RNA virus

Last updated

Taxonomy and replication strategies of different types of RNA viruses 18 2014 1695 Fig1 HTML.webp
Taxonomy and replication strategies of different types of RNA viruses

An RNA virus is a virus characterized by a ribonucleic acid (RNA) based genome. [1] The genome can be single-stranded RNA (ssRNA) or double-stranded (dsRNA). [2] Notable human diseases caused by RNA viruses include influenza, SARS, MERS, COVID-19, Dengue virus, hepatitis C, hepatitis E, West Nile fever, Ebola virus disease, rabies, polio, mumps, and measles.

Contents

All known RNA viruses, that is viruses that use a homologous RNA-dependent polymerase for replication, are categorized by the International Committee on Taxonomy of Viruses (ICTV) into the realm Riboviria . [3] This includes RNA viruses belonging to Group III, Group IV or Group V of the Baltimore classification system as well as Group VI. Group VI viruses are retroviruses, viruses with RNA genetic material that use DNA intermediates in their life cycle including HIV-1 and HIV-2 which cause AIDS.

The majority of such RNA viruses fall into the kingdom Orthornavirae and the rest have a positioning not yet defined. [4] The realm does not contain all RNA viruses: Deltavirus , Avsunviroidae , and Pospiviroidae are taxa of RNA viruses that were mistakenly included in 2019, [a] but corrected in 2020. [5]

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-dependent RNA polymerase before translation. Purified RNA of a positive-sense virus can directly cause infection though it may be less infectious than the whole virus particle. In contrast, 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 translate genes from their negative and positive strands. [6]

Double-stranded RNA viruses

Structure of the reovirus virion Structure of the reovirus virion.png
Structure of the reovirus virion

The double-stranded (ds)RNA viruses represent a diverse group of viruses that vary widely in host range (humans, animals, plants, fungi, [b] and bacteria), genome segment number (one to twelve), and virion organization (Triangulation number, capsid layers, spikes, turrets, etc.). Members of this group include the rotaviruses, which are the most common cause of gastroenteritis in young children, and picobirnaviruses, which are the most common virus in fecal samples of both humans and animals with or without signs of diarrhea. Bluetongue virus is an economically important pathogen that infects cattle and sheep. In recent years, progress has been made in determining atomic and subnanometer resolution structures of a number of key viral proteins and virion capsids of several dsRNA viruses, highlighting the significant parallels in the structure and replicative processes of many of these viruses. [2] [ page needed ]

Mutation rates

RNA viruses generally have very high mutation rates compared to DNA viruses, [8] because viral RNA polymerases lack the proofreading ability of DNA polymerases. [9] The genetic diversity of RNA viruses is one reason why it is difficult to make effective vaccines against them. [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]

Sequence complexity

On average, dsRNA viruses show a lower sequence redundancy relative to ssRNA viruses. Contrarily, dsDNA viruses contain the most redundant genome sequences while ssDNA viruses have the least. [14] The sequence complexity of viruses has been shown to be a key characteristic for accurate reference-free viral classification. [14]

Replication

There are three distinct groups of RNA viruses depending on their genome and mode of replication:

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.

Recombination

Numerous RNA viruses are capable of genetic recombination when at least two viral genomes are present in the same host cell. [15] Very rarely viral RNA can recombine with host RNA. [16] RNA recombination appears to be a major driving force in determining genome architecture and the course of viral evolution among Picornaviridae ((+)ssRNA), e.g. poliovirus. [17] In the Retroviridae ((+)ssRNA), e.g. HIV, damage in the RNA genome appears to be avoided during reverse transcription by strand switching, a form of recombination. [18] [19] [20] Recombination also occurs in the Reoviridae (dsRNA), e.g. reovirus; Orthomyxoviridae ((-)ssRNA), e.g. influenza virus; [20] and Coronaviridae ((+)ssRNA), e.g. SARS. [21] Recombination in RNA viruses appears to be an adaptation for coping with genome damage. [15] Recombination can occur infrequently between animal viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans. [21]

Classification

Classification is based principally on the type of genome (double-stranded, negative- or positive-single-strand) and gene number and organization. Currently, there are 5 orders and 47 families of RNA viruses recognized. 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.

