Novel SERS Assay Could Identify Superspreaders Carrying Coronavirus Mutations

Scientists have developed 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 or make some people “superspreaders.”

Based on the new technique, scientists from Rutgers University (New Brunswick, NJ, USA) are now developing COVID-19 diagnostic tests to identify superspreaders, or people carrying unusually high amounts of the SARS-CoV-2 virus and infecting many others. In order to understand how populations respond to the SARS-CoV-2 virus, as well as how individuals interact with it, the researchers focused their efforts on studying viral replication in single cells, which has been technically challenging earlier. In their results presented at the American Chemical Society (ACS) Fall 2020 Virtual Meeting & Expo, the researchers highlighted how analyzing individual cells instead of large populations could go a long way toward better understanding many facets of viral outbreaks, such as superspreaders. Some cells or people carry unusually high amounts of virus and therefore can infect many others. 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.

As a result, the researchers focused on developing an assay that was sensitive enough to detect viral RNA, and its mutations, in single living cells. The team based their technique on surface enhanced Raman spectroscopy (SERS), a sensitive method that detects interactions between molecules through changes in how they scatter light. The researchers decided to use the method to study influenza A. To detect the virus’s RNA, they added to gold nanoparticles a “beacon DNA” specific to influenza A. In the presence of influenza A RNA, the beacon produced a strong SERS signal, whereas in the absence of this RNA, it did not. The beacon produced weaker SERS signals with increasing numbers of viral mutations, allowing the researchers to detect as few as two nucleotide changes. Importantly, the nanoparticles could enter human cells in a dish, and they produced a SERS signal only in those cells expressing influenza A RNA.

The researchers are now making a version of the assay that produces a fluorescent signal, instead of a SERS signal, when viral RNA is detected. In collaboration with virologists and mathematicians at other universities, the team is developing microfluidic devices, or “lab-on-a-chip” technologies, to 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 (known as RT-PCR), it could prove ideal for detecting and studying viruses in the future. The researchers are also working on identifying regions of the SARS-CoV-2 genome to target with SERS probes.

“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. So we’ve focused our efforts on studying viral replication in single cells, which in the past has been technically challenging,” said Laura Fabris, Ph.D., the project’s principal investigator. “We’re in the process of obtaining funding to work on possible SARS-CoV-2 diagnostics with the SERS method we developed.”

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