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). Notable human diseases caused by RNA viruses include SARS, influenza, hepatitis C, West Nile fever, polio and measles.
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 in their life cycle as RNA viruses. Viruses with RNA as their genetic material but that 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.
- 1 Characteristics
- 2 Replication
- 3 Classification
- 4 Group III—dsRNA viruses
- 5 Group IV—positive-sense ssRNA viruses
- 6 Group V—negative-sense ssRNA viruses
- 7 Notes
- 8 See also
- 9 References
- 10 External links
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 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; 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.
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 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, 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.
RNA viruses generally have very high mutation rates compared to DNA viruses, because viral RNA polymerases lack the proof-reading ability of DNA polymerases. This is one reason why it is difficult to make effective vaccines to prevent diseases caused by RNA viruses. 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. 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, because it contains an RNA structure involved in an internal ribosome entry site.
- Double-stranded RNA viruses (Group III) contain from one to a dozen different RNA molecules, each of which coding for one or more viral proteins.
- Positive-sense ssRNA viruses (Group IV) have their genome directly utilized as if it were mRNA, with host ribosomes translating it into a single protein that is modified by host and viral proteins to form the various proteins needed for replication. One of these includes RNA-dependent RNA polymerase (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 ssRNA viruses (Group V) must have their genome copied by an RNA-dependent RNA polymerase to form positive-sense RNA. This means that the virus must bring along with it the RNA replicase 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, in general, are 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 into the host genome using the viral enzyme integrase, expression of the encoded genes may lead to the formation of new virions.
Classification of the RNA viruses has proven to be a difficult problem. This is in part due to the high mutation rates these genomes undergo. Classification is based principally on the type of genome (double-stranded, negative- or positive-single-strand) and gene number and organisation. Currently there are 5 orders and 47 families of RNA viruses recognised. There are also many unassigned species and genera.
Positive strand RNA viruses
This is the single largest group of RNA viruses with 30 families. Attempts have been made to group these families in higher orders. These proposals were based on an analysis of the RNA polymerases and are still under consideration. To date, the suggestions proposed have not been broadly accepted because of doubts over the suitability of a single gene to determine the taxonomy of the clade.
The proposed classification of positive-strand RNA viruses is based on the RNA-dependent RNA polymerase. Three groups have been recognised:
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).
A division of the alpha-like (Sindbis-like) supergroup on the basis of a novel domain located near the N termini of the proteins involved in viral replication has been proposed. The two groups proposed are: the 'altovirus' group (alphaviruses, furoviruses, hepatitis E virus, hordeiviruses, tobamoviruses, tobraviruses, tricornaviruses and probably rubiviruses); and the 'typovirus' group (apple chlorotic leaf spot virus, carlaviruses, potexviruses and tymoviruses).
Additional work has identified five groups of positive-stranded RNA viruses containing four, three, three, three, and one order(s), respectively. 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.
The evolution of the picornaviruses based on an analysis of their RNA polymerases and helicases appears to date to the divergence of the eukaryotes. Their putative ancestors include the bacterial group II retroelements, the family of HtrA proteases and DNA bacteriophages.
Double-stranded RNA viruses
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.
One study has suggested a that there are two large clades: One includes the Caliciviridae, Flaviviridae, and Picornaviridae families and a second that includes the Alphatetraviridae, Birnaviridae and Cystoviridae, Nodaviridae, and Permutotretraviridae families.
Group III—dsRNA viruses
There are nine families and a number of unassigned genera and species recognised in this group.
- Family Birnaviridae
- Family Chrysoviridae
- Family Cystoviridae
- Family Endornaviridae
- Family Hypoviridae
- Family Megabirnaviridae
- Family Partitiviridae
- Family Picobirnaviridae
- Family Reoviridae—includes Rotavirus
- Family Totiviridae
- Unassigned species
Group IV—positive-sense ssRNA viruses
There are three orders and 33 families recognised in this group. In addition, there are a number of unclassified species and genera.
- Order Nidovirales
- Order Picornavirales
- Order Tymovirales
- Family Alphatetraviridae
- Family Alvernaviridae
- Family Astroviridae
- Family Barnaviridae
- Family Bromoviridae
- Family Caliciviridae—includes Norwalk virus
- Family Carmotetraviridae
- Family Closteroviridae
- Family Flaviviridae—includes Yellow fever virus, West Nile virus, Hepatitis C virus, Dengue fever virus
- Family Leviviridae
- Family Luteoviridae—includes Barley yellow dwarf virus
- Family Narnaviridae
- Family Nodaviridae
- Family Permutotetraviridae
- Family Potyviridae
- Family Togaviridae—includes Rubella virus, Ross River virus, Sindbis virus, Chikungunya virus
- Family Tombusviridae
- Family Virgaviridae
- Unassigned species
- Blueberry necrotic ring blotch virus
- Botrytis virus F
- Canine picodicistrovirus
- Chronic bee paralysis associated satellite virus
- Extra small virus
- Heterocapsa circularisquama RNA virus
- Kelp fly virus
- Le Blanc virus
- Plasmopara halstedii virus
- Orsay virus
- Santeuil virus
- Solenopsis invicta virus 2
- Solenopsis invicta virus 3
- Unassigned species
Group V—negative-sense ssRNA viruses
There are two orders and eight families recognised in this group. There are also a number of unassigned species and genera.