A study of several thousand RNA viruses has shown the presence of at least five main taxa: a levivirus and relatives group; a picornavirus supergroup; an alphavirus supergroup plus a flavivirus supergroup; the dsRNA viruses; and the -ve strand viruses. [22] The lentivirus group appears to be basal to all the remaining RNA viruses. The next major division lies between the picornasupragroup and the remaining viruses. The dsRNA viruses appear to have evolved from a +ve RNA ancestor and the -ve RNA viruses from within the dsRNA viruses. The closest relation to the -ve stranded RNA viruses is the Reoviridae.

Positive-strand RNA viruses

This is the single largest group of RNA viruses [23] and has been organized by the ICTV into the phyla Kitrinoviricota , Lenarviricota , and Pisuviricota in the kingdom Orthornavirae and realm Riboviria . [24]

Positive-strand RNA viruses can also be classified based on the RNA-dependent RNA polymerase. Three groups have been recognised: [25]

  1. 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).
  2. Carmoviruses, dianthoviruses, flaviviruses, pestiviruses, statoviruses, tombusviruses, single-stranded RNA bacteriophages, hepatitis C virus and a subset of luteoviruses (barley yellow dwarf virus)—the flavi like group (Flavivirata).
  3. 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. [26] 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. [27]

Additional work has identified five groups of positive-stranded RNA viruses containing four, three, three, three, and one order(s), respectively. [28] 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 eukaryotes. [29] Their putative ancestors include the bacterial group II retroelements, the family of HtrA proteases and DNA bacteriophages.

Partitiviruses are related to and may have evolved from a totivirus ancestor. [30]

Hypoviruses and barnaviruses appear to share an ancestry with the potyvirus and sobemovirus lineages respectively. [30]

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 that there are two large clades: One includes the families Caliciviridae, Flaviviridae, and Picornaviridae and a second that includes the families Alphatetraviridae, Birnaviridae, Cystoviridae, Nodaviridae, and Permutotretraviridae. [31]

Negative strand RNA viruses

These viruses have multiple types of genome ranging from a single RNA molecule up to eight segments. Despite their diversity it appears that they may have originated in arthropods and to have diversified from there. [32]

Satellite viruses

A number of satellite viruses—viruses that require the assistance of another virus to complete their life cycle—are also known. Their taxonomy has yet to be settled. The following four genera have been proposed for positive sense single stranded RNA satellite viruses that infect plants—Albetovirus, Aumaivirus, Papanivirus and Virtovirus. [33] A family—Sarthroviridae which includes the genus Macronovirus—has been proposed for the positive sense single stranded RNA satellite viruses that infect arthropods.

Group III – dsRNA viruses

There are twelve families and a number of unassigned genera and species recognised in this group. [9]

Group IV – positive-sense ssRNA viruses

There are three orders and 34 families recognised in this group. In addition, there are a number of unclassified species and genera.

Satellite viruses

An unclassified astrovirus/hepevirus-like virus has also been described. [35]

Group V – negative-sense ssRNA viruses

With the exception of the Hepatitis D virus, this group of viruses has been placed into a single phylum—Negarnaviricota. This phylum has been divided into two subphyla—Haploviricotina and Polyploviricotina. Within the subphylum Haploviricotina four classes are currently recognised: Chunqiuviricetes, Milneviricetes, Monjiviricetes and Yunchangviricetes. In the subphylum Polyploviricotina two classes are recognised: Ellioviricetes and Insthoviricetes.

Six classes, seven orders and twenty four families are currently recognized in this group. A number of unassigned species and genera are yet to be classified. [9]

See also

Notes

  1. ↑ This inclusion was due to TaxoProp 2017.006G, which proposed Riboviria. The confusion might be due to the TaxoProp's reference to a "monophyly of all RNA viruses", improperly termed as it was only demonstrated with RdRP. On the other hand, the proposed definition of Riboviria did correctly mention RdRP .
  2. ↑ 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. [7]

Related Research Articles

<span class="mw-page-title-main">DNA virus</span> Virus that has DNA as its genetic material

A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase. They can be divided between those that have two strands of DNA in their genome, called double-stranded DNA (dsDNA) viruses, and those that have one strand of DNA in their genome, called single-stranded DNA (ssDNA) viruses. dsDNA viruses primarily belong to two realms: Duplodnaviria and Varidnaviria, and ssDNA viruses are almost exclusively assigned to the realm Monodnaviria, which also includes some dsDNA viruses. Additionally, many DNA viruses are unassigned to higher taxa. Reverse transcribing viruses, which have a DNA genome that is replicated through an RNA intermediate by a reverse transcriptase, are classified into the kingdom Pararnavirae in the realm Riboviria.

