Family Partitiviridae Research Articles

Complete genome sequence of a novel partitivirus infecting the phytopathogenic fungus Alternaria tenuissima.

In the present study, a novel double-stranded RNA (dsRNA) mycovirus designated as "Alternaria tenuissima partitivirus 2" (AttPV2), was isolated from Alternaria tenuissima strain BJ-SY-1, a phytopathogenic fungus causing muskmelon leaf blight in Beijing municipality of China. The genome of AttPV2 comprises two dsRNA segments. The larger segment is 1829 bp in length and has a single open reading frame (ORF), potentially encoding a 65.8-kDa RNA-dependent RNA polymerase (RdRp), and the smaller segment is 1681 bp in length and also contains a single ORF, encoding a putative coat protein (CP) with a molecular mass of 56.0 kDa. BLASTp analysis revealed that the RdRp and CP encoded by the two ORFs of AttPV2 have the highest sequence identity, 85.9% and 75.0%, respectively, to their counterparts in Colletotrichum eremochloae partitivirus 1 (CePV1). Phylogenetic analysis based on RdRp sequences showed that AttPV2 clustered most closely with CePV1, a member of the proposed genus "Epsilonpartitivirus" in the family Partitiviridae. Hence, we propose that AttPV2 is a new epsilonpartitivirus from A. tenuissima. To the best of our knowledge, this is the first report of an epsilonpartitivirus infecting A. tenuissima.

Identification and complete genome sequence of mulberry cryptic virus 1.

A cryptic virus, named mulberry cryptic virus 1 (MuCV1), was identified in a mulberry (Morus alba) transcriptome dataset and confirmed using RACE methods. The genome of MuCV1 is composed of two double-stranded RNAs, 1605 bp and 1627 bp in size, encoding an RNA-dependent RNA polymerase (RdRp) and a coat protein (CP), respectively. The 5'-AGAAUU-3' sequence in the 5' untranslated region was conserved in the two dsRNAs. Sequence comparisons and phylogenetic analysis based on RdRp and CP sequences both indicated that MuCV1 is a deltapartitivirus (family Partitiviridae).

Genome Organizations and Functional Analyses of a Novel Gammapartitivirus from Rhizoctonia solani AG-1 IA Strain D122.

Here, we describe a novel double-stranded (ds) RNA mycovirus designated Rhizoctonia solani dsRNA virus 5 (RsRV5) from strain D122 of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight. The RsRV5 genome consists of two segments of dsRNA (dsRNA-1, 1894 bp and dsRNA-2, 1755 bp), each possessing a single open reading frame (ORF). Sequence alignments and phylogenetic analyses showed that RsRV5 is a new member of the genus Gammapartitivirus in the family Partitiviridae. Transmission electron microscope (TEM) images revealed that RsRV5 has isometric viral particles with a diameter of approximately 20 nm. The mycovirus RsRV5 was successfully removed from strain D122 by using the protoplast regeneration technique, thus resulting in derivative isogenic RsRV5-cured strain D122-P being obtained. RsRV5-cured strain D122-P possessed the traits of accelerated mycelial growth rate, increased sclerotia production and enhanced pathogenicity to rice leaves compared with wild type RsRV5-infection strain D122. Transcriptome analysis showed that three genes were differentially expressed between two isogenic strains, D122 and D122-P. These findings provided new insights into the molecular mechanism of the interaction between RsRV5 and its host, D122 of R. solani AG-1 IA.

Genomic characterization of silvergrass cryptic virus 1, a novel partitivirus infecting Miscanthus sinensis.

