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Basics of Viruses

Viruses do not belong to any of the three domains of life. This is because they aren't considered to be living things (like vampires and zombies). They are not living because they cannot replicate without the (forced) assistance 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 shell made out 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.

Viruses are not cells. They do not breathe or eat or drink or require energy. They are just bits of genetic information and protein that hang around the planet hoping they will get close enough to a living cell to get inside. The basic (non) life story of every virus is:

1) Enter a host cell
2) Hijack the host machinery
3) Replicate
4) New viruses are released, starting the process over again

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 was the Tobacco Mosaic Virus which was discovered in 1898. Today there is 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 waiting for a host, but others can barely survive outside a host. Viruses can vary in size but they are very itty bitty, even smaller than most bacteria. Think about it. They have to be smaller than a cell if they are 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 a favorite host or favorite type of host cell that it typically infects: blonde, brunette, red-head, emu, tobacco plant, or E-coli.

As mentioned previously, most viruses will be killed by the host's immune system without causing any illness. Other times, they will successfully infect a host but will not cause an infectious disease… at least it might not right away. In a latent infection, viruses hibernate and can cause infection years later.

In fact, it is beneficial for a virus NOT to kill the host that it has infected (at least not as soon as it sets up shop) because viruses cannot replicate in a dead host. This is why there are vector animals which are healthy carriers of the virus. Of course, there are also many virus infections that can be deadly too. We will discuss these types of infections in more detail.

The way that the virus gets into the host depends on the type of virus and the type of host. Many viruses are similar to bacteria and can be picked up from a surface or inhaled when someone coughs or sneezes. 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. These viruses must be transmitted directly from host to host. Therefore, they can often only be transferred through 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?

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.

However, viral infections are generally more systemic than bacterial infections. This means that the virus affects your entire body. We are 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 do NOT work against viruses.

Antiviral drugs are typically designed to work against a specific species of virus. It is difficult to make an antiviral that can affect multiple viruses 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. Viruses are renegades out on their own with no rules to follow.

The only thing many viruses have in common is the host machinery that they hijack in order 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 risks outweigh the benefits.

Antivirals, just like antibiotics, can cause drug resistance if they are used too frequently. Many viruses are frequently mutating, especially RNA viruses. This is because the in-house copy machine of an RNA virus is not very good. It makes mistakes and causes mutations so often that they should have aliens beat it with a folding chair.

If one of these mutations causes a drug to be less effective (like we discussed above 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 Speedy Gonzalez.

Vaccines are also an important step in preventing infectious diseases caused by viruses. Vaccines must be designed against a particular strain of virus. You might have heard of or had to get a "flu shot." This is a vaccine to protect against influenza virus. Since the most prevalent influenza strain changes each year, they 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). 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, recently just less than 2 million people per year. That is 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 or from mother to child at birth. There is 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.

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.

"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 is usually caused by a norovirus or a rotavirus infection, which causes severe diarrhea/dehydration and occasional vomiting. Both viral infections can start from contaminated food or water, or by touching contaminated surfaces and then touching your mouth.

In the United States 1 out of 14 people will become ill with a norovirus each year. This sounds like a lot, but most people in the United States do not 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 from 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 which can last up to two weeks. It can be caused by an infection with over 200 possible viruses. However, it is most frequently 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. An affected animal or person is described as rabid. (Spoiler Alert.) This is the same disease which infamously led to the demise of 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.

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 is unknown whether she is a long lost American cousin of Harry Potter. You can read about it 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

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

Young boy with Chickenpox, still smiling!

Shingles is a different form of disease caused by varicella virions leftover from a childhood case of Chickenpox. Basically, the virions can hide in the body in a latent form and can 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 which 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 is 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 the symptoms of "mono" to disappear.

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 (as mentioned in the introduction section).

HPV virus particle.

The virus is transferred through sexual intercourse even if the partner shows no sign of warts at the time. Warts may not appear on an infected person for a long time and they may pass the virus on without knowing they are infected.

Cancer does not always occur and it typically does not occur until years after initial infection. There is a vaccine that is effective at preventing some strains of HPV. There is no treatment once you have HPV although the warts may be treated with ointments.

Viral Hemorrhagic Fever

This infectious disease can be caused by infection with a number of rare viruses. The most common are Ebola and Marburg. These viruses are rare although 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 are deadly and there is no vaccine, treatment, or cure available. They would be a great subject of a horror movie. Oh wait, they were; this is the type of virus that is described in the movie Outbreak.

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 which was defeated by human effort. Now, it exists only in research laboratories. In the wrong hands, it could be a dangerous bioweapon.

Vial of smallpox vaccine.

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