Watch a virus in the moments right before it attacks
3D tracking and imaging (3D-TrIm). a, Experimental setup. Fluorescently labeled VLPs are added to live cells plated on a coverslip. The sample is placed on a heated sample holder mounted on a piezoelectric stage. Inset, sampling rate comparison among spinning disk, light sheet and 3D-TrIm. FPS, frames per second. b, Overview of 3D-SMART tracking of single viruses. The EOD and TAG lens rapidly scan the focused laser spot around the local particle area. Photon arrival times and the current laser position are used to calculate the position of the virus within the scan area. Using the measured position, the piezoelectric stage moves to recenter the virus within the scan area. c, Concept of 3D-FASTR volumetric imaging. By outfitting a traditional two-photon LSM with an ETL, a repeatable, tessellated 3D sampling pattern can be generated during each frame-time. Over a set number of frame-times, the entire volume is sampled. d, Construction of global volumes in 3D-TrIm. As the virus diffuses, 3D-SMART moves the sample, and the 3D-FASTR imaging system collects sequential volumes from different areas around the particle (black dot). These time-resolved local volumes can be used to generate an integrated global volume. Credit: Nature Methods (2022). DOI: 10.1038/s41592-022-01672-3

It's like she's watching an attempted break-in on a home security camera when she pulls up the video from her PhD.

The person looking for a point of entry doesn't need to set a foot inside. This is a different type of person. It is a Viruses.

Filmed over two and a half minutes, the footage shows a tiny virus particle, thousands of times smaller than a grain of sand, as it lurches and bobs among tightly packed humans.

The virus skims along the surface of a cell, but doesn't stick, for a short time. If this were an actual home break-in, Johnson says, this would be the part where the person hasn't broken the window.

A microscopic video shows a virus (purple track) as it finds its way to the surface of human intestinal cells (green). Credit: The Welsher lab, Duke University

Kevin Welsher is a chemistry professor at Duke University. Welsher and Jack Exell have collaborated to come up with a way to capture real-time 3D footage of viruses as they approach their cellular targets. The journal Nature Methods contains their research.

Every day we take in millions of Viruses. Some of them can be dangerous, such as the viruses that cause the flu or COVID-19.

Demonstration of 3D-TrIm operating principle. Animation sequence begins with overview of experimental setup in which a heated sample containing virus-like particles (VLP) and live cells are mounted on a piezoelectric stage with an objective lens shared by both tracking and imaging microscope sources. This overview is followed by an animation of 3D-SMART real-time tracking, demonstrating how a pair of Electro-Optic Deflectors (EOD) create a lateral Knight's Tour grid pattern, followed by the use of a Tunable Acoustic Gradient (TAG lens) to scan a focal range above and below the center of the focal volume. A final animation demonstrates the principle of 3D-FASTR point-scan imaging. Credit: Nature Methods (2022). DOI: 10.1038/s41592-022-01672-3

When a Viruses enters a cell it hijacks the cellular machinery to make copies of itself A virus has to get to the cell first before it can break in.

One of the first lines of defense against infections is the mucus and cells in the airway and gut.

VSV-G exploring the extracellular matrix, related to Fig. 2a,b. 3D reconstruction of real-time VSV-G VLP trajectory in extracellular matrix of live GM701 cells (stained with F-actin label SiR650-actin), from a 4D dataset covering 10 local volumes, at 16 FPV. Trajectory (~162 s) is segmented into 25 segments per second (25 frames per second when playback rate is 1×) and color mapped by time. The progress bar shows how the trajectory is further categorized: (1) Free diffusion period (playback rate: 2×): 0–14 s, 18–38 s, 44–62 s, 70–108 s. (2) Skimming period (playback rate: 1×): 14–18 s, 38–44 s, 62–70 s, 108–122 s. (3) Detachment (playback rate: 2×): 122–162 s. Sphere represents the VLP position in the current frame (refreshing rate is consistent with the trajectory, that is, 25 FPS at 1× playback rate). Image volumes formed from maximum intensity projection over time from local volumes acquired over 16 frame-times. In a, cells are color-coded by imaging intensity, while in b, cells are color-coded depending on distance of the virus from the cell surface. Panels a and b share the same trajectory color scale, camera angle and camera path; however, a is magnified compared with b. Credit: Nature Methods (2022). DOI: 10.1038/s41592-022-01672-3

The researchers wanted to understand how viruses are able to penetrate these defenses. How do viruses get around? Welsher spoke. It has long been difficult to watch the critical early moments before infections begin.

Viruses move two to three orders of magnitude quicker in the unConfined space outside of the cell than they do inside. Viruses are hundreds of times smaller than cells and this makes them difficult to image.

This is a difficult problem to study because of that. It's like taking a picture of a person in front of a skyscraper. It's not possible to see the details of the person in front of the skyscraper with a single picture.

The team developed a new method that combines two microscopes in one. The first microscope "locks on" to the fast- moving virus, using a laser to calculate and update its position tens of thousands of times per second. The microscope stage constantly adjusts to keep it in focus as the viruses bounce around in the cell.

3D images of the surrounding cells are taken by the second microscope. Welsher said that the combined effect is similar to navigating with Google Maps, showing your current location as you drive, as well as the terrain, landmarks and the overall lay of the land.

When presenting his work, Johnson sometimes gets asked if it's a video game or a simulation. This is from a real microscope.

The researchers can't just watch a healthy person breathe in virus particles from a sick person. They need to attach a fluorescent label to a virus before they can use a microscope to see it. They can only keep an eye on a virus for a short time.

Exell said that the biggest challenge for them is to make brighter viruses.

Welsher hopes the technique will make it possible to follow infections in action beyond the coverslip and in more realistic environments.

Welsher said that this is the real promise of the method. We think we have the chance to do that now.

There is more information about Capturing the start point of the virus–cell interaction with high-speed 3D single-viruses. It's 10.1038

Journal information: Nature Methods

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