Intro to viruses

What a virus is. The structure of a virus and how it infects a cell.

Key points:

  • A virus is an infectious particle that reproduces by "commandeering" a host cell and using its machinery to make more viruses.
  • A virus is made up of a DNA or RNA genome inside a protein shell called a capsid. Some viruses have an internal or external membrane envelope.
  • Viruses are very diverse. They come in different shapes and structures, have different kinds of genomes, and infect different hosts.
  • Viruses reproduce by infecting their host cells and reprogramming them to become virus-making "factories."

Introduction

Scientists estimate that there are roughly 103110^\text{31} viruses at any given moment1^1. That’s a one with 3131 zeroes after it! If you were somehow able to wrangle up all 103110^\text{31} of these viruses and line them end-to-end, your virus column would extend nearly 200200 light years into space. To put it another way, there are over ten million times more viruses on Earth than there are stars in the entire universe2^2.
Does that mean there are 103110^\text{31} viruses just waiting to infect us? Actually, most of these viruses are found in oceans, where they attack bacteria and other microbes3^3. It may seem odd that bacteria can get a virus, but scientists think that every kind of living organism is probably host to at least one virus!

What is a virus?

A virus is an tiny, infectious particle that can reproduce only by infecting a host cell. Viruses "commandeer" the host cell and use its resources to make more viruses, basically reprogramming it to become a virus factory. Because they can't reproduce by themselves (without a host), viruses are not considered living. Nor do viruses have cells: they're very small, much smaller than the cells of living things, and are basically just packages of nucleic acid and protein.
Still, viruses have some important features in common with cell-based life. For instance, they have nucleic acid genomes based on the same genetic code that's used in your cells (and the cells of all living creatures). Also, like cell-based life, viruses have genetic variation and can evolve. So, even though they don't meet the definition of life, viruses seem to be in a "questionable" zone. (Maybe viruses are actually undead, like zombies or vampires!)

How are viruses different from bacteria?

Even though they can both make us sick, bacteria and viruses are very different at the biological level. Bacteria are small and single-celled, but they are living organisms that do not depend on a host cell to reproduce. Because of these differences, bacterial and viral infections are treated very differently. For instance, antibiotics are only helpful against bacteria, not viruses.
Bacteria are also much bigger than viruses. The diameter of a typical virus is about 2020 300300 nanometers\text{nanometers} (11 nm\text{nm} == 10-910^\text{-9} m\text{m})4^4. This is considerably smaller than a typical E. coli bacterium, which has a diameter of roughly 10001000 nm\text{nm}! Tens of millions of viruses could fit on the head of a pin.
Well, it depends when you ask! In recent years, larger and larger viruses have kept getting discovered. At the moment, the largest known virus is called Pithovirus. It infects amoebas and is rod-shaped, with a length of 1.51.5 and diameter of 0.50.5 .5^5 That's larger than some cells!
To be clear, Pithovirus is definitely an exception to the rule. The vast majority of viruses fall into the range of 2020 300300 nm\text{nm} in diameter and are much smaller than cells.

The structure of a virus

There are a lot of different viruses in the world. So, viruses vary a ton in their sizes, shapes, and life cycles. If you're curious just how much, I recommend playing around with the ViralZone website. Click on a few virus names at random, and see what bizarre shapes and features you find!
Viruses do, however, have a few key features in common. These include:
  • A protective protein shell, or capsid
  • A nucleic acid genome made of DNA or RNA, tucked inside of the capsid
  • A layer of membrane called the envelope (some but not all viruses)
Let's take a closer look at these features.
Diagram of a virus. The exterior layer is a membrane envelope. Inside the envelope is a protein capsid, which contains the nucleic acid genome.
Image modified from "Scheme of a CMV virus." by Emmanuel Boutet, CC BY-SA 2.5. The modified image is licensed under a CC BY-SA 2.5 license.

Virus capsids

The capsid, or protein shell, of a virus is made up of many protein molecules (not just one big, hollow one). The proteins join to make units called capsomers, which together make up the capsid. Capsid proteins are always encoded by the virus genome, meaning that it’s the virus (not the host cell) that provides instructions for making them.
You can think of the capsid as a soccer ball, and the white hexagons and black pentagons as capsomers.
Comparison of a soccer ball with a virus capsid. The hexagons are one type of capsomer while the pentagon are another type. Both types of capsomer are assembled from individual virus proteins.
Left panel: modified from "Parvoviridae virion," by ViralZone/Swiss Institute of Bioinformatics, CC BY-NC 4.0. Right panel: "Soccer ball," by Pumbaa80, CC BY-SA 3.0.
The capsids of some viruses are relatively simple and are made from multiple copies of a single protein. Canine parvovirus, a very small virus that infects dogs, has a capsid made from 6060 copies of the same capsid protein. The capsid is organized into 1212 capsomers, each of which is made from 55 capsid proteins. The capsids of other viruses are more complex and consist of multiple copies of several different proteins.
Capsid protein
5 capsid proteins = 1 capsomer
12 capsomers = one full capsid
Image modified from "T = 1 icosahedral capsid protein," by ViralZone/Swiss Institute of Bioinformatics, CC BY-NC 4.0.
Capsids come in many forms, but they often take one of the following shapes (or a variation of these shapes):
  1. Icosahedral – Icosahedral capsids have twenty faces, and are named after the twenty-sided shape called an icosahedron.
  2. Filamentous – Filamentous capsids are named after their linear, thin, thread-like appearance. They may also be called rod-shaped or helical.
  3. Head-tail –These capsids are kind of a hybrid between the filamentous and icosahedral shapes. They basically consist of an icosahedral head attached to a filamentous tail.
    Diagram of icosahedral (roughly spherical), filamentous (rod-like), and head-tail (icosahedral head attached to filamentous tail) virus capsid shapes.
    Image modified from "Non-enveloped icosahedral virus," "Non-enveloped helical virus," and "Head-tail phage," by Anderson Brito, CC BY-SA 3.0. The modified image is licensed under a CC BY-SA 3.0 license.

