Unclassified Viruses

Edited by: Stuart G. Siddell

Summary

Although many viruses have been assigned as members of species in different genera and families (https://ictv.global/taxonomy), a number of relatively well-characterized viruses remain, for various reasons, unclassified. In some instances this is because they are sufficiently distinguished from recognized members of existing taxa to suggest that they form members of new genera or families. The examples listed here are unclassified viruses for which certain key characteristics are known, most notably a significant amount of sequence data or some well-described biological and biophysical properties. Of the 35 unclassified viruses listed in the Ninth ICTV Report (https://ictv.global/report_9th/), 15 have now been classified into taxa. 

A much larger number of viruses, not included here and known only from their genome sequence, remain unclassified; it is the policy of the ICTV that such viruses should be incorporated into the taxonomic structure even in the absence of knowledge of their biology or pathogenicity (Simmonds et al., 2017). Suggestions for additions to this list should be submitted to the appropriate Subcommittee Chair. 

Archaeal viruses

None

Bacterial viruses 

Mycoplasma phage MAV1 is a temperate phage of Mycoplasma arthritidis with a linear dsDNA genome of about 16 kbp (Maniloff and Dybvig 2006). Lysogenic bacterial strains have been observed to have higher virulence in a murine arthritis 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. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.]

Staphylococcus phage P954 and Staphylococcus phage ROSA are phages of Staphylococcus aureus with dsDNA genomes of about 40 kbp (Kwan et al., 2005). 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 related to 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. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.] 

Fungal viruses

Curvularia thermal tolerance virus has a bipartite genome comprising two dsRNA segments of 2.2 and 1.8 kbp (Márquez et al., 2007). 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; those of dsRNA1 encode 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. Isometric virus particles of approximately 27 nm in diameter appear to be associated with Curvularia thermal tolerance virus, but no virus particles have been detected with isolates of seven other related viruses. The RdRP sequences of these viruses form a distinct phylogenetic clade. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R. and the Partitiviridae Study Group (2017): Eeva Vainio, Sotaro Chiba, Said A. Ghabrial, Edgar Maiss, Marilyn Roossinck, Sead Sabanadzovic, Nobuhiro Suzuki, Jiatao Xie and Max Nibert]  

Diaporthe RNA virus (DRV) was originally named Diaporthe ambigua RNA virus (DaRV) (Preisig et al., 2000). However, the host fungus was later correctly identified as Diaporthe perjuncta, not D. ambigua (Moleleki et al., 2003). No particles are associated with DRV; its positive-sense ssRNA genome is 4,113 bases. DRV is associated with hypovirulence of its fungal host. Its genome has two large ORFs present in the same reading frame, the second of which is most likely translated by readthrough of a UAG stop codon located in the central part of the genome that terminates the first ORF. Taking into account all potential readthrough sites, the longest translation product has a predicted molecular mass of about 125 kDa, and shows significant similarity to the nonstructural proteins of carmoviruses of the positive-sense RNA virus family Tombusviridae. Transcripts derived from full-length cDNA clones are infectious when inoculated to spheroplasts. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.] 

Fusarium graminearum virus DK21 confers a hypovirulent phenotype to its plant pathogenic fungal host Fusarium graminearum (Kwon et al., 2007). The RNA genome (6,624 bases) comprises five putative ORFs (ORF1-5) encoding proteins of 174, 17, 6.2, 4.8, and 41 kDa, respectively. The 5′- and 3′-NCRs are 53 and 46 nt respectively. ORF1 encodes a putative RNA-dependent RNA polymerase, which is phylogenetically related to the RdRP of hypoviruses (Figure 3. Hypoviridae). 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 mRNAs. However, note that no subgenomic RNAs are confirmed in the other FgV-DK21-related viruses listed above. No typical virions are associated with FgV-DK21. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R., and Hypoviridae Study Group (2018) Nobuhiro Suzuki, Said A. Ghabrial, Kook-Hyung Kim, Michael N.Pearson, Shin-Yi L.Marzano, Hajime Yaegashi, Jiatao Xie, Lihua Guo, Hideki Kondo, Igor Koloniuk, and Bradley I. Hillman]  

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′-NCRs are 865 and 44 bp, respectively. Although FgV3 is closely related phylogenetically to members of the families Totiviriridae and Chrysoviridae, it is placed outside of their main clusters (Yu et al., 2009). FgV3 and FgV4 can co-infect Fusarium graminearum, the causal agent of important head and seedling blights of small grains. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.]  