<span class="mw-page-title-main">Retrovirus</span> Family of viruses

A retrovirus is a type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. After invading a host cell's cytoplasm, the virus uses its own reverse transcriptase enzyme to produce DNA from its RNA genome, the reverse of the usual pattern, thus retro (backward). The new DNA is then incorporated into the host cell genome by an integrase enzyme, at which point the retroviral DNA is referred to as a provirus. The host cell then treats the viral DNA as part of its own genome, transcribing and translating the viral genes along with the cell's own genes, producing the proteins required to assemble new copies of the virus. Many retroviruses cause serious diseases in humans, other mammals, and birds.

<span class="mw-page-title-main">Reverse transcriptase</span> Enzyme which generates DNA

A reverse transcriptase (RT) is an enzyme used to convert RNA genome to DNA, a process termed reverse transcription. Reverse transcriptases are used by viruses such as HIV and hepatitis B to replicate their genomes, by retrotransposon mobile genetic elements to proliferate within the host genome, and by eukaryotic cells to extend the telomeres at the ends of their linear chromosomes. Contrary to a widely held belief, the process does not violate the flows of genetic information as described by the classical central dogma, as transfers of information from RNA to DNA are explicitly held possible.

Virus classification is the process of naming viruses and placing them into a taxonomic system similar to the classification systems used for cellular organisms.

<i>Hepadnaviridae</i> Family of viruses

Hepadnaviridae is a family of viruses. Humans, apes, and birds serve as natural hosts. There are currently 18 species in this family, divided among 5 genera. Its best-known member is hepatitis B virus. Diseases associated with this family include: liver infections, such as hepatitis, hepatocellular carcinomas, and cirrhosis. It is the sole accepted family in the order Blubervirales.

<i>Geminiviridae</i> Family of viruses

Geminiviridae is a family of plant viruses that encode their genetic information on a circular genome of single-stranded (ss) DNA. There are 520 species in this family, assigned to 14 genera. Diseases associated with this family include: bright yellow mosaic, yellow mosaic, yellow mottle, leaf curling, stunting, streaks, reduced yields. They have single-stranded circular DNA genomes encoding genes that diverge in both directions from a virion strand origin of replication. According to the Baltimore classification they are considered class II viruses. It is the largest known family of single stranded DNA viruses.

<i>Tombusviridae</i> Family of viruses

Tombusviridae is a family of single-stranded positive sense RNA plant viruses. There are three subfamilies, 17 genera, and 95 species in this family. The name is derived from Tomato bushy stunt virus (TBSV).

<span class="mw-page-title-main">Viral replication</span> Formation of biological viruses during the infection process

Viral replication is the formation of biological viruses during the infection process in the target host cells. Viruses must first get into the cell before viral replication can occur. Through the generation of abundant copies of its genome and packaging these copies, the virus continues infecting new hosts. Replication between viruses is greatly varied and depends on the type of genes involved in them. Most DNA viruses assemble in the nucleus while most RNA viruses develop solely in cytoplasm.

Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a distinct group. Seven Baltimore groups are described that take into consideration whether the viral genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), whether the genome is single- or double-stranded, and whether the sense of a single-stranded RNA genome is positive or negative.

<i>Murine leukemia virus</i> Species of virus

The murine leukemia viruses are retroviruses named for their ability to cause cancer in murine (mouse) hosts. Some MLVs may infect other vertebrates. MLVs include both exogenous and endogenous viruses. Replicating MLVs have a positive sense, single-stranded RNA (ssRNA) genome that replicates through a DNA intermediate via the process of reverse transcription.

In molecular biology and genetics, the sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the context, sense may have slightly different meanings. For example, the negative-sense strand of DNA is equivalent to the template strand, whereas the positive-sense strand is the non-template strand whose nucleotide sequence is equivalent to the sequence of the mRNA transcript.