Virus envelopes

In addition to the capsid, some viruses also have a lipid membrane known as an envelope. Virus envelopes can be external, surrounding the entire capsid, or internal, found beneath the capsid.
Viruses with envelopes do not provide instructions for the envelope lipids. Instead, they "borrow" a patch from the host membranes on their way out of the cell. Envelopes do, however, contain proteins that are specified by the virus, which often help viral particles bind to host cells.
Diagram of enveloped icosahedral virus.
Image modified from "Enveloped icosahedral virus," by Anderson Brito, CC BY-SA 3.0. The modified image is licensed under a CC BY-SA 3.0 license.
Although envelopes are common, especially among animal viruses, they are not found in every virus (i.e., are not a universal virus feature).

Virus genomes

All viruses have genetic material (a genome) made of nucleic acid. You, like all other cell-based life, use DNA as your genetic material. Viruses, on the other hand, may use either RNA or DNA, both of which are types of nucleic acid.
We often think of DNA as double-stranded and RNA as single-stranded, since that's typically the case in our own cells. However, viruses can have all possible combos of strandedness and nucleic acid type (double-stranded DNA, double-stranded RNA, single-stranded DNA, or single-stranded RNA). Viral genomes also come in various shapes, sizes, and varieties, though they are generally much smaller than the genomes of cellular organisms.
Virus genomes are pretty small! They typically range from 2,2,000000 to several hundred thousand nucleotides in length6^6. (A nucleotide is a "unit" of DNA or RNA).
For comparison, the bacterium E. coli has a genome that's 4.64.6 million\text{million} nucleotides long, and you have a genome that's 6.66.6 billion\text{billion} nucleotides long!
Notably, DNA and RNA viruses always use the same genetic code as living cells. If they didn't, they would have no way to reprogram their host cells!

What is a viral infection?