The genome of FgV4 comprises two dsRNA segments (dsRNAs 1 and 2) of 2,383 bp and 1,739 bp, respectively (Yu et al., 2009). FgV4 dsRNA1 contains a single ORF, which has a conserved RdRP motif, whereas dsRNA2 contains two ORFs coding for putative products of unknown function. The 5′- and 3′- NCRs of dsRNAs 1 and 2 share conserved sequences, including stretches of 48 and 67 nucleotides with 100% identity. The FgV4 genome does not encode a capsid protein and no typical virions can be isolated. FgV4 genomes form a distinct clade, which is closest to members of the family Partitiviridae. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.]  

Virions are isometric, 27 nm in diameter, with a monopartite positive-sense ssRNA genome (5,784 bases) and a coat protein of approximately 28.5 kDa (Yu et al., 2003). The oyster mushroom spherical virus 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 the ORF1 sequence, each with a −1 frameshift, whereas ORF7 overlaps ORF2. The genomic organization and amino acid sequence analysis of RdRP and helicase domains indicate similarity to those of tymoviruses. Oyster mushroom spherical virus is associated with a devastating oyster mushroom die-back disease. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.] 

Sclerophthora macrospora virus A virions are isometric, 30 nm in diameter, and contain three segments of positive-sense ssRNA (RNAs 1, 2, and 3) (Yokoi et al., 2003). RNA 1 (2,928 bases) encodes an RdRP and RNA 2 (1,981 bases) encodes a capsid protein. RNA 3 (977 bases) is a satellite RNA. Sequence analysis of the RdRP (100 kDa) shows similarity to RdRPs of nodaviruses. The amino acid sequence of the viral capsid protein, on the other hand, shows similarity to members of 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. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.] 

Particles are isometric, 32 nm in diameter, containing a monopartite positive-sense ssRNA genome (Yokoi et al., 1999). The viral genome (5,533 bases) 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 viruses belonging to the genera Sobemovirus, Barnavirus and Polerovirus. The putative domains for the serine protease, VPg, RdRP, and the capsid protein are located in this order, from the 5′-terminus to the 3′-terminus of the genomic RNA. 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. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.] 

This virus is one of a number cloned and sequenced from dsRNAs isolated from a debilitated strain of the plant pathogenic fungus Sclerotinia sclerotiorum (Liu et al., 2009). The sequence of 6,043 bases has a single ORF encoding a protein with 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. Virions have not been observed and the genome sequence lacks any ORF that might encode a coat protein. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.] 

Invertebrate viruses

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 (van der Wilk et al., 1997). The genome contains two large ORFs with ORF2 overlapping ORF1. The latter is thought to be expressed by a −1 translational frameshift. The capsid proteins 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. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.] 

The virus was first isolated from honey bees, Apis mellifera (Hymenoptera: Apidae), in the United Kingdom (Ribière et al., 2010). 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 positive-sense ssRNA species (3,674 bases and 2,305 bases), 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. 

[From 9^thReport, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.]  

Originally isolated from a laboratory colony of Drosophila melanogaster in France, Drosophila A virus 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 positive-sense ssRNA genome of 4,806 bases contains two ORFs: one (5′) encoding an RdRP, and the other a major coat protein. The RdRP has a permuted organization similar to that found in members of the Birnaviridae and Tetraviridae (Ambrose et al., 2009). 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.] 

The virus was originally isolated from kelp fly, Chaetocoelopa sydneyensis (Diptera: Coelopidae) collected in New South Wales, Australia (Hartley et al., 2005). 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 11 kb. 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 currently an unclassified virus related to viruses within the family Solinviviviridae (https://ictv.global/filebrowser/download/5040). 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.]

