This article is part of the Science in Sci-fi, Fact in Fantasy blog series. Each week, we tackle one of the scientific or technological concepts pervasive in science fiction — space travel, genetic engineering, artificial intelligence, etc. — with input from an expert.

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About the Expert

E.E. Giorgi is a computational biologist at the Los Alamos National Laboratory. She has been working on HIV since 2006. She spends her days analyzing genetic data, her evenings chasing sunsets, and her nights pretending she’s somebody else. On her blog, E.E. discusses science for the inquiring mind, especially the kind that sparks fantastic premises and engaging stories.

Her detective thriller CHIMERAS, a medical mystery, is a 2014 Readers’ Favorite International Book Award winner, and her futuristic sci-fi thriller GENE CARDS is a Stargazer Literary Prizes finalist winner.

8 THings Authors Should Know About Viruses

My 12-year-old is a very picky reader. I never managed to get him hooked on Harry Potter, Percy Jackson or any of those bestselling characters, but he’s read the Hobbit and all three books in The Lord of the Rings trilogy when he was 10. So when he came home with a new book from the library and devoured it in three days I was in awe. I picked up the book and started reading it, eager to find out what this author had done to enthuse my child.

The premise hooked me, but the ending had my jaw drop. I put the book down, called my 12-year-old, and lectured him on viruses from A to Z. My kid knows I work on HIV, so I told him about some very special people—we call them elite controllers—who have the virus but, unlike the vast majority of HIV-infected people, they never get sick with AIDS. I told my son that we do not kill those people to study their brains, we do not torture them to see how they react, we do not keep infecting them over and over again, and we do not use them as guinea pigs.

My son listened to everything I had to say, then nodded and went back to read the rest of the books in the awful-virus trilogy.

I’ll admit that viruses make fantastic plot devices for science fiction. I’m a writer myself and I’ve used them in virtually every book I’ve written so far. They are the subtlest of serial killers. And if you ever want to see how an investigation is conducted to catch any of these microscopic serial killers, watch And The Band Played On, a movie/documentary on how the spread of AIDS was linked to an infective agent and how its transmission route was discovered.

Now that most information is available on the Internet through Wikipedia and many fantastic websites like This Week in Virology and MedlinePlus, there’s no excuse for not researching these fascinating little machines and getting the basic facts right. It makes for a much more enjoyable reading experience and, as you’ll see, viruses will surprise you with plot twists that are even better than what your own imagination would’ve come up with.

1. What is a virus?

A virus is a microscopic machine that carries genetic material and has one purpose: replicate. Too small to carry all the genes they need to self-replicate, viruses infect cells so they can hijack the cell’s own machinery in order to replicate. By doing so, they disrupt the cell’s own processes that keeps it alive and that’s how they make us sick. Some viruses can cause long-lasting inflammation that, if not treated, can eventually lead to cancer, as is the case, for example, with the human papilloma virus, which can cause cervical cancer.

The fact that they carry genetic material is what makes viruses so special and, as it turns out, so useful, too. In order to replicate, some viruses insert their DNA inside the cell’s genome and, once there, they are able to turn ‘on’ or ‘off’ some of the genes. Indeed, these pesky little machines can tap into the deepest wiring of our cells and induce changes in gene expression (called epigenetic changes). And if you are looking for a way your fictional virus can make the most damage, how about this: some of the epigenetic changes induced by a virus can be not only permanent, but also heritable.

So far I told you that bad news. But there are some good news, too.

2. Without viruses we wouldn’t have vaccines.

I know, it probably sounds like a tautology, since we wouldn’t have discovered vaccines if we didn’t have viruses. A vaccine is an inactivated form of the virus that can be presented to the immune system without the aftermath of an infection. It’s like giving a hunting hound an olfactory clue to sniff so he knows what to hunt. But the inactivated virus still needs to be presented to the immune system, and what better way than to put it inside another virus?

Indeed, a vaccine is made of two components: an outer shell, or viral vector, and an inside, which is the inactivated virus that needs to be presented to the immune system. Common viruses like the cold virus (adenovirus) are often used as vectors for vaccines because we know they can’t do much damage. The virus is modified in the lab, and its contents are removed and replaced by the vaccine strains.

In the past, vaccine trials have gone wrong because of unexpected immune reactions to the viral vector in use. So, if you need a plot twist for the fictional vaccine in your book, one way to go is to create a really bad immune reaction to the vector.

3. Without viruses we wouldn’t have gene therapy.

Viruses can be very specific, and infect certain cells only. For example, HIV infects T-cells, which are part of our immune system. Hepatitis viruses instead infect liver cells. This ability to inject their genetic material into specific cells can be exploited for therapeutic purposes. Gene therapy is a way to replace damaged or defective genes with healthy ones. Like vaccines, gene therapy too makes use of a viral vector as the carrier for the replacement genes.

