Lecture 2: Virus Structure

All viruses contain the following two components: 1) a nucleic acid genome and 2) a protein capsid that covers the genome. Together this is called the nucleocapsid. In addition, many animal viruses contain a 3) lipid envelope. The entire intact virus is called the virion. The structure and composition of these components can vary widely.

A: Viral Genomes: While the genomes of all known cells are comprised of double stranded DNA, the genomes of viruses can be comprised of single or double stranded DNA or RNA. They can vary greatly in size, from approximately 5-10 kb (Papovaviridae, Parvoviridae, etc.) to greater than 100-200 kb (Herpesviridae, Poxviridae). The known structures of viral genomes are summarized below.

DNA: Double Stranded - linear or circular

          Single Stranded - linear or circular

          Other Structures - gapped circles

RNA: Double Stranded - linear

          Single Stranded - linear : These single stranded genomes can be either + sense, - sense, or ambisense The sense         strand is the one that can serve directly as mRNA and code for protein, so for these viruses, the viral RNA is infectious. The viral mRNA from - strand viruses is not infectious, since it needs to be copied into the + strand before it can be translated. In an ambisense virus, part of the genome is the sense strand, and part is the antisense.

The genome of some RNA viruses is segmented, meaning that a virus particle contains several different molecules of RNA, like different chromosomes.

B: Protein Capsid

Viral genomes are surrounded by protein shells known as capsids. One interesting question is how capsid proteins recognize viral, but not cellular RNA or DNA. The answer is that there is often some type of "packaging" signal (sequence) on the viral genome that is recognized by the capsid proteins. A capsid is almost always made up of repeating structural subunits that are arranged in one of two symmetrical structures, a helix or an icosahedron. In the simplest case, these "subunits" consist of a single polypeptide. In many cases, however, these structural subunits (also called protomers) are made up of several polypeptides. Both helical and icosahedral structures are described in more detail below.

1) Helical Capsids: The first and best studied example is the plant tobacco mosaic virus (TMV), which contains a SS RNA genome and a protein coat made up of a single, 17.5 kd protein. This protein is arranged in a helix around the viral RNA, with 3 nt of RNA fitting into a groove in each subunit. Helical capsids can also be more complex, and involve more than one protein subunit.

A helix can be defined by two parameters, its amplitude (diameter) and pitch, where pitch is defined as the distance covered by each turn of the helix. P = m x p, where m is the number of subunits per turn and p is the axial rise per subunit. For TMV, m = 16.3 and p= 0.14 nm, so P=2.28 nm. This structure is very stable, and can be dissociated and re-associated readily by changing ionic strength, pH, temperature, etc. The interactions that hold these molecules together are non-covalent, and involve H-bonds, salt bridges, hydrophobic interactions, and vander Waals forces.

Several families of animal virus contain helical nucleocapsids, including the Orthomyxoviridae (influenza), the Paramyxoviridae (bovine respiratory syncytial virus), and the Rhabdoviridae (rabies). All of these are enveloped viruses (see below).

2) Icosahedral Capsids: In these structures, the subunits are arranged in the form of a hollow, quasi spherical structure, with the genome within. An icosahedron is defined as being made up of 20 equilateral triangular faces arranged around the surface of a sphere. They display 2-3-5 fold symmetry as follows:

- an axis of 2 fold rotational symmetry through the center of each edge.

- an axis of 3 fold rotational symmetry through the center of each face.

- an axis of 5 fold rotational symmetry through the center of each corner.

These corners are also called Vertices, and each icosahedron has 12.

Since proteins are not equilateral triangles, each face of an icosahedron contains more than one protein subunit. The simplest icosahedron is made by using 3 identical subunits to form each face, so the minimum # of subunits is 60 (20 x 3). Remember, that each of these subunits could be a single protein or, more likely, a complex of several polypeptides.

