions with four different proteins from the coronavirus. Because the test gives a more exact understanding of antibody response, it has the potential to answer several questions about COVID-19 that scientists have been grappling with.
“In COVID-19 [antibody] quantity is potentially important,” says Ingrid Stuiver, senior director of translational research at La Jolla Institute for Immunology, a nonprofit institution that has been conducting research on immunity and COVID-19. She works with researchers at La Jolla to understand how their findings can have commercial or public applications. She says that lots of commercial test developers are looking for new tools to understand the complex way COVID-19 works: “We want to know if you mount an immune response and you have a neutralizing antibody, how long is that antibody going to be around for? If you just have a minuscule amount and your body is only producing a little bit, is that going to be protective enough next time you get exposed to COVID?”
Such insights could help scientist develop better diagnostic methods as well as treatments and vaccines, providing a pathway out of the pandemic. But Quanterix believes there’s another opportunity for its testing platform. SIMOA only requires a small amount of blood. The company sees an opportunity to use its technology to create a highly sensitive and specific at-home finger-prick antibody test, which could help individuals and public officials get better insight immunity to COVID-19, especially as governments continue to wrangle over the idea of immunity passports.
The challenges of COVID-19
For researchers, the new coronavirus has been confounding, and not just because it’s new. The way it behaves in the body makes it particularly difficult to test. Stuiver says that the virus appears to cycle through the body in unusual ways. A frequent story she’s heard from hospital doctors is that patients who are suffering extreme effects from the virus will test positive and enter intensive care. But just four days later, the same patients will test negative. A day or two after that, they’ll test positive again.
“That’s why [test] sensitivity has been all over the map,” she says. The level of virus in the body may reach undetectable levels depending on where a person is in this cycle. This doesn’t necessarily render diagnostic tests useless, but it does mean that doctors have to test patients repeatedly to get an accurate picture of their illness. Researchers at Harvard’s T.H. Chan School of Public Health noted as much in a recent paper, suggesting it is more important to test patients frequently and isolate cases than it is to have a highly sensitive diagnostic test.
Stuiver says that research now shows 15 to 28 days post-infection may be the optimal window for testing antibodies.
These molecular tests, or PCR tests—where a doctor swabs high up in a person’s nasal cavity or deep into the lung—can have a fairly high false-negative rate, one that can fluctuate depending on how far along a person is into an infection, according to research from Johns Hopkins. They also take days to get results. The U.S. in particular has suffered an overwhelming backlog of testing, which has made it difficult to know who has COVID-19.
There have also been issues with antibody tests, which look at whether a person had the disease and recovered from it. The Food and Drug Administration allowed commercial laboratories to begin selling antibody tests without explicit FDA validation so long as they met certain criteria. The result was a deluge of rapid blood tests, which can deliver results in less than 15 minutes. But some of these have proved inaccurate. For tests that may have been appropriately sensitive and specific, there weren’t clear guidelines on how and when to use them to yield the best results.
Stuiver says that research now shows 15 to 28 days post-infection may be the optimal window for testing antibodies. “If you don’t test in that window— if you’re way outside that window—your antibody test may not work very well,” she says. “[Health professionals] are trialing anybody and anything, and there’s limited standardization simply because there isn’t knowledge out there yet.” That may be affecting test outcomes and thus our understanding of COVID-19, she adds.
Building a new testing paradigm
The SIMOA platform enables tests that can see evidence of an immune response seven-days post infection and beyond. “We end up with 12 different signals that we’re able to to detect,” Walt says. “What that allows us to do is if we look at . . . an infected patient over time, we can see the dynamics of that individual’s response to the virus.”
Being able to see how quickly antibodies develop and in what quantity at the population level will also be helpful in planning interventions.
These initial studies were performed to prove out the efficacy of the test. Quanterix is licensing the test from Walt and made it available to other research institutions for use in studies at the end of June. CEO Kevin Hrusovsky says that big research hospitals and other health organizations are most interested in using the test to understand how many people in a broad pool test positive for COVID-19 antibodies. He says that hospitals in particular are interested in having patients mail in samples from home.
“We’ve always had a vision in our powering precision health that would enable asymptomatic home care, which means that we would routinely monitor people, populations from home through dry blood spots to measure a lot of different biomarkers,” he says.
Being able to see how quickly antibodies develop and in what quantity at the population level will also be helpful in planning interventions. For example, scientists are exploring the use of convalescent plasma, or antibody-infused blood from recovered COVID-19 patients, in patients who have a weak response to COVID-19.
“There’s been mixed results on that,” says Stuvier. “I think it’s timing of delivery—is there an optimal time?” Understanding how many antibodies and what kind of antibodies a donor has could be integral to identifying the best time to draw blood and use it on a sick patient. A recent pre-published study shows that at 23 days post infection, 60% of a cohort of COVID-19 patients had a potent antibody response. By 65 days post infection, that figure had dwindled to 16.7%. The study suggests that immune response to COVID-19 may wane fairly rapidly.
Still, the amount of antibodies does not necessarily indicate that someone is recovering from COVID-19. Not all antibodies have a neutralizing effect, and there is still plenty that researchers and doctors don’t understand about how the body combats COVD-19.
“Unfortunately most of these [methods] are just looking for the total amount of antibody that’s being produced. It’s not answering the question, ‘What is the quality of the antibodies that are being produced?” Walt says. The body mounts a variety of immune responses to disease. A recent study shows that a potential hallmark among people who have the most severe manifestation of COVID-19 is that they don’t develop as many antiviral proteins called interferons.
To figure out how effective a person’s immune response is, scientists will ultimately have to track the elimination of the virus. Walt is currently working on an antigen test that can be run in parallel to his 12-plex antibody test to monitor the virus. The latter would identify viral proteins in a sample. There are already several antigen tests on the market, though there is some concern about the rate of false negatives. However, antigen tests can be performed much more quickly than the molecular PCR test. Conducted in tandem at a regular frequency, a rapid antigen test and a reliable finger-prick antibody test could serve as the foundation for understanding how well a patient is fighting the virus.
Walt says that doctors need to consider a different approach to figuring out who is infected with or has been infected with COVID-19 than the well-used nasal scrape. “I think that’s going to be a fight in the field,” he says. “Right now, too many people are relying on PCR as the gold standard and there’s going to have to be a turn around on what corresponds to actively infected individuals.”