The Unassigned Viruses

Chapter Version: ICTV Ninth Report; 2009 Taxonomy Release

Although many viruses have been classified into genera in this Report, a number of relatively well-characterized viruses are yet, for various reasons, to be assigned to existing genera/families or have been sufficiently distinguished from recognized viruses to form types and members for new genera. Some examples are listed here for which certain key characteristics are known, most notably a significant amount of sequence data along with some well-described biological and biophysical properties. Some of the unassigned viruses listed in the Eighth ICTV Report are now classified or are in the process of being classified into recognized taxa. There are, however, a number of viruses that are new to this list and the emphasis has been placed upon those viruses that are likely to represent as yet undescribed genera and families, and that underline the fact that developing a universally applicable virus taxonomy is a continuously evolving process.

Archaeal Viruses

Haloarcula phage SH1

This icosahedral phage was originally isolated from the archaeon Haloarcula hispanica and have virions that have no visible tail and are about 70 nm in diameter. The virions contain a genome of linear dsDNA of approximately 30 kb in length, and a lipid envelope. The virions have a T=28 symmetry, which is shared with another archaeal virus, Thermus phage P23–77. The genome shares little homology with any other virus but the structure and lipid content indicates distant relationships with P23–77-like phages and the bacterial tectiviruses.

Sequence accession number: AY950802.

Bamford, D.H., Ravantti, J.J., Ronnholm, G., Laurinavicius, S., Kukkaro, P., Dyall-Smith, M., Somerharju, P., Kalkkinen, N. and Bamford, J.K. (2005). Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica. J. Virol.79, 9097–9107.

Haloarcula hispanica pleomorphic virus 1 (HHPV-1)

This pleiomorphic virus was isolated from the halophilic archaeon Haloarcula hispanica, and contains a circular dsDNA genome of around 8 kbp. The organization of the genome shows remarkable synteny and amino acid sequence similarity to the genome and predicted proteins of the archaeal virus HRPV-1, a ssDNA containing pleiomorphic virus from a Halorubrum sp. These viruses have no known relationships to any described genus.

Sequence accession number: GU321093.

Roine, E., Kukkaro, P., Paulin, L., Laurinavicius, S., Domanska, A., Somerharju, P. and Bamford, D.H. (2010). New, closely related haloarchaeal viral elements with different nucleic acid types. J. Virol., 84, 3682–3689.

Halorubrum pleomorphic virus 1 (HRPV-1)

Originally isolated from a host belonging to the genus Halorubrum, this virus has an enveloped virion with pleiomorphic morphology and is approximately 44×55 nm in size. Like the archaeal virus HHPV-1, HRPV-1 has a ssDNA genome, in this instance of about 7 kb. The pleomorphic membrane vesicle carries the two major virion proteins: VP4 forms glycosylated spikes on the virion surface and VP3 resides on the inner surface of the membrane vesicle. Related to HHPV-1 but otherwise has no known relationships.

Sequence accession number: FJ685651.

Pietila, M.K., Roine, E., Paulin, L., Kalkkinen, N. and Bamford, D.H. (2009). A ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope. Mol. Microbiol., 72, 307–319.

Thermus phage IN93

Thermus phage P23-77

These two tailless icosahedral phages were originally isolated from the thermophilic archaea Thermus aquaticus and T. thermophilus. The virions are about 90 nm in diameter from vertex to vertex and have 15 nm projections on the vertices. The virion has T=28 architecture and contains an internal lipid envelope and a circular dsDNA genome of 17–19 kbp. The two viruses have very similar ORF composition and translated sequences of the virion structural protein genes available show about 75% amino acid identity. These viruses share the unusual T=28 architecture with the archaeal Haloarcula phage SH1.

Sequence accession numbers: AB063393 (IN93), GQ403789 (P23-77).

Jalasvuori M., Jaatinen S.T., Laurinavicius S., Ahola-Iivarinen E., Kalkkinen N., Bamford D.H. and Bamford J.K. (2009). The closest relatives of icosahedral viruses of thermophilic bacteria are among viruses and plasmids of the halophilic archaea. J. Virol., 83, 9388–9397.

