Rhabdoviridae

Genus: Sigmavirus


Genus: Sigmavirus

Distinguishing features

Viruses assigned to the genus Sigmavirus form a distinct monophyletic group based on well-supported maximum-likelihood trees inferred from complete or partial L sequences. Sigmaviruses each infect a dipteran insect of single species (Drosophilidae or Muscidae) in which they are transmitted only vertically; other dipterans also appear to harbour sigmaviruses. Sigmavirus genomes may feature an additional gene (X) located between the P and M genes, encoding a protein of unknown function.

Virion

Morphology

Bullet-shaped particles of approximately 80 nm x 100 nm with prominent surface projections have been reported for Drosophila melanogaster sigmavirus (DMelSV) (Richard-Molard et al., 1984, L'Heritier 1958, Teninges 1968).

Nucleic acid

Sigmavirus genomes consist of a single molecule of negative-sense, single-stranded RNA and range from approximately 12.4–14.5 kb (Longdon et al., 2010, Longdon et al., 2015, Teninges et al., 1993).

Proteins

The N, P, M, G and L share sequence homology and/or structural characteristics with the cognate proteins of other rhabdoviruses (Teninges et al., 1993, Landes-Devauchelle et al., 1995, Bras et al., 1994, Teninges and Bras-Herreng 1987). The X (U1) proteins are of unknown function. They range from 224 to 321 amino acids (~25.0 kDa to ~36.9 kDa) and generally share very low or no detectable sequence homology amongst viruses assigned to different species. The DMelSV X protein has been observed to contain 3 sequence motifs that are related to conserved motifs in reverse transcriptases but the significance of this is not known (Landes-Devauchelle et al., 1995). Other likely sigmaviruses (currently unclassified) may encode other accessory proteins of unknown function (Longdon et al., 2015).

Genome organisation and replication

Sigmavirus genomes include five genes (N, P, M, G and L) encoding the structural proteins and may contain an additional long ORF between the P and M genes encoding a protein of unknown function (X or U1) (Figure 1.Sigmavirus) (Teninges et al., 1993). All ORFs occur in discrete transcriptional units including conserved transcription initiation and transcription termination/polyadenylation sequences. Variations in genome length are due primarily to significant variations in the length of 3' and 5' non-coding regions which may be very long (e.g., 664 nt 3' non-coding region in the G mRNA of Drosophila affinis sigmavirus (DAffSV) (Longdon et al., 2015).

Figure 1.Sigmavirus. Schematic representation of sigmavirus genome organisations. N, P, M, G and L represent ORFs encoding the structural proteins. ORF X (U1) encoding a protein of unknown function is highlighted (turquoise).

Antigenicity

DMelSV has been shown to cross-react in indirect immunofluorescence tests with several rhabdoviruses including Parry Creek virus (genus Hapavirus) , Humpty Doo virus (related, unclassified rhabdovirus) and Tibrogargan virus (genus Tibrovirus) and Tupaia rhabdovirus (genus Tupavirus) (Calisher et al., 1989).

Biology

Sigmaviruses infect insects in the order Diptera. Although currently classified sigmaviruses infect flies in either the families Drosophilidae or Muscidae, recent evidence indicates that sigmaviruses may occur in a much a wider range of dipteran insects (Longdon et al., 2015). Sigmaviruses are transmitted only vertically through eggs or sperm (Fleuriet 1988, Longdon et al., 2011). Sigmaviruses have not been associated with disease but flies infected with sigmaviruses become paralysed or die upon exposure to high concentrations of carbon dioxide (L'Heritier 1958, Longdon et al., 2010); however, this property has also been associated with other rhabdoviruses (Rosen 1980, Bussereau and Contamine 1980).

Species demarcation criteria

Viruses assigned to different species within the genus Sigmavirus have several of the following characteristics: A) minimum amino acid sequence divergence of 20% in L; and B) occupy different ecological niches as evidenced by differences in hosts.

As sigmaviruses are transmitted only verthttps://talk.ictvonline.org/ictv-reports/ictv_online_report/negative-sense-rna-viruses/w/rhabdoviridae/799/genus-sigmavirus/edit#ically, resulting in extreme host fidelity over ecological time scales, viruses found within different host species are likely to represent different virus species. Although host switching does occur over evolutionary time scales, it is possible that highly related viruses could be found in hosts of different species but host switching events are likely to be rare.  Species demarcation based upon the host species should be supported by phylogenetic analysis based upon L gene sequences to indicate that the proposed virus species represents a distinct lineage and, if possible, estimates of genetic diversity to demonstrate much lower diversity within than between viruses assigned to different species. Typically, these will be <5% L amino acid sequence diversity for viruses within species and >20% diversity between species.

Member Species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus Abbreviation(s)
Drosophila affinis sigmavirusDrosophila affinis sigmavirus10KR822811Complete coding genomeDAffSV
Drosophila ananassae sigmavirusDrosophila ananassae sigmavirusKilifi KenyaKR822812Complete coding genomeDAnaSV
Drosophila immigrans sigmavirusDrosophila immigrans sigmavirusSCM45623KX884434Complete coding genomeDImmSV
Drosophila melanogaster sigmavirusDrosophila melanogaster sigmavirusHAP23GQ375258Complete coding genomeDMelSV
Drosophila obscura sigmavirusDrosophila obscura sigmavirus10AGQ410979NC_022580Complete coding genomeDObsSV
Drosophila tristis sigmavirusDrosophila tristis sigmavirusKR822818Partial genomeDTriSV
Muscina stabulans sigmavirusMuscina stabulans sigmavirusCa1JF311402Partial genomeMStaSV

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.

Derivation of names

The genus name is taken from the naming of the original virus discovered in fruit flies (Drosophila melanogaster) that was named virus “sigma” (L'Heritier 1958).

Related, Unclassified Viruses

Virus name

Accession number

Virus abbreviation

Drosophila sturtevanti sigmavirus

KR822816

DStuSV

Drosophila montana sigmavirus

KR822815*

DMonSV

Drosophila algonquin sigmavirus

KR822824*

DAlgSV

Ceratitis capitata sigmavirus

KR822825

CCapSV

Gata virus

KX852388

GATV

Hubei dimarhabdovirus 1

KX884431

HbDRV-1

Hubei diptera virus 9

KX884429

HbDV-9

Hubei diptera virus 10

KX884433

HbDV-10

Scaptodrosophila deflexa sigmavirus

KR822820*, KR822821*, KR822822*

SDefSV

Shayang fly virus 2

KM817635

SyFV-2

Wuhan fly virus 2

KM817646

WhFV-2

Wuhan house fly virus 1

KM817648

WhHFV-1

Wuhan louse fly virus 8

KM817655*

WhLFV-8

Wuhan louse fly virus 9

KM817656

WhLFV-9

Wuhan louse fly virus 10

KM817657

WhLFV-10

* Coding region sequence incomplete
Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.
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