Understanding the structure of viruses

Photo by CDC on Unsplash


Viruses are infectious particles existing in nature. As discussed in the previous post, viruses come in a variety of sizes.

In this post, we will look at the basic structural components of a virus particle.

Although viruses are not as complex as other living organisms and they lack the ability to reproduce on their own, their structures do not lack any sophistication.

All viruses carry their viral genomic materials in the form of nucleic acid (DNA or RNA). They act as the blueprint for making more viral proteins essential for their propagation inside the host cell.  The DNA or RNA in a virus particle is packaged inside a protein shell called a capsid. On top of that, viruses can be enclosed by an envelope layer. But not all viruses have an envelope.

ENVELOPE

The envelope layer is composed of a lipid bilayer. The lipid bilayer is like that of a cell membrane. Very often viruses get their lipid bilayers from the host cells’ cell membrane during their release from the host cells. This process is called budding.

A virus particle’s lipid bilayer can be embedded with various viral proteins. These envelope proteins are also called matrix proteins. For example, coronaviruses develop spikes, made of matrix proteins called glycoproteins. Together with the envelope, they form the “crown” like the outer layer, a trademark of coronavirus. There are two main types of virus particles. They are either “enveloped” or “nonenveloped”. Take a look at the schematic of a typical “enveloped” and “nonenveloped” viruses. Virus lacking the envelope layer is sometimes called a “naked virus”.

Credit: Reference [1]

CAPSID

Capsid is the protective shell that encloses the viruses’ genomic materials. Together, it is called a nucleocapsid. This protective shell is made up of viral structural proteins. A basic subunit of the capsid is called a capsomere. Multiple capsomers together make up the capsid.  Capsid can come in two basic structures: spherical (icosahedral or polygon-shaped) or helical.

Example of helical virus
Left: Model of Tobacco Mosaic Virus (TMV); Right: Electron micrograph of  TMV. The white bar represents 100nm
Credit link
Molecular models of icosahedral viruses
Credit: Reference [2]

There is a third structure: complex or head-tail. Complex capsids are a kind of hybrid between both helical and icosahedral capsids. For example, a T4 bacteriophage, a virus that infects bacteria has an elongated icosahedral head, helical body, and tail structures.

Credit: Adapted by Petr Leiman (Purdue University) from a drawing by Fred Eiserling (UCLA)

What is a T number?

First described in 1962 by Caspar and King, the T (triangular) number is used to explain the size and complexity of icosahedral capsids. Over the years, this concept has evolved as more icosahedral capsids are discovered and analyzed. For example, a virus with a T number of 1 (for example, a parvovirus) represents a simple icosahedral assembly of 20 triangular faces and 60 structural subunits.

Examples of large and small icosahedral capsids.
Credit: Reference [2]

Three main functions of a capsid

  • Protects the viral nucleic acids
  • Aids in the attachment of the virus particle to a host cell
  • Delivers the viral genome by penetrating the host cell membrane

The assembly and stability of the capsid structure are very important. The capsid must be able to protect the nucleic acids from harmful radiation such as UV, environments of varying pH, temperature and exposure to enzymes that can break down proteins and nucleic acids.

For naked viruses, they lack the envelope layer for additional protection. The capsid serves as the main protective layer as well as aiding in the penetration of the host cell membrane.

Check out this video on the self-assembly of the virus capsid using 3D printed model

NUCLEIC ACID

Nucleic acids in the form of DNA and RNA contain important genetic blueprint for the synthesis of all the viral proteins that are required in the assembly and making of new virus particles. They are safely packaged inside the capsid. Once inside a host cell, they are released.

Generally, DNAs are double-stranded (ds) while RNAs are single-stranded(ss). However, in viruses, there are many potential combinations: dsDNA, dsRNA, ssDNA, or ssRNA.

How are viruses classified?

Generally, viruses are classified based on the organisms they infect. They are further classified into families, subfamilies, genera, and species based on 3 main conditions:

  • Viral genome (size and type of nucleic acids, ss or ds)
  • Presence of envelope
  • Size and shape of the capsid 

Other considerations such as the physicochemical properties, proteins, lipids, antigenic and biological properties, and genomic replication strategies also influence the classification of viruses. 

The classification of viruses is complex and constantly evolving as more and more viruses are discovered. 

If you are curious about the different kinds of viruses and virus taxonomy, Viralzone is a great website for you to explore.

Looking for something to do while self-isolating, how about making some origami icosahedrons?

References:
1. Computational Virology: from the Inside Out – Scientific Figure on ResearchGate. Available from: https://www.researchgate.net/figure/Non-enveloped-and-enveloped-viruses-a-simple-schematic-diagram-illustrating-the_fig1_294110884 [accessed 1 Apr, 2020]
2. Payne, S. (2017). Virus Structure. Viruses, 13–21. doi:10.1016/b978-0-12-803109-4.00002-7 

About the Author

Ameline Lim, Ph.D.
Ameline Lim, Ph.D., is a research scientist and biologist. She received her PhD from the University of New South Wales at Sydney, Australia. She has broad interests in medicine, history of science, and behavioural science. She is particularly interested in science education and the public understanding of scientific research. Her blog 'Science with Amy' celebrates the pleasures of finding things out and general curiosity.

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