In the present study we report the identification of a novel partitivirus recovered from Miscanthus sinensis, for which the provisional name "silvergrass cryptic virus 1" (SgCV-1) is proposed. High-throughput sequencing (HTS) and rapid amplification of cDNA ends (RACE) allowed the assembly of the complete sequence of each double-stranded RNA genome segment of this novel virus. The largest dsRNA segment, dsRNA1 (1699 bp), was predicted to encode a viral RNA-dependent RNA polymerase protein (RdRp) with 478 aa, and dsRNA2 (1490 bp) and dsRNA3 (1508 bp) were predicted to encode putative capsid proteins (CPs) with 347 and 348 aa, respectively. SgCV-1 has the highest amino acid sequence identity (≤70.80% in RdPp and ≤34.5% in CPs) to members of the genus Deltapartitivirus, family Partitiviridae, especially to unclassified viruses related to members of this genus. Its genome segment and protein lengths are also within the range of those of deltapartitiviruses. Moreover, phylogenetic analysis based on RdRp amino acid sequences also showed clustering of this novel virus with the related unclassified deltapartitiviruses. An RT-PCR survey of 94 imported M. sinensis samples held in quarantine identified seven additional samples carrying SgCV-1. This new virus fulfils all ICTV criteria to be considered a new member of the genus Deltapartitivirus.

A novel alphapartitivirus from binucleate Rhizoctonia fumigata AG-Ba isolate C-314 Baishi.

The full-length nucleotide sequence and genome organization of a novel mycovirus designated as "Rhizoctonia fumigata partitivirus 1" (RfPV1) from Rhizoctonia fumigata AG-Ba strain C-314 Baishi was determined. The genome of RfPV1 consists of two double-stranded RNAs (dsRNAs): dsRNA1 (2003 bp) and dsRNA2 (1802bp). Each of the two dsRNAs contains one open reading frame, coding for a putative RNA-dependent RNA polymerase and a coat protein, respectively. The 5' untranslated regions (UTRs) of both dsRNAs were conserved, and the 3'-UTRs of the two dsRNAs had interrupted poly(A) tails, similar to other partitiviruses. Phylogenetic analysis indicated that RfPV1 is a new species in the genus Alphapartitivirus, family Partitiviridae.

First report of Raphanus sativus cryptic virus 2 on cabbage seeds (Brassica rapa subsp. pekinensis) imported from Italy.

The online version contains supplementary material available at 10.1007/s13337-021-00744-w.

Molecular characterization of the complete genome of a novel partitivirus hosted by the saprobic mushroom Leucocybe candicans.

Virus communities of uncultivated fungi stay largely unknown. In the current study, we characterized a new partitivirus species detected in the basidiomycetous, saprobic mushroom Leucocybe candicans, named "Leucocybe candicans partitivirus 1" (LcPV1). The full-length genome of LcPV1, determined using deep sequencing and RLM-RACE approaches, consists of two dsRNA segments with each having the same size of 1984bp. Both dsRNA genome segments comprise a single open reading frame (ORF), encoding an RNA-dependent RNA polymerase (RdRp), and a capsid protein (CP), respectively. Based on BLASTp search, the sequences of the RdRp and CP show the highest identity (50.09% and 35.71% similarity, respectively) to those of partitiviruses reported from an oomycetous, plant pathogenic, stramenopile algae Plasmopara viticola and basidiomycetous, plant pathogenic fungus Ceratobasidium sp., respectively. Phylogenetic analyses performed based on the RdRp and CP sequences revealed that LcPV1 falls within a cluster that includes different alphapartitivirus species from the family Partitiviridae. In this study, we propose that LcPV1 is a new member of a species belonging to the genus Alphapartitivirus. To our knowledge, this is the first study reporting on a new fungal virus (mycovirus) identified in the basidiomycetous, saprobic mushroom Leucocybe candicans.

A Novel Partitivirus That Confer Hypovirulence to the Plant Pathogenic Fungus Colletotrichum liriopes.

