Viruses are the only organisms on this planet to still have RNA as their sole genetic material. They are also the only autonomously replicating organisms to have single-stranded DNA. The range of virus genomes as found in virions encompasses single-component dsDNA, linear or circular (occasionally circularly permuted linear); single, double or multi-component circular ssDNA; single-component linear ssDNA; single or multi- component dsRNA; single or multiple component ssRNA genomes which may be totally "positive"(or messenger) polarity, totally "negative" (or anti-messenger) polarity, or partially positive negative-sense; "diploid" positive-sense ssRNA genomes which replicate via reverse transcription to and transcription from longer-than-genome-length dsDNA, and nicked and/or partially dsDNAs which replicate via transcription to and reverse transcription from longer-than-genome-length positive-sense ssRNA. In contrast, prokaryotes have only single-component circular (mainly) or linear (Streptomyces, Helicobacter) dsDNA while all eukaryotes have multi-component dsDNA, and all the genomes replicate via the classic semi-conservative route.
Briefly, the types are classified by type of nucleic acid in virions (see also genomes.gif), and replication strategy. The types are:
dsDNA viruses include viruses infecting Bacteria and Archaea, or phages (eg. the T-even and lambda coliphages of E coli); viruses of higher animals (pox- and herpes- and adeno- and polyomaviruses); viruses of insects (baculo- and irido- and polydnaviruses); and viruses of eukaryotic algae (phycodnaviruses). These range in size from 5000 bp (polydnaviruses) through 30-40 kb (lambda phage and adenoviruses) to about 200 kb (baculoviruses) to over 300 kb (herpes- and pox- and irido- and phycodnaviruses). They may have circular genomes (polyoma- and baculo- and polydnaviruses); linear genomes (adeno- and herpesviruses, some phages); have linear genomes which are circularly permuted (phage T4, some iridoviruses); or linear genomes which have covalently closed ends (pox- and phycodnaviruses).
All viruses except polydnaviruses have single-component genomes; the latter have multiple components ranging in size from 2 - 20 kb, and the number which constitute an individual genome is not known.
Replication of the viruses is in all cases by the semi-conservative method favoured by cellular genomes; however, smaller circular genomes (eg. polyomaviruses) replicate by means of bidirectional replication forks from a single origin. like some plasmids. Among the viruses of Eukarya, replication mainly occurs in the nucleus, using cellular enzymes such as polymerases, methylases, etc. However,the replication of poxviruses, some baculoviruses (granulosis group), and some of the replication of iridoviruses, takes place in virus-specified "inclusion bodies" in the cytoplasm, using viral-coded enzymes, most important of which are DNA-dependent DNA polymerases.
Virus Taxonomy: Sixth report of the International Committee on Taxonomy of Viruses (FA Murphy et al., Eds.); Springer-Verlag, Wien, 1995.
B) Type II: ssDNA
ssDNA viruses include organisms infecting bacteria ("bacteriophages", eg. Inoviridae, Microviridae), mammals (circoviruses, Parvoviridae), birds (circovirus-like organisms), and plants (Geminiviridae, banana bunchy top-like viruses). They can have linear single-component genomes (Parvoviridae), circular single-component genomes (Microviridae, Inoviridae, circoviruses, some Geminiviridae), circular two-component genomes (some Geminiviridae), or circular multicomponent (>3) genomes (banana bunchy top-related viruses, BBTRV). The genomes are all relatively small: the circovirus-like agents have genomes of about 3 kb; Parvoviridae have genomes of 4-5 kb; the Geminiviridae about 2.7 - 5.4 kb (depending on whether are mono- or bi-component); the Microviridae (including the famous phiX 174) about 4.5 kb; the Inoviridae and the banana bunchy top-like viruses about 5-6 kb.
Replication of all of the viruses requires formation of a "replicative form" (RF) double- stranded DNA intermediate: this is formed soon after infection, almost certainly by the host cell DNA polymerases engaging in "repair" of the ssDNA. In the case of circular genomes in Eukarya (circoviruses, eg. porcine circovirus; also psittacine beak-and-feather disease agent, chicken infectious aneamia agent; Geminiviridae; BBTRV), these get converted into cccds-(plasmid-like)-DNA in the nucleus, and become associated with nuclear proteins and complexes such as nucleosomes. Parvoviruses have an interesting strategy for replicating their genomes, which uses internal or self-complementarity of genome ends to get around the problem of how to replicate a linear DNA genome. A virus-specific process is required both to nick RF DNA, and to sequester newly-formed genomic ssDNA into assembling particles: in the case of Parvoviridae the first is done by a NS1 protein (which binds the new 5'-terminus resulting from the nick) and the second by the coat protein; in Geminiviridae it appears as if the first is done by a similarly-acting rep protein, and the second also by the coat protein.
Parvoviridae: Fields Virology (2nd Edn), Chapter 62
Virus Taxonomy: Sixth report of the International Committee on Taxonomy of Viruses (FA Murphy et al., Eds.); Springer-Verlag, Wien, 1995.
Type III viruses include enveloped phages (Cystoviridae), the animal- plant- and insect-infecting Reoviridae, the vertebrate and invertebrate infecting Birnaviridae, the Totiviridae, which appear limited to primitive Eukarya (fungi and protozoa, though one report describes a virus apparently infecting stinkbugs), Partitiviridae, which only infect fungi, and the Cryptoviruses, which occur in plants but are apparently only transmissible via seed or pollen. The viruses have single-component (Totiviridae), two-component (Birna-, crypto- and Partitiviruses), three-component (Cystoviridae) and multi- component (Reoviridae) genomes. Reoviruses have 10-12 segments of dsRNA per genome, all encapsidated in a single particle.
Virus Taxonomy: Sixth report of the International Committee on Taxonomy of Viruses (FA Murphy et al., Eds.); Springer-Verlag, Wien, 1995.
B) Type IV: (+)ve-sense ssRNA
C) Type V: (-)ve-sense ssRNA
B) TypeVII: dsDNA genomes replicating via
longer-than-genome-length ssRNA intermediates
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