In everyday life, we tend to think of a viral infection as the nasty collection of symptoms we get when catch a virus, such as the flu or the chicken pox. But what's actually happening in your body when you have a virus?
At the microscopic scale, a viral infection means that many viruses are using your cells to make more copies of themselves. The viral lifecycle is the set of steps in which a virus recognizes and enters a host cell, "reprograms" the host by providing instructions in the form of viral DNA or RNA, and uses the host's resources to make more virus particles (the output of the viral "program").
For a typical virus, the lifecycle can be divided into five broad steps (though the details of these steps will be different for each virus):
Steps of a viral infection, illustrated generically for a virus with a + sense RNA genome.
  1. Attachment. Virus binds to receptor on cell surface.
  2. Entry. Virus enters cell by endocytosis. In the cytoplasm, the capsid comes apart, releasing the RNA genome.
  3. Replication and gene expression. The RNA genome is copied (this would be done by a viral enzyme, not shown) and translated into viral proteins using a host ribosome. The viral proteins produced include capsid proteins.
  4. Assembly. Capsid proteins and RNA genomes come together to make new viral particles.
  5. Release. The cell lyses (bursts), releasing the viral particles, which can then infect other host cells.
  1. Attachment. The virus recognizes and binds to a host cell via a receptor molecule on the cell surface.
    Virus binding to its receptor on the cell surface.
    Image modified from "Viral attachment to host cell," by ViralZone/Swiss Institute of Bioinformatics, CC BY-NC 4.0.
    In attachment, a specific protein on the capsid of the virus physically "sticks" to a specific molecule on the membrane of the host cell.
    This molecule, called a receptor, is usually a protein. A virus recognizes its host cells based on the receptors they carry, and a cell without receptors for a virus can't be infected by that virus.
  2. Entry. The virus or its genetic material enters the cell.
    One typical route for viral entry is fusion with the membrane, which is most common in viruses with envelopes. Viruses may also trick the cell into taking them in by a bulk transport process called endocytosis. Some even inject their DNA into the cell!
    Routes of entry include endocytosis (in which the membrane folds inward to bring the virus into the cell in a bubble) and direct fusion of the viral particle with the membrane, releasing its contents into the cell.
    Image modified from "Virus entry," by ViralZone/Swiss Institute of Bioinformatics, CC BY-NC 4.0.
  3. Genome replication and gene expression. The viral genome is copied and its genes are expressed to make viral proteins.
    The viral genome is copied, and its genes are also expressed to make viral proteins.
    Image modified from "Positive stranded RNA virus replication, by ViralZone/Swiss Institute of Bioinformatics, CC BY-NC 4.0.
    This step involves copying the viral genome and making more viral proteins, so that new virus particles can be assembled.
    The materials for these processes (such as nucleotides to make new DNA or RNA) come from the host cell, not the virus. Most of the "machinery" for replication and gene expression is also provided by the host cell. For instance, the messenger RNAs (mRNAs) encoding viral genes are translated into viral proteins using the host cell's ribosomes. However, certain steps, such as the copying of an RNA virus's genome, cannot be performed by host cell enzymes. In such cases, the viruses must encode their own enzymes.
    The viral proteins produced vary from virus to virus. All viruses must encode capsid proteins, and enveloped viruses typically also encode envelope proteins (which often aid in host recognition). Viruses may also encode proteins that manipulate the host genome (e.g., by blocking host defenses or driving expression of genes to benefit the virus), help with viral genome replication, or play a role in other parts of the viral lifecycle.
  4. Assembly. New viral particles are assembled from the genome copies and viral proteins.
    During assembly, newly synthesized capsid proteins come together to form capsomers, which interact with other capsomers to form the full-sized capsid.
    Some viruses, like head-tail viruses, first assemble an “empty” capsid and then stuff the viral genome inside. Other viruses build the capsid around the viral genome, as shown below.
    Proteins of the capsid assemble around the viral genome, forming a new viral particle with the genome on the inside (encased by the capsid).
    Image modified from "Cytoplasmic capsid assembly/packaging, by ViralZone/Swiss Institute of Bioinformatics, CC BY-NC 4.0.
  5. Release. Completed viral particles exit the cell and can infect other cells.
    Viruses may exit through lysis of the cell, exocytosis, or budding at the plasma membrane.
    Image modified from "Virus exit," by ViralZone/Swiss Institute of Bioinformatics, CC BY-NC 4.0.
    The last step in the virus lifecycle is the release of newly made viruses from the host cell. Different types of viruses exit the cell by different routes: some make the host cell burst (a process called lysis), while others exit through the cell's own export pathways (exocytosis), and others yet bud from the plasma membrane, taking a patch of it with them as they go.
    In some cases, the release of the new viruses kills the host cell. (For instance, a host cell that bursts will not survive.) In other cases, the exiting viruses leave the host cell intact so it can continue cranking out more virus particles.
The diagram above shows how these steps might occur for a virus with a single-stranded RNA genome. You can see real examples of viral lifecycles in the articles on bacteriophages (bacteria-infecting viruses) and animal viruses.
This article is licensed under a CC BY-NC-SA 4.0 license.

Works cited:

  1. Weitz, J. S., and Wilhelm, S. W. (2013, July 1). An ocean of viruses. In The scientist. Retrieved from http://www.the-scientist.com/?articles.view/articleNo/36120/title/An-Ocean-of-Viruses/.
  2. Zimmer, C. (2013, Feb 20). An infinity of viruses. In The loom: A blog by Carl Zimmer. Retrieved from http://phenomena.nationalgeographic.com/2013/02/20/an-infinity-of-viruses/.
  3. Suttle, C. A. (2007). Marine viruses - major players in the global ecosystem. Nat. Rev. Microbiol.,. 5(10), 801-12.
  4. Virus. (2016, May 4). Retrieved May 10, 2016 from Wikipedia: https://en.wikipedia.org/wiki/Virus.
  5. Pithovirus. (2016, March 26). Retrieved May 10,2016 from Wikipedia: https://en.wikipedia.org/wiki/Pithovirus.
  6. Pierson, T. C. (2012, November 2). The flavivirus lifecycle. In Labs at NIAID. Retrieved from https://www.niaid.nih.gov/research/ted-c-pierson-phd

Additional references:

Acheson, N. H. (2007). Introduction to virology. In Fundamentals of molecular virology. (1st ed., pp. 1-17). Hoboken, NJ: Wiley.
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Racaniello, V. (2013, September 6). How many viruses on Earth? In Virology blog: About viruses and viral disease. Retrieved from http://www.virology.ws/2013/09/06/how-many-viruses-on-earth/.
Raven, P. H. and Johnson, G. B. (2002). The nature of viruses. In Biology (6th ed., p. 667). Boston, MA: McGraw-Hill.
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Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., and Jackson, R. B. (2011). Structure of viruses. In Campbell biology (10th ed., pp. 394-395). San Francisco, CA: Pearson.
Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., and Jackson, R. B. (2011). Viruses replicate only in cells . In Campbell biology (10th ed., pp. 395-403). San Francisco, CA: Pearson.
Travis, J. (2009). All the world's a phage. Science News, 2(164), 26-27. http://www.jstor.org/stable/3982016.
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