Here, we report a novel double-stranded RNA virus designated Colletotrichum liriopes partitivirus 1 (ClPV1) from the plant pathogenic fungus C. liriopes. ClPV1 genome has two double stranded RNAs (dsRNAs), named as dsRNA 1 and dsRNA 2, which in the lengths of 1,807 and 1,706 bp, respectively. The dsRNA 1 and dsRNA 2 encoded proteins showing significant amino acid (aa) sequence identity to the RNA-dependent RNA polymerase (RdRp) and coat protein (CP) of partitiviruses, respectively. Phylogenetic analysis using the aa sequences of RdRp and CP indicated that ClPV1 was grouped to members of the putative Epsilonpartitivirus genus in the Partitiviridae family. Spherical viral particles in approximately 35 nm in diameter and packaging the ClPV1 genome were isolated. Virus elimination and virus transfection with purified viral particles, and biological comparison revealed that ClPV1 could reduce the virulence and conidia production of C. liriopes. To the best of our knowledge, this is the first report of mycovirus in C. liriopes fungus.

Molecular characterization of a novel partitivirus and a fusarivirus coinfecting the fungus Nigrospora sphaerica.

In this report, we describe the molecular characterization of two novel mycoviruses coinfecting the plant pathogenic fungus Nigrospora sphaerica, which were designated "Nigrospora sphaerica fusarivirus 1" (NsFV1) and "Nigrospora sphaerica partitivirus 1" (NsPV1). NsFV1 has an undivided genome measuring 6,147 nt, excluding the polyA tail, and was predicted to contain two nonoverlapping open reading frames (ORF1 and 2). The larger ORF1 encodes a polyprotein containing a conserved RNA-dependent RNA polymerase (RdRp) and a helicase domain that has functions related to RNA replication, and the smaller ORF2 encodes a putative protein with an unknown function. NsPV1 consists of two genome segments, which measure 1,796 bp and 1,455 bp in length. Each of the two dsRNAs has a single ORF, and they are predicted to encode proteins with homology to viral RdRps and coat proteins of members of the family Partitiviridae. Phylogenetic analysis indicated that NsFV1 is a member of the recently proposed family "Fusariviridae", while NsPV1 was determined to belong to the genus Gammapartitivirus in the family Partitiviridae. To the best of our knowledge, this report is the first to describe mycoviruses infecting N. sphaerica.

Complete nucleotide sequence of a novel partitivirus from Brassica campestris L. ssp. chinensis.

In the present work, we report the discovery and complete genome sequence of a novel partitivirus identified from Brassica campestris L. ssp. chinensis, which we have named "Brassica campestris chinensis cryptic virus 1" (BCCV1). Next-generation sequencing (NGS) combined with adapter-ligation-mediated amplification allowed assembly of the full-length genome sequence of BCCV1. The genome of BCCV1 contains two dsRNA segments, dsRNA1 (1595 bp) and dsRNA2 (1591 bp), which encode a conserved RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP), respectively. Homology searches and phylogenetic analysis of the 479-aa RdRp and 438-aa CP showed that BCCV1 is a new member of the genus Deltapartitivirus, family Partitiviridae. This is the first report of the identification of a member of the family Partitiviridae in Brassica campestris L. ssp. chinensis.

Genomic and biological characterization of a novel partitivirus infecting Fusarium equiseti

This study describes a new mycovirus infecting a strain from the Fusarium incarnatum-equiseti species complex. Based on phylogenetic and genomic analyses, this virus belongs to the recently proposed genus “Zetapartitivirus” in the family Partitiviridae. The name “Fusarium equiseti partitivirus 1″ (FePV1) is therefore suggested for this novel viral species. Similar to other partitiviruses, FePV1 genome is composed by two dsRNA segments that exhibit each one large ORF encoding for an RdRp and a CP, respectively. A smaller dsRNA was also detected in infected mycelium and could be a satellite RNA of FePV1. In addition to characterized zetapartitiviruses, other FePV1-related sequences were retrieved from online databases and their significance is discussed. Following conidial isolation, an FePV1-free isogenic line of the fungal host was obtained. In comparison with the original infected strain, this line showed higher growth, biomass production and pathogenicity on tomato, advocating that FePV1 induces hypovirulence on its host.

A novel mycovirus isolated from the plant-pathogenic fungus Botryosphaeria dothidea.

