Covid-19: Optical scientists and engineers push back

It is hardly a surprise that this year's SPIE Photonics West conference sessions were peppered with presentations relevant to Covid-19. Be it methods to screen for the virus, systems that identify fast-flying Covid-19 droplets or non-invasive techniques to assess patients, researchers worldwide have been adapting existing instrumentation or developing new ways to tackle the pandemic.

When SARS-CoV-2 emerged, Professor Gabriel Popescu, Neha Goswami, and colleagues from the University of Illinois Urbana-Champaign and University of Illinois at Chicago knew they could apply their quantitative phase imaging method, Spatial Light Interference Microscopy (SLIM), to directly image unlabelled viral particles. Used with a conventional light microscope, a SLIM module converts interference patterns recorded by the microscope's CCD camera to quantitative phase images, producing incredibly high-resolution images of unstained cells.

However, they also realized that if they merged their method with deep learning, specifically trained to detect and classify virus particles, they would have a very fast, high-throughput and accurate method to identify SARS-CoV-2 in people. They trained a convolutional neural network to recognize SLIM, label-free images of SARS-CoV-2 particles and to discern the coronavirus from other particles including dusts, beads, as well as additional pathogens — influenza, adenovirus, and the Zika virus.

"Our phase imaging is sensitive enough to pick up the structural information of a particle down to the nanometer level," highlights Goswami. "For example, Zika is much smoother than SARS-CoV-2 which is covered with protrusions — so the method is detecting those very small, nanoscale-differences and can differentiate between these different classes."

Pre-clinical studies using a CellVista SLIM instrument from Popescu's spin-out company, Phi Optics, have shown the neural network can identify SARS-CoV-2 versus the other viruses with a 96% accuracy. Clinical trials are now underway using face shields with integrated glass slides — breath condensates are transferred from a subject to the slide ready for analysis. According to the researchers, image acquisition and inference take 100 ms, so an entire test could be performed in just one minute. They also reckon throughputs can be easily scaled if slides are automatically fed into the whole slide scanners used in digital pathology.

"We're collecting breath samples from actual patients in Chicago right now," says Popescu. "If the breath testing [set-up] works, I think that every school would probably benefit from having one... We also envision that at an airport, someone could simply breathe on a slide that is automatically passed onto the imaging system and you have results within a matter of seconds."

The researchers' label-free method could also detect many infectious diseases, including bacterial infections. As Popescu points out, he and colleagues have been particularly interested in other label-free approaches where you can bypass sample preparation and reduce time to assay. Quantitative-phase imaging methods have already been applied to other viruses such as the herpes simplex virus (HSV) while scattering techniques are known to hold huge potential for virus detection.

"The pandemic has pushed technology development on faster tracks than usual and many researchers, including ourselves, have really benefited from US fast-track government grants," he says. "We've seen many developments on the photonics side that just wouldn't have happened on a regular time-scale."

Covid-specific photonic sensor platforms

Professor Benjamin Miller, from the University of Rochester Medical Center, agrees, saying: "You have to get some good out of this and it's been amazing to watch how the scientific world has responded to Covid-19. The technological development that's occurred over the last couple of years has been amazing, particularly in the in the sensor realm." Since the onset of the pandemic, Miller and colleagues have been working on photonic sensor platforms designed to profile the human immune response to Covid-19 infection and vaccination. Miller presented his results in the Photonics West presentation "Design and Quality for Biomedical Technologies XV."

In a first set-up, a multiplexed, label-free optical biosensing method — arrayed imaging reflectometry — analyzes human response to disease. In this, a silicon chip is coated with a near-perfect anti-reflective, silica layer that contains immobilized "capture" molecules, such as antigens (proteins), that can bind viral biomarkers in blood samples. The binding changes the surface thickness of the layer, causing incident light to now partially reflect — this light can be measured using a CCD camera and analyzed to detect the presence of a virus in the blood sample.

Ben Miller's graduate student, John Cognetti, adding a serum sample to the disposable photonics sensor card. Credit: Courtesy of Benjamin Miller/University of Rochester Medical Center.

According to Miller, the biosensor chip is sensitive down the molecular level and can handle many targets per sensor. "You can have so much data on a single chip," he says. "You get a full profile of what's going on with someone's immune system in half an hour." The set-up has already been widely used to measure influenza immune response in humans. But as Miller highlights: "As soon as it became clear that SARS-CoV-2 was going to be important, we recognized this could be useful to study the antibody response to this virus."

He and colleagues selected proteins from SARS-CoV-2 and fine-tuned the biosensor coating to include antigen proteins that would bind the coronavirus and other viral biomarkers. This process took just two weeks, and the results so far are fascinating. The latest platform can detect antibodies to SARS-CoV-2, including mutants, SAR-SCoV-1, MERS, three circulating coronavirus strains (HKU1, 229E, OC43, NL63), seventeen strains of influenza and respiratory syncytial virus (RSV), which can be fatal to children. "One thing that is nice about this is we can put large numbers of antigens on a single chip and study the response all at once," says Miller. "For example, we were curious about whether we would see a cross-reactivity between SARS-CoV-2 and other coronavirus antigens."

