RNA Genome Diversity and Genomic Replication Strategies

See also section on "RNA Virus Replication"

RNA Genome Types:

A) Type III: dsRNA

Replication Scheme Diagram

Type III viruses include:

enveloped phages (Cystoviridae),
the animal- plant- and insect-infecting Reoviridae,
the vertebrate- and invertebrate-infecting Birnaviridae
the Totiviridae, in primitive Eukarya (fungi and protozoa, and perhaps in insects)
Partitiviridae, which mainly infect fungi, and the
Cryptoviruses (family Partitiviridae), which occur in plants, transmissible only via seed or pollen.

The viruses have:

single-component (Totiviridae)
two-component (Birna-, Crypto- and Partitiviruses)
three-component (Cystoviridae) and
multi-component (Reoviridae, 10-12 segments) genomes

All multiple component genomes are encapsidated in a single particle.

Virus genome sizes:

Partitiviridae: 4-9 kb
Birnaviridae: about 6 kb
Totiviridae: 4-7 kb
Hypoviridae: 10-13 kb
Cystoviridae: 13 kb
Reoviridae: 20-27 kb

All genomes apparently replicate by a conservative mechanism, wherein ds input RNA is transcribed by viral enzyme to mRNA, which both codes for protein, and acts as template for second strand synthesis.

Reference:

Virus Taxonomy: Sixth report of the International Committee on Taxonomy of Viruses (FA Murphy et al., Eds.); Springer-Verlag, Wien, 1995.

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B) Type IV: (+)ve-sense ssRNA

Class IV viruses include:

Viruses infecting Eubacteria (Leviviridae)
Viruses of insects (Noda-, Tetraviridae)
Viruses of fungi (Barnaviridae)
Viruses of plants (Bromo-, Como-, Poty-, Sequi- and Tombusviridae, and 19 unassigned genera)
Viruses of vertebrates (Astro-, Calici-, Corona-, Flavi-, Picorna- and Togaviridae, and genus Arterivirus)

The viruses have:

single-component genomes with single ORFs (Poty-, Picorna-, Sequiviridae)
single components with multiple ORFs (Toga-, Caliciviridae, Tobamovirus)
two components with single ORFs (Como-, Noda-, Tetri- and Potyviridae genus Bymovirus)
two components with multiple ORFs (Tobra-, Furo-, Enamovirus)
three components with multiple ORFs (Hordeivirus, Bromoviridae)

Genome sizes range from:

less than 5 kb (Levi-, Barna-, Tombusviridae), to
7-12 kb (Astro-, Como-, Picorna-, Calici-, Bromo-, Poty-, Sequi-, Toga-, Flaviviridae, Tobraviruses)
to 13 kb (Arteriviruses) - 15.5 kb (Closteroviruses)
to 20 - 30 kb (Coronaviridae)

Genome expression strategies range from :

expressing a single polyprotein from each genome component and proteolytically processing it (Picorna-, Poty-, Sequi-, Como-, Nodaviridae)
expressing proteins from 5'-proximal ORFs and from subgenomic messengers (Tobamoviruses, Bromoviridae)
a mixture of the two strategies (Togaviridae, Tymoviruses, Caliciviridae)

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C) Type V: (-)ve-sense ssRNA

Type V viruses include:

viruses infecting vertebrates only (Arena-, Orthomyxo-, Paramyxoviridae);
viruses infecting vertebrates and arthropods (Bunya-, Rhabdoviridae);
viruses infecting plants and arthropds (Bunya-, Rhabdoviridae);
viruses infecting plants only (Tenuiviruses)

The viruses have:

single-component genomes with multiple ORFs (Filo-, Paramyxo-, Rhabdoviridae)
two-component ambisense genomes (Arenaviruses)
three-component, occasionally ambisense genomes (Bunyaviridae, Tenuivirus (4))
six to eight component genomes (Orthomyxoviridae)

The families Paramyxo-, Rhabdo and Filoviridae are grouped together in the Order Mononegavirales, due to similarities in virion structure, gene order and transcription.

Virus genome sizes:

single component, 11-19 kb: Mononegavirales
6 - 8 component, 10-14 kb: Orthomyxoviridae
3 component, 11-20 kb: Bunyaviridae

Class V viruses are probably a late evolutionary development, as they occur only among higher Eukarya (arthropods and vertebrates): viruses infecting plants probably do so as a result of close association of insects and host plants in recent evolutionary times.

dsDNA viruses

ssDNA viruses

dsRNA viruses

ssRNA (+)-sense viruses

ssRNA (-)sense viruses

ssRNA retroid viruses

dsDNA retroid viruses

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