Bacterial Viruses

Mycoplasma phage MAV1

Mycoplasma phage MAV1 is a lysogenic phage of Mycoplasma arthritidis with ds linear DNA genome of about 16 kb. Lysogenic bacterial strains have been observed to have higher virulence in a murine arithritis model than non-lysogenic strains and a putative virulence factor in the phage genome has been identified; more recent studies have however questioned the effect of MAV1 on virulence in this model. The phage can be grown in a plaquing system and while isolated virions have not been observed, they are known to be proteinase K resistant.

Sequence accession number: AF074945.

Maniloff, J. and Dybvig, K. (2006). Mycoplasma phages. In R. Carpenter (Ed.), The Bacteriophages. New York, Oxford University Press, pp. 636–652.

Staphylococcus phage P954

Staphylococcus phage ROSA

Staphylococcus phage PT1028

Staphylococcus phage P954 and Staphylococcus phage ROSA are phages of Staphylococcus aureus with dsDNA genomes of about 40 kbp. They show close relationships to a number of other phages with similar sized genomes isolated from the same host. Although the morphology of P954 and ROSA have not been reported, related viruses show a morphotype with isometric heads and long non-contractile tails. These phages and their relatives are probably members of the Siphoviridae. Staphylococcus phage PT1028 is a phage of Staphylococcus aureus with an unknown morphology and a dsDNA genome of around 20 kbp that shows little relationship to any other phage.

Sequence accession numbers: GQ398772 (P945), AY954961 (ROSA), AY954948 (PT1028).

Kwan, T., Liu, J, DuBow, M., Gros, P. and Pelletier, J. (2005). The complete genomes and proteomes of 27 Staphylococcus areus bacteriophages. Proc. Natl Acad. Sci., U S A102, 5174–5179.

Stenotrophomonas phage phiSMA9

A filamentous phage of the opportunistic nosocomial pathogen Stenotrophomonas maltophilia, this phage has a genome of 6.9 kb that encodes seven genes, the largest being an orthologue of the gene encoding the toxin of the filamentous bacteriophage of Vibrio cholerae.

Sequence accession number: AM040673.

Hagemann, M., Hasse, D. and Berg, G. (2006). Detection of a phage genome carrying a zonula occludens like toxin gene (zot) in clinical isolates of Stenotrophomonas maltophiliaArch. Microbiol., 185, 449–458.

Fungal Viruses

Curvularia thermal tolerance virus (CThTV)

Curvularia thermal tolerance virus has a bipartite genome comprising two dsRNA segments, 2.2 and 1.8 kbp in size. A defective dsRNA of less than 1 kbp may also be present. Isometric particles, 27 nm in diameter, can be isolated from the infected fungal host and are thought to package the genomic dsRNAs. Each of the genomic dsRNAs has two ORFs; dsRNA1 ORF codes for replication proteins. The two ORFs of dsRNA 2 have no similarity to any known protein. Infection of the fungal endophyte Curvularia protuberata with CThTV confers thermal tolerance to its tropical panic grass host and allows both fungus and plant to grow at high soil temperatures.

Sequence accession numbers: EF120984/5.

Márquez, L.M., Redman, R.S., Rodriguez, R.J. and M.J. Roossinck. (2007). A virus in a fungus in a plant: Three-way symbiosis required for thermal tolerance. Science315, 513–515.

Diaporthe RNA virus (DRV)

Diaporthe RNA virus (DRV) was originally named Diaporthe ambigua RNA virus (DaRV). However, the host fungus was later correctly identified as Diaporthe perjuncta, not D. ambigua. No particles are associated with DRV and its ssRNA genome is 4,113 nt in length. DRV is associated with hypovirulence of its fungal host. It has two large ORFs present in the same reading frame, which are most likely translated by readthrough of a UAG stop codon in the central part of the genome. The longest possible translation product has a predicted molecular mass of about 125 kDa, which shows significant similarity to the nonstructural proteins of carmoviruses of the positive-strand RNA virus family Tombusviridae. Transcripts derived from full-length cDNA clones are infectious when inoculated to spheroplasts.

Sequence accession number: AF142094.

Moleleki, N., van Heerden, S.W., Wingfield, M.J., Wingfield, B.D. and Preisig, O. (2003). Transfection of Diaporthe perjuncta with Diaporthe RNA virus. Appl. Environ. Microbiol., 69, 3952–3956.