<span class="mw-page-title-main">RNA-dependent RNA polymerase</span> Enzyme that synthesizes RNA from an RNA template

RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to typical DNA-dependent RNA polymerases, which all organisms use to catalyze the transcription of RNA from a DNA template.

<span class="mw-page-title-main">Viral disease</span> Animal or plant disease resulting from a viral infection

A viral disease occurs when an organism's body is invaded by pathogenic viruses, and infectious virus particles (virions) attach to and enter susceptible cells.

<span class="mw-page-title-main">Positive-strand RNA virus</span> Class of viruses in the Baltimore classification

Positive-strand RNA viruses are a group of related viruses that have positive-sense, single-stranded genomes made of ribonucleic acid. The positive-sense genome can act as messenger RNA (mRNA) and can be directly translated into viral proteins by the host cell's ribosomes. Positive-strand RNA viruses encode an RNA-dependent RNA polymerase (RdRp) which is used during replication of the genome to synthesize a negative-sense antigenome that is then used as a template to create a new positive-sense viral genome.

<span class="mw-page-title-main">Negative-strand RNA virus</span> Phylum of viruses

Negative-strand RNA viruses are a group of related viruses that have negative-sense, single-stranded genomes made of ribonucleic acid (RNA). They have genomes that act as complementary strands from which messenger RNA (mRNA) is synthesized by the viral enzyme RNA-dependent RNA polymerase (RdRp). During replication of the viral genome, RdRp synthesizes a positive-sense antigenome that it uses as a template to create genomic negative-sense RNA. Negative-strand RNA viruses also share a number of other characteristics: most contain a viral envelope that surrounds the capsid, which encases the viral genome, −ssRNA virus genomes are usually linear, and it is common for their genome to be segmented.

<i>Riboviria</i> Realm of viruses

Riboviria is a realm of viruses that includes all viruses that use a homologous RNA-dependent polymerase for replication. It includes RNA viruses that encode an RNA-dependent RNA polymerase, as well as reverse-transcribing viruses that encode an RNA-dependent DNA polymerase. RNA-dependent RNA polymerase (RdRp), also called RNA replicase, produces RNA from RNA. RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), produces DNA from RNA. These enzymes are essential for replicating the viral genome and transcribing viral genes into messenger RNA (mRNA) for translation of viral proteins.

In virology, realm is the highest taxonomic rank established for viruses by the International Committee on Taxonomy of Viruses (ICTV), which oversees virus taxonomy. Six virus realms are recognized and united by specific highly conserved traits:

<i>Ground squirrel hepatitis virus</i> Species of virus

Ground squirrel hepatitis virus, abbreviated GSHV, is a partially double-stranded DNA virus that is closely related to human Hepatitis B virus (HBV) and Woodchuck hepatitis virus (WHV). It is a member of the family of viruses Hepadnaviridae and the genus Orthohepadnavirus. Like the other members of its family, GSHV has high degree of species and tissue specificity. It was discovered in Beechey ground squirrels, Spermophilus beecheyi, but also infects Arctic ground squirrels, Spermophilus parryi. Commonalities between GSHV and HBV include morphology, DNA polymerase activity in genome repair, cross-reacting viral antigens, and the resulting persistent infection with viral antigen in the blood (antigenemia). As a result, GSHV is used as an experimental model for HBV.

<i>Monodnaviria</i> Realm of viruses

Monodnaviria is a realm of viruses that includes all single-stranded DNA viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication of the circular viral genome. Viruses descended from such viruses are also included in the realm, including certain linear single-stranded DNA (ssDNA) viruses and circular double-stranded DNA (dsDNA) viruses. These atypical members typically replicate through means other than rolling circle replication.

<i>Orthornavirae</i> Kingdom of viruses

Orthornavirae is a kingdom of viruses that have genomes made of ribonucleic acid (RNA), including genes which encode an RNA-dependent RNA polymerase (RdRp). The RdRp is used to transcribe the viral RNA genome into messenger RNA (mRNA) and to replicate the genome. Viruses in this kingdom share a number of characteristics which promote rapid evolution, including high rates of genetic mutation, recombination, and reassortment.

References

  1. ↑ Wagner, Edward K.; Hewlett, Martinez J. (1999). Basic virology. Malden, MA: Blackwell Science, Inc. p. 249. ISBN   0-632-04299-0 . Retrieved 30 March 2020.
  2. 1 2 Patton JT, ed. (2008). Segmented Double-stranded RNA Viruses: Structure and Molecular Biology. Caister Academic Press. ISBN   978-1-904455-21-9.
  3. ↑ International Committee on Taxonomy of Viruses Executive Committee (May 2020). "The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks". Nature Microbiology. 5 (5): 668–674. doi: 10.1038/s41564-020-0709-x . PMC   7186216 . PMID   32341570.
  4. ↑ TaxoProp 2019.006G
  5. ↑ TaxoProp 2019.009G
  6. ↑ Nguyen M, Haenni AL (June 2003). "Expression strategies of ambisense viruses". Virus Research. 93 (2): 141–50. doi:10.1016/S0168-1702(03)00094-7. PMID   12782362.
  7. ↑ Kondo H, Chiba S, Toyoda K, Suzuki N (January 2013). "Evidence for negative-strand RNA virus infection in fungi". Virology. 435 (2): 201–09. doi: 10.1016/j.virol.2012.10.002 . PMID   23099204.
  8. ↑ Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R (October 2010). "Viral mutation rates". Journal of Virology. 84 (19): 9733–48. doi:10.1128/JVI.00694-10. PMC   2937809 . PMID   20660197.
  9. 1 2 3 Klein DW, Prescott LM, Harley J (1993). Microbiology. Dubuque, Iowa: Wm. C. Brown. ISBN   978-0-697-01372-9.
  10. ↑ Steinhauer DA, Holland JJ (1987). "Rapid evolution of RNA viruses". Annual Review of Microbiology. 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". The Journal of Infectious Diseases. 202 (Suppl 2): S309–14. doi:10.1086/655653. PMC   2945609 . PMID   20846038.
  12. ↑ Bukh J, Purcell RH, Miller RH (August 1994). "Sequence analysis of the core gene of 14 hepatitis C virus genotypes". Proceedings of the National Academy of Sciences of the United States of America. 91 (17): 8239–43. Bibcode:1994PNAS...91.8239B. doi: 10.1073/pnas.91.17.8239 . PMC   44581 . 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". The Journal of General Virology. 85 (Pt 10): 3037–47. doi: 10.1099/vir.0.80141-0 . PMID   15448367.
  14. 1 2 Silva JM, Pratas D, Caetano T, Matos D (August 2022). "The complexity landscape of viral genomes". GigaScience. 11: 1–16. doi:10.1093/gigascience/giac079. PMC   9366995 . PMID   35950839.
  15. 1 2 Barr JN, Fearns R (June 2010). "How RNA viruses maintain their genome integrity". The Journal of General Virology. 91 (Pt 6): 1373–87. doi: 10.1099/vir.0.020818-0 . PMID   20335491.
  16. ↑ Stedman, Kenneth M. (2015). "Deep Recombination: RNA and ssDNA Virus Genes in DNA Virus and Host Genomes". Annual Review of Virology. 2 (1): 203–217. doi: 10.1146/annurev-virology-100114-055127 . ISSN   2327-0578. PMID   26958913. S2CID   207745438.
  17. ↑ Muslin C, Mac Kain A, Bessaud M, Blondel B, Delpeyroux F (September 2019). "Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process". Viruses. 11 (9): 859. doi: 10.3390/v11090859 . PMC   6784155 . PMID   31540135.
  18. ↑ Hu WS, Temin HM (November 1990). "Retroviral recombination and reverse transcription". Science. 250 (4985): 1227–33. Bibcode:1990Sci...250.1227H. doi:10.1126/science.1700865. PMID   1700865.
  19. ↑ Rawson JM, Nikolaitchik OA, Keele BF, Pathak VK, Hu WS (November 2018). "Recombination is required for efficient HIV-1 replication and the maintenance of viral genome integrity". Nucleic Acids Research. 46 (20): 10535–45. doi:10.1093/nar/gky910. PMC   6237782 . PMID   30307534.
  20. 1 2 Bernstein H, Bernstein C, Michod RE (January 2018). "Sex in microbial pathogens". Infection, Genetics and Evolution. 57: 8–25. Bibcode:2018InfGE..57....8B. doi: 10.1016/j.meegid.2017.10.024 . PMID   29111273.
