RNA virus

An RNA virus is a virus that has RNA (ribonucleic acid) as its genetic material. This nucleic acid is usually single-stranded RNA (ssRNA) but may be double-stranded RNA (dsRNA). The ICTV classifies RNA viruses as those that belong to Group III, Group IV or Group V of the Baltimore classification system of classifying viruses, and does not consider viruses with DNA intermediates as RNA viruses. Notable human diseases caused by RNA viruses include SARS, influenza and hepatitis C.

Another term for RNA viruses that explicitly excludes retroviruses is ribovirus.

Characteristics

Single-stranded RNA viruses and RNA Sense

RNA viruses can be further classified according to the sense or polarity o

f 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 resemble negative-sense RNA viruses, except they also translate genes from the positive 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 have a high mutation rate even though their DNA intermediate integrates into the host genome (and is thus subject to host DNA proofreading once integrated), because errors during reverse transcription are embedded into both strands of DNA prior to integration.

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 are classified into three distinct groups depending on their genome and mode of replication (and the numerical groups based on the older Baltimore classification):

• Double-stranded RNA viruses (Group III) contain from one to a dozen different RNA molecules, each of which codes for one or more viral proteins.
• Positive-sense ssRNA viruses (Group IV) 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-d ependent RNA polymerase, which copies the viral RNA to form a double-stranded replicative form, in turn this directs the formation of new virions.
• Negative-sense ssRNA viruses (Group V) must have their genome copied by an RNA polymerase 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.

  

Retroviruses (Group VI) have a single-stranded RNA genome but are generally not considered RNA viruses because 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. After this DNA is integrated, expression of the encoded genes may lead 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,Chikungunya 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