Fusarium graminearum virus DK21 (FgV-DK21)

Fusarium graminearum virus DK21 confers a hypovirulent phenotype to its plant pathogenic fungal host Fusarium graminearum. The RNA genome (6624 nt in length) comprises five putative ORFs (ORF1-5) encoding proteins of 174, 17, 6.2, 4.8, and 41 kDa, respectively. The 5′ and 3′ UTRs are 53 and 46 nt in length. ORF1 encodes a putative RNA-dependent RNA polymerase, which is phylogenetically related to hypoviruses. The genome organization and expression strategy of FgV-DK21, however, are more similar to those of the plant ssRNA alphaflexiviruses. The putative proteins encoded in ORFs 2 through 5 appear to be expressed from at least two different subgenomic RNAs. No typical virions are associated with FgV-DK21.

Sequence accession number: AY533037.

Kwon, S.-J., Lim, W.-S., Park, S.-H., Park, M.-R. and Kim, K.-H. (2007). Molecular characterization of a dsRNA mycovirus, Fusarium graminearum virus-DK21, which is phylogenetically related to hypoviruses but has a genome organization and gene expression strategy resembling those of plant potex-like viruses. Mol. Cells23, 304–315.

Fusarium graminearum virus 3 (FgV3)

No particles are associated with FgV3. Its dsRNA genome comprises 9,098 bp and contains two ORFs; ORF1 codes for a protein of unknown function (145 kDa) and ORF2 codes for a putative RNA-dependent RNA polymerase (RdRp; 151 kDa). The two ORFs are separated by 143 nucleotides. The 5′ and 3′ UTRs are 865 and 44 bp long, respectively. Although FgV3 is closely related phylogenetically to members of the families Totiviriridae and Chrysoviridae, it is placed outside of their main clusters. FgV3 and FgV4 can co-infect Fusarium graminearum, the causal agent of important head and seedling blights of small grains.

Sequence accession number: GQ140626.

Yu, J., Kwon, S.-J., Lee, K.-M., Son, M. and Kim, K.-H. (2009). Complete nucleotide sequence of double-stranded RNA viruses from Fusarium graminearum strain DK3. Arch. Virol., 154, 1855–1858.

Fusarium graminearum virus 4 (FgV4)

The genome of FgV4 comprises two dsRNA segments (dsRNAs 1 and 2) of 2,383 bp and 1,739 bp, respectively. FgV4 dsRNA1 contains a single ORF, which has a conserved RdRp motif, whereas dsRNA2 contains two putative ORFs coding for products of unknown function. The 5′ and 3′ UTRs of dsRNAs 1 and 2 share conserved sequences, including stretches of 48 and 67 nucleotides with 100% identity. FgV4 does not code for a capsid protein and no typical virions can be isolated. FgV4 forms a distinct clade within the family Partitiviridae.

Sequence accession numbers: GQ140627/8.

Yu, J., Kwon, S.-J., Lee, K.-M., Son, M. and Kim, K.H. (2009). Complete nucleotide sequence of double-stranded RNA viruses from Fusarium graminearum strain DK3. Arch. Virol., 154, 1855–1858.

Oyster mushroom spherical virus (OMSV)

Virions are isometric 27 nm in diameter containing a monopartite positive sense ssRNA genome (5784 nt in length) and a coat protein of approximately 28.5 kDa. The OMSV genome comprises seven ORFs; ORF1 has the motifs of RNA-dependent RNA polymerases (RdRp), and helicase and ORF2 encodes a coat protein. None of the putative polypeptides potentially encoded by ORFs 3–7 have similarities to any known proteins. ORFs 3 to 6 are located within ORF1 sequence with a −1 frameshift, whereas ORF7 overlaps ORF2. Genomic organization and amino acid sequence analysis of RdRp and helicase domains are most similar to those of tymoviruses. OMSV is associated with a devastating oyster mushroom die-back disease.

Sequence accession number: AY182001.

Yu, H.J., Lim, D. and Lee, H.-S. (2003). Characterization of a novel single-stranded RNA mycovirus in Pleurotus ostreatusVirology314, 9–15.

Sclerophthora macrospora virus A (SmV-A)

Virions are isometric 30 nm in diameter and contain three segments of positive-sense ssRNA (RNAs 1, 2, and 3). RNA 1 (2928 nt) contains the RdRp motif and RNA 2 (1981 nt) codes for a capsid protein. RNA 3 (977 nt) is a satellite RNA. Sequence analysis of RdRp (100 kDa) shows similarity to RdRps of nodaviruses. The amino acid sequence of the viral CP, on the other hand, shows similarity to those of members in the family Tombusviridae. The capsid of SmV-A comprises two capsid proteins, CP1 (43 kDa) and CP2 (39 kDa), both encoded in ORF2. CP2 is derived from CP1 via proteolytic cleavage. The genome organization of SmV-A is distinct from those of other known fungal RNA viruses.

