Real SARS-CoV-2 virion in 3D

Previously, we have visualized scientifically accurate atomistic models of SARS-CoV-2. Now we offer you the look at a real SARS-CoV-2 virion, in 3D. Our scientific collaborators at Tsinghua University scanned SARS-CoV-2 virions with cryo-electron tomography (cryo-ET) to obtain images of the virus in extreme resolution. However, these images were still too noisy to be displayed in 3D. With the help of our colleagues at KAUST, we were able to turn these scans into stunning visualization showing the shape of SARS-CoV-2 virions. By identifying different parts of the virus particles and coloring them with artificial colors, we are able to show you, for the first time, real coronavirus in unprecedented detail.

With our interactive 360° viewer, you can compare the original cryo-ET data (left) and our visualization revealing the details of the virion (right). You can rotate the virion around to look at it from different directions. By clicking the 360° icon, you can get the html code to embed the viewer in your own webpage or blog.


Updated on January 19, 2021

What does a virus actually look like?

This is the first time you can see real (flash-frozen) coronavirus in 3D. We used machine learning and advanced visualization algorithms to show you the most detailed view of a real SARS-CoV-2 virion, in 3D, directly from Cryo-ET data.

The Cryo-ET data were provided by Sai Li of Tsinghua University, Beijing, China.

High resolution renderings of SARS-CoV-2 Cryo-ET

We made high resolution renders of the SARS-CoV-2 cryo-electron tomography scans. We release these images under Creative Commons Attribution license, so that you can use them freely in your work.

Creative Commons License
The images are licensed under a Creative Commons Attribution 4.0 International License.

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If you'd like to showcase your research with similar visualizations, interactive, pre-rendered, or in virtual reality, or if you're interested in biological visualization, contact us! We are looking forward to hear about your project!

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You can read the paper on the architecture of SARS-CoV-2 virus discovered based on Cryo-ET imaging here. More resources on SARS-CoV-2 are also available here.

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cross section of a coronavirus particle

There are already many pictures of coronavirus. What is unique about these images?

These are the first 3D images of coronavirus made from a single cryo-electron tomography scan. Previous images were either man-made models of coronavirus, or they were composited from many different scans. We show you, for the first time, an actual, existing virion of SARS-CoV-2.

Are these the real colors of the coronavirus?

No. For objects on such tiny scale as viruses are, colors do not exist in the same sense as we are familiar with them. The 3D images of the virus were not captured with photons of visible light (those give things their colors), but with electrons. Electrons are not associated with any color that our eyes can see. Therefore, to display a scan from an electron microscope, we have to use artificial colors.

But why?

Colors are nothing but our perceptions of photons of visible light with different wavelengths. Objects seem to have colors because they emit or reflect photons of certain wavelengths. Those photons that find their way into our eyes are then interpreted by our brains as different colors. The smallest thing we can theoretically see this way is about half the size of the shortest visible wavelength. However, most viruses (including coronavirus) are even smaller than that (coronavirus is approximately 100 nm accross, while the shortest visible wavelength is around 380 nm) and so they don't have any visible color.

Instead of using photons of visible light, we can use electrons. Electrons have much shorter wavelengths, so they can resolve something as small as a virus, but the resulting scan will contain no color information. To produce a picture that can be displayed on the screen, we have to asign colors to individual measured electron densities. Usually, scans from electron microscopes are displayed in shades of grey, but any color scheme can be used.

Why did you chose this particular color scheme?

We wanted to use different colors to distinguish various parts of the virus from each other, because otherwise they would blend in together. We chose bright pink for the spikes, to signify that they are the part of the virus responsible for attaching to the host cells and infecting them. The rest of the virus is shown in muted, cold colors, to suggest that a virus is not a living thing.

So, if you chose the colors arbitrarily, how are these images “real”?

You can look at it this way: when you take a photo with your phone, what happens is that an image sensor consisting of a grid of cells, or pixels, converts the energy from the incoming photons into voltage values. Then, the processor in your phone modifies these measured values by a complex chain of mathematical functions. This steps is called postprocessing and it makes sure that the resulting picture is as clear and as aesthetically pleasing as possible. Indeed, there's no such thing as #nofilter in digital photography. However, since the resulting picture somehow reflects the measurement from the camera's sensor, it is natural to call digital photographs real.

When looking at viruses, we have to use electrons instead of photons. The electrons are shot at the specimen and scattered depending on the density of the specimen at focused area. The scattered electrons are then picked up by a sensor, which allows us to measure the density across the specimen. From these measured densities, the picture is then reconstructed by showing each density in different color. The picture reflects the measurement of the sensor, and so again, it is natural to call it real.

The electron microscope does not allow us to see the colors - because there aren't any - but it allows us to see shapes. And thanks to the artificial colors that we added to the images, we can see the shapes of the virus particles even better.

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