RNA virus

Overview
An RNA virus is a virus that has ribonucleic acid (RNA) as its genetic material and does not replicate using a DNA intermediate. RNA viruses belong to either Group III, Group IV or Group V of the Baltimore classification system of classifying viruses. Their nucleic acid is usually single-stranded RNA (ssRNA) but may be double-stranded RNA (dsRNA). Notable human pathogenic RNA viruses include SARS, Influenza and Hepatitis C.

Single-stranded RNA viruses and RNA Sense
RNA viruses can be further classified according to the sense or polarity of their RNA into negative-sense and positive-sense, or ambisense RNA viruses. Positive-sense viral RNA is identical to viral mRNA and thus can be immediately translated by the host cell. Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA polymerase before translation. As such, purified RNA of a positive-sense virus can directly cause infection though it may be less infectious than the whole virus particle. Purified RNA of a negative-sense virus is not infectious by itself as it needs to be transcribed into positive-sense RNA. Ambisense RNA viruses transcribe genes from both the positive or negative strand.

Double-stranded RNA viruses
The double-stranded (ds)RNA viruses represent a diverse group of viruses that vary widely in host range (humans, animals, plants, fungi, and bacteria), genome segment number (one to twelve), and virion organization (T-number, capsid layers, or turrets). Members of this group include the rotaviruses, renowned globally as the commonest cause of gastroenteritis in young children, and bluetongue virus, an economically important pathogen of cattle and sheep. In recent years, remarkable progress has been made in determining, at atomic and subnanometeric levels, the structures of a number of key viral proteins and of the virion capsids of several dsRNA viruses, highlighting the significant parallels in the structure and replicative processes of many of these viruses.

Mutation rates
RNA viruses generally have very high mutation rates as they lack DNA polymerases which can find and fix mistakes, and are therefore unable to conduct DNA repair of damaged genetic material. DNA viruses have considerably lower mutation rates due to the proof-reading ability of DNA polymerases within the host cell. Retroviruses integrate a DNA intermediate of their RNA genome into the host genome, and therefore have a higher chance of correcting any mistakes in their genome thanks to the action of proof-reading DNA polymerases belonging to the host cell.

Although RNA usually mutates rapidly, recent work found that the SARS virus and related RNA viruses contain a gene that mutates very slowly. The gene in question has a complex three-dimensional structure which is hypothesized to provide a chemical function necessary for viral propagation, perhaps as a ribozyme. If so, most mutations would render it unfit for that purpose and would not propagate.

Replication
Animal RNA viruses can be placed into about four different groups depending on their mode of replication.


 * Positive-sense viruses have their genome directly utilized as if it were mRNA, producing a single protein which is modified by host and viral proteins to form the various proteins needed for replication. One of these includes RNA replicase, which copies the viral RNA to form a double-stranded replicative form, in turn this directs the formation of new virions.
 * Negative-sense viruses must have their genome copied by an RNA polymerase or transcriptase to form positive-sense RNA. This means that the virus must bring along with it the RNA-dependent RNA polymerase enzyme. The positive-sense RNA molecule then acts as viral mRNA, which is translated into proteins by the host ribosomes. The resultant protein goes on to direct the synthesis of new virions, such as capsid proteins and RNA replicase, which is used to produce new negative-sense RNA molecules.
 * Double-stranded reoviruses contain up to a dozen different RNA molecules which each code for an mRNA. These all associate with proteins to form a single large complex which is replicated using virally-encoded replicase to form new virions.
 * Retroviruses are single-stranded but unlike other single-stranded RNA viruses they use DNA intermediates to replicate. Reverse transcriptase, a viral enzyme that comes from the virus itself after it is uncoated, converts the viral RNA into a complementary strand of DNA, which is copied to produce a double stranded molecule of viral DNA. This DNA goes on to direct the formation of new virions.

Group III - dsRNA viruses

 * Family Birnaviridae
 * Family Chrysoviridae
 * Family Cystoviridae
 * Family Hypoviridae
 * Family Partitiviridae
 * Family Reoviridae - includes Rotavirus
 * Family Totiviridae
 * Unassigned genera
 * Endornavirus

Group IV - positive-sense ssRNA viruses

 * Order Nidovirales
 * Family Arteriviridae
 * Family Coronaviridae - includes Coronavirus, SARS
 * Family Roniviridae
 * Unassigned
 * Family Astroviridae
 * Family Barnaviridae
 * Family Bromoviridae
 * Family Caliciviridae - includes Norwalk virus
 * Family Closteroviridae
 * Family Comoviridae
 * Family Dicistroviridae
 * Family Flaviviridae - includes Yellow fever virus, West Nile virus, Hepatitis C virus, Dengue fever virus
 * Family Flexiviridae
 * Family Leviviridae
 * Family Luteoviridae - includes Barley yellow dwarf virus
 * Family Marnaviridae
 * Family Narnaviridae
 * Family Nodaviridae
 * Family Picornaviridae - includes Poliovirus, the common cold virus, Hepatitis A virus
 * Family Potyviridae
 * Family Sequiviridae
 * Family Tetraviridae
 * Family Togaviridae - includes Rubella virus, Ross River virus, Sindbis virus
 * Family Tombusviridae
 * Family Tymoviridae
 * Unassigned genera
 * Genus Benyvirus
 * Genus Cheravirus
 * Genus Furovirus
 * Genus Hepevirus - includes Hepatitis E virus
 * Genus Hordeivirus
 * Genus Idaeovirus
 * Genus Ourmiavirus
 * Genus Pecluvirus
 * Genus Pomovirus
 * Genus Sadwavirus
 * Genus Sobemovirus
 * Genus Tobamovirus - includes tobacco mosaic virus
 * Genus Tobravirus
 * Genus Umbravirus

Group V - negative-sense ssRNA viruses

 * Order Mononegavirales
 * Family Bornaviridae - Borna disease virus
 * Family Filoviridae - includes Ebola virus, Marburg virus
 * Family Paramyxoviridae - includes Measles virus, Mumps virus, Nipah virus, Hendra virus
 * Family Rhabdoviridae - includes Rabies virus
 * Unassigned
 * Family Arenaviridae - includes Lassa virus
 * Family Bunyaviridae - includes Hantavirus
 * Family Orthomyxoviridae - includes Influenza viruses
 * Unassigned genera:
 * Genus Deltavirus
 * Genus Ophiovirus
 * Genus Tenuivirus
 * Genus Varicosavirus