ICTV Virus Taxonomy Profile: Yadokariviridae 2023.

The family Yadokariviridae, with the genera Alphayadokarivirus and Betayadokarivirus, includes capsidless non-segmented positive-sense (+) RNA viruses that hijack capsids from phylogenetically distant double-stranded RNA viruses. Yadokarivirids likely replicate inside the hijacked heterocapsids using their own RNA-directed RNA polymerase, mimicking dsRNA viruses despite their phylogenetic placement in a (+) RNA virus lineage. Yadokarivirids can have negative or positive impacts on their host fungi, through interactions with the capsid donor dsRNA viruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Yadokariviridae, which is available at ictv.global/report/yadokariviridae.

A novel alphapartitivirus detected in Japanese pear.

Pyrus pyrifolia cryptic virus (PpCV) had been previously reported from Japanese pear (Pyrus pyrifolia). In analyses of Japanese pear, two other double-stranded (ds) RNA molecules (dsRNA4 and 5) were observed along with the three dsRNA segments from PpCV on an electrophoretic profile of isolated dsRNA. When the purified dsRNA sample was deep sequenced by a next-generation sequencer, two de novo assembled contigs corresponding to dsRNA4 and 5, with predicted amino acid sequences showing homologies to the RNA-dependent RNA polymerase and the capsid protein of Rose partitivirus, respectively, were found by BLAST analysis. The relationships between the two contigs and dsRNA4, 5 were confirmed by northern blot analyses with probes amplified using primers designed from the contigs. Terminal sequence analyses by rapid amplification of cDNA ends revealed that dsRNA4 and 5 were 1945 and 1788 bp long, respectively. The 5' terminal sequences (GUCAAAUU) of dsRNA4 and 5 were conserved. Based on genome size and phylogenetic analyses, the newly found virus is thought to be a member of the genus Alphapartitivirus. Thus, it has been designated as Pyrus pyrifolia partitivirus 2.

Genome segments encoding capsid protein-like variants of Pyrus pyrifolia cryptic virus.

According to previous studies, three double-stranded (ds) RNA molecules (dsRNA1, 2, and 3) detected in Japanese pear are transmitted to the next generation with high frequency through both ovules and pollen. Nucleotide sequence analysis of dsRNA1-encoding RNA-dependent RNA polymerase (RdRp) has suggested that these dsRNAs are related to a cryptovirus named Pyrus pyrifolia cryptic virus (PpCV). In this study, purified dsRNA prepared from a PpCV-infected Japanese pear cultivar was subjected to next-generation deep sequencing. This sequencing generated two de novo assembled contigs corresponding to dsRNA2 and 3, with BLAST analysis of the predicted amino acid sequences indicating homology to capsid proteins (CPs) of the cryptoviruses persimmon cryptic virus and Sinapis alba cryptic virus 1, respectively. Relationships between the two contigs and dsRNA2 and 3 were confirmed by northern blot hybridization with probes generated using primers designed from the assembled contigs. Rapid amplification of cDNA ends analyses of 5'- and 3'-terminal sequences of dsRNA2 and 3 revealed that these two dsRNAs consist of 1523 and 1481bp, respectively. The 5'-terminal sequences (AGAAUUUC) of dsRNA1, 2 and 3 were found to be conserved. Phylogenetic analysis of deduced amino acid sequences of the two CP-like variants indicated that PpCV belongs to Deltapartitivirus (Partitiviridae). Our results imply that PpCV is tri-segmented.

Multiple virus infection in a single strain of Fusarium poae shown by deep sequencing.

Many bands were detected on an electrophoretic profile of double-stranded (ds) RNA preparation from a single strain of Fusarium poae isolated from wheat. When the purified dsRNA sample was deep-sequenced by a next-generation sequencer, sixteen virus-like assembled contigs with predicted amino acid sequences showing homologies to respective viral RNA-dependent RNA polymerases (RdRps) were found by BLAST analysis. Fourteen out of sixteen sequences showed homologies to RdRps of known mycoviruses, that is, four mitoviruses, two narnaviruses, two partitiviruses, an alternavirus, a fusarivirus, a hypovirus, a victorivirus, and two unclassified mycoviruses, Sclerotinia sclerotiorum dsRNA mycovirus-L and Aspergillus foetidus slow virus 2, respectively. The other two putative viral RdRp sequences showed homologies to those of members of negative-stranded RNA viruses, the Ophiovirus and the Phlebovirus respectively, which mycoviruses had been not ever assigned to. Based on genome structure and phylogenetic analysis, both viruses were thought to be members of novel respective negative-stranded RNA virus groups. The presences of all sixteen viral RdRp sequences identified by BLAST analysis were confirmed by sequencing RT-PCR products generated from the starting dsRNA material using primers designed from the de novo assembled sequences of respective putative mycoviruses. Since the single strain of F. poae was considered to be multiply infected with mycoviruses from novel taxonomical groups in addition to many common mycoviruses, the RNA virome of the strain was found to be highly diverse.

Isolation and characterization of two mitoviruses and a putative alphapartitivirus from Fusarium spp.

