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Type Species |
(DmeCopV) |
Two elements in this genus encode a single ORF with similarity to retroviral gag and pol proteins (Fig. 2); 1731 contains gag and pol in a +1 frameshift arrangement similar to the yeast SceTy1V, SceTy2V and SceTy4V of the genus Pseudovirus. For DmeCopV, gag is encoded on a spliced 2 kb mRNA, and differential splicing is the mechanism by which gag and gag-pol stoichiometry are regulated. The mechanism(s) that regulate gag and gag-pol expression for other members of this genus remain to be determined.
Species in this genus use an initiator methionine tRNA as the primer for minus-strand DNA synthesis during reverse transcription. Hemiviruses, unlike members of the families Retroviridae, Metaviridae and genus Pseudovirus, use an initiator methionine tRNA half-molecule as a primer, which is generated by cleaving the initiator tRNA in the anticodon stem. However relatively little is known about the detailed mechanism of this reaction. Phylogenetic analysis (Fig. 3) does not fully resolve those elements, but we suggest that half-tRNA priming is a useful character for defining this genus.
List of Species Demarcation Criteria in the Genus
Individual species in the genus all have less than 50% identity in their Gag protein sequences to all other species.
Official virus species names are in italics. Tentative virus species names, alternative names ( ), strains or serotypes are not italicized. Virus names, genome sequence accession numbers [ ], and assigned abbreviations ( ) are:
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Drosophila melanogaster 1731 virus |
[X07656] |
(Dme1731V) |
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Drosophila melanogaster copia virus |
[M11240] |
(DmeCopV) |
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Volvox carteri Osser virus |
[X69552] |
(VcaOssV) |
|
Saccharomyces cerevisiae Ty5 virus |
[U19263] |
(SceTy5V) |
Tentative Species in the Genus
None reported.
List of Unassigned Species in the Family
None reported.
Phylogenetic Relationships within the Family
See Fig. 3.
Like the members of the families Hepadnaviridae and Metaviridae, the members of the family Pseudoviridae are clearly related to the members of the family Retroviridae. All four families are linked by reverse transcription and a viral core structure made up of gag-like proteins. Members of the family Pseudoviridae are different from the other two in that all lack env-like genes and have the unusual organization (PR-IN-RT-RH) of pol. Members of the families Pseudoviridae, Metaviridae and Retroviridae also share the following: a proviral form characterized by LTRs, protease, RNase H and integrase activities essential for multiplication, readthrough-mediated gag-pol gene expression and tRNA primers (in most species).
An important and controversial question is the extent of the relationship between the members of the families Pseudoviridae, Metaviridae and Retroviridae. Because the genomic structures of elements in the families Pseudoviridae and Metaviridae are clearly related to, but simpler than those of members of the family Retroviridae, many authors who have considered the problem have concluded that the families Pseudoviridae and Metaviridae represent more primitive groups; the members of the family Metaviridae probably spawned the members of the family Retroviridae (presumably by transducing genes encoding ligands for cell-surface receptors). This conclusion makes sense within the context of the enormous diversity of other types of retroelements, which are all clearly phylogenetically related by the presence of RT (Fig. 4), but not all of which encode a virus-like intermediate. An alternative viewpoint that cannot be ruled out, but for which there is less support, is that members of the family Metaviridae represent degenerate forms of members of the family Retroviridae.
Hemi: from Greek hemi, “half”, referring to the half-molecule of tRNA used as a primer for reverse transcription.
Pseudo: from Greek pseudo, “false”: To connote some uncertainty as to whether these are true viruses.
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