Have You Gone Viral?

All the basic information you need to know about viruses that infect people.

What do you actually know about viruses?

Most people just know that viruses infect them and make them sick. So in these trying times with COVID-19, maybe it’s a good idea for us to all learn some basic viral biology.

There’s so much information out there about COVID-19 that I’m not going to say much about it. This article tells you about the main categories of viruses, how they reproduce, how they infect cells, their physical characteristics, and much more.

Let’s get started.

What are viruses?

Viruses are infectious particles.  We call them particles because they are not the same as cells and here’s why.

They lack any of the normal internal subcellular “machinery” that all other living organisms’ cells have. This includes the structures needed to make proteins or the proteins that are needed for independent metabolism and to make new copies of their nucleic acid genome.

Because of this, they fall into the category of what we call obligate intracellular parasites.  They can only reproduce inside a host cell.

Are they alive?

The perennial viral question.  It depends how you define life so some folks say yes and some say no.  As we stated above, they need to be inside a host cell to reproduce. No host cell available, no more viruses made.

But they do contain all the instructional material necessary to make new copies of themselves once inside a host.  So is that a form of life? You get to decide for yourself.

How big are viruses?

This is a very important question to answer.  Do you want to protect yourself from getting a viral infection? Then you need to either destroy or deactivate the viral particles or hide behind a barrier that the virus can’t penetrate.

To construct a viral barrier you need to make sure that the pore size is small enough to keep them from getting through it.  And know what CAN pass through it.

Viruses range in size from 20 nanometres (nm) up to about 250 nm. But what does that actually mean?  How can I “picture” that? Do you remember the microscope you used in high school Biology? Well, the smallest thing we can see with it is about 500 nm.

The width of a human hair is 80,000 to 100,00 nm wide.

The largest virus is around 250 nm. It would take about 300-400 of them stacked up on top of each other to equal the width of a single human hair!

And a few million of the 20 nm large viruses will fit on the head of a pin!

Now think for a moment about those face masks everyone is wearing these days to guard against COVID-19.  Do you think they can filter out something that small? Or even slow them down? Nope, they can’t. You can wear it if it makes you feel better to do so but it doesn’t serve any real purpose.

From Wikipedia “Surgical masks are not designed to protect the wearer from inhaling airborne bacteria or virus particles…” 

So let’s talk a bit about what makes a virus.

Viral structure

The general structure of most viruses is quite simple.  Their genome is a piece of DNA or RNA packaged inside a capsule made of proteins.  This structure is called the capsid.

Then, depending on what kind of virus it is, the capsid may be enclosed in a membranous structure called an envelope.

When there is an envelope, it usually contains additional molecules that protrude from the envelope.  Viruses like SARS or COVID-19 are called coronaviruses because the protruding molecules make them look like a sun with coronal flares.

The figure below is an electron microscope picture of typical SARS virus particles. You can see the protein molecules that stick out from the envelope quite nicely.

Kinds of Virus

Viruses were originally classified into 2 types, DNA viruses and RNA viruses. As we learned more, we discovered it wasn’t quite that simple!

By looking at their genomes and the proteins included in the capsid, modern viral taxonomy has distinguished 7 different classes of viruses.

This figure shows the 7 classes of viruses.  Here’s what the abbreviations mean if you’re curious but I’m not going to get into any detail about them in this article. Too technical!  ds is double-stranded, ss is single-stranded, (+) is the plus strand, (-) is the minus strand, RT is reverse transcriptase.

Viral structure

What do viruses look like? What are they made of?

In Biology, we call the appearance of an entity its morphology.  As an example, human morphology includes a trunk (abdomen and chest) supported on 2 legs which also has 2 arms that extend from it on either side.  And then there is a short tube at the top of the trunk that has another structure that has several openings and has 2 eyes, a nose and a mouth and 2 ears etc.  You get the idea. It can get very detailed! I barely started here.

This figure shows just how different the morphology for some of the 7 different types is.

How do viruses infect their hosts and reproduce?

Again, I don’t want to get too technical here.  This is not a course to teach you everything about viruses but is a quick overview of what viruses are and how they do what they do.

Because different kinds of viruses infect all the other kinds of creatures on this planet, there is no one method of infection that they all use.  And even looking just at the ones that infect humans, there are a few different ways they do this.

One of the most common ways viruses infect humans is by essentially “merging” with the cells to enter them.  How did they come to be able to do that?

This is sort of a chicken and egg question because we don’t exactly know how viruses evolved this method.  What we do know is the ones that use this method have a membranous coating that they picked up from the last cell they invaded.