The filamentous fungus Fusarium spp. includes several important plant pathogens. We attempted to reveal presence of double-stranded (ds) RNAs in the genus. Thirty-seven Fusarium spp. at the MAFF collection were analyzed. In the strains of Fusarium coeruleum, Fusarium globosum and Fusarium solani f. sp. pisi, single dsRNA bands were detected. The strains of F. coeruleum and F. solani f. sp. pisi cause potato dry rot and mulberry twig blight, respectively. Sequence analyses revealed that dsRNAs in F. coeruleum and F. globosum consisted of 2423 and 2414 bp, respectively. Using the fungal mitochondrial translation table, the positive strands of these cDNAs were found to contain single open reading frames with the potential to encode a protein of putative 757 and 717 amino acids (molecular mass 88.5 and 84.0 kDa, respectively), similar to RNA-dependent RNA polymerases of members of the genus Mitovirus. These dsRNAs in F. coeruleum and F. globosum were assigned to the genus Mitovirus (family Narnaviridae), and these two mitoviruses were designated as Fusarium coeruleum mitovirus 1 and Fusarium globosum mitovirus 1. On the other hand, a positive strand of cDNA (1950 bp) from dsRNA in F. solani f. sp. pisi contained an ORF potentially encoding a putative RdRp of 608 amino acids (72.0 kDa). The putative RdRp was shown to be related to those of members of the genus of Alphapartitivirus (family Partitiviridae). We coined the name Fusarium solani partitivirus 2 for dsRNA in F. solani f. sp. pisi.

An endornavirus from a hypovirulent strain of the violet root rot fungus, Helicobasidium mompa.

We determined the complete nucleotide (nt) sequence (16,614 nt) of a large double-stranded (ds) RNA (referred to as L1 dsRNA), previously identified as the hypovirulence factor from strain V670 of the violet root rot fungus, Helicobasidium mompa. The positive-strand of L1 dsRNA contained a long open reading frame (ORF) potentially encoding a protein of 5,373 amino acids (molecular mass 603,080 Da) with conserved motifs characteristic of RNA-dependent RNA polymerase (RdRp) and helicase. The ORF is the longest so far reported in the fungal kingdom. The putative RdRp and helicase were shown to be related to putative RdRps and helicases of members of the genus Endornavirus. As is the case with endornaviruses, the coding (sense) strand of L1 dsRNA contained a discontinuity (nick) at nt position 2,552. A region between the RdRp and helicase domains of the polyprotein also had an amino acid sequence, resembling UDP glycosyltransferases (UGTs) in Oryza sativa endornavirus and Phytophthora endornavirus 1. Regions in the L1 dsRNA-encoded protein presumed to contain putative helicase, UGT and RdRp motifs were present at comparable positions to those in other endornaviruses. L1 dsRNA of H. mompa strain V670 was assigned to the genus Endornavirus, and here, we designate it as H. mompa endornavirus 1-670 (HmEV1-670). This represents the first report of a fungal endornavirus whose complete nucleotide sequence has been determined.

Nucleotide sequence of a mitochondrial RNA virus from the plant pathogenic fungus, Helicobasidium mompa Tanaka.

A double-stranded (ds) RNA (2411 bp) from a strain V18 of the violet root rot basidiomycetous fungus, Helicobasidium mompa was sequenced. Using the fungal mitochondrial genetic code in which UGA codes for tryptophan, the positive strand of V18 dsRNA was found to contain a long open-reading frame with the potential to encode a protein of 700 amino acids (molecular mass 79,805 Da), including conserved motifs characteristic of RNA-dependent RNA polymerase (RDRP). This putative RDRP was shown to be related to putative RDRPs of several fungal mitochondrial viruses. It is proposed that V18 dsRNA is assigned to the genus Mitovirus in the family Narnaviridae and designated as H. mompa mitovirus 1-18 (HmMV1-18). Like other mitoviruses, HmMV1-18 RNA can be folded into potentially stable stem-loop structures at both the 5'- and 3'-termini, and both terminal sequences have inverted complementarity with the potential to form panhandle structure. BLAST analysis indicates that the RDRP encoded by HmMV1-18 is more closely related to those encoded by mitochondrial viruses of some ascomycetes than to that of the unassigned RsM2-1A1 dsRNA in the basidiomycetous Rhizoctonia solani. HmMV1-18 is the first member of the genus Mitovirus from basidiomycete fungi.

Characterization of double-stranded RNA elements in the violet root rot fungus Helicobasidium mompa.

Double-stranded (ds) RNA of various types was detected by electrophoresis in 23 of 25 isolates of Helicobasidium mompa. These dsRNAs varied in size from ca. 2 kbp to more than 10 kbp. dsRNAs from an isolate V1 had two distinct nucleotide sequences for putative RNA-dependent RNA polymerase (RDRP). Their complete sequences revealed that V1 dsRNA1 was 2247 bp in length, with a single ORF that encoded a 706-amino acid residue polypeptide with a predicted molecular mass of 82.6 kDa, and that V1 dsRNA3 was 1776 bp in length, with a single ORF that encoded a 538-amino acid residue polypeptide with a predicted molecular mass of 62.6 kDa. RDRP-conserved motifs were identified in both predicted amino acid sequences. Phylogenetic analysis indicated that V1 dsRNA1 was most closely related to Fusarium poae virus 1, while V1 dsRNA3 was most closely related to Helicobasidium mompa 70 virus. These results indicate coinfection of isolate V1 by two distinct partitiviruses.

