Study Guide

Infectious Diseases - Viruses

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Basics of Viruses

Viruses don't belong to any of the three domains of life. That's because they aren't really considered living things (maybe they're undead things, like vampires and zombies). They're not living because they can't replicate without a hostile takeover of a living host cell.

A single virus particle is called a virion (pronounced veer- ee-on). A basic virion consists of:

  • Genome: genetic information encoded in either DNA or RNA
  • Capsid: outer candy coated shell made of proteins
  • Envelope (optional): lipid membrane with an additional layer of proteins outside the capsid

Example of an Influenza virus particle. The squiggly strands are the genome. The yellow layer is the protein capsid. The blue layer is the envelope of lipids, and the orange and pink spikes are glycoproteins on the surface on the envelope. Image from here.

Viruses aren't cells. They don't breathe or eat or drink or require energy. They're just bits of genetic material and some proteins that hang out waiting to hitch a ride with an unsuspecting host (or hostess). The basic (non)life story of every virus is:

  1. Enter a host cell
  2. Hijack the host machinery
  3. Replicate
  4. Release new viruses
  5. Rinse and repeat

Basically, the entire purpose of a virus is to infect something, which is why they are a major cause of infectious diseases.

You can see how the computer virus got its name. A computer virus silently enters a hard drive just like a real virus. It hijacks a computer and uses the computer's own machinery to help it spread. Users often don't know they have been infected until they experience the devastating consequences.

The first virus discovered (we're back to actual viruses, not the IT kind) was the Tobacco Mosaic Virus, which was discovered in 1898. Today there's an entire field of science dedicated to studying viruses, called virology.

Viruses can be found all over the place. Some viruses can exist in the environment for decades, waiting for a host. Others tend to be a bit wimpy, barely surviving outside a host. Viruses can vary in size, but they are all very itty bitty, even smaller than most bacteria. Think about it. They have to be smaller than a cell if they're going to infect it and then replicate inside it. Isn't it great when everything makes sense in the world?

Viral Infection

Viruses have been shown to infect a wide variety of living things, including plants, animals, and even bacteria. Each type of virus has its favorite host or even a favorite type of cell within the host.

Now, most viruses will be killed by the host's immune system without causing any illness. Sometimes they'll successfully infect a host but won't cause any disease symptoms…at least it might not right away. In a latent infection, viruses hibernate and can cause infection years later.

In fact, it's beneficial for a virus to not kill the host that it's infected (at least not immediately after setting up shop). That's because viruses can't replicate in a dead host (unless it's a zombie host, and then we're all in trouble).

The way that the virus gets into the host depends on the type of virus and the type of host. Lots of viruses can be picked up from a surface, like a table or telephone, or inhaled when someone coughs or sneezes in your general direction. In fact, we believe that covering your mouth when you cough or sneeze should count for community service (if you happen to also be helping an elderly person with their groceries while it happens).

However, some viruses wither away like a fish out of water when outside of a host. There are two options for these kinds of viruses. One way to deal with this is for a virus to set up temporary housing in an animal vector, like a mosquito or a flea, and wait hitch a ride to its desired host, like a dog or a human.

Otherwise, these viruses must be transmitted directly from host to host. A side effect of this is that the virus can often only be transferred through the host's bodily fluid, like blood or semen. This is the case for HIV.

Below is a chart showing different types of viruses and the parts of the body that they typically infect in humans. Do you recognize any of these viruses? Rabies? Herpes? Influenza?

Image from here.

Symptoms of a Viral Infection

Viral symptoms vary depending on which virus it is, how many virions were in the infecting posse, and the host that has been infected. Just as with a bacterial infection, there are certain symptoms that are common of many viral infections because they are actually symptoms of the immune system reacting to the virus. For example, many people experience fever or inflammation at the site of infection.

Viral infections tend to be more systemic than bacterial infections, meaning that the virus affects your entire body. We're talking about fatigue and whole body aches rather than just being sore at one place. Viruses also tend to cause lower fevers than bacterial infections, but these are just some general trends. There are bacteria that can spread throughout the body like a tsunami. There are also viruses that can cause a fever that is hot, hot, hot. Without a chat with your immune cells or a lab test to verify it, there is no way to tell if it is a viral infection or a bacterial infection.

Treating and Preventing Viral Infections

The top two ways of combating viruses are with:

  • Antiviral drugs
  • Preventative vaccines

Remember, antibiotics don't work against viruses.

Antiviral drugs are typically designed to work against a specific type of virus. It's difficult to make an antiviral that can affect multiple viruses, just because viruses are all very different.

Note: Bacteria are different too, but at least bacteria are all alive and have to follow all of the rules of life for basic cellular processes. Antibiotics can target these cellular processes to stop bacteria in their tracks. Viruses are renegades out on their own with no rules to follow.

