A virus is a small infectious agent that replicates only inside the living cells of other organisms. Viruses can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.
While not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent particles. These viral particles, also known as virions, consist of two or three parts: (i) the genetic material made from either DNA or RNA, long molecules that carry genetic information; (ii) a protein coat, called the capsid, which surrounds and protects the genetic material; and in some cases (iii) an envelope of lipids that surrounds the protein coat when they are outside a cell.
The shapes of these virus particles range from simple helical and icosahedral forms for some virus species to more complex structures for others. Most virus species have virions that are too small to be seen with an optical microscope. The average virion is about one one-hundredth the size of the average bacterium.
Viruses are not usually classified into conventional taxonomic groups but are usually grouped according to such properties as size, the type of nucleic acid they contain, the structure of the capsid and the number of protein subunits in it, host species, and immunological characteristics.
Two classification systems exist: The Hierarchical virus classification system and the Baltimore Classification System.
The Hierarchical virus classification system
In 1962 Lwoff, R. W. Horne, and P. Tournier advanced a comprehensive scheme for the classification of all viruses consisting of phylum – class – order – family – subfamily – genus – species – strain/type.
The most important principle embodied in this system was that viruses should be grouped according to their shared properties rather than the properties of the cells or organisms they infect. Four main characteristics are used:
- Nature of the nucleic acid: RNA or DNA
Viruses may use either DNA or RNA as their genetic material. The virus core contains the genome or total genetic content of the virus. Viral genomes tend to be small, containing only those genes that encode proteins that the virus cannot obtain from the host cell. This genetic material may be single- or double-stranded. It may also be linear or circular. While most viruses contain a single nucleic acid, others have genomes that have several, which are called segments. The type of genetic material (DNA or RNA) and its structure (single- or double-stranded, linear or circular, and segmented or non-segmented) are used to classify the virus core structures .
- Dimension and symmetry of the capsid
Viruses can also be classified by the design of their capsids. Isometric viruses have shapes that are roughly spherical, such as poliovirus or herpesviruses. Enveloped viruses have membranes surrounding capsids. Animal viruses, such as HIV, are frequently enveloped. Head and tail viruses infect bacteria and have a head that is similar to icosahedral viruses and a tail shape like filamentous viruses.
Capsids are classified as naked icosahedral, enveloped icosahedral, enveloped helical, naked helical, and complex .For example, the tobacco mosaic virus has a naked helical capsid . The adenovirus has an icosahedral capsid .
- Presence or absence of an envelope
Virus can be classified as enveloped or non-enveloped virus based on the presence and absence of the envelope round the protein coat.
Enveloped virus : Examples are Herpes simplex virus, varicella-zoster virus, cytomegalovirus, Epstein–Barr virus.
Non-enveloped virus : Examples are Adenovirus, infectious canine hepatitis virus.
Baltimore Classification System
The Baltimore system of virus classification provides a useful guide with regard to the various mechanisms of viral genome replication. The central theme here is that all viruses must generate positive strand mRNAs from their genomes, in order to produce proteins and replicate themselves. The precise mechanisms whereby this is achieved differ for each virus family.
These various types of virus genomes can be broken down into seven fundamentally different groups, which obviously require different basic strategies for their replication. David Baltimore, who originated the scheme, has given his name to the so-called “Baltimore Classification” of virus genomes.
By convention the top strand of coding DNA written in the 5′ – 3′ direction is + sense. Positive polarity means that the genomic RNA can serve directly as mRNA and a negative polarity means that their sequence is complementary to the mRNA .The replication strategy of the virus depends on the nature of its genome.
Viruses can be classified into seven (arbitrary) groups:
- Double-stranded DNA
Include the viruses such as Adenoviruses, Herpesviruses, Poxviruses, etc. Some replicate in the nucleus e.g adenoviruses using cellular proteins. Poxviruses replicate in the cytoplasm and make their own enzymes for nucleic acid replication.
- Single-stranded (+) sense DNA
Replication occurs in the nucleus, involving the formation of a (-)sense strand, which serves as a template for (+) strand RNA and DNA synthesis. Example is Parvoviruses.
- Double-stranded RNA
These viruses have segmented genomes. Each genome segment is transcribed separately to produce monocistronic mRNAs. Examples are Reoviruses, Birnaviruses
- Single-stranded (+) sense RNA
a) Polycistronic mRNA : Genome RNA = mRNA. Means naked RNA is infectious, no virion particle associated polymerase. Translation results in the formation of a polyprotein product, which is subsequently cleaved to form the mature proteins. Examples are Picornaviruses, Hepatitis A.
b) Complex Transcription : Two or more rounds of translation are necessary to produce the genomic RNA. Example is Togaviruses.
- Single-stranded (-) sense RNA
Must have a virion particle RNA directed RNA polymerase.
a) Segmented : First step in replication is transcription of the (-) sense RNA genome by the virion RNA-dependent RNA polymerase to produce monocistronic mRNAs, which also serve as the template for genome replication. Example is Orthomyxoviruses.
b) Non-segmented : Replication occurs as above and monocistronic mRNAs are produced. Example is Rhabdoviruses.
- Single-stranded (+) sense RNA with DNA intermediate in life-cycle
Genome is (+) sense but unique among viruses in that it is diploid, and does not serve as mRNA, but as a template for reverse transcription. Example is Retroviruses.
- Double-stranded DNA with RNA intermediate
This group of viruses also relies on reverse transcription, but unlike the Retroviruses, this occurs inside the virus particle on maturation. On infection of a new cell, the first event to occur is repair of the gapped genome, followed by transcription .Example is Hepadnaviruses.