SARS E!

How does this virus assemble and get out of the cell? The key proteins are named S, M, N, and E.

True to their tiny size, viruses typically have short genomes and short names for their genes, which are relatively few. Coronaviruses generally have two halves to their genomes- a big polyprotein that gets translated right away from the genome RNA, and encodes key proteins, some of which interfere with host functions, and others of which include its own replicase, and proteases that cleave itself into those pieces. The other half of the genome is expressed later, into the proteins that make up the baby virions- the envelope and nucleocapsid, along with a slew of smaller proteins that have other, and sometimes still unknown, functions.

Once all this has gotten going, the virions have to assemble and escape from the cell- a complicated and interesting process, not completely understood, though blowing up the cell through inflammation, apoptosis, and general tissue destruction certainly helps. Genomic viral RNAs, as they are made in the cell cytoplasm by the viral replicase, get bound by the N protein, which is the viral protein that binds and packages the genome, and also has binding sites for the M protein, which organizes the outside envelope. N has other roles in controlling host processes, but this is its major function. These N+genome RNA complexes (which are regarded as the nucleocapsid) find their M partners sticking out of the endoplasmic reticulum (ER, or actually a post-ER compartment called ERGIC) that is the major site in cells of protein synthesis of membrane proteins and secreted proteins. Binding promotes budding of the genome complex into the ER, forming a nascent virion, now inside the ERGIC.

Final portion of the SARS life cycle. Virion proteins are made by ribosomes (green) from gene-sized portions of the viral genome, at lower left. The nucleocapsid protein (yellow) gathers up the replicated RNA genomes into packages, and then docks onto the membranes of the ERGIC, or endoplasmic reticulum-golgi intermediate membrane compartment, specifically on the M proteins (red) exposed there, that have been translated into the endoplasmic reticulum and formed homogenous rafts. Then all that is left is to follow the endocytic pathway out of the cell, or wait for the cell to blow up by other means. In actual virions, there are many more M proteins than S proteins, and extremely few E proteins.

The M protein has in the mean-time been synthesized in vast amounts and has several important properties, being the main protein that constitutes and drives formation of the viral envelope. It is an integral membrane protein, and associates with itself, in a particular array that prefigures the complete virion and excludes non-viral membrane proteins. M protein also, in these rafts of itself, makes space for the S protein- the surface spike which gives the virus its name (corona) and which binds to the next target cell- in someone else's lung tissue. And it binds to the N protein, so that the virus envelope engulfs the packaged genome as it docks from the cytoplasm.

E protein from original SARS. That is it! Red denotes hydrophobic amino acids, blue hydrophilic, and stars the charged amino acids.

That leaves the E protein.. what is it doing? It is a tiny (76 amino acid) membrane protein, important, though not essential, for viable viruses. Indeed it is so important that viruses with this gene experimentally removed, while able to limp along at low levels, quickly evolve a new one from scratch. But it is present in virions only in very small amounts. Its structure indicates one transmembrane domain, but predictions have been ambiguous- some methods predict two, some only one. This may suggest that this protein truly has somewhat ambiguous membrane localization, which might suggest a key function in the budding process, encouraging the last, critical transition from membrane invagination to true, fully enclosed virion.

You might not need many E proteins to do this, just a small ring around the final lip of the M-protein led vesicle. E binds to M protein, and the two of them alone are sufficient to make virion-like particles in experimental cells. N protein is not needed at all, nor a genome! Yet E is thought to also be able to bind to S, helping anchor it in the viral envelope. E can also bind to itself in complexes form membrane pores, one of whose effects is to promote inflammation and apoptosis, i.e. cell death. As if that weren't enough, E protein also contains a regulatory domain (PBM) that can bind hundreds of cellular proteins to regulate cell function, particularly dysregulating cell-cell junctions to form multi-cellular synctia that allow viral spread to neighboring cells, while impeding immune responses. A lot to do for such a small protein!

Virions lacking E, made with only M, are abnormally shaped, and ones made with mutant E proteins have novel, still abnormal, shapes. This leads to the idea that M forms flat sheets, and E helps the viral envelope curve, as it must to form the spherical virion. As mentioned above, it is also quite possible that E helps with the ultimate encirclement of the virion, the final membrane-fusing stage of budding that is actually rather tricky to accomplish and requires specialized machinery in the cell and in most membrane-envelope viruses. So there remains quite a bit to learn about the machinery of this virus, for all we know so far. And we are naturally even more curious about more practical matters, like whether all this can help create a vaccine, how exactly it spreads, whether it provides immunity after infection and for how long, and how much each of our protective measures, like masks, gloves, washing, disinfecting, etc., really help.

• Social networks, evolution, the friendship paradox, and epidemic modeling.
• Coronaviruses remain viable for over an hour in aerosol, and for many hours on hard surfaces. So they spread everywhere, mask or no mask.