Many viruses have too large a genome to be packaged inside an icosahedron made up of only 60 polypeptides (or even 60 subunits), so many are more complicated. In these cases, each of the 20 triangular faces is divided into smaller triangles; and each of these smaller triangles is defined by 3 subunits. However, the total number of subunits is always a multiple of 60. The total number of subunits can be defined as 60 X N, where N is sometimes called the Triangulation Number, or T. Values for T of 1,3,4,7,9, 12 and more are permitted.

When virus nucleocapsids are observed in the electron microscope, one often sees apparent "lumps" or clusters on the surface of the particle. These are usually protein subunits clustered around an axis of symmetry, and have been called "morphological units" or capsomers.

C: Viral Envelope

In some animal viruses, the nucleocapsid is surrounded by a membrane, also called an envelope. This envelope is made up of a lipid bilayer, and is comprised of host-cell lipids. It also contains virally encoded proteins, often glycoproteins which are trans-membrane proteins. These viral proteins serve many purposes, such as binding to receptors on the host cell, playing a role in membrane fusion and cell entry, etc. They can also form channels in the viral membrane.

Many enveloped viruses also contain matrix proteins, which are internal proteins that link the nucleocapsid to the envelope. They are very abundant (ie, many copies per virion), and are usually not glycosylated. Some virions also contain other, non-structural proteins that are used in the viral life cycle. Examples of this are replicases, transcription factors, etc. These non-structural proteins are present in low amounts in the virion.

Enveloped viruses are formed by budding through cellular membranes, usually the plasma membrane but sometimes an internal membrane such as the ER, golgi, or nucleus. In these cases, the assembly of viral components (genome, capsid, matrix) occurs on the inside face of the membrane, the envelope glycoproteins cluster in that region of the membrane, and the virus buds out. This ability to bud allows the virus to exit the host cell without lysing, or killing the host. In contrast, non-enveloped viruses, and some enveloped viruses, kill the host cell in order to escape.

D: Virus Classification/Nomenclature

Viruses are classified using a combination of characteristics, including the following

1) Morphology: size, shape, presence of envelope, etc.

2) Physicochemical properties: thermal stability, detergent stability, molecular mass, etc.

3) Genome: size, type of nucleic acid, strandedness, etc.

4) Proteins: number, size, sequence, etc.

5) Lipids: content, character, etc.

6) Carbohydrates: content, character, etc.

7) Genome organization and replication: strategy of replication, number and position of open reading frames, transcriptional and translational strategies, site of virion assembly and release.

8) Antigenic properties: serological relationships.

9) Biological properties: Host range, mode of transmission, pathogenicity, tissue tropisms, geographic distribution, etc.

Using these and other criteria, the International Committee on Nomenclature of Viruses (ICTV) produced the following the hierarchical system for viral classification.

1) Orders (virales): Groupings of families of viruses that share common characteristics and are distinct from other orders and families.

2) Families (-viridae): Groupings of genera of viruses that share common characteristics and are distinct from the member viruses of other families.

3) Subfamilies (-virinae): Not used in all families, but allows for more complex hierarchy of taxa.

4) Genera (-virus): Groupings of species of viruses that share common characteristics and are distinct from the member viruses of other species.

5) Species (virus); The definition accepted by ICTV is "a virus species is defined as a polythetic class of viruses that constitutes a replicating lineage and occupies a particular ecological niche". A species can be further broken down into strains, variants, etc.

In addition to this formal taxonomy, David Baltimore proposed that viruses be classified according to the nature of their genome and the relationship between the genome and the viral mRNA. The classes that he proposed are the following:

Class I: Double Stranded DNA Genomes

Class II: Single Stranded DNA Genomes

Class III: Double Stranded RNA Genomes

Class IV: Positive Strand RNA Genomes

Class V: Negative Strand RNA Genomes

Class VI: Retroviruses

So, the classification of viruses is quite complex, and to some extent is constantly evolving.

For further information, go to on-line course 224 lecture on virus structure or on-line course 109 lecture on virus structure