To best get the idea, let’s start with the virus already having entered the cell.  Enzymes inside the cell digest the envelope (if there is one) and the capsid, which releases the viral genomic nucleic acids (DNA or RNA). The genome contains the “instructions” to make the proteins that make more viral genomes. The viral genome is then “read” by the cell’s “machinery” that it uses to read its own genome and makes the proteins encoded in the viral genome.

These viral proteins now co-opt other parts of the subcellular “production line” and use them to manufacture more viral genomes, viral capsid proteins and envelope glycoproteins.

The capsid proteins then assemble and form new capsids around a strand of the new viral genome, one or two genomes per capsid.  At the same time, the cell transports the new viral envelope glycoproteins to its cellular membrane. The new genome-containing capsids are transported to the cell membrane where they bud out from the cell.  They surround themselves with the host cell membrane which also contains viral envelope proteins.

Here’s a nice figure to summarize all that information.

It turns out that these viral glycoproteins in the envelope actually bind to receptor molecules embedded in that particular type of cell’s membrane.  Let’s use our lung cells as an example. All the lung’s cells have that receptor molecule in and on their membranes.

The new viral particles’ envelopes bind to the same receptors present on other nearby cells and the cycle repeats over and over.  In some cases, the original host cell is killed but in others, it is not. Even if it is not killed, it is making new viral particles so it can’t perform the function it was originally designed for nearly as well, if at all. That plus the inflammatory response from the immune system is what causes the sickness or disease the creature suffers from. Especially when a high percentage of that particular cell type is infected.

Why are viruses specific to a particular host?

Let’s stay with the virus that infected our lungs. Its envelope only contains glycoproteins recognized by receptors on other lung cells.  It is not recognized by the liver, brain, kidney or any other tissue lacking the receptor. This is why viruses are so specific.  For example, the hepatitis virus only infects liver tissue cells and HIV only infects a specific kind of immune cell called a T cell. HIV kills this class of T cells which are a critical component of our immune system. The whole immune system is disabled without these T cells.

Some viruses can actually remain latent in the cell.  Herpes virus is one example. It actually makes copies of itself inside the cell nucleus. Then it buds from the nucleus with an envelope made from the nuclear membrane, not the cell’s outer membrane.  Some copies do not actually bud out of the nucleus but remain inside it as minichromosomes.

These minichromosomes stay inside the nucleus until some kind of stress signal activates them to open up and start producing more virus particles.  These particles then cause blisters such as cold sores or genital sores. And that’s why herpes infection is life-long. Some particles always remain behind just “waiting” to become active again!

What are other viral hosts?

Viruses are found in every other life form.  All the other creatures in the plant and animal kingdoms, and they also infect other microorganisms including bacteria and archaea, single-celled organisms that are not bacteria.

Viruses that infect bacteria are called bacteriophages. “The term comes from “bacteria” and the Greek φαγεῖν (phagein), meaning “to devour”. They are often referred to simply as phages.

Many early molecular biology studies used phage particles and their bacterial hosts as model systems to begin to understand basic molecular genetic and genomic biology.

 What else do I need to know?

I’ve covered all the basic biology of viruses you need to feel a bit more knowledgeable about them.

You know how small they are and the different parts that make a virus particle. You also know the different classes of viruses, how they infect humans, how they reproduce and the different organisms they use as hosts.

Any more information would start to get us into serious viral biology.

Note: I have specifically avoided talking about the COVID-19 coronavirus. Because there is so much information out there, I would just be repeating everything everyone else has already written about.

I hope you found this interesting and worth spending a few minutes of your time to read.

Until next time,

Rich

Hey! If you enjoyed this article then please subscribe to my newsletter to hear about my latest articles and grab my free ebook here.

Carl Zimmer’s Newsletter About the Covid-19 Virus

Do you know who Carl Zimmer is? If you are a regular reader of this blog, then you probably do know. And if you don’t know who he is, then read on.

Carl is one of the premier biological science columnists at the New York Times. He has his own website and blog, and he publishes a weekly newsletter, Friday’s Elk, that I avidly subscribe to. And you should too!

This past Friday’s Elk was about the Covid-19 virus and is one of the best-unbiased sources of information about this outbreak that I have read, yet.

I asked Carl for his permission to share it with you, my readers, and he graciously granted that. Here is what Carl has to say.

“Things have certainly changed since the last Friday’s Elk. The world has experienced over 100,000 infections of Covid-19, caused by a virus, SARS-CoV-2, that we didn’t even know about till a few weeks ago.

