What are viruses, the different types of viruses?

This is part of a mini series where I will look at the following
Article 1: What are viruses, the different types of viruses?
Article 2: How are viruses replicated?
Article 3: What is the relation between viruses and cancer.

What is a virus?

A sub-cellular organism, no metabolic activity outside a host cell which it requires for replication. It is an obligate, intracellular parasite.

Structure of Viruses

The size of viruses range from 10-400nm in diameter, there are those that can be seen through a light microscope, but most viruses can only be seen through an electron microscope.

Smallpox – 200nm

Poliovirus – 28nm

Parvovirus – 18-22nm

The largest viruses can be seen in the electron microscope transmission but cannot be seen under light microscope. They usually consist of nucleic acid (either one or more DNA or RNA molecules [not both] wrapped in a coat of protein. They depend entirely on the host cell for their metabolism and multiplication. Some viruses can have additional layers that consist of carbohydrates, lipids and additional proteins. They can exist in the following phases: extracellular and intracellular.

Extracellular viruses consist of few enzymes and cannot reproduce independent of living cell. Intracellular viruses exist as replicating nucleic acids that induce host metabolism to synthesize virion particles.

Viruses are the most widespread of all pathogens affecting nearly every species from animals to protozoa, bacteria and plants (well known tobacco mosaic virus).

 The basic structure a virus consists of following: 

Viral genomes:

Viruses can have four possible nucleic acids: (single stranded DNA) ssDNA, (Double-stranded DNA) dsDNA, (SingleStranded RNA) ssRNA, (Double-stranded RNA)dsRNA. All four of these can be found in animal viruses, most plant viruses will have ssRNA and most bacterial viruses contain dsDNA. The size of the genetic material will also vary depending on the virus: e.g. MS2 viruses have 4000 nucleotides - code for 3/4 proteins. T-phages can have genomes of 1.0-2.0 x 105 nucleotides – synthesize 100s of proteins.

Viral Envelopes

Many viruses are bound by an outer membrane layer called an envelope that covers the protein caspid. Animal virus envelopes usually arise from host cell nuclear or plasma membranes (their lipids and carbohydrates are normal host constituents). These envelopes help the virus enter the host cell, and glycoprotein help to indentify and bind to receptor sites on the hosts membrane. The viral can then fuse with the host’s membrane. However the virus buds will often die or be weakened this is because the lipid bilayer envelops are sensitive to desiccation (dryness), heat and detergents.

Envelope proteins are coded for by virus genes and may even be projected on the envelope surface as spikes (peplomers). These spikes are involved in helping the virus attach to the surface of the host cell. These spikes differ amongst viruses therefore can be used to identify certain viruses.

The envelope is flexible membrane structure giving the virus a variable shape (pleomorphic). Some envelopes (e.g. in the bullet-shaped rabies) the envelope is attached to the underlying nucleocaspid giving the virus a constant shape.

Influenza virus is an example of an enveloped virus. Spikes project about 10nm from the surface. These spikes posses the enzyme neuraminidase which helps in the release of mature virions form the host cell. Other spikes will have hemagglutinin proteins. These proteins attach the virion to red blood cells and cause them to clump together (agglutinate).  Proteins that are found on the outer envelope surface are generally glycoproteins. A nonglycosylated protein, (M) or ‘matrix protein’ are found on the inner surface of the envelope and helps stabilize it.

Caspid

A caspid is a protein shell of the virus that consists of oligimeric structural subunits made of protein called protomers; the basic sub units of caspids are capsomers that is an outer covering of the protein that protects the genetic material of viruses.

The nucleic acid encodes the genetic information of a virus that is arranged in to genomes. There are different types of genomes usually single stranded DNA (ssDNA) or double stranded DNA (dsDNA). DNA viruses usually belong to the group one or group two of the Baltimore classification system for the viruses. However in infected cells ssDNA is usually expanded to ds DNA genome in infected cells. Some viruses are naked and some contain envelopes.

The spike of a virus usually helps the virus to invade the host for example the influenza virus has two types of spikes, one which is the haemagglutinin protein (HA), that fusses with the host cell, and The neuraminidase that helps the newly formed particles to bud out from the host cell membrane.

What are the different types of caspids?

Caspids can be present in three forms: helical, icosahedral and complex.

Helical:

Shaped like hollow tubes with protein walls. A virus example with this type of caspid is the tobacco mosaic virus. The protomers arrange themselves into a helical arrangement which produces a long, rigid tube, 15-18nm in diameter and 300nm long. The caspid enclose an RNA nucleic acid. The size of the helical caspid is influenced by both the protomers and the nucleic acid it encloses.

Icosahedral:

This is a regular polyhedron with 20 equilateral triangle faces and 12 vertices. The icosahedral is the most efficient way to enclose a space. Very few genes are required to form this type of caspid. The caspid is constructed from ring or knob-shaped units called capsomeres, each made up of 5/6 protomers. Pentamers- Have 5 sub-units. Hexamers- Have 6 sub-units.  Pentamers are usually at the vertices of the icosahedron, while hexamers form the edges and triangular faces. 

Complex:

Most viruses will have an icosahedral or helical caspid, but there are also viruses that do not fit into either category (e.g. poxviruses and bacteriophages). Poxviruses are the largest animal viruses and can be seen through a phase-contrast microscope.  In the poxvirus the dsDNA is contained in a nucleoid which is shaped like a biconcave disk and surrounded by a membrane. Two elliptical or lateral bodies lye between the nucleoid and the outer envelope: a membrane and a thick layer covered by an array of tubules or fibres. 

Viral enzymes

Most viral enzymes are located within the caspid. E.g. influenza virus: it uses RNA as its genetic material and carries an enzyme that synthesizes RNA using RNA as a template. This enzyme is called RNA-dependent RNA polymerases.

Bacteriophages

Bacteriophages are more complex such as T2, T4 and T6 phages have a binal symmetry structure. It is called this as the phages contain a head that resembles an icosahedron and a tail that resembles a helical. The head is elongated by one or two rows of hexamers in the middle and contains the DNA genome. The tail is made up of a collar joining it to the head, a central hollow tube, a sheath surrounding the tube, and a complex base plate. The sheath is made up from 144 copies of the gp18 protein arranged in 24 rings, each containing six copies. In T phages the base plate is hexagonal and has a pin and a jointed fibre at each corner. Not all phages will have the all the structures mentioned above (T1-lack sheath, T3 – lack tail fibres). 

Baltimore Classification – 7 classes

1. dsDNA             Adenoviruses, Herpesviruses, Poxviruses

2. ssDNA (+) sense          Parvoviruses

3. dsRNA                              Reoviruses

4. ssRNA(+ ) sense          Picornaviruses, Togaviruses

5. ssRNA(-) sense            Orthomyxoviruses, Rhabdoviruses

6. ssRNA(+)sense with DNA intermediate. Retroviruses

7. dsDNA with RNA intermediate             Hepadnaviruses (e.g. hepatitis B)

On sunday I will look at how Viruses are replicated.
Stay tuned!