For example, HIV has been used in a gene therapy trial to cure a type of leukemia characterized by an abnormal proliferation of B-cells. B-cells and T-cells are part of our immune system. HIV targets and kills T-cells. Researchers modified the HIV virus so that it would still “attack” T-cells but this time, instead of inserting its own genetic material inside the cell, it inserted a particular gene that enabled the T-cells to recognize and kill the malignant B-cells. Pretty ingenious, right?

4. Don’t forget the incubation time!

Incubation is the time that elapses between the moment the very first viral particle enters the host and the onset of symptoms. It can be hours, days, years, but it’s never, never zero. That’s because the immune system doesn’t react immediately. It takes time for those viral proteins to be chopped up and presented to the surface of the cell. Once there, they are like red flags ready to be seen. Once recognized as a threat, the immune system mounts its counterattack by creating many T-cells and antibodies exactly like the ones that recognized the enemy in the first place. For example, in the case of HIV, it usually takes around three weeks before we start seeing an immune response.

Now, here is the fun part for writers: incubation time is what makes viruses so elusive. The only clues viruses leave are symptoms, but if they happen days or even weeks after the virus entered the body, how are you going to find out when and where the contamination happened? That’s why authors shouldn’t ignore incubation time, rather, they should make it part of the plot and have fun with it. Not only you can make incubation last as long as you want or need, but it is perfectly reasonable that different people will have different incubation times. Try and catch a killer without knowing when, exactly, it struck the victim!

5. There’s more to incubation time: latency.

Some viruses can enter a cell and do nothing for days, months, years. They enter a state called “latency.” They are “sleeping”, in a way, a Trojan horse hidden inside the body. Sometimes all it takes is a stressful week to weaken the immune system and present the perfect opportunity for the virus to wake up and strike. HIV is one of such viruses. In March 2013 the first child to ever be cured of HIV was announced to the world. The child, born HIV-positive, had been on antiretroviral drugs for about a year and a half until the mother stopped taking her to the doctor and giving her the medications.

When the child was seen by doctors again, she had no detectible viral load. Had she been cured of HIV? That’s what everybody thought. It took one year, but eventually the virus came back. It had remained dormant and well hidden inside the child’s body, but in due time it started replicating again and sure enough, the child’s viral load started growing again. There are viruses in the herpes family that can hide in this latency state for decades, just waiting to catch the immune system at a low point.

Latency is a great plot device if you want to turn your fictional virus into a bioweapon. Put your source in an airplane and then watch it spread. If you delay the onset of symptoms, it will create a great puzzle for the investigators to try and retrace the origin of the contamination.

6. Some viruses spread easily, and some do not

If your virus is a bioweapon, you want to make it easy to spread, and the best way to do that is to make it airborne: it’ll spread through saliva aerosol with a sneeze. The influenza virus is the perfect example. On the other hand, Ebola (though deadly) is too big to be airborne. If you need your virus to be less efficient, make it spreadable through fluids like blood or semen. You can even play around with genetics, and make only some people with a certain genetic mutation be prone to develop symptoms, while the others can still spread the virus without ever showing symptoms.

7. Viruses can cause many different symptoms

This is one aspect of viruses where you can do virtually whatever you want, so long as you remember to account for that critical incubation time. Viruses can affect any part of your body: muscles, respiratory tracts, stomach and bowels, brain. HIV affects the immune system, for example. Patients who develop AIDS end up dying of any opportunistic infection because by then, the virus has debilitated the immune system to the point that a common cold becomes deadly. And because viruses have the ability to mess up with the on/off switches of our genes (the epigenetic changes I explained earlier), you can even have your virus trigger some weird autoimmune disorder.

Or, you can twist it the other way around: you can have the virus actually kill malignant cells in the body. Such viruses exist and are called oncolytic viruses because they infect tumor cells. Researchers are currently experimenting with a modified poliovirus that could potentially kill certain types of brain tumors.

8. The viruses inside us: endogenous retroviruses.

Earlier I said that what makes viruses so special is the fact that they carry genetic material. Retroviruses in particular have the ability to insert their genome inside the host cell’s DNA. Now, imagine one of those viruses inserting its genome inside a germ line cell and then becoming latent. Germ line cells are those cells that become spermatozoa in men and oocytes in women. If such cell now carries the inserted viral genomes and becomes a fertilized egg, the viral genome will indeed be passed on to the offspring.

You think this is far-fetched? Think again: roughly 10% of our genome originated exactly like that, from retroviruses that, millions of years ago, infected germ line cells. Again, another potentially great plot element, with an even creepier factor, as now the killer is hidden inside our very own genome.

In reality these proteins, though initially completely silent, have over time found new functions throughout evolution. For example, some of these retroviral proteins are expressed in the mammalian placenta, which makes sense if you think that what viruses do to survive is hide from the immune system. In a way, a fetus too has to be hidden from the immune system because it represents extraneous tissues (hence, an antigen) growing inside the mother’s body.

I hope you’ve enjoyed this overview on viruses. Viruses are not only fun to write about, but they are also very versatile: they can be your serial killer or your deus ex machina, they can work for the bad guys as bioweapons, or for the good guys as the unexpected cure in a bad twist of events.

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