At first, we Americans complacently looked at the news as just another overseas disaster. As of this afternoon, there are 370 confirmed cases in the United States (one just a thirty-minute drive from where I live in Connecticut). Because our testing program is a mess, it’s certain there are many more–and transmission will bring more in weeks to come.

Anyone who says that no one could imagine this happening is ignorant or lying. Virologists have been tracing the origin of new human diseases from animal hosts for decades. The new virus, SARS-CoV-2, belongs to a lineage of bat viruses that has already produced two worrisome human diseases, SARS and MERS, in the past two decades. We know a fair amount now how viruses circulate in other species, how they spill over into ours, and then how they spread–either a little or a lot. You didn’t have to read virology journals to know about this. We science writers have been writing this story over and over again.

When I started out in journalism, my senior colleagues were writing about emerging diseases like Ebola and Four Corners Disease and HIV. Laurie Garrett published the far-sighted book The Coming Plague in 1994. Other books followed. I later wrote a short primer, A Planet of Viruses, in which I emphasized that viruses have always been with us, indeed even making up a sizable part of our genome. But even as we triumphed over smallpox and rinderpest, we were coming to appreciate just how many viruses we might run up against as we continued to devastate the natural world. David Quammen’s 2012 Spillover documented this threat in vivid detail.

So here we are, facing a new virus with which we have no experience whatsoever–both scientifically and immunologically. Scientists are working hard to estimate the key variables about this virus–such as how quickly it spreads from person to person and how likely an infection is to turn fatal. Those are not fixed values like the mass of an electron or the speed of light. Viruses spread more slowly when public health systems put up barriers between their hosts. Viruses can be deadlier when people can’t get decent medical care.

Roughly speaking, Covid-19 is much less deadly than SARS, but much more deadly than seasonal flu. While SARS had trouble spreading outside of hospitals, Covid-19 is spreading readily on cruise ships, within families at home, and among the elderly in long-term care facilities. While everyone seems vulnerable to infection, children typically only develop mild symptoms, while older people are at greater risk for serious illness or death.

For most people who get the virus, it will be a mild infection. But according to one rough estimate from Marc Lipsitch at Harvard, 20 to 60 percent of all adults may get infected. That could translate into a terrible toll, not just in terms of deaths but in terms of patients who need ventilators to stay alive. If thousands of cases hit American hospitals at once, it’s not clear how well the healthy system will hold up.

We don’t know if the virus will keep spreading into the spring and summer, or if it will fade as other winter respiratory viruses do. If it ebbs, chances are it will come back in the fall, perhaps in a roaring second wave. Vaccines won’t be ready till next year at the earliest. It’s possible that an effective antiviral may emerge in the coming months, which might help the desperately ill.

But for now, the best weapons against this virus are the classic ones. Social distancing, including school closures, may help to slow the coming wave so that fewer people need help at any moment. And washing hands keeps the virus from using them as a springboard to get into your mucous membranes–and ultimately your lungs. 

So let us give thanks to Ignaz Semmelweis! Washing hands may seem tediously obvious as a way to stop diseases, but it wasn’t until the mid-1800s that Semmelweis noticed that doctors themselves could spread fevers from patient to patient. If you find yourself looking for books to read during self-imposed quarantine, let me recommend The Doctor’s Plague by Sherwin Nuland, a short, potent account of Semmelweis’s struggle to make hand-washing our best weapon against enemies we can’t see and struggle to understand.

Check in on the CDC Covid-19 page for updated information on the disease and what to do about it.

If you still find yourself hankering for something to read–perhaps something not about viruses–I have a feature in the Atlantic this week about one of the strangest stories of the nuclear age. We released a vast pulse of radiocarbon into the atmosphere in the 1950s, which has infiltrated the biosphere ever since, including our own brains and bones. I’ve written a biography of the “bomb spike,” and what it has told us about our world.

Usually at the end of these emails, I list my upcoming talks. I’m going to skip them this time around because I’m honestly not sure how much traveling I’m going to do for the next few months. I’d rather not help spread SARS-CoV-2 any further than it’s going to get without me. I’ll update as the situation clarifies.

Stay well!

My award-winning book, She Has Her Mother’s Laugh, is now out in paperback. You can order it now from fine book mongers, including Amazon, Barnes and Noble, BAM, Hudson Booksellers, and IndieBound.

You can find information and ordering links for my books here. You can also follow me on Twitter, Facebook, Goodreads, and LinkedIn. If someone forwarded this email to you, you can subscribe to it here.

Best wishes, Carl“

Friday’s Elk by Carl ZimmerYale University English Department P.O. Box 208302 New Haven, CT 06520-8302 USA

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