A novel virus, Botryosphaeria dothidea bipartite mycovirus 1 (BdBMV1), was isolated from the plant-pathogenic fungus Botryosphaeria dothidea strain HNDT1, and the complete nucleotide sequence of its genome was determined. BdBMV1 consists of two genomic segments. The first segment is 1,976bp in length and contains a single open reading frame (ORF) encoding the RNA-dependent RNA polymerase (RdRp) (68.95kDa). The second segment is 1,786bp in length and also contains a single ORF encoding a hypothetical protein of 35.19kDa of unknown function. Based on the sequence of its RdRp, BdBMV1 is phylogenetically related to several other unclassified dsRNA mycoviruses, including Cryphonectria parasitica bipartite mycovirus 1 (CpBV1), and has a distant relationship to members of the family Partitiviridae.

Molecular characterization of a novel partitivirus hosted by the false morel mushroom Gyromitra esculenta.

Virus populations of uncultivated fungi remain scarcely studied. In the present study, we characterized a new partitivirus isolated from the false morel mushroom Gyromitra esculenta, named "Gyromitra esculenta partitivirus 1" (GePV1). The complete genome of GePV1, whose sequence was determined by combining high-throughput sequencing and RLM-RACE approaches, comprises two dsRNA segments of 1971 bp and 1799 bp, respectively. Each dsRNA genome segment contains a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp) and a capsid protein (CP), respectively. The sequences of the RdRp and CP exhibited the highest similarity (69.77% and 47.00% identity, respectively) to those of Rosellinia necatrix partitivirus 2 (RnPV2). Phylogenetic analysis based on the CP and RdRp sequences demonstrated that GePV1 clusters within a clade that includes members of the genus Alphapartitivirus, family Partitiviridae. We propose that GePV1 is a new member of the genus Alphapartitivirus. This is the first study reporting on a new partitivirus identified in the false morel mushroom Gyromitra esculenta.

Molecular characterization of a novel partitivirus isolated from the phytopathogenic fungus Aplosporella javeedii.

Aplosporella javeedii is a pathogenic fungus that causes canker and dieback of jujube in China. In this study, we report a new mycovirus, Aplosporella javeedii partitivirus 1 (AjPV1), isolated from A. javeedii strain NX55-3. The AjPV1 genome contains two double-stranded RNA elements (dsRNA1 and dsRNA2). The size of dsRNA1 is 2,360 bp, and it encodes a putative RNA-dependent RNA polymerase (RdRp), while dsRNA2 is 2,301 bp in length and encodes a putative capsid protein (CP). The sequences of RdRp and CP have significant similarity to those of members of the family Partitiviridae. Sequence alignment and phylogenetic analysis showed that AjPV1 is a new member of the family Partitiviridae that is related to members of the genus Betapartitivirus. To our knowledge, AjPV1 is the first mycovirus reported from A. javeedii.

A novel gammapartitivirus from the entomopathogenic fungus Metarhizium brunneum.

Here, we report a novel partitivirus infecting Metarhizium brunneum, which was designated "Metarhizium brunneum partitivirus 2" (MbPV2). The complete genome of MbPV2 consists of two segments, dsRNA1 and dsRNA2, with each dsRNA possessing a single open reading frame (ORF). dsRNA1 (1,775 bp) encodes a conserved RNA-dependent RNA polymerase (RdRp) with the highest sequence similarity to Plasmopara viticola associated partitivirus 1 (PvAPV1), while dsRNA2 (1,568 bp) encodes a coat protein (CP) with the highest sequence similarity to Colletotrichum partitivirus 1 (CtParV1). Phylogenetic analysis based on RdRp sequences showed that MbPV2 is a new member of the genus Gammapartitivirus, family Partitiviridae. This is the first report of a gammapartitivirus that infects the entomopathogenic fungus Metarhizium brunneum.

A novel mycovirus infecting Aspergillus nidulans that is closely related to viruses in a new genus of the family Partitiviridae.

