What’s a virus, anyway? Part 1: The bare-bones basics

As the coronavirus pandemic spreads across the globe, the term "virus" gets a lot of airplay. But what exactly are viruses, and how do they spread? Here's a primer, with a hat tip to Stanford virologist Jan Carette, PhD.

For starters, viruses are easily the most abundant life form on Earth, if you accept the proposition that they're alive. Try multiplying a billion by a billion, then multiply that by ten trillion, and that (10 to the 31st power) is the mind-numbing estimate of how many individual viral particles are estimated to populate the planet.

Is a virus a living thing? Maybe. Sometimes. It depends on location. "Outside of a cell, a viral particle is inert," Carette told me. On its own, it can't reproduce itself or, for that matter, produce anything at all. It's the ultimate parasite.

Or, you could say more charitably, very efficient. Viruses travel light, packing only the baggage they absolutely need to hack into a cell, commandeer its molecular machinery, multiply and make an escape.

When it comes to viruses, there are exceptions to nearly every rule. But they do have things in common, said Carette.

A virus's travel kit always includes its genome and a surrounding protein shell, or capsid, which keeps the viral genome safe, helps the virus latch onto cells and climb inside and, on occasion, abets its offspring's getaway. The capsid consists of identical protein subunits, whose unique shapes and properties determine the capsid's structure and function.

Some viruses also wear greasy overcoats, called envelopes, made from stolen shards of the membranes of the last cell they infected. Influenza and hepatitis C viruses have envelopes, as do coronaviruses, herpesviruses and HIV. Rhinoviruses, which are responsible for most common colds, and polioviruses don't. Here's a practical takeaway: Enveloped viruses particularly despise soap because it disrupts greasy membranes. Soap and water are to these viruses what exhaling garlic is to a vampire, which is why washing your hands works wonders.

How do viruses enter cells, replicate and head for the exits?

For a virus to spread, it must first find a way into a cell. But, said Carette, "penetrating a cell's perimeter isn't easy." Cells' outer membranes are normally tough to penetrate without some kind of special pass. But viruses have ways of tricking cells into letting them in. Typically, a portion of the viral capsid will have a strong affinity to bind with one or another protein dotting the surfaces of one or another particular cell type. The binding of the viral capsid with that cell-surface protein serves as an admission ticket, easing the virus's invasion of the cell.

The viral genome, like ours, is an instruction kit for the production of proteins the virus needs. This genome can be made up of either DNA, as is the case with virtually all other creatures, or its close chemical relative RNA, which encodes genetic information just as DNA does but is much more flexible and somewhat less stable. Most mammal-infecting viruses' genomes are made of RNA. (Not herpesviruses, though.)

In addition to the gene coding for its capsid protein, every virus needs another gene for its own version of an enzyme known as a polymerase. Inside the cell, viral polymerases generate numerous copies of the invader's genes, from whose instructions the cell's obedient molecular assembly line produces capsid subunits and other viral proteins.

Capsids -- a virus's protein shell -- self-assemble from their subunits, often with help from proteins originally made by the cell for other purposes, but co-opted by the virus. These fresh copies of the viral genome are packaged inside newly-made capsids for export.

Viral genomes can also contain genes for proteins that can co-opt the cellular machinery to help viruses replicate and escape, or that can tweak the virus's own genome -- or ours. The genome can contain as few as two genes -- one for the protein from which the capsid is built, the other for the polymerase -- or as many as hundreds (as in herpesviruses, for example).

Often, the virus's plentiful progeny punish the good deed of the cell that produced them by lysing it -- punching holes in its outer membrane, busting out of it and destroying the cell in the process. But enveloped viruses can escape by an alternative process called budding, whereby they wrap themselves in a piece of membrane from the infected cell and, in these newly acquired greasy overcoats, diffuse through the cell's outer membrane without structurally damaging it. Even then, the cell, having birthed myriad baby viruses, is often left fatally weakened.

 Author: Bruce Goldman