Isolated from Drosophila melanogaster, the virions of nora virus (nora meaning new in Armenian) are approximately 30 nm in diameter (Habayeb et al., 2006). The virions contain a single species of polyadenylated positive-sense ssRNA of 11,908 bases 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. Nora virus 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. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.] 

Plant viruses

The virus has quasi-spherical particles 30–40 nm in diameter and two genomic, positive-sense ssRNAs of about 6.2 and 3.0 kb (Valverde and Sabanadzovic 2009). 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 positive-sense ssRNA viruses infecting angiosperms, specifically in the genera Idaeovirus and Umbravirus respectively, but Japanese holly fern mottle virus differs from members of these genera in both its genome organisation and host. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.] 

Protozoan viruses

Faustovirus, a virus infecting amoeba, has a double-stranded DNA genome of 466,000 bp with 451 predicted ORFs sharing distant similarity with African swine fever virus (ASFV, Asfarviridae) (Figure 4. Asfarviridae), although with a larger genome  (Klose et al., 2016, Andreani et al., 2017). A 17,000 bp region includes five putative ORFs that encode polypeptides related to parts of the ASFV major capsid protein. However, the architecture of the related gene of the prototypic Faustovirus E12 (Reteno et al., 2015) is clearly different from that of ASFV as it contains putative introns and exons. In contrast, capsid-encoding genes with introns and exons can be found in other viruses of amoeba such as a mimivirus infecting Acanthamoeba polyphaga. Faustovirus virions have an icosahedral shape and a unique double layered protein capsid. The presence of an inner and outer capsid (with double jelly-roll folds) with spikes and the absence of an internal membrane are other distinct features of the faustovirus virion. Faustovirus infects amoeba (Vermamoeba vermiformis) (Reteno et al., 2015) and was detected in biting midges (Culicoides imicola) (Temmam et al., 2015). 

[Asfarviridae Study Group (2018): Covadonga Alonso, Manuel Borca, Linda Dixon, Yolanda Revilla, Fernando Rodriguez, and José M. Escribano]

Pacmanvirus, a virus infecting the amoeba Acanthamoeba castellanii, has a linear DNA genome of at least 395,000 bp with 465 genes, of which 31 are similar to those of Faustovirus and kaumoebavirus (Andreani et al., 2017). Phylogenetic analysis of the RNA polymerase genes shows that Pacmanvirus is distinct from Faustovirus, kamoeabavirus and African swine fever virus (Figure 4. Asfarviridae). The major capsid protein locus of Pacmanvirus appears to be different from those of kaumoebavirus and Faustovirus.

[Asfarviridae Study Group (2018): Covadonga Alonso, Manuel Borca, Linda Dixon, Yolanda Revilla, Fernando Rodriguez, and José M. Escribano]

Kaumoebavirus (the name is derived from King Abdulaziz University amoebavirus) has 250 nm icosahedral capsids and a DNA genome of at least 350,000 bp including 465 genes (Bajrai et al., 2016). The closest similarities to kaumoebavirus proteins are for proteins encoded by Faustovirus and African swine fever virus (Andreani et al., 2017) (Figure 4. Asfarviridae), although the genome organization is distinct.The kaumoebavirus genome contains introns and exons, similar to that of Faustovirus. 

[Asfarviridae Study Group (2018): Covadonga Alonso, Manuel Borca, Linda Dixon, Yolanda Revilla, Fernando Rodriguez, and José M. Escribano]

Vertebrate viruses 

Sea turtle tornovirus 1 is a virus isolated from fibropapillomas collected from a green sea turtle (Ng et al., 2009). Identified in a fraction with buoyant density in CsCl of between 1.2 and 1.5 g cm⁻³, it has a circular single-stranded DNA genome of approximately 1.8 kb. STTV1 has 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. 

[From 9^th Report, Adams, M.J., Christian, P., Ghabrial, S.A., Knowles, N.J. and Lavigne, R.]