![Viral RNA labeled with a fluorescent dye is clustered around the nucleus of SARS-CoV-2-infected cells captured through super-resolution microscopy. Source: Nature Communications (2024). DOI: 10.1038/s41467-024-48991-x A new way to check virus activity](https://scx1.b-cdn.net/csz/news/800a/2024/a-new-way-to-see-virus.jpg)
Viral RNA labeled with a fluorescent dye is clustered around the nucleus of SARS-CoV-2-infected cells captured through super-resolution microscopy. Credit Transactions: Nature Communications (2024). DOI: 10.1038/s41467-024-48991-x
New nanoscale observations of how the SARS-CoV-2 virus replicates in cells could provide greater precision for drug development, a Stanford University team reports. Nature Communications. Using advanced microscopy techniques, researchers have produced the clearest images yet of the virus's RNA and replication structure, and have seen it form a spherical shape around the nucleus of infected cells.
“We’ve never seen COVID-19 infected cells at this high resolution, and we didn’t know what we were looking at before,” said Stanley Qi, co-author of the paper and associate professor of biomedical engineering at the Stanford School of Engineering. “Being able to know what we are seeing at this high resolution over time will fundamentally benefit future viral research, including virology and antiviral drug development.”
blinking RNA
This study illuminates molecular-scale details of viral activity inside host cells. To spread, viruses essentially take over cells and transform them into virus production factories equipped with specialized replication organelles. Within this factory, the viral RNA must continue to replicate until enough genetic material is collected to travel to new cells, infect them, and start the process over again.
Stanford scientists sought to reveal this replication step in the clearest detail yet. To do this, they first labeled viral RNA and replication-related proteins with fluorescent molecules of different colors. However, imaging glowing RNA alone can result in blurry blobs in conventional microscopes. So they added a chemical that temporarily suppressed the fluorescence. The molecules then blink again randomly, with only a few lighting up at a time. This made it easier to pinpoint the flashes and revealed the positions of individual molecules.
Using a setup that included a laser, a powerful microscope, and a camera that took pictures every 10 milliseconds, the researchers collected snapshots of the blinking molecules. By combining these sets of images, they were able to create a highly detailed picture showing the viral RNA and replication structures in the cell.
“We have a very sensitive and specific method and high resolution,” said co-author Leonid Andronov, a Stanford postdoctoral fellow in chemistry. “I see a single virus molecule inside the cell.”
The resulting images, with a resolution of 10 nanometers, provide the most detailed view yet of how the virus replicates inside cells. The image shows magenta RNA forming clumps around the cell's nucleus and accumulating in large repeating patterns. “We discovered for the first time that viral genomic RNA forms distinct spherical structures at high resolution,” said co-author Mengting Han, a Stanford bioengineering postdoctoral fellow.
These clusters help show how viruses evade cellular defenses, said WE Moerner, the Harry S. Mosher Professor of Chemistry in the College of Arts and Sciences and co-author of the paper. “They gather together inside a membrane that isolates them from the rest of the cell, so they aren’t attacked by the rest of the cell.”
Nanoscale drug testing
Compared to using an electron microscope, the new imaging technique allows researchers to know more reliably where viral components are within the cell, thanks to blinking fluorescent labels. Additionally, medical research conducted through biochemical analysis can provide nanoscale details about invisible cellular processes.
“Existing techniques are completely different from spatially recording where an object actually is in a cell, and are capable of much higher resolution,” Moerner said. “We have the advantage of basing it on fluorescent labeling because we know where the light is coming from.”
Determining exactly how the virus progresses through its stages of infection opens up new possibilities for medicine. Observing how different viruses take over cells can help answer questions such as why some pathogens cause mild symptoms while others are life-threatening. Super-resolution microscopy can also aid drug development. “These nanoscale structures of replicating organelles may provide us with several new therapeutic targets,” Han said. “We can use this method to screen different drugs and determine their effect on nanoscale structures.”
In fact, that's what the team plans to do. They will repeat the experiment and see how the structure of the virus changes in the presence of drugs such as paxlovid or remdesivir. If a candidate drug can inhibit the viral replication step, this means that the drug is effective in suppressing the pathogen and making it easier for the host to fight the infection.
Researchers also plan to map all 29 proteins that make up SARS-CoV-2 and determine what role they play during infection. “We want to be ready to really use these methods for the next challenge so we can quickly see and better understand what’s going on inside,” Qi said.
Additional information:
Leonid Andronov et al., Nanoscale cellular organization of viral RNA and proteins of SARS-CoV-2 replication organelles; Nature Communications (2024). DOI: 10.1038/s41467-024-48991-x
Provided by Stanford University
Summons: A new way to see viruses in action: Super-resolution microscopy gives a nanoscale look, Retrieved May 31, 2024, from https://phys.org/news/2024-05-viruses-action-super (2024 May 31, 2012). -resolution-microscope.html
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