- Order Mononegavirales
- Unassigned families:
- Unassigned genera:
- Unassigned species:
The majority of fungal viruses are double-stranded RNA viruses. A small number of positive-strand RNA viruses have been described. One report has suggested the possibility of a negative stranded virus.
- Virus classification
- Viral replication
- Animal viruses
- Double-stranded RNA viruses
- DNA viruses
- Norovirus cis-acting replication element
- MeSH, retrieved on 12 April 2008.
- "Listing in Taxonomic Order—Index to ICTV Species Lists". Retrieved 2008-04-11.
- Drake JW, Holland JJ (November 1999). "Mutation rates among RNA viruses". Proc. Natl. Acad. Sci. U.S.A. 96 (24): 13910–3. doi:10.1073/pnas.96.24.13910. PMC 24164. PMID 10570172.
- Nguyen M, Haenni AL (2003). "Expression strategies of ambisense viruses". Virus Res. 93 (2): 141–50. doi:10.1016/S0168-1702(03)00094-7. PMID 12782362.
- Roy P (2008). "Molecular Dissection of Bluetongue Virus". Animal Viruses: Molecular Biology. Caister Academic Press. isbn=978-1-904455-22-6.
- Roy P (2008). "Structure and Function of Bluetongue Virus and its Proteins". Segmented Double-stranded RNA Viruses: Structure and Molecular Biology. Caister Academic Press. isbn=978-1-904455-21-9.
- Klein, Donald W.; Prescott, Lansing M.; Harley, John (1993). Microbiology. Dubuque, Iowa: Wm. C. Brown. ISBN 0-697-01372-3.
- Steinhauer DA, Holland JJ (1987). "Rapid evolution of RNA viruses". Annu. Rev. Microbiol. 41: 409–33. doi:10.1146/annurev.mi.41.100187.002205. PMID 3318675.
- Boutwell CL, Rolland MM, Herbeck JT, Mullins JI, Allen TM (October 2010). "Viral Evolution and Escape during Acute HIV-1 Infection". J. Infect. Dis. 202 Suppl 2 (Suppl 2): S309–14. doi:10.1086/655653. PMC 2945609. PMID 20846038.
- Bukh J, Purcell RH, Miller RH (August 1994). "Sequence analysis of the core gene of 14 hepatitis C virus genotypes". Proc. Natl. Acad. Sci. U.S.A. 91 (17): 8239–43. doi:10.1073/pnas.91.17.8239. PMC 44581. PMID 8058787.
- Tuplin A, Evans DJ, Simmonds P (October 2004). "Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods". J. Gen. Virol. 85 (Pt 10): 3037–47. doi:10.1099/vir.0.80141-0. PMID 15448367.
- Koonin EV (1991). "The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses". J Gen Virol 72 (9): 2197–206. doi:10.1099/0022-1317-72-9-2197.
- Rozanov MN, Koonin EV, Gorbalenya AE (1992) Conservation of the putative methyltransferase domain: a hallmark of the 'Sindbis-like' supergroup of positive-strand RNA viruses. J Gen Virol 73 (8):2129–2134
- Koonin, EV, Dolja VV (1993) Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28:375–430
- Ward CW (1993). "Progress towards a higher taxonomy of viruses". Res Virol 144 (6): 419–453. doi:10.1016/S0923-2516(06)80059-2. PMID 8140287.
- Koonin EV, Wolf YI, Nagasaki K, Dolja VV (2008) The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat Rev Microbiol 6(12):925–939
- Gibrat, J. F.; Mariadassou, M.; Boudinot, P.; Delmas, B. (2013). "Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods". BMC Evol Biol 13: 154. doi:10.1186/1471-2148-13-154.
- Adams MJ, Antoniw JF, Kreuze J (2009). "Virgaviridae: a new family of rod-shaped plant viruses". Arch Virol 154 (12): 1967–1972. doi:10.1007/s00705-009-0506-6. PMID 19862474.
- Mihindukulasuriya, K. A.; Nguyen, N. L.; Wu, G.; Huang, H. V.; Travassos da Rosa, A. P.; Popov, V. L.; Tesh, R. B.; Wang, D. (2009). "Nyamanini and Midway viruses define a novel taxon of RNA viruses in the order Mononegavirales". J. Virol. 83 (10): 5109–5116. doi:10.1128/JVI.02667-08. PMC 2682064. PMID 19279111.
- Kondo, H.; Chiba, S.; Toyoda, K.; Suzuki, N. (2012). "Evidence for negative-strand RNA virus infection in fungi". Virology 435 (2): 201–209. doi:10.1016/j.virol.2012.10.002. PMID 23099204.