The bisegmented genome of a novel double-stranded (ds) RNA mycovirus, named "Aspergillus nidulans partitivirus 1" (AnPV1), isolated from the fungus Aspergillus nidulans strain HJ5-47, was sequenced and analyzed. AnPV1 contains two segments, AnPV1-1 and AnPV1-2. AnPV1-1 has 1837 bp with an open reading frame (ORF) that potentially encodes a putative RNA-dependent RNA polymerase (RdRp) of 572 amino acids (aa). AnPV1-2 has 1583 bp with an ORF encoding a putative capsid protein (CP) of 488 aa. Phylogenetic analyses indicated that AnPV1 and related viruses clustered in a group that could represent a new unclassified genus in the family Partitiviridae.

Full-length genome characterization of a novel alphapartitivirus detected in the ectomycorrhizal fungus Hygrophorus penarioides

Virus populations of ectomycorrhizal fungi remain poorly studied. In the present study, we characterized a new partitivirus isolated from the basidiomycetous, ectomycorrhizal fungus Hygrophorus penarioides, named "Hygrophorus penarioides partitivirus 1" (HpPV1). The whole genome of HpPV1, determined by merging deep sequencing and RLM-RACE approaches, comprised two dsRNA segments of 2053bp and 2072bp, respectively. Both dsRNA genome segments included a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp), and a capsid protein (CP), respectively. Based on BLASTp search, the sequences of the RdRp and CP exhibits the highest similarity (67.49% and 75.61% identity, respectively) to those of partitiviruses identified from an ascomycetous ectomycorrhizal fungus Sarcosphaera coronaria. Phylogenetic analyses performed based on the CP and RdRp sequences demonstrated that HpPV1 clusters within a clade that includes members of the genus Alphapartitivirus, belonging to the family Partitiviridae. Here, we propose that HpPV1 is a new member of the genus Alphapartitivirus. This is the first study reporting on a new partitivirus identified from the basidiomycetous, ectomycorrhizal fungus Hygrophorus penarioides.

Divergent RNA viruses in Macrophomina phaseolina exhibit potential as virocontrol agents

Macrophomina phaseolina is an important necrotrophic phytopathogenic fungus and cause extensive damage in many oilseed crops. Twelve M.phaseolina isolates with diverse biological phenotypes were selected for a high-throughput sequencing-based metatranscriptomic and bioinformatics analysis to identify viruses infecting M.phaseolina. The analysis identified 40 partial or nearly complete viral genome segments, 31 of which were novel viruses. Among these viral sequences, 43% of the viral genomes were double-stranded RNA (dsRNA), 47% were positive single-stranded RNA (ssRNA+), and the remaining 10% were negative sense-stranded RNA (ssRNA−). The 40 viruses showed affinity to 13 distinct viral lineages, including Bunyavirales (four viruses), Totiviridae (three viruses), Chrysoviridae (five viruses), Partitiviridae (four viruses), Hypoviridae (one virus), Endornaviridae (two viruses), Tombusviridae (three viruses), Narnaviridae (one virus), Potyviridae (one virus), Bromoviridae (one virus), Virgaviridae (six viruses), ‘Fusagraviridae’ (five viruses), and Ourmiavirus (four viruses). Two viruses are closely related to two families, Potyviridae and Bromoviridae, which previously contained no mycovirus species. Moreover, nine novel viruses associated with M.phaseolina were identified in the family Totiviridae, Endornaviridae, and Partitiviridae. Coinfection with multiple viruses is prevalent in M.phaseolina, with each isolate harboring different numbers of viruses, ranging from three to eighteen. Furthermore, the effects of the viruses on the fungal host were analyzed according to the biological characteristics of each isolate. The results suggested that M.phaseolina hypovirus 2, M.phaseolina fusagravirus virus 1-5 (MpFV1-5), M.phaseolina endornavirus 1-2 (MpEV1-2), M.phaseolina ourmia-like virus 1-3 (MpOLV1-3), M.phaseolina mitovirus 4 (MpMV4), and M.phaseolina mycobunyavirus 1-4 (MpMBV1-4) were only detected in hypovirulent isolates. Those viruses associated with hypovirulence might be used as biological control agents as an environmentally friendly alternative to chemical fungicides. These findings considerably expand our understanding of mycoviruses in M.phaseolina and unvailed the presence of a huge difference among viruses in isolates from different hosts in distant geographical regions. Together, the present study provides new knowledge about viral evolution and fungus-virus coevolution.

