An RNA virus is a virus that has RNA (ribonucleic acid) as its genetic material.[1] This nucleic acid is usually single-stranded RNA (ssRNA), but may be double-stranded RNA (dsRNA).[2] 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.[3] Notable human diseases caused by RNA viruses include SARS, influenza, hepatitis C and polio.
Viruses with RNA as their genetic material but which include DNA intermediates in their replication cycle are called retroviruses, and comprise Group VI of the Baltimore classification. Notable human retroviruses include HIV-1 and HIV-2, the cause of the disease AIDS.
Another term for RNA viruses that explicitly excludes retroviruses is ribovirus.[4]
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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 similar to 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, however each virion can be transcribed to several positive-sense RNAs. Ambisense RNA viruses resemble negative-sense RNA viruses, except they also translate genes from the positive strand.[5]
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 most common cause of gastroenteritis in young children, picobirnaviruses, renowned worldwide as the most commonly occurring virus in fecal samples of both humans and animals with or without signs of diarrhea. Picobirnaviruses, have also been recently reported in respiratory tract samples of pigs and bluetongue virus,[6][7] 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.[2]
RNA viruses generally have very high mutation rates compared to DNA viruses, because viral RNA polymerases lack the proof-reading ability of DNA polymerases.[8] This is one reason why it is difficult to make effective vaccines to prevent diseases caused by RNA viruses.[9] Retroviruses also 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 before integration.[10] Some genes of RNA virus are important to the viral replication cycles and mutations are not tolerated. For example, the region of the hepatitis C virus genome that encodes the core protein is highly conserved,[11] because it contains an RNA structure involved in an internal ribosome entry site.[12]
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):
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.
Classification of the positive strand RNA viruses is based on the RNA dependent RNA polymerase. Three groups have been recognised:[13]
I. Bymoviruses, comoviruses, nepoviruses, nodaviruses, picornaviruses, potyviruses, sobemoviruses and a subset of luteoviruses (beet western yellows virus and potato leafroll virus) - the picorna like group (Picornavirata).
II. Carmoviruses, dianthoviruses, flaviviruses, pestiviruses, tombusviruses, single-stranded RNA bacteriophages, hepatitis C virus and a subset of luteoviruses (barley yellow dwarf virus) - the flavi like group (Flavivirata).
III. Alphaviruses, carlaviruses, furoviruses, hordeiviruses, potexviruses, rubiviruses, tobraviruses, tricornaviruses, tymoviruses, apple chlorotic leaf spot virus, beet yellows virus and hepatitis E virus - the alpha like group (Rubivirata).
The alpha like groups can be further divided into three clades: the rubi-like, tobamo-like, and tymo-like viruses.[14]
Additional work has identified five groups of positive stranded RNA viruses containing four, three, three, three and one order(s) respectively.[15] These fourteen orders contain 31 virus families (including 17 families of plant viruses) and 48 genera (including 30 genera of plant viruses). This analysis suggests that alphaviruses and flaviviruses can be separated into two families - the Togaviridae and Flaviridae respectively - but suggests that other taxonomic assignments, such as the pestiviruses, hepatitis C virus, rubiviruses, hepatitis E virus and arteriviruses, may be incorrect. The coronaviruses and toroviruses appear to be distinct families in distinct orders and not distinct genera of the same family as currently classified. The luteoviruses appear to be two families rather than one and apple chlorotic leaf spot virus appears not to be a closterovirus but a new genus of the Potexviridae.
This analysis also suggests that the dsRNA viruses are not closely related to each other but instead belong to four additional classes - Birnaviridae, Cystoviridae, Partitiviridae and Reoviridae - and one additional order (Totiviridae) of one of the classes of positive ssRNA viruses in the same subphylum as the positive strand RNA viruses.
These proposals were based on an analysis of the RNA polymerases and are still under consideration. To date they have not been broadly accepted because of doubts over the suitability of a single gene to determine the taxonomy of the clade.
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