Graphical abstract

During its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IVs) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped intracellular mature virions (IMVs) that lack D13. Here, we performed cryo-electron tomography (cryo-ET) of frozen-hydrated vaccinia-infected cells to structurally characterise the maturation process in situ. During IMV formation, a new viral core forms inside IV with a wall consisting of trimeric pillars arranged in a new pseudohexagonal lattice. This lattice appears as a palisade in cross-section. As maturation occurs, which involves a 50% reduction in particle volume, the viral membrane becomes corrugated as it adapts to the newly formed viral core in a process that does not appear to require membrane removal. Our study suggests that the length of this core is determined by the D13 lattice and that the consecutive D13 and palisade lattices control virion shape and dimensions during vaccinia assembly and maturation.

SARS-CoV-2 is a lipid-enveloped Betacoronavirus and cause of the Covid-19 pandemic. To study the three-dimensional architecture of the virus, we perform electron cryotomography (cryo-ET) on SARS-Cov-2 virions and three variants revealing particles of regular cylindrical morphology. The ribonucleoprotein particles packaging the genome in the virion interior form a dense, double layer assembly with a cylindrical shape related to the overall particle morphology. This organisation suggests structural interactions important to virus assembly.

During replication, vaccinia virus and other poxviruses such as monkeypox first assemble non-infectious spherical immature virions (IV) in the cytoplasm of infected cells. The IV membrane, which is fully coated by a viral D13 lattice, encapsidates both viral proteins and the DNA genome. Subsequently, the D13 lattice is lost and IV transitions into the brick-shaped intracellular mature virus (IMV) with an organised core enclosing the genome. We have an overview of the maturation of IV into IMV but our structural understanding remains limited. Here, we performed cryo-electron tomography of frozen-hydrated vaccinia-infected cells to structurally characterise the maturation process in situ. We found that D13-coated IV have similar diameters and lattice dimensions to spherical D13 assemblies formed in vitro, confirming the size of IV is determined by D13. During IMV formation a new pseudohexagonal lattice forms inside IV to produce the viral core. This lattice is composed of trimeric pillars with outward projections that appears as a palisade in cross-section. Strikingly, the diameter of IV precisely matches the IMV long axis, suggesting the length of the core, and hence the IMV, is determined by the D13 lattice. During maturation the viral membrane becomes corrugated as it adapts to the shape of the core. This suggests that the 50% reduction in volume during the transition of IV to IMV does not require membrane removal. Our observations suggest that the consecutive D13 and palisade lattices structurally define vaccinia assembly and maturation.