Track a virus in the moments just before it attacks

When Courtney “CJ” Johnson takes footage of her Ph.D. thesis, it’s like watching a burglary attempt on a home security camera.

The attacker grabs their target without setting foot inside, looking for an entry point. But this intruder is not your typical burglar. It’s a virus.

Filmed in two and a half minutes by tracking its position 1,000 times a second, the footage shows a tiny virus particle, thousands of times smaller than a grain of sand, as it drifts between tightly packed human intestinal cells.

For a fleeting moment, the virus makes contact with a cell and passes along its surface, but does not stick before detaching again. If it was an actual home burglary, Johnson says, “that would be the place where the burglar hasn’t broken the window yet.”

Johnson is part of a Duke University team led by assistant professor of chemistry Kevin Welsher. Along with Welsher’s postdoctoral associate Jack Exell and colleagues, they have found a way to capture real-time 3D footage of viruses as they approach their cellular targets. Their research is published today in the journal Nature Methods.

We inhale, swallow and ingest millions of viruses every day. Most of them are harmless, but some of them—like the viruses that cause the flu or COVID-19—can make us sick.

Infection begins when a virus binds to and enters a cell, where it tricks the cellular machinery into making copies of itself. But before it can enter, a virus must first reach the cell, Johnson said.

This often means that it passes through the protective layer of cells and mucus that line the airways and gut – one of the body’s first lines of defense against infection.

Researchers wanted to understand how viruses breach these first-line defenses. “How do viruses navigate these complex barriers?” Welsher said. But these critical early moments before infection begins have long been difficult, if not impossible, to track with existing microscopy methods, he added.

Part of the reason is that viruses move two to three orders of magnitude faster in the unbounded space outside the cell, compared to its crowded interior. To make matters even more difficult from a visual perspective, viruses are hundreds of times smaller than the cells they infect.

“That’s why this problem is so hard to study,” Johnson said. Under the microscope, “it’s like trying to take a picture of a person standing in front of a skyscraper. You can’t take the whole skyscraper and see the details of the person in front of it with a picture.”

So the team developed a new method called 3D Tracking and Imaging Microscopy (3D-TrIm), which essentially combines two microscopes into one. The first microscope “locks on” to the fast-moving virus, scanning a laser around the virus tens of thousands of times a second to calculate and update its position. As the virus bounces and tumbles around the soupy exterior of the cell, the microscope stage constantly adjusts to keep it in focus.

While the first microscope tracks the virus, the second microscope takes 3D images of the surrounding cells. The combined effect, Welsher said, is similar to navigating with Google Maps: it doesn’t just show your current location as you drive, it also shows terrain, landmarks and the overall landmass, but in 3D.

“Sometimes when I present this project, people ask, ‘is this a video game or a simulation?’ said Johnson, now a postdoctoral fellow at the Howard Hughes Medical Institute, Janelia Research Campus. “No, that’s something that came from a real microscope.”

With their method, researchers can’t just, say, watch a healthy person breathe in virus particles from an infected person’s cough or sneeze. First, they have to attach a special fluorescent tag to a virus before they can track it—what the microscope follows is the movement of the glowing spot. And currently they can only watch a virus for a few minutes at a time before it fades.

“The biggest challenge for us now is to produce brighter viruses,” Exell said.

However, Welsher said he hopes the technique will make it possible to watch viruses in action beyond coverage, and in more realistic tissue-like environments where infections start to take hold.

“That’s the real promise of this method,” Welsher said. “We think that’s something we have the ability to do now.”