Sequence accession numbers: AB083060-62.

Yokoi T., Yamashita S. and Hibi, T. (2003). The nucleotide sequence and genome organization of Sclerophthora macrospora virus A. Virology311, 394–399.

Sclerophthora macrospora virus B (SmV-B)

Particles are isometric, 32 nm in diameter, containing a monopartite positive sense ssRNA genome. The viral genome (5533 nt) has two large ORFs: ORF1 encodes a putative polyprotein (145 kDa) containing the motifs of chymotrypsin-related serine protease and RdRp, and ORF2 encodes a capsid protein (41 kDa). The genome arrangement of SmV-B is similar to those belonging to the genera SobemovirusBarnavirus and Polerovirus. The putative domains for the serine protease, VPg, RdRp, and the CP are located in this order from the 5′ terminus to the 3′ terminus. SmV B, however, is distinctive since its genome has only two ORFs. S. macrospora, the plant pathogenic fungal host of SMV-B, is the causal agent of downy mildew of gramineous plants.

Sequence accession number: AB012756.

Yokoi, T., Takemoto, Y., Suzuki, M., Yamashita, S. and Hibi, T. (1999). The nucleotide sequence and genome organization of Sclerophthora macrospora virus B. Virology264, 344–349.

Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1)

SsHADV-1 is the first reported DNA mycovirus (viruses infecting fungi). It has a circular ssDNA genome of 2166 nt, coding for a replication initiation protein (Rep) and a coat protein (CP). SsHADV-1 is phylogenetically related to the geminiviruses based on Rep sequences. However, it is distinct from geminiviruses both in genome organization and particle morphology. Particles are non-twinned, isometric, 20–22 nm in diameter. SsHADV-1 confers hypovirulence to its plant pathogenic fungal host Sclerotinia sclerotiorum. Purified SsHADV-1 particles or viral DNA, isolated directly from mycelium, are infectious when transfected to virus-free fungal protoplasts. Transfected isolates exhibit the hypovirulence phenotype typical of the naturally infected isolate.

Sequence accession number: GQ365709.

Yua, X., Li, B., Fu, Y., Jiang, D., Ghabrial, S.A., Li, G., Peng, Y., Xie, J., Cheng, J., Huang, J. and Yi, X. (2010). A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proc. Natl Acad. Sci., U S A107, 8387–8392.

Sclerotinia sclerotiorum RNA virus L (SsRV-L)

This virus is one of a number cloned and sequenced from dsRNAs isolated from a debilitated strain of the plant pathogenic fungus Sclerotinia sclerotiorum. The sequence of 6,043 nt has a single ORF encoding a protein with significant similarity to the replication proteins of the “alphavirus-like” supergroup of positive-strand RNA viruses. Phylogenetic analyses suggest a relationship to positive sense ssRNA viruses infecting plants (clostero-, beny- and tobamoviruses), insects (omegatetraviruses) and vertebrates (hepeviruses). There is evidence that the RNA can replicate independently within its fungus host but appears to have little effect on its growth. No virions have been observed and the sequence lacks any ORF that might encode a coat protein.

Sequence accession number: EU779934.

Liu, H., Fu, Y., Jiang, D., Li, G., Xie, J., Peng, Y., Yi, X. and Ghabrial, S.A. (2009). A novel mycovirus that is related to the human pathogen Hepatitis E virus and rubi-like viruses. J. Virol., 83, 1981–1991.

Invertebrate Viruses

Acyrthosiphon pisum virus (APV)

Acyrthosiphon pisum virus particles are icosahedral and 31 nm in diameter. The virus was isolated from Acyrthosiphon pisum (Hemiptera: Aphididae) but is able to infect many other aphid species. The virus capsid is composed of a major protein of 34 kDa and three minor proteins of 23, 24 and 66 kDa. The genome has been completely sequenced and consists of a single stranded polyadenylated ssRNA molecule of approximately 10 kb. The genome contains two large ORFs with ORF2 overlapping ORF1. The latter is thought to be expressed by a −1 translational frameshift. The CPs are encoded at the 3′ end of ORF1 and the 5′ end of ORF2. The ORF1 product contains motifs characteristic for RdRp, Hel and cysteine proteases.

