Mixed infection by a partitivirus and a negative-sense RNA virus related to mymonaviruses in the polypore fungus Bondarzewia berkeleyi

Seven new mycoviruses identified from isolated ascomycetous macrofungi

Mycoviruses have been described in all major fungal taxonomic groups. There has been much focus on commercially cultivated basidiomycetous macrofungi, while attention to viruses from ascomycetous macrofungi is lacking. Therefore, in this study, we conducted viral screening against fungal mycelia that were regenerated from ascomycetous macrofungi using agarose gel electrophoresis (AGE) and fragmented and primer-ligated dsRNA sequencing (FLDS). Among the 57 isolates, four isolates were detected with virus-like bands through screening with AGE, and subsequent FLDS analyses determined the viral sequences. Other isolates without virus-like bands in AGE were pooled to check for viral sequences. Using FLDS analysis, a total of seven new mycoviruses were identified, including two double-stranded RNA (dsRNA) viruses belonging to Quadriviridae and Partitiviridae, five positive-sense single-stranded RNA (ssRNA) viruses (three belonging to Mitoviridae, one belonging to Endornaviridae and one belonging to Virgaviridae). All viruses characterized in this study are novel species, and all the hosts are firstly reported to be infected by mycoviruses. These findings expand our knowledge of the diversity of mycoviruses from macrofungi in natural environments.

Oyster Mushroom Spherical Virus Crosses the Species Barrier and Is Pathogenic to a New Host Pleurotus pulmonarius

Oyster mushroom spherical virus (OMSV) is a mycovirus with a positive-sense single-stranded RNA genome that infects the edible mushroom Pleurotus ostreatus. OMSV is horizontally transferred from an infected strain to a cured strain via mycelia. The infection results in significant inhibition of mycelial growth, malformation of fruiting bodies, and yield loss in oyster mushrooms. This study successfully transferred OMSV from P. ostreatus to Pleurotus pulmonarius. However, transmission was not successful in other Pleurotus species including P. citrinopileatus, P. eryngii, P. nebrodensis, and P. salmoneostramineus. The successful OMSV infection in P. pulmonarius was further verified with Western blot analysis using a newly prepared polyclonal antiserum against the OMSV coat protein. Furthermore, OMSV infection reduