RNA virus

RNA virus

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 and hepatitis C.

Another term for RNA viruses that explicitly excludes retroviruses is ribovirus.[4]

Contents

Characteristics

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, 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]

Double-stranded RNA viruses

Further information: 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, 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]

Mutation rates

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]

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-dependent 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.

Classification

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.

Group III - dsRNA viruses

  • Unassigned species
    • Sclerotinia sclerotiorum debilitation-associated virus

Source:[8]

Group IV - positive-sense ssRNA viruses



  • Order Tymovirales
    • Family Alphaflexiviridae
    • Family Betaflexiviridae
    • Family Gammaflexiviridae
    • Family Tymoviridae




    • Unassigned species
      • Chronic bee paralysis associated satellite virus
      • Extra small virus

Group V - negative-sense ssRNA viruses

  • Unassigned genera:
  • Unassigned species:
    • Taastrup virus

Source:[8]

See also

References

  1. ^ MeSH, retrieved on 12 April 2008.
  2. ^ a b Patton JT (editor). (2008). Segmented Double-stranded RNA Viruses: Structure and Molecular Biology. Caister Academic Press. ISBN [[Special:BookSources/978-1-904455-21-9]|978-1-904455-21-9]]]. [http://www.horizonpress.com/rnav. http://www.horizonpress.com/rnav. 
  3. ^ "Listing in Taxonomic Order - Index to ICTV Species Lists". http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/fr-fst-g.htm. Retrieved 2008-04-11. 
  4. ^ 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. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=10570172. 
  5. ^ 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. 
  6. ^ Roy P (2008). "Molecular Dissection of Bluetongue Virus". Animal Viruses: Molecular Biology. Caister Academic Press. ISBN [[Special:BookSources/978-1-904455-22-6]|978-1-904455-22-6]]]. [http://www.horizonpress.com/avir. http://www.horizonpress.com/avir. 
  7. ^ 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 [[Special:BookSources/978-1-904455-21-9]|978-1-904455-21-9]]]. [http://www.horizonpress.com/rnav. http://www.horizonpress.com/rnav. 
  8. ^ a b c Klein, Donald W.; Prescott, Lansing M.; Harley, John (1993). Microbiology. Dubuque, Iowa: Wm. C. Brown. ISBN 0-697-01372-3. 
  9. ^ 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. 
  10. ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2945609. 
  11. ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=44581. 
  12. ^ 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. 
  13. ^ Koonin EV (1991) The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J Gen Virol 72 (9):2197-206.
  14. ^ Koonin, E. V., and V. V. Dolja. 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.
  15. ^ Ward CW (1993) Progress towards a higher taxonomy of viruses. Res Virol. 144(6):419-453
  16. ^ Adams MJ, Antoniw JF, Kreuze J (2009) Virgaviridae: a new family of rod-shaped plant viruses. Arch Virol 154(12):1967-1972
  17. ^ 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.

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