  21. 1 2 Su S, Wong G, Shi W, Liu J, Lai AC, Zhou J, et al. (June 2016). "Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses". Trends in Microbiology. 24 (6): 490–502. doi: 10.1016/j.tim.2016.03.003 . PMC   7125511 . PMID   27012512.
  22. ↑ Wolf YI, Kazlauskas D, Iranzo J, Lucía-Sanz A, Kuhn JH, Krupovic M, Dolja VV, Koonin EV (November 2018). "Origins and Evolution of the Global RNA Virome". mBio. 9 (6). doi:10.1128/mBio.02329-18. PMC   6282212 . PMID   30482837.
  23. ↑ Francki RI, Fauquet CM, Knudson DL, Brown F (1991). Classification and nomenclature of viruses. Fifth report of the International Committee on Taxonomy of Viruses, Archives of Virology (Suppl. 2). Springer. ISBN   978-3-7091-9163-7.
  24. ↑ "Current ICTV Taxonomy Release | ICTV". ictv.global. Retrieved 3 April 2023.
  25. ↑ Koonin EV (September 1991). "The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses". The Journal of General Virology. 72 (Pt 9): 2197–206. doi: 10.1099/0022-1317-72-9-2197 . PMID   1895057.
  26. ↑ 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". The Journal of General Virology. 73 (Pt 8): 2129–34. CiteSeerX   10.1.1.532.7367 . doi:10.1099/0022-1317-73-8-2129. PMID   1645151.
  27. ↑ Koonin EV, Dolja VV (1993). "Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences". Critical Reviews in Biochemistry and Molecular Biology. 28 (5): 375–430. doi:10.3109/10409239309078440. PMID   8269709.
  28. ↑ Ward CW (1993). "Progress towards a higher taxonomy of viruses". Research in Virology. 144 (6): 419–53. doi:10.1016/S0923-2516(06)80059-2. PMC   7135741 . PMID   8140287.
  29. ↑ Koonin EV, Wolf YI, Nagasaki K, Dolja VV (December 2008). "The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups". Nature Reviews. Microbiology. 6 (12): 925–39. doi: 10.1038/nrmicro2030 . PMID   18997823.
  30. 1 2 Ghabrial SA (1998). "Origin, adaptation and evolutionary pathways of fungal viruses". Virus Genes. 16 (1): 119–31. doi:10.1023/a:1007966229595. PMC   7089520 . PMID   9562896.
  31. ↑ Gibrat JF, Mariadassou M, Boudinot P, Delmas B (July 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 Evolutionary Biology. 13 (1): 154. Bibcode:2013BMCEE..13..154G. doi: 10.1186/1471-2148-13-154 . PMC   3724706 . PMID   23865988.
  32. ↑ Li CX, Shi M, Tian JH, Lin XD, Kang YJ, Chen LJ, et al. (January 2015). "Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses". eLife. 4. doi: 10.7554/eLife.05378 . PMC   4384744 . PMID   25633976.
  33. ↑ Krupovic M, Kuhn JH, Fischer MG (January 2016). "A classification system for virophages and satellite viruses". Archives of Virology. 161 (1): 233–47. doi: 10.1007/s00705-015-2622-9 . hdl: 11858/00-001M-0000-0028-DC34-F . PMID   26446887.
  34. ↑ Adams MJ, Antoniw JF, Kreuze J (2009). "Virgaviridae: a new family of rod-shaped plant viruses". Archives of Virology. 154 (12): 1967–72. doi: 10.1007/s00705-009-0506-6 . PMID   19862474.
  35. ↑ Pankovics P, Boros Á, Kiss T, Engelmann P, Reuter G (2019) Genetically highly divergent RNA virus with astrovirus-like (5'-end) and hepevirus-like (3'-end) genome organization in carnivorous birds, European roller (Coracias garrulus). Infect Genet Evol
  36. ↑ "Virus Taxonomy: 2018 Release". International Committee on Taxonomy of Viruses . Retrieved 13 November 2018.
  37. ↑ Mihindukulasuriya KA, Nguyen NL, Wu G, Huang HV, da Rosa AP, Popov VL, et al. (May 2009). "Nyamanini and midway viruses define a novel taxon of RNA viruses in the order Mononegavirales". Journal of Virology. 83 (10): 5109–16. doi:10.1128/JVI.02667-08. PMC   2682064 . PMID   19279111.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.