While the world is familiar with the SARS-CoV-2 spike (S) protein, the biosensor also detects the virus' nucleocapsid (N) protein, which is abundantly expressed during infection. "The vaccine is all spike but if someone gets sick [from Covid-19], they're going to have a strong immune response to the N-protein — so we can very easily discriminate between someone who's been vaccinated and someone who's had the virus," says Miller. "Now we've put different mutant antigens of SARS-CoV-2 on an array, we can also say ‘well we know they've been vaccinated against one strain but do their antibodies still bind to the antigens of other variants'," he adds. "So [the array] will let you know if there's a variant that people's antibodies are no longer binding to."

Miller is hoping to set-up a new venture to apply the technology to diagnostics applications and vaccine development. "We already have a commercial instrument that we can tune very quickly, and we can scale manufacturing to [print] thousands of chips very easily," he says.

Miller's second platform stems from a massive $1.7 million US Department of Defense Manufacturing Technology project with the American Institute for Manufacturing Integrated Photonics (AIM Photonics) and collaborators, US in-vitro diagnostics company, Ortho Clinical Diagnostics, and polymer optics manufacturer, Syntec Optics. Additional research input comes from the NY CREATES 300mm microelectronics research facility in Albany, New York, the University of California at Santa Barbara and the US Naval Research Laboratory in Washington DC.

In a similar vein to arrayed imaging reflectometry, this platform detects antibodies in Covid-19 patients and vaccinated subjects and tracks post-vaccination changes to SARS-CoV-2 antibodies over time, but this time the emphasis is on cost and speed. "When you interact with researchers from government and industry, there's another set of success criteria that drive interesting research goals," highlights Miller. "For example, Ortho Clinical Diagnostics would say to us, ‘the results are great but how can we get this down to 10 cents a test?' And this led us to our disposable photonics platform."

This biosensor comprises a rice grainsized (1mm × 4 mm) silicon nitride ring resonator to analyze serum samples for the antibodies that humans develop within two days of exposure to the SARS-CoV-2. The sensor chip is coupled onto a plastic micropillar fluidic card that pulls a sample through its winding chamber via capillary action, enabling cheap, high throughput Covid-19 antibody detection in a minute.

The researchers continue to work with commercial partners, honing the platform for swift, high throughput clinical diagnostics and large-scale manufacturing. "This is a completely new diagnostic platform — we think it will be valuable in very broad applications for clinical diagnostics, not just Covid-19," says Miller.

From antibodies to mechanisms

Photonics West also hosted many presentations that revealed novel ways in which optics are being used to examine Covid-19's underlying mechanisms. Dr. Hui Min Leung from Massachusetts General Hospital, has been working with colleagues at Harvard Medical School and the University of Alabama at Birmingham, including Professors Guillermo Tearney and Steven Rowe, as well as Healthcare Innovation Partners researchers, to develop label-free micro-optical coherence tomography (µOCT) to image the nasal airways of Covid-19 patients.

Dr. Hui Min Leung from Massachusetts General Hospital, has been working with colleagues at Harvard Medical School and the University of Alabama at Birmingham to examine Covid-19's underlying mechanisms. Credit: Courtesy of Hui Min Leung/Mass. Gen. Hospital

As Leung points out, the latest Covid-19 work follows ten years of development of the technique for cystic fibrosis, in which sticky mucus builds up in the lungs and digestive system. Many of the entry factors that SARS-CoV-2 relies on to enter human cells are also expressed in nasal epithelial tissue, making the lining of the nose a key target to understand how infection takes place.

As part of the set-up, a fiber-optic catheter is connected to an imaging console, based on spectral domain OCT, to study nasal airways and provide live images of unsedated patients to sub-cellular resolution. Studies take place in a negative pressure booth installed with HEPA filters, designed to protect both participants and clinicians. The Covid-19 patient will sit inside the booth while the clinician operates the intranasal probe from the outside through a glove port.

"It typically takes 20 minutes or less to perform intra-nasal µOCT on a person... and during that time we use the optical probe to take µOCT videos in different regions within the nasal airways," highlights Leung. "We can get high-resolution cross-sectional views of the epithelium, the thickness of hydration layers, motion of motile cilia and resulting transport of mucus. Data analysis is still underway, but we've seen several abnormalities at the microscopic level in our Covid-19 study cohort."

Researching Covid-19's underlying mechanisms. Credit: Courtesy of Hui Min Leung/Mass. Gen. Hospital

As a technique, µOCT has been prized for how it can resolve highly detailed images of micro-anatomical features, such as cilia and mucus layers in airways, and holds great potential for Covid-19 analysis. For now, Leung says their research-grade instrument currently needs regular maintenance to optimize performance, but commercialization of the method is plausible.

Echoing the sentiments of Popescu and Miller, the Harvard researcher adds: "The pandemic prompted us to apply our intranasal µOCT to study a relatively unknown disease."

"Being one of the few people to be able to see what happens to the airways of Covid patients at the cellular level, and having the chance to uncover new knowledge about this clinical phenotypes of this disease, is so very exciting," she adds.

Rebecca Pool is a UK-based freelance writer. A version of this article originally appeared in the 2022 SPIE Photonics West Show Daily.