Sequence accession number: AF024514.

Van der Wilk, F., Dullemans, A.M., Verbeek, M. and van den Heuvel, J.F.J.M. (1997). Nucleotide sequence and genomic organization of Acyrthosiphon pisum virus. Virology238, 353–362.

Chronic bee paralysis virus (CBPV)

The virus was first isolated from honey bees, Apis mellifera (HymenopteraApidae), in the United Kingdom. The virions have an unusual anisometric shape and are heterogeneous in size, usually of about 60 nm in length but ranging in diameter from 20 to 30 nm. Purified virion preparations contain two ssRNA species (3674 nt and 2305 nt), the larger encoding the RdRp. Virions contain a single structural protein of 23.5 kDa. The virus is readily transmitted orally to adult honey bees and has been identified in colonies almost everywhere that honey bees are maintained.

Sequence accession numbers: EU122229/30.

Ribière, M., Olivier, V. and Blanchard P. (2010). Chronic bee paralysis: a disease and a virus like no other? J. Invertebr. Pathol.103 Suppl. 1, S120–S131.

Drosophila A virus (DAV)

Originally isolated from a laboratory colony of Drosophila melanogaster in France, it has subsequently been found widely distributed in laboratory and natural populations of Drosophila spp. from around the world. The virions are 30 nm in diameter, have icosahedral T=3 symmetry and comprise a single major coat protein of 42 kDa. The ssRNA genome is 4806 nucleotides long and contains two ORFs: one (5′) encoding an RdRp, and the other the major coat protein. The RdRp has a permuted organization similar to that found in members of the Birnaviridae and Tetraviridae.

Sequence accession number: FJ150422.

Ambrose, R.L., Lander, G.C., Maaty, W.S., Bothner, B., Johnson, J.E. and Johnson, K.N. (2009). Drosophila A virus is an unusual RNA virus with a T=3 icosahedral core and permuted RNA-dependent RNA polymerase. J. Gen. Virol.90, 2191–2200.

Gryllus bimaculatus nudivirus (GbNV)

Gryllus bimaculatus nudivirus infects nymphs and adults of the cricket Gryllus bimaculatus. Like the other nudiviruses, Heliothis zea nudivirus 1 (HzNV-1) and Oryctes rhinoceros nudivirus (OrNV), the virions of GbNV have enveloped rod-shaped nucleocapsids similar in size to those of baculoviruses. The circular dsDNA genome of GbNV is about 97 kbp and encodes approximately 100 ORFs, 33 of which are shared with the other nudiviruses. Previously considered to be non-occluded baculoviruses, the nudiviruses are a distinct sister-group to the baculoviruses that probably warrant separate taxonomic treatment.

Sequence accession number: EF203088.

Wang, Y. and Jehle, J.A. (2009). Nudiviruses and other large, double-stranded circular DNA viruses of invertebrates: new insights on an old topic. J. Invertebr. Pathol.101, 187–193.

Heliothis zea virus 1 (HzV-1)

Gonad specific virus (Hz2-V)

Heliothis zea virus 1 (also known as Heliothis zea nudivirus 1; HzNV-1) was isolated as a persistent virus of an insect cell line derived from Helicoverpa zea (Lepidoptera: Noctuidae), although the virus can also infect a number of other insect (lepidopteran) cell lines. Related to the nudiviruses Gryllus bimaculatus nudivirus and Oryctes rhinoceros nudivirus (OrNV), the HzV-1 genome consists of a single molecule of circular dsDNA, approximately 228 kbp in length. The closely related Gonad specific virus Hz2-V is found in larvae and adults of Helicoverpa zea and is associated with an agonadal disease.

Sequence accession number: AF451898.

Burand, J. (1998). Nudiviruses. In L. Miller and L.A. Ball (Eds.), The Insect Viruses. New York: Plenum Press. pp. 69–90.

Kelp fly virus (KFV)

The virus was originally isolated from kelp fly, Chaetocoelopa sydneyensis (Diptera: Coelopidae) collected in New South Wales, Australia. The virus has isometric particles 29 nm in diameter with surface projections that gives the particles the appearance of a small reovirus. The genome comprises ssRNA of about 11kb. The genome encodes a single ORF with the CPs (75 and 28 kDa) towards the 5′ end of the genome and the RdRp towards the 3′ end. KFV is a structurally distinctive virus that is possibly a member of the Picornavirales.

