Raman Spectroscopy Pinpoints Viral RNA in Single Cells

A new technique for identifying and quantifying viral RNA in living cells, based on surface-enhanced Raman spectroscopy (SERS) and developed by scientists at Rutgers University, can detect minor changes in RNA sequences that could give viruses an edge or make some people “superspreaders.”

If researchers could identify single cells with high viral loads in superspreaders and then study the viral sequences in those cells, they could perhaps learn how viruses evolve to become more infectious or to outwit therapies and vaccines. In addition, features of the host cell itself could aid various viral processes and thus become targets for therapies. On the other end of the spectrum, some cells produce mutated viruses that are no longer infectious. Understanding how this happens could also lead to new antiviral therapies and vaccines.

“For studying a new virus like SARS-CoV-2, it’s important to understand not only how populations respond to the virus, but how individuals — either people or cells — interact with it,” professor Laura Fabris said. “So we’ve focused our efforts on studying viral replication in single cells, which in the past has been technically challenging.”

The researchers used SERS to develop an assay that was sensitive enough to detect viral RNA and its mutations in single living cells. They applied their technique to the study of influenza A. To detect the virus’s RNA, they added a “beacon DNA” specific to influenza A to gold nanoparticles. In the presence of influenza A RNA, the beacon produced a strong SERS signal, but in the absence of RNA, it did not.

The beacon produced weaker SERS signals when presented with increasing numbers of viral mutations, allowing the researchers to detect as few as two nucleotide changes. The researchers found that the nanoparticles could enter human cells in a dish and when they did so produced a SERS signal only in those cells expressing influenza A RNA.

The team is developing a version of the assay that produces a fluorescent signal instead of a SERS signal when viral RNA is detected. “SERS is not a clinically approved technology. It’s just now breaking into the clinic,” Fabris said. “So we wanted to provide clinicians and virologists with an approach they would be more familiar with and have the technology to use right now.” In collaboration with virologists and mathematicians at other universities, the team is developing “lab-on-a-chip” technologies that will read many fluorescent samples simultaneously.

Because SERS is more sensitive, cheaper, faster, and easier to perform than other assays based on fluorescence or the reverse transcriptase-polymerase chain reaction (RT-PCR), it could be useful for detecting and studying viruses in the future. Fabris is collaborating with a company that makes a low-cost, portable Raman spectrometer, which would enable the SERS assay to be easily conducted in the field.

The team is also working on identifying regions of the SARS-CoV-2 genome to target with SERS probes. “We’re in the process of obtaining funding to work on possible SARS-CoV-2 diagnostics with the SERS method we developed,” Fabris said.

The research was presented at the American Chemical Society Fall 2020 Virtual Meeting, Aug. 17-20, 2020.

Scientists report a new technique that can not only identify and quantify viral RNA in living cells, but also detect minor changes in RNA sequences that might give viruses an edge. Courtesy of the American Chemical Society.