Newly identified Cryptosporidium parvum virus-1 from newborn calf diarrhoea in Turkey.

Cryptosporidium is a common enteric parasite that primarily affects those immunocompromised susceptible individuals and newborns. Detailed investigations have revealed that Cryptosporidium (C.) oocysts contain dsRNA segments which are recently classified under the Partitiviridae family. The relationship between parasite and virus whether or not affect the clinical outcomes of newborn calf diarrhoea is not apparent. The aim of this study was the identification and characterization of Cryptosporidium parvum virus-1 (CSpV1) from newborn calves. We also aimed to understand that parasite-virus symbiont relationship role in the severity of disease cases. Parasitic screening was performed with the help of morphological examinations, immunoassay and molecular polymerase chain reaction (PCR) methods. To further identification of C.parvum oocysts, confocal laser, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) image analysis were used for the morphological investigations. Software-based in silico comparison and identity analyses were conducted from the CSpV1 genome for the genomic sequence characterizations. Cryptosporidium prevalence was 56.2% in newborn calf diarrhoeal cases. Virus dsRNA segments isolated from purified and clarified oocysts. Sequence results showed that we have successfully isolated CSpV1 from C.parvum oocysts. Virus RNA-dependent RNA polymerase (RdRp) was found to be highly variable and showed a species-specific relationship with their carriers. We also identified that CSpV1 frequency was around 8.8% from diarrhoea-showing newborn calves. Cryptosporidium was strongly associated with diarrhoea at early ages of newborns, but the parasite and CSpV1 relationship is not associated with the severity of newborn calf diarrhoea. The current study provides the first report and molecular characterization of CSpV1 in Turkey.

Co-infection of a novel fusagravirus and a partitivirus in a Korean isolate of Rosellinia necatrix KACC40168.

We report here the presence of dsRNA mycoviruses in a Korean isolate of Rosellinia necatrix. A multiple band pattern of double-stranded RNA (dsRNA) from R. necatrix suggested mixed mycovirus infection. Next-generation sequencing analysis of purified dsRNAs indicated the presence of two dsRNA mycoviruses related to the members of families "Fusagraviridae" (proposed) and Partitiviridae. The first dsRNA virus revealed that the complete genome sequence was 8868bp in size and contained two large open reading frames (ORFs 1 and 2), overlapped by 22bp containing a canonical (- 1) slippery heptanucelotide sequence of UUUAAAC. The deduced amino acid sequence of ORF1 and ORF2 showed highest similarity to the hypothetical protein and RNA-dependent RNA polymerase (RdRp) of Rosellinia necatrix fusagravirus 3 (RnFGV3). Phylogenetic analysis showed that this dsRNA virus clustered with RnFGV3 and other fusagraviruses. Gene organization, sequence similarity, and phylogenetic analysis indicate that this virus seems to belong to a novel species of "Fusagraviridae", which we have named Rosellinia necatrix fusagravirus 4. The second virus has two dsRNA segments with sizes of 1907bp and 1918bp, each of which encoded a single ORF showing highest similarity to the RdRp and capsid protein of known members of Partitiviridae. Evaluation of genome structure, sequence similarity, and phylogeny indicate this to be a new member of the genus Alphapartitivirus in the family Partitiviridae, hereafter designated as Rosellinia necatrix partitivirus 26. This is the first report of the presence of a fusagravirus in an Asian R. necatrix isolate and of its mixed infection with a partitivirus.