Sequence accession number: DQ112227.

Hartley, C.J., Greenwood, D.R., Gilbert, R.J., Masoumi, A., Gordon, K.H., Hanzlik, T.N., Fry, E.E., Stuart, D.I. and Scotti, P.D. (2005). Kelp fly virus: a novel group of insect picorna-like viruses as defined by genome sequence analysis and a distinctive virion structure. J. Virol.79, 13385–13398.

Nora virus (NV)

Isolated from Drosophila melanogaster, the virions of Nora virus are approximately 30 nm in diameter. The virions contain a single species of a 11908 nt polyadenylated ssRNA, encoding four ORFs. The RdRp (ORF2) is towards the 5′ end (the other three ORFs are not closely related to any other viral sequences), and the putative coat protein encoding sequences are at the 3′ end of the genome. NV occurs commonly as a persistent infection in laboratory stocks of drosophila, the major site of replication is the intestine and the virus is readily transmitted horizontally.

Sequence accession number: DQ321720.

Habayeb, M.S., Ekengren, S.K. and Hultmark, D. (2006). Nora virus, a persistent virus in Drosophila, defines a new picorna-like virus family. J. Gen. Virol.87, 3045–3051.

Solenopsis invicta virus 2 (SINV-2)

SINV-2 was originally isolated from the red imported fire ant Solenopsis invicta and is an icosahedral ssRNA-containing virus with a genome of about 11 kb. The genome is organized with the structural proteins at the 5′ end and the RdRp at the 3′ end (like the picornaviruses and iflaviruses) but with an apparent polycistronic structure like the dicistroviruses. SINV-2 is a probable member of the Picornavirales but it is phylogenetically distinct from all other viruses in the order.

Sequence accession number: EF428566.

Valles, S.M., Strong, C.A. and Hashimoto, Y. (2007). A new positive-strand RNA virus with unique genome characteristics from the red imported fire ant, Solenopsis invictaVirology365, 457–463.

Solenopsis invicta virus 3 (SINV-3)

An isometric virus approximately 27 nm in diameter with distinct surface projections, this ssRNA-containing virus of the red imported fire ant, Solenopsis invicta, has a genome of about 11.5 kb and a genomic organization similar to the dicistroviruses (5′RdRp, 3′CPs). The two coat proteins are approximately 41 and 36 kDa and appear to be driven by an IRES element (also like the dicistroviruses). However, phylogenetically SINV3, appear to be only distantly related to currently known dicistroviruses and its probable affinities are poorly understood.

Sequence accession number: FJ528584.

Valles, S.M. and Hashimoto, Y. (2009). Isolation and characterization of Solenopsis invicta virus 3, a new positive-strand RNA virus infecting the red imported fire ant, Solenopsis invictaVirology388, 354–361.

Plant Viruses

Japanese holly fern mottle virus (JHFMoV)

The virus has quasi-spherical particles 30–40 nm in diameter and two genomic ssRNAs of about 6.2 and 3.0 kb. It causes a disease in Japanese holly fern (Cyrtomium falcatum), and can be transmitted by grafting and through spores from infected plants. The larger RNA encodes a 214 kDa replication polyprotein and a putative 12 kDa protein of unknown function. RNA2 encodes three proteins: a 32 kDa movement protein, a 37 kDa protein and a 29 kDa coat protein. In phylogenetic analyses, the replication protein and movement protein show some relationships to those of ssRNA+viruses infecting angiosperms, more particularly in the genera Idaeovirus and Umbravirus respectively. The unique genome organization and distinctive host make this a candidate for a novel genus.

Sequence accession numbers: FJ907327/8.

Valverde, R.A. and Sabanadzovic, S. (2009). A novel plant virus with unique properties infecting Japanese holly fern. J. Gen. Virol., 90, 2542–2549.

