Studying viral outbreaks in single cells could reveal new ways to defeat
them

Date:
August 20, 2020
Source:
American Chemical Society
Summary:
Many viruses mutate so quickly that identifying effective vaccines
or treatments is like trying to hit a moving target. A better
understanding of viral propagation and evolution in single cells
could help. Now, scientists report a new technique that can detect
minor changes in RNA sequences in living cells that might give
viruses an edge.



FULL STORY ==========================================================================
Many viruses, including HIV and influenza A, mutate so quickly that
identifying effective vaccines or treatments is like trying to hit a
moving target. A better understanding of viral propagation and evolution
in single cells could help. Today, 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 or make some people "superspreaders."

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The researchers will present their results at the American Chemical
Society (ACS) Fall 2020 Virtual Meeting & Expo.

"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," says Laura Fabris, Ph.D.,
the project's principal investigator. "So we've focused our efforts on
studying viral replication in single cells, which in the past has been technically challenging." Analyzing individual cells instead of large populations could go a long way toward better understanding many facets
of viral outbreaks, such as superspreaders. That's a phenomenon in which
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.

But first, Fabris and colleagues at Rutgers University needed to
develop 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.

Now, Fabris and colleagues are making 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 notes. "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 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. Fabris is now 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.

Fabris and her team are 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 says.

A brand-new video about the research is available at http://www.acs.org/ fall2020-outbreaks.


========================================================================== Story Source: Materials provided by American_Chemical_Society. Note:
Content may be edited for style and length.


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Link to news story: https://www.sciencedaily.com/releases/2020/08/200820102454.htm

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