Though viruses are all very different, they do have one thing in common: they hijack the host machinery to replicate. But, the host machinery can be difficult to target because, obviously, the host needs it too. Still, many labs are trying to develop antiviral drugs that target the host machinery because the benefits might just outweigh the risks sometimes.

Antivirals, just like antibiotics, can cause drug resistance if they are used too frequently. Like all genetic material in all species, mutations are frequent in viruses. RNA viruses are especially good at mutating. This is because the in-house copier of an RNA virus isn't very good. It makes mistakes and causes mutations so often that it's more like AutoCorrect than a copier. Do yucca underwear what werewolf trekking about?

But imagine if you were so bad at something that it actually made you better at everything. These mutations can sometimes be beneficial, and if one of them causes a drug to be less effective (like we discussed in the bacteria section), then it will be naturally selected for. Research is constantly trying to keep up with this ever-changing problem, developing new antivirals like mad.

Vaccines are also an important step in preventing infectious diseases caused by viruses. Vaccines are designed against a particular strain of virus. The flu shot is a vaccine that protects against influenza virus. Since the most prevalent influenza strains change each year, drug companies have to make a new vaccine every year. This means that the influenza vaccine changes faster than most fashion trends. You can read more about this in the In the Real World section.

Examples of Infectious Diseases Caused by Viral Infection


Acquired immune deficiency syndrome (AIDS) is caused by infection with the Human Immunodeficiency Virus (HIV). HIV is the virus, and AIDS is the disease caused by the virus. Not all people infected with HIV will develop AIDS.

HIV is currently the deadliest pathogen on the planet. It has caused more than 25 million deaths over the past three decades (that's about 2 million people per year). That's like the number of people holding hands in a chain stretching from New York City to Los Angeles. In 2011, it was estimated that there were 34 million people living with HIV, over half of which live in Sub-Saharan Africa. There are approximately one million people infected in the United States.

HIV is transmitted through bodily fluids, and is usually transferred from person to person during unsafe sex, sharing of intravenous drug needles, or from mother to child at birth. There's no vaccine for HIV, although a combination of antiviral drugs is often quite effective at keeping the virus from replicating. There have been two cases where a person has supposedly been "cured," which means that there are almost no viruses detected in their bodies.

Estimated HIV/AIDS prevalence among young adults (age 15-49) by country as of 2011. Image from here.

The Flu

The flu is one virus you were probably unlucky enough to catch once or twice already. The flu is caused by infection with the Influenza A Virus. Symptoms of the flu include coughing, sneezing, weakness, aches, and fever. In addition to the vaccine, which has to be modified every year, there are several antiviral drugs available to treat influenza infection.

Although flu viruses circulate the entire year, the number of infections peaks during the dry, colder months (which is the perfect time to enjoy some hot chicken soup). Each year, 3–5 million people are sick and 250,000–500,000 people die from the flu. Influenza also infects many animals, especially wild aquatic birds like ducks and geese.

The influenza virus has two proteins that stick out of the viral envelope like spikes. These proteins are called HA and NA. The different types of influenza are named for the type of spikes that each strain has. For example, H3N8 (the type of flu that a dog gets) has type 3 HA and type 8 NA. The 2009 "swine flu" strain was an H1N1.

As mentioned earlier in this section, influenza viruses continually mutate and change. The seasonal strain from one year to the next can be quite different; either because the spikes are a teensy bit changed or because they have a completely different type of spike.

Sometimes these differences can make one influenza virus strain particularly deadly. This type of strain can appear quickly and spread around the globe, causing a pandemic. A pandemic is more likely when a virus switches to humans from another species like pigs or birds. This is where the names "swine flu" and "bird flu" come from, not because Miss Piggy and Big Bird were among the first victims. These types are more dangerous because they are new strains that humans have no antibodies against.

Image from here.

"The Stomach Flu"/"Stomach bug"/"24 hour flu"

Don't let these misnomers fool you. The stomach flu isn't really caused by the flu virus at all, and it rarely lasts less than 24 hours. It's usually caused by a norovirus or a rotavirus infection, which leaves you with severe diarrhea/dehydration and occasional vomiting. These infections are transmitted through fecal material from infected people…think about that for a moment. Food, water, or surfaces that are contaminated with virus particles make their way into another host's mouth. Hope you've washed your hands today.

In the United States, 1 out of 14 people will become ill with norovirus each year. This sounds like a lot, but most people in the United States don't die. On the other hand, noroviruses and rotaviruses cause an estimated 200,000–500,000 deaths each year worldwide. Nearly all of these deaths are in children under 5 years old in developing counties. The next time you drink some clean water, don't forget to feel lucky.

Norovirus particles. Image from here.