Molecular characterization of dsRNA segments 2 and 5 and electron microscopy of a novel reovirus from a hypovirulent isolate, W370, of the plant pathogen Rosellinia necatrix.

A hypovirulent isolate, W370, of the white root rot fungus Rosellinia necatrix has previously been shown to harbour 12 dsRNA segments. In this study, complete nucleotide sequences of segments 2 and 5 of W370 dsRNAs were determined. The nucleotide sequence of genome segment 2 was 3773 bases long with a single long open reading frame (ORF) encoding 1226 amino acid residues with a predicted molecular mass of approximately 138.5 kDa. The nucleotide sequence of segment 5 was 2089 bases long with a single long ORF, whose deduced polypeptide contained 646 amino acid residues with a predicted molecular mass of about 72 kDa. Comparative analysis showed that the deduced protein sequence of segment 2 had significant homology with the putative VP2 of Colorado tick fever virus (CTFV) and European Eyach virus (EYAV) in the genus Coltivirus, but the deduced protein sequence of segment 5 had no similarity with other virus proteins. Double-shelled spherical particles approximately 80 nm in diameter associated with W370 dsRNAs were observed in a preparation from the mycelial tissue of isolate W370. The results demonstrated that the virus associated with W370 dsRNAs is a novel reovirus of the family Reoviridae. The virus was named Rosellinia anti-rot virus (RArV).

Cloning and characterization of a totivirus double-stranded RNA from the plant pathogenic fungus, Helicobasidium mompa Tanaka.

Virus-like particles (VLPs, named HmTV1-17), about 40 nm in diameter were found in the violet root rot fungus Helicobasidium mompa Tanaka strain No. 17, which had been isolated from an apple tree. Purified preparations of HmTV1-17 contained two species of double-stranded RNA (dsRNA), designated 17L and 17S. cDNAs were constructed from HmTV1-17 genomic dsRNAs purified using CF-11 cellulose column chromatography. The sequences of 17L and 17S cDNA comprised 5,207 and 2,096 bp, respectively. Although 17S has no large open reading flame (ORF) on either strand, 17L has two large overlapping ORFs. The 5' located ORF1 encodes the coat protein (CP, 788 amino acids), whereas the gene product of ORF2, which is in the -1 frame relative to ORF1, shows the typical features of a RNA dependent RNA polymerase (RDRP, 845 amino acids). Phylogenetic analysis based on RDRP showed that HmTV1-17 is closely related to Sphaeropsis sapinea SsRV1, a member of the genus Totivirus from filamentous fungus S. sapinea.

Detection of a double-stranded RNA virus from a strain of the violet root rot fungus Helicobasidium mompa Tanaka.

Three double-stranded (ds) RNA species (ca. 1.30, 1.27 and 1.23 x 106) were isolated by CF-11 cellulose chromatography from a strain of the violet root rot fungus Helicobasidium mompa recovered from apple roots. Purified virion preparations contained isometric particles about 25 nm in diameter, and also the same three species of dsRNA isolated from total extracts by CF-11 cellulose chromatography. The molecular mass of the coat protein was about 67 K when estimated by SDS-PAGE. The largest dsRNA (referred to as dsRNA1) contains a single, long open reading frame of 1794 nucleotides that encodes a putative polypeptide containing 598 amino acid residues with a molecular mass of 69.9 K. This polypeptide contains amino acid sequence motifs conserved in putative RNA-dependent RNA polymerases of RNA viruses. Phylogenetic analysis revealed similarities to RNA-dependent RNA polymerases from Atkinsonella hypoxylon 2H virus, a member of the family Partitiviridae.

Nucleotide sequences of double-stranded RNA segments from a hypovirulent strain of the white root rot fungus Rosellinia necatrix: possibility of the first member of the Reoviridae from fungus.

Twelve double-stranded (ds) RNA segments were detected from a hypovirulent strain W370 of the white root rot fungus Rosellinia necatrix. The estimated molecular weights ranged from 0.41 x 10(6) to 2.95 x 10(6). Full length cDNA clones for eight segments were obtained. Northern blot analysis suggested that each segment was genetically unique. The nucleotide sequences of eight full length dsRNA segments were determined. One long open reading frame was found in each segment. Conserved sequences at the 5'-end (5'-ACAAUUU-3') and at the 3'-end (5'-UGCAGAC-3') were identified in all eight segments. Segment-specific panhandle structures, formed by inverted terminal repeats, were also found in all segments. Comparative analyses of the predicted translational products of eight dsRNA segments showed that the deduced amino acid sequence partially matched those of the Reoviridae family members: Colorado tick fever virus, Nilaparvata lugens reovirus, and rice black streaked dwarf virus. The results suggested that W370 dsRNA is derived from a new member of the family Reoviridae detected in fungus.