Virus

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A **virus** is a tiny parasite. Viruses reproduce inside other living things; they are not free-living. A virus makes copies of itself inside another organism's cells. When viruses infect living organisms, they can cause disease. There are many types of diseases caused by viruses, such as polio, ebola and hepatitis. Viruses outnumber all other forms of life on the planet by a long way. Viruses are everywhere in the environment, and all organisms can be infected by them.

With eukaryotic cells, the virus protein coat is able to enter the target cells by certain cell membrane receptors. With prokaryote bacteria cells, the bacteriophage physically injects the nucleic acid strand into the host cell.

When the host cell has finished making more viruses, it undergoes lysis, or breaks apart. The viruses are released and are then able to infect other cells. Viruses can remain "silent" (inactive) for a long time, and will infect cells when the time and conditions are right.

Some special viruses are worth noting. Bacteriophages have evolved to enter bacterial cells, which have a different type of cell wall from eukaryote cell membranes. *Envelope viruses*, when they reproduce, cover themselves with a modified form of the host cell membrane, thus gaining an outer lipid layer that helps entry. Some of the most difficult viruses to combat, like influenza and HIV, use this method.

Viral infections in animals trigger an immune response which usually destroys the infecting virus. Vaccines can also produce immune responses. They give an artificially acquired immunity to the specific viral infection. However, some viruses (including those causing AIDS and viral hepatitis) escape from these immune responses and cause chronic infections. Antibiotics have no effect on viruses, but there are some other drugs which can be used against viruses. Virology is the study of viruses.

## Genome 
There are many genomic structures in viruses. As a group they are more diverse than plants, animals, archaea, or bacteria. There are millions of different types of viruses,96/99

Fewer than 7,000 types have been described in detail. but there are doubtlessly many more to be discovered.

## Replication cycle 
Viral populations do not grow through cell division, because they do not have cells. Instead, they use the machinery and metabolism of a host cell to produce many copies of themselves, and they *assemble* (put together) in the cell.

The life cycle of viruses differs greatly between species but there are six *basic* stages in the life cycle of viruses:
* Viruses can be *released* from the host cell by lysis, a process that kills the cell by bursting its membrane and cell wall. This is a feature of many bacterial and some animal viruses. In some viruses  the viral genome is put by genetic recombination into a specific place in the host's chromosome. The viral genome is then known as a "provirus" or, in the case of bacteriophages a "prophage". They are susceptible to antiviral drugs that inhibit the reverse transcriptase enzyme. An example of the first type is HIV, which is a retrovirus. Examples of the second type are the Hepadnaviridae, which includes Hepatitis B virus.

RNA interference is an important innate defence against viruses. Many viruses have a replication strategy that involves double-stranded RNA (dsRNA). When such a virus infects a cell, it releases its RNA molecule. A protein complex called dicer sticks to it and chops the RNA into pieces. Then a biochemical pathway, called the RISC complex, starts up. This attacks the viral mRNA, and the cell survives the infection.

es: the one on the right is coated with antibodies which stop it attaching to cells and infecting them|alt=Two spherical rotavirus particles, one is coated with antibody which looks like many small birds, regularly spaced on the surface of the virus]]
Rotaviruses avoid this by not uncoating fully inside the cell and by releasing newly produced mRNA through pores in the particle's inner capsid. The genomic dsRNA remains protected inside the core of the virion.

The production of interferon is an important host defence mechanism. This is a hormone produced by the body when viruses are present. Its role in immunity is complex; it eventually stops the viruses from reproducing by killing the infected cell and its close neighbours.

### Adaptive immune system 
Vertebrates have a second, more specific, immune system. It is called the adaptive immune system. When it meets a virus, it produces specific antibodies that bind to the virus and render it non-infectious. Two types of antibodies are important.

The first, called IgM, is highly effective at neutralizing viruses but is produced by the cells of the immune system only for a few weeks. The second, called IgG, is produced indefinitely. The presence of IgM in the blood of the host is used to test for acute infection, whereas IgG indicates an infection sometime in the past. IgG antibody is measured when tests for immunity are carried out.

Another vertebrate defence against viruses involves immune cells known as T cells. The body's cells constantly display short fragments of their proteins on the cell's surface, and, if a T cell recognises a suspicious viral fragment there, the host cell is destroyed by *killer T* cells and the virus-specific T-cells proliferate. Cells such as macrophages are specialists at this antigen presentation.

### Evading the immune system 
Not all virus infections produce a protective immune response. These persistent viruses evade immune control by sequestration (hiding away); cytokine resistance; evading natural killer cell activity; escape from apoptosis (cell death), and antigenic shift (changing surface proteins). HIV evades the immune system by constantly changing the amino acid sequence of the proteins on the surface of the virion. Other viruses move along nerves to places the immune system cannot reach.

## Evolution 
Viruses do not belong to any group of living organisms, including any of the kingdoms or domains. They are not seen as living organisms because they are not active until the point of infection. However, that is just a verbal point.

Their structure and mode of operation means they have evolved from other living things, and the loss of normal structure occurs in many endoparasites. The origins of viruses in the evolutionary history of life are unclear; some may have evolved from plasmids – pieces of DNA that can move between cells – while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity.

## Recent discoveries 
A recent project discovered nearly 1500 new RNA viruses by sampling over 200 invertebrate species. "The research team... extracted their RNA and, using next-generation sequencing, deciphered the sequence of a staggering six trillion letters present in the invertebrate RNA libraries". The research showed that viruses changed bits and pieces of their RNA by a variety of genetic mechanisms. "The invertebrate virome [shows] remarkable genomic flexibility that includes frequent recombination, lateral gene transfer among viruses and hosts, gene gain and loss, and complex genomic rearrangements".

### How bacteria and archaea deal with viruses 
Viruses have been on this planet a long time. We now know that bacteria and archaea had to deal with them first, before our type of cellular life evolved. Details of the defence mechanisms used by archaea and bacteria are discussed on the page CRISPR, which briefly introduces the topic of early defences against viruses.

### Largest virus 
A group of large viruses infect amoebae. The largest is *Pithovirus*. Others in order of size are *Pandoravirus*, then *Megavirus*, then *Mimivirus*. They are bigger than some bacteria, and visible under a light microscope.

### Viruses in the sea 
Viruses are everywhere in the sea. They may outnumber all other forms of marine life by at least an order of magnitude. Through selective infection, viruses influence nutrient cycling and evolution in the ocean.

## Uses 
Viruses are used widely in cell biology. Geneticists often use viruses as vectors to introduce genes into cells that they are studying. This is useful for making the cell produce a foreign substance, or to study the effect of introducing a new gene into the genome. Eastern European scientists have used phage therapy as an alternative to antibiotics for some time, and interest in this approach is increasing, because of the high level of antibiotic resistance now found in some pathogenic bacteria.

### List of the viruses
## Related pages 
*Viroid

## References