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I assumed a virus to be something with a very specific geometry,
similar to a crystal, but more complex.

In an answer to What is the size (diameter) of the SARS-CoV-2 virus? some SARS-CoV-2 virus particles are shown.

It looks like they do not have the same geometry.

They may be soft and influenced by external forces, but they could also be of different, but similar shape. Also, they could simply be defective in some way.

I assume a structure of the size of a virus is not rigid. Assuming no external forces, would multiple exemplars of the same kind of virus have the same shape?
Can a virus have a different molecular arrangement, but be equivalent for biological purposes?

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    $\begingroup$ You should check literature on VLP (virus like particles) for vaccine purposes. They spend a lot of time charactering their modified virus shells a lot as capsid protein don't tolerate fusions well. $\endgroup$ Mar 24 '20 at 0:48
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    $\begingroup$ The caption to the figure in the source linked in that answer says Figure 3. Visualization of 2019-nCoV with Transmission Electron Microscopy. Negative-stained 2019-nCoV particles are shown in Panel A, and 2019-nCoV particles in the human airway epithelial cell ultrathin sections are shown in Panel B... They've been through quite a lot and I'm not completely sure those techniques can faithfully preserve the shapes of the virus particles. $\endgroup$
    – uhoh
    Mar 24 '20 at 2:05
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Some parts of viruses are consistently shaped, in particular anything that is made of multiple copies of a protein sticking together. There are methods to determine the structures of these regular components to high precision, like single particle analysis (eg. zika) and X-ray crystallography (bacteriophage HK97). Other parts of the virus are less consistent, either because they are flexible or because they are produced slightly differently each time. The nucleic acid core is often arranged semi-randomly, and the lipid envelope of many viruses can vary greatly, dependent on the process by which parts of the host cell's membrane is pinched off to create new viral particles. Here's an example of pretty extreme variability of influenza particles, based on what cell type they have infected. Virus particles with different shapes can be just as infectious, but if they are too large the number of new viruses produced by an infected cell may be too low.

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