Fig. 1: Electron cryotomography of SARS-CoV-2 virions.

a Tomogram section of Wuhan virions in cross-section showing surface spike proteins surrounding the viral membrane bilayer and the nucleocapsid in the virus interior. b Same field of view with models for the virus membrane (pale blue), nucleocapsid (red), and the spike glycoprotein (purple) overlaid. The glycoprotein map (inset) was obtained by subtomogram averaging of spikes and fitted with a pre-fusion S model (pdbid 6zge). c Gallery shows cross-sections through narrow side views and circular top views of Wuhan virions. The side view shows two layers of density for RNP subunits in the nucleocapsid assembly (indicated by two red lines), which is separated from the top and bottom membrane bilayer. The circular top views show dense RNP subunits that extend to the bilayer. d Virion dimensions for 4 variants (Wuhan n = 75, Alpha n = 26, Beta n = 26, Delta n = 31). Box and whisker plot of the measurements of 3 orthogonal dimensions as shown in inset: circular view major axis (blue), circular view minor axis (yellow), side view (green). The boxes represent the interquartile range of measurements, line across box = median, x inside box = mean (see Supplementary Table 1 for values), whiskers extend to minimum and maximum measurements, circles = outliers. e Wuhan virions of aberrant ellipsoidal morphology show a two layer nucleocapsid, which abuts the membrane at the highly-curved sides while remaining separated from the membrane bilayers above and below.