Common Cold

The symptoms of the common cold are sore throat, runny nose, sneezing, and coughing, all of which can last up to two weeks. There are over 200 cold viruses, which is one of the reasons there's no cure for "the" cold. There's just too many viruses to cure, and they're always mutating to come back and infect us again. Most colds are caused by a rhinovirus. Yep, that's right, rhino as in rhinoceros. This is because the infection primarily affects the nose and upper respiratory tract. Therefore, they named it using the Greek word for nose, which is "rhin," the same root used in rhinoceros.


Rabies is a disease caused by infection with a rhabdovirus. It primarily affects wild animals, but it doesn't discriminate and will infect just about any mammal it finds. An affected animal or person is described as rabid. This is the same disease which infamously led to the demise of (spoiler alert) Old Yeller.

Symptoms in humans begin as fever, headache, and weakness. However, later symptoms include confusion, insomnia, anxiety, slight or partial paralysis, hallucinations, increase in saliva, difficulty swallowing, and fear of water. Death can occur within a few days of these severe symptoms.

A rabid dog with excess saliva. Image from here.

Approximately 55,000 people die each year from rabies, mostly in Africa and Asia from encounters with infected dogs. There is a preventative vaccine available, which is commonly administered to pet cats and dogs. If a human is bitten by a rabid animal, then a series of post-exposure injections can be done immediately to prevent the disease. However, once symptoms have set in, the disease is almost always fatal.

In 2004, the first person known to have survived full-blown Rabies without any injections was a young girl who soon became known as "the girl who lived." It's unknown whether she's a long lost American cousin of Harry Potter. You can listen to her story here.

Chickenpox and Shingles

Both Chickenpox and Shingles are infectious diseases caused by the Varicella zoster virus, although the diseases are very different. Chickenpox is highly contagious and usually affects children less than 10 years of age. The symptoms are fever, weakness, loss of appetite, and a characteristic rash that develops into fluid-filled blisters and scabs that look like oversized connect-the-dots.

The virus is transmitted from person to person through the air by coughing and sneezing, or through direct contact with the oozy blister fluid (gross). In the 1990's, there were nearly 4 million cases of chickenpox each year. However, there's now a vaccine available that has drastically reduced the number of cases.

Young boy with Chickenpox, still smiling! Image from here.

Shingles is a different disease, which is caused by varicella virions that were left over from a childhood case of chickenpox. Basically, the virions can hide in the body in a latent form and reactivate later in life. In about 10–20% of cases they can cause disease again, usually in people over 50. Shingles is a painful rash that can sometimes cause nerve damage or visual impairment. Each year there are over 1 million cases of shingles in the United States.

"Mono," Mononucleosis, "The Kissing Disease"

Mononucleosis (mono) is caused by infection with the Epstein-Barr virus (EBV). In the United States, 95% of adults 35–40 have been infected with EBV at some point. It often causes no symptoms at all. However, infection with EBV during adolescence causes infectious mononucleosis about 35–50% of the time.

It's spread through close contact with another person's saliva, thus earning the nickname "the kissing disease." Typical symptoms of mono are fever, sore throat, fatigue, and swollen lymph nodes. It can take 1–2 months for a person to get over the symptoms of mono. So that's 1–2 months of sticking to a strict no-smooching policy.

Genital Warts

Genital warts are caused by infection with the Human Papillomavirus (HPV). There are more than 40 strains of HPV. Symptoms are small bumps in the genital area of various sizes and shapes. In addition, certain strains of HPV have been shown to cause cervical cancer. Yikes.

HPV virus particle. Image from here.

The virus is transferred through sexual intercourse, and it can be passed along even when the partner shows no symptoms. Warts may not appear on an infected person for a long time, so they may pass the virus on without knowing they are infected.

Cancer doesn't always occur with HPV infection, and when it does, it typically isn't for years after initial infection. There's a vaccine that is effective at preventing some strains of HPV; however, there's no cure once you have HPV. Symptoms of the disease (warts) can be treated with ointments.

Viral Hemorrhagic Fever

There are a number of viruses that can cause viral hemorrhagic fever. The most common are Ebola and Marburg. Though these viruses are rare, there are occasional outbreaks in Africa. The fatality rate for both viruses is pretty high, with sometimes 80% of people who become infected dying.

These viruses cause multiple organ systems to fail and blood can leak out of blood vessels. They are among the scariest viruses on the planet, because they're plenty deadly and there are no vaccines, treatments, or cures available. They would be a great subject of a horror movie. Oh wait, they were; the virus at the center of the movie Outbreak was based on the Ebola virus.

Brain Snack

Smallpox is caused by infection with the Variola virus. Symptoms include high fever and fatigue, followed by a rash of spots on the arms and legs. Smallpox was a serious deadly disease for thousands of years, until the WHO said NO MORE.

The WHO started a program to vaccinate people left, right, and center around the world. In 1979, it was declared that smallpox was eradicated (you can cheer now). It was the first infectious disease that was defeated by human effort. Now, it exists only in a handful of research laboratories.

Vial of smallpox vaccine. Image from here.

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