SARS COV-19 3D visualization Case Study

Visualizing COVID-19: a 3D visualization of SARS-CoV-2

SARS-CoV-2, the novel Coronavirus, is the cause of COVID-19, the severe acute respiratory disease we are all familiar with by now. The spread of COVID-19 is an emerging global health risk that has already had a significant impact on the global economy and our daily lives, directly or indirectly.
We have seen many coronavirus visualizations since the beginning of the pandemic, and we wanted to share our insights too. We have created a 3D visualization and illustrations of the SARS-CoV-2 virus particle. We worked with structures based on literature accessed in March 2020 (listed below).

Our Model

The COVID-19 virus is spherical with spikes on its surface, similar to SARS-CoV-1. Our animation model is based on what we know so far, what we’ve already learned about the structurally similar virus SARS-CoV-1, plus one very important reference, the accurate CDC image, which gives us a very good idea of what the virus looks like and the proportions of each component.

The Technicals

For our visualization, we created molecular structures using UCSF Chimera and ePMV. We assembled and animated the models in Cinema4D and the developed materials and rendered the images using Cinema 4D, using After Effects to add effects.

The Challenge

Specific techniques allow scientists to study these viral protein components separately and render 3D models of them, which results in pretty faithful visualizations. For some other pieces, we need to make our best guess as to how to visualize them and support the scientific understanding of the structure, even if the evidence is not yet available.

The animation story line

We wanted our animation peak point to be the moment at which the S protein binds to the host ACE2 cellular receptor of a lung cell. By binding to this specific receptor, the virus makes its way into the cell, starting the infection. So, back to SARS-CoV-2. Much of the virus’s outer membrane is made up of:

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S (spike) glycoprotein: This large protein made up of smaller subunits plays an important role in the transmission process – it attaches to a molecule called a receptor on the human cell so the virus can infect it. S proteins cover the outside of the virus – they are embedded in a lipid bilayer. M (membrane) protein: Membrane proteins, visualized in our model in green, are diffusely present on the virus surface, but had not yet been mapped at the time of our research. We decided to use a very simple substitute model for this, similar to the N protein. HE (hemagglutinin esterase) protein Hemagglutinin esterase is a glycoprotein on the surface of the virus that some enveloped viruses, including some Coronaviruses, use as invasion mechanism. HEs are responsible for several important functions in genome maintenance and virus replication. They help the virus attach to and destroy certain sialic acid receptors found on the host cell surface. The HE protein carries out several enzyme activities, including receptor binding, receptor hydrolysis and membrane fusion.

E (envelope) protein: The third protein that makes up the viral envelope, or outer layer, is the envelope protein. This had also not been mapped at the time of our research, so we decided to use a very simple substitute model. N (nucleocapsid) protein: N proteins bind to the virus’s RNA (its genetic material, visualized in red) to help organize and protect it. The host cell translates viral RNA into new viral proteins, some of which are assembled into new copies of the virus, which then continue the cycle by infecting other cells. The N proteins have different orientations, relative to each other and relative to the disordered amino acid strings of the RNA. Since this orientation is still not entirely clear, and given the technical challenge and time limitations for this animation, we applied some artistic license when it came to their organization around the RNA chain.

 

We wanted our animation peak point to be the moment at which the S protein binds to the host ACE2 cellular receptor of a lung cell. By binding to this specific receptor, the virus makes its way into the cell, starting the infection.  For the rendering, we imagined the animation to play out against a warm, pinkish background. We chose this as it could help the viewer imagine the tissues inside the human body, where the virus infects cells. Before settling on this background, we tried other options. We hope you like the animation! Please feel free to provide your contribution should any of the content be revised.

Notes

The understanding of the structure of this virus will undoubtedly change as research continues
The organization of the nucleoprotein region within the membrane is a rough approximation, as stated above
The illustrated visualization is not the result of simulation or direct data acquisition
This animation is not based on molecular dynamics simulation, temperature factors, or other data sources

References/Data sources

RCSB’s Corona Virus Resources Page: https://www.rcsb.org/news?year=2020&a
PDB entries for proteins: (from SARS-CoV) 6VXX, 6VSB, 5X29, M-Protein predicted by DeepMind, N-Protein as predicted by the Zhang Lab at UMich, HE – Protein Hemagglutinin Esterase 4ZXN, ACE2 cell receptor 6M17, 6M1D, 6M18.
The SARS coronavirus nucleocapsid protein – Forms and functions https://www.sciencedirect.com/science/article/pii/S0166354213003781.
Genotype and phenotype of COVID-19: Their roles in pathogenesis https://www.sciencedirect.com/science/article/pii/S1684118220300827
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