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] Notable human diseases caused by RNA viruses include Ebola hemorrhoragic fever, SARS, the common cold, 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.[3] 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.[4]

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 a 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.[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 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]

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][9] This is one reason why it is difficult to make effective vaccines to prevent diseases caused by RNA viruses.[10] 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.[11] 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,[12] because it contains an RNA structure involved in an internal ribosome entry site.[13]

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):

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

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.

Related to but distinct from the RNA viruses are the viroids and the RNA satellite viruses. These are not currently classified as RNA viruses and are described on their own pages.

Positive strand RNA viruses

This is the single largest group of RNA viruses[14] 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:[15]

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.[16] 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).

The alpha like supergroup can be further divided into three clades: the rubi-like, tobamo-like, and tymo-like viruses.[17]

Additional work has identified five groups of positive-stranded RNA viruses containing four, three, three, three, and one order(s), respectively.[18] 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.

Evolution

The evolution of the picornaviruses based on an analysis of their RNA polymerases and helicases appears to date to the divergence of the eukaryotes.[19] 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.[20]

Group III—dsRNA viruses

There are eleven families and a number of unassigned genera and species recognised in this group.[8]

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.

Group V—negative-sense ssRNA viruses

This groups consist of twelve families recognised and a number of unassigned genera and species.

Source:[22]

Notes

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.[23]

See also

References

  1. ↑ MeSH, retrieved on 12 April 2008.
  2. 1 2 Patton JT (editor). (2008). Segmented Double-stranded RNA Viruses: Structure and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-21-9.
  3. ↑ "Listing in Taxonomic Order—Index to ICTV Species Lists". 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 24164Freely accessible. 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. ISBN 978-1-904455-22-6.
  7. ↑ Roy P (2008). "Structure and Function of Bluetongue Virus and its Proteins". Segmented Double-stranded RNA Viruses: Structure and Molecular Biology. Caister Academic. ISBN 978-1-904455-21-9.
  8. 1 2 Klein, Donald W.; Prescott, Lansing M.; Harley, John (1993). Microbiology. Dubuque, Iowa: Wm. C. Brown. ISBN 0-697-01372-3.
  9. ↑ Martinez MA, et al. (2012). "Quasispecies Dynamics of RNA Viruses". In Witzany, G. Viruses: Essential Agents of Life. Springer. pp. 21–42. ISBN 978-94-007-4898-9.
  10. ↑ 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.
  11. ↑ 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): S309–14. doi:10.1086/655653. PMC 2945609Freely accessible. PMID 20846038.
  12. ↑ 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 44581Freely accessible. PMID 8058787.
  13. ↑ 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.
  14. ↑ Francki, R.I.B; Fauquet, C. M.; Knudson, D. L.; Brown, F. (1991). Classification and nomenclature of viruses. Fifth report of the International Committee on Taxonomy of Viruses, Archives of Virology (Suppl. 2). ISBN 978-3-7091-9163-7.
  15. ↑ Koonin EV (September 1991). "The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses". J. Gen. Virol. 72 (Pt 9): 2197–206. doi:10.1099/0022-1317-72-9-2197. PMID 1895057.
  16. ↑ Rozanov MN, Koonin EV, Gorbalenya AE (August 1992). "Conservation of the putative methyltransferase domain: a hallmark of the 'Sindbis-like' supergroup of positive-strand RNA viruses". J. Gen. Virol. 73 (Pt 8): 2129–34. doi:10.1099/0022-1317-73-8-2129. PMID 1645151.
  17. ↑ 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 (5): 375–430. doi:10.3109/10409239309078440. PMID 8269709.
  18. ↑ 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.
  19. ↑ Koonin EV, Wolf YI, Nagasaki K, Dolja VV (December 2008). "The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups". Nat. Rev. Microbiol. 6 (12): 925–39. doi:10.1038/nrmicro2030. PMID 18997823.
  20. ↑ Gibrat JF, 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. PMC 3724706Freely accessible. PMID 23865988.
  21. ↑ Adams MJ, Antoniw JF, Kreuze J (2009). "Virgaviridae: a new family of rod-shaped plant viruses". Arch Virol. 154 (12): 1967–72. doi:10.1007/s00705-009-0506-6. PMID 19862474.
  22. ↑ Afonso, Claudio L.; Amarasinghe, Gaya K.; Bányai, Krisztián; Bào, Yīmíng; Basler, Christopher F.; Bavari, Sina; Bejerman, Nicolás; Blasdell, Kim R.; Briand, François-Xavier (2016-08-01). "Taxonomy of the order Mononegavirales: update 2016". Archives of Virology. 161 (8): 2351–2360. doi:10.1007/s00705-016-2880-1. ISSN 1432-8798. PMC 4947412Freely accessible. PMID 27216929.
  23. ↑ Kondo, H.; Chiba, S.; Toyoda, K.; Suzuki, N. (2012). "Evidence for negative-strand RNA virus infection in fungi". Virology. 435 (2): 201–9. doi:10.1016/j.virol.2012.10.002. PMID 23099204.

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