The physics of the SARS-CoV-2 virion

 Some progress is being made in understanding the structure and dynamics of the SARS-CoV-2 virions (virus particles) that are responsible for the pandemic. A nice starting point for the non-expert is a recent article in The New York Times.

A fundamental question is what is the structure and symmetry of the virion? In particular, does it have the icosahedral symmetry possessed by many virions, as discussed in a talk I gave earlier this year and in a recent review (with lots of nice pictures). As far as I am aware, there are still no definitive results on the overall structure and symmetry. 

This preprint has some really nice images and videos such as the video below. 

SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography

 View ORCID ProfileSteffen Klein,  View ORCID ProfileMirko Cortese,  View ORCID ProfileSophie L. Winter,  View ORCID ProfileMoritz Wachsmuth-Melm,  View ORCID ProfileChristopher J. Neufeldt, Berati Cerikan,  View ORCID ProfileMegan L. Stanifer,  View ORCID ProfileSteeve Boulant,  View ORCID ProfileRalf Bartenschlager,  Petr Chlanda

View ORCID Profile

Mathematical aside: the authors note that the geometric problem of how to place the spike protein (S) trimers on the surface of the virion is related to the "Tammes Problem" or the seventh unsolved mathematical problem listed by Steve Smale: how do you arrange a specific number of points on a sphere with the largest possible minimum distance between the points.

The paper below shows that the nucleocapsid protein (N) is similar to that for SARS-CoV and MERS. The protein can form dimers and tetramers, steps in the self-assembly of the whole virion.

Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate

Christiane Iserman, Christine Roden, Mark Boerneke, Rachel Sealfon, Grace McLaughlin, Irwin Jungreis,  View ORCID ProfileChris Park, Avinash Boppana, Ethan Fritch, Yixuan J. Hou, Chandra Theesfeld, Olga G Troyanskaya, Ralph S. Baric,  View ORCID ProfileTimothy P. Sheahan, Kevin Weeks, Amy S. Gladfelter

Some nice soft matter physics is in the preprint below. It argues that the N protein can undergo liquid-liquid phase separation with the viral genome. Aside: even before covid, liquid-liquid phase separation was quite a hot topic in cell biology, as recently discussed by Tom McLeish. 

Architecture and self‐assembly of the SARS‐CoV‐2 nucleocapsid protein 

Qiaozhen Ye, Alan M. V. West, Steve Silletti, Kevin D. Corbett

Finally, the paper below combines molecular dynamics simulations with experiments to argue that the stalk of the spike protein has three hinges giving the head of the spike unexpected orientational freedom so it can scan the host cell surface.

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

1. View ORCID ProfileBeata Turoňová1,2,*, 
2. View ORCID ProfileMateusz Sikora3,*, 
3. View ORCID ProfileChristoph Schürmann4,*, 
4. View ORCID ProfileWim J. H. Hagen1, 
5. View ORCID ProfileSonja Welsch5, 
6. View ORCID ProfileFlorian E. C. Blanc3, 
7. View ORCID ProfileSören von Bülow3, 
8. View ORCID ProfileMichael Gecht3, 
9. View ORCID ProfileKatrin Bagola6, 
10. View ORCID ProfileCindy Hörner4,7, 
11. View ORCID ProfileGer van Zandbergen6,8,9, 
12. View ORCID ProfileJonathan Landry10, 
13. View ORCID ProfileNayara Trevisan Doimo de Azevedo10, 
14. View ORCID ProfileShyamal Mosalaganti1,2, 
15. View ORCID ProfileAndre Schwarz1, 
16. View ORCID ProfileRoberto Covino3,11, 
17. View ORCID ProfileMichael D. Mühlebach4,7, 
18. View ORCID ProfileGerhard Hummer3,12,†, 
19. View ORCID ProfileJacomine Krijnse Locker13,†, 
20. View ORCID ProfileMartin Beck1,2,†
21.