By harnessing expertise in lasers, nanoscience, and biology, researchers at Berkeley Lab have developed an ultrasensitive technique for detecting the COVID-19 virus.
A multi-disciplinary team led by researchers from the Accelerator Technology & Applied Physics (ATAP) and Biological Systems & Engineering (BSE) divisions at Berkeley Lab has developed a novel and highly-sensitive technique for detecting SARS-CoV-2 spike protein molecules in solutions. The technique could lay the foundations for rapid, low-cost methods for detecting and monitoring pathogens, potentially helping to prevent and mitigate future pandemics.
“It was in the spring of 2020,” says Thomas Schenkel, a Senior Scientist who leads ATAP’s Fusion Science & Ion Beam Technology Program and who spearheaded the development of the technique, “when the team responded to a ‘call-for-action’ from the Department of Energy and other Federal agencies for the development of a test for COVID-19 and a better understanding of how the virus is transmitted.”
At that time, he continues, there were no tests or vaccines for COVID-19, and “we felt that it was important to see how we could contribute to global efforts on limiting the spread of the virus—so, we joined a lab-wide task force to study COVID-19 and develop a method for testing the presence of the virus in biological fluids, like saliva.”
With funding from an emergency Laboratory Directed Research & Development (LDRD) program, the team, which included ATAP Staff Scientists Kei Nakamura and Peter Seidl and Senior Scientist Antoine Snijders who heads up the BioEngineering & BioMedical Sciences Department at BSE, used a technique called matrix-assisted laser desorption-ionization mass spectrometry (MALDI-MS), which is used for determining the mass of proteins, to investigate the microenvironments of SARS-CoV-2 spike protein complexes—a fingerprint signature for the COVID-19 virus.
“We wanted to learn more about the virus,” explains Schenkel, “for example, what it binds to in droplets and how it reacts to compounds mixed into the droplets.”
Towards this end, the researchers added samples of the spike proteins to droplets containing sinapinic acid, a commonly used matrix in MALDI-MS. They then deposited the droplets on carbon nanotube (CNT) substrates placed on silicon wafers. (CNTs are cylindrical molecules consisting of rolled-up sheets of single-layers of carbon atoms, commonly referred to as graphene.)
While Schenkel noted that using nanostructured substrates in MALDI-MS has been shown to effectively detect proteins with masses below ten kilodaltons (kDa), the SARS-CoV-2 spike protein has a mass of 75 kDa. He says that using MALDI-MS on proteins of these masses causes desorption and ionization processes in the matrix-analyte, which can lead to fragmentation of the protein into a series of poly-peptide and small fragment ions, “making the identification of the virus very challenging.”
To overcome this, instead of using standard flat substrates, the researchers used “CNT forests” that had been grown on silicon wafers.
“We found that spike protein ion yields were strongly enhanced when using the CNT substrates compared to the flat substates,” he says, “with a 50-fold increase in spike protein ion yields observed when the matrix-analyte solution was placed on substrates coated with these CNT forests compared with yields from uncoated substrates.”
Peter Seidl (left) and Kei Nakamura (right) at the MALDI-MS experiment. The metal cylinder in the foreground is the flight tube with detector for spike protein ions. (Credit: Berkeley Lab/Thomas Schenkel)
From these observations, the researchers concluded that the deposition of drops of matrix-analyte solutions on the CNT forest-coated substrates leads to the formation of denser matrix-analyte crystal assemblies compared to the flat surfaces, and that the CNT forests enhance the absorption of laser light and energy transfer to the molecules. Both effects, notes Schenkel, contribute to the enhanced ion signal seen in the CNT samples.
He says the work demonstrates an efficient method for the formation and detection of characteristic fingerprint ions for detecting pathogens such as SARS-CoV-2 with high sensitivity and selectivity. “It also shows that the use of CNT substrates allows for the efficient absorption of laser light, leading to significant increases in the yields of the SARS-CoV-2 spike protein ions.”
Antoine Snijders added that: “In the future, using laser-mass spectrometry with high power lasers we can identify characteristic bio-molecular fingerprints enabling the rapid identification of SARS-CoV-2 in liquids and potentially identify biochemical targets for the development of aerosols designed to decrease viral viability by modifying the microenvironment of SARS-CoV-2-laden droplets limiting the rapid spread of COVID-19.”
The team is now exploring how analyte ion intensities from samples of intact viruses and pathogens deposited on CNT substrates can be enhanced, which could lay the groundwork for instruments capable of “the rapid and reliable testing and environmental monitoring of pathogens that could be deployed to hospitals and laboratories at relatively low costs,” says Schenkel.
He noted that in parallel to this work, Jeroen van Tilborg from the BELLA Center led a theoretical study on imaging of viruses in droplets using laser-driven X-ray pulses.
The research described in this article was supported by the Laboratory Directed Research & Development (LDRD) program.
Learn More
- Schenkel, T., Snijders, A.M., Nakamura, K., Seidl, P.A., Mak, B., Obst-Huebl, L., Knobel, H., Pong, I., Persaud, A., van Tilborg, J., Ostermayr, T., Steinke, S., Blakely,1 E.A., Ji, Q., Javey, A., Kapadia, R. Geddes, C.G.R., and Esarey, E., “Carbon nanotube substrates enhance SARS-CoV-2 spike protein ion yields in matrix-assisted laser desorption–ionization mass spectrometry,” Applied Physics Letters 122, 2023, https://doi.org/10.1063/5.0128667
- van Tilborg, J., Ostermayr, T., Tsai, H.-E., Schenkel, T., Geddes, C.G.R., Schroeder, C., and Esarey, E. “Phase-contrast imaging with laser-plasma-accelerator betatron sources”, Proc. of SPIE Vol. 11886, 2021, https://doi.org/10.1117/12.2592437
- ATAP Newsletter, August 2020
