Pleolipoviridae

Genus: Alphapleolipovirus


Genus: Alphapleolipovirus

Distinguishing features

The viral genomes encode putative rolling circle replication initiation proteins (RCR Reps) that have not been detected among the members of the other genera. Viruses of the genus Alphapleolipovirus contain different types of circular genomes: either a circular double-stranded or single-stranded DNA molecule (Pietilä et al., 2009, Senčilo et al., 2012, Roine et al., 2010, Li et al., 2014).

Virion

Morphology

Virions are 40-55 nm in diameter and pleomorphic in shape with a membrane vesicle and irregularly distributed spike complexes attached on the vesicle. Mature virions contain a single internal membrane protein and a spike protein. The virion structure of HRPV-1 has been determined by cryo-electron microscopy and tomography (Pietilä et al., 2012). The virion contains a continuous, approximately 4.2 nm thick membrane, which includes the internal membrane protein VP3. The club-shaped VP4 spike complexes protrude from the membrane surface and are irregularly distributed. The ~7 nm long complexes are anchored to the membrane by their C-terminal domains.

Physicochemical and physical properties

The buoyant density of the virion is about 1.26-1.29 g cm−3 in CsCl (Pietilä et al., 2009, Pietilä et al., 2012, Roine et al., 2010). The buoyant density of Haloarcula hispanica pleomorphic virus 2 (HHPV-2) has not been determined. Virions are stable at high NaCl concentration (above 2.5 M), but are readily inactivated by low NaCl concentrations or the absence of NaCl, temperatures above 60 °C, or detergents. In general, the organic solvent chloroform inactivates the members of the genus Alphapleolipovirus. Virion stability of HHPV-2 has not been determined.

Nucleic acid

The genomes consist of a circular single-stranded DNA of 7.0-10.7 kilonucleotides [HRPV-1, Halorubrum pleomorphic virus 2 (HRPV-2), Halorubrum pleomorphic virus 6 (HRPV-6) and HHPV-2] or of a circular double-stranded DNA of about 8.1 kbp [Haloarcula hispanica pleomorphic virus 1 (HHPV-1)].

Proteins

Virions contain two major structural proteins: an internal membrane protein (VP3 for HRPV-1 and HHPV-1; VP4 for HRPV-2 and HRPV-6), and a spike protein (VP4 for HRPV-1 and HHPV1; VP5 for HRPV-2 and HRPV-6). The structural proteins of HHPV-2 have not been determined, but based on the sequence similarity, the putative ORF3 and ORF4 products are the major structural proteins of HHPV-2. HRPV-1 has also been identified to contain a minor structural protein VP8, which is predicted to be an NTPase.

Lipids

Virions contain lipids derived non-selectively from host cell membranes. Polar lipids identified in HRPV-1 virions are cardiolipin (CL), phosphatidylglycerol (PG), phosphatidylglycerophosphate methyl ester (PGP-Me), and phosphatidylglycerosulfate (PGS) (Pietilä et al., 2010). In addition, virions of HRPV-1 contain neutral lipids and glycolipids (Pietilä et al., 2010). HRPV-6 virions contains archaeal phosphatidic acid (PA), unsaturated PG, PG, PGP-Me, PGS, and sulphated diglycosyl diphytanylglycerol (S-DGD-5) (Vitale et al., 2013). Based on thin-layer chromatography, CL, PG, PGP-Me, and PGS are present in the virions of the other alphapleolipoviruses (Pietilä et al., 2012).

Carbohydrates

The protein VP4 of HRPV-1 (spike protein) is glycosylated (Pietilä et al., 2010) with a pentasaccharide as the major N-glycan (Kandiba et al., 2012).

Genome organization and replication

Genomes contain from eight to fifteen predicted ORFs (Figure 2.Pleolipoviridae). In addition to the conserved cluster of two genes and three predicted ORFs found in the members of the family Pleolipoviridae, alphapleolipoviruses share two ORFs: one encoding a putative RCR Rep, and another one encoding a putative protein of unknown function (Figure 1.Alphapleolipovirus).

 Figure 1.AlphapleolipovirusGenome organization of Halorubrum pleomorphic virus 1. Genes encoding structural proteins are coloured purple, ORFs in grey. VP, viral protein; Rep, replication initiation protein; NTPase, nucleoside triphosphate hydrolase. The position of the first nucleotide (1 nt) is indicated.

In all alphapleolipoviruses, the latter ORF is located between the ORF for RCR Rep and the conserved cluster of five genes/ORFs. Alphapleolipoviruses are suggested to replicate their genomes via rolling-circle replication mechanism, although direct experimental evidence is not available. As with other Pleolipoviridae members, alphapleolipoviruses display a non-lytic life cycle and are suggested to exit the host cell via budding (Pietilä et al., 2009, Pietilä et al., 2012, Roine et al., 2010).

Biology

Host range

Alphapleolipoviruses are known to infect their original isolation hosts belonging to either the family Halorubraceae or Haloarculaceae. HRPV-1, HRPV-2 and HRPV-6 infect Halorubrum sp. strains PV6, SS5-4 and SS7-4, respectively, and HHPV-1 and HHPV2 infect Haloarcula hispanica (ATCC 33960) (Pietilä et al., 2012, Roine et al., 2010, Atanasova et al., 2012, Li et al., 2014). 

Geographical distribution

In all cases except for HHPV-1 and HHPV-2, the hosts were isolated from the same geographical locations as the viruses themselves, i.e. from Trapani, Italy and Samut Sakhon, Thailand (Pietilä et al., 2012, Atanasova et al., 2012). HHPV-1 was isolated from Margherita di Savoia, Italy and HHPV-2 was isolated from saltern on Hulu Island, China (Atanasova et al., 2012, Li et al., 2014).

Species demarcation criteria

Not currently defined.

Member Species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus Abbreviation(s)
Haloarcula virus HHPV1Haloarcula hispanica pleomorphic virus 1GU321093NC_013758Complete genomeHHPV-1
Haloarcula virus HHPV2Haloarcula hispanica pleomorphic virus 2KF056323NC_023592Complete genomeHHPV-2
Halorubrum virus HRPV1Halorubrum pleomorphic virus 1FJ685651NC_012558Complete genomeHRPV-1
Halorubrum virus HRPV2Halorubrum pleomorphic virus 2JN882264NC_017087Complete genomeHRPV-2
Halorubrum virus HRPV6Halorubrum pleomorphic virus 6JN882266NC_017089Complete genomeHRPV-6

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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