Orchid fleck virus (OFV)

Preparations of purified virus contain bacilliform and non-enveloped particles of 150 ×40 nm. Enveloped particles are sometimes seen in infected plant tissues. The genome comprises two molecules: RNA1 (6,413 nt) and RNA2 (6,001 nt). The RNAs have conserved and complementary terminal sequences. RNA1 contains five ORFs, and RNA2 has a single ORF encoding an RNA polymerase. Some of the encoded proteins, particularly the polymerase, have sequences similar to those of proteins of rhabdoviruses. OFV was previously classified as a tentative rhabdovirus and it has been suggested that it should be included in a new genus named Dichorhabdovirus. However, this poses a taxonomic challenge because the family Rhabdoviridae is included in the order Mononegavirales and includes only viruses with undivided genomes.

Sequence accession numbers: AB244417/8.

Kondo, H., Maeda, T., Shirako, Y. and Tamada, T. (2006). Orchid fleck is a rhabdovirus with an unusual bipartite genome. J. Gen. Virol., 87, 2413–2416.

Southern tomato virus (STV)

The virus has a monopartite dsRNA genome of 3.5 kbp and is consistently associated with a disease of field and glasshouse-grown tomatoes in California, Mexico and Mississippi. No virions have been detected. The genome has two partially overlapping ORFs with a genomic organization resembling members of the family Totiviridae. However, there is very little sequence similarity to totiviruses (which infect fungi and protozoa) and a similarly remote relationship to members of the family Partitiviridae, some of which infect plants but which have a divided genome. The virus was efficiently transmitted by seed but not mechanically or by grafting.

Sequence accession number: EF442780.

Sabanadzovic, S., Vlaverde, R.A., Brown, J.K., Martin, R.R. and Tzanetakis, I.E. (2009). Southern tomato virus: the link between the families Totiviridae and PartitiviridaeVirus Res., 140, 130–137.

Vertebrate Viruses

Nyamanini virus (NYMV)

Midway virus (MIDWV)

Nyamanini virus was first isolated from Bubulcus ibis (cattle egret) collected in 1957 in South Africa and has since been widely isolated from cattle egrets and ticks in Africa. Serologically related to Midway Virus (originally isolated in 1966 from seabird ticks collected on several Pacific islands) both viruses have negative sense ssRNA genomes of about 11.5 kbp contained within roughly spherical, pleiomorphic enveloped virions of between 100 and 130 nm in diameter. Both viruses are pathogenic for certain laboratory vertebrates and cell cultures. Phylogenetic analysis of the deduced nucleocapsid and viral polymerase proteins indicate that these viruses form a distinct lineage in the order Mononegavirales.

Sequence accession numbers: FJ554526 (NYMV); FJ554525 (MIDWV).

Mihindukulasuriya, K.A., Nguyen, N.L., Wu, G., Huang, H.V., da Rosa, A.P., Popov, V.L., Tesh, R.B. and Wang, D. (2009). Nyamanini and midway viruses define a novel taxon of RNA viruses in the order MononegaviralesJ. Virol., 83, 5109–5116.

Sea turtle tornovirus 1 (STTV1)

Sea turtle tornovirus 1 is a putative virus isolated from fibropapillomas collected from a green sea turtle. Identified in a fraction with buoyant density in CsCl of between 1.2 and 1.5 g cm−3, it has a circular genome of approximately 1.8 kb. STTV1 has only weak amino acid level identities (25%) to chicken anaemia virus in short regions of its genome but most of the genome shows no homology with any other viral sequences.

Sequence accession numbers: EU867823.

Ng, T.F., Manire, C., Borrowman, K., Langer, T., Ehrhart, L. and Breitbart, M. (2009). Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics. J. Virol.83, 2500–2509.

Chimpanzee stool-associated circular virus (ChiSCV)

Originally isolated from stool samples collected from wild-living chimpanzees, chimpanzee stool-associated circular virus (ChiSCV) has a single-stranded circular DNA genome with organizational similarities to vertebrate circoviruses and plant geminiviruses, but with a different location for the stem-loop structure involved in rolling circle DNA replication.

Sequence accession numbers: GQ351272-78.

Blinkova, O., Victoria, J., Li, Y., Keele, B.F., Sanz, C., Ndjango, J.B., Peeters, M., Travis, D., Lonsdorf, E.V., Wilson, M.L., Pusey, A.E., Hahn, B.H. and Delwart, E.L. (2010). Novel circular DNA viruses in stool samples of wild-living chimpanzees. J. Gen. Virol., 91, 74–86.

Contributed by

Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.

(240 rows affected) Completion time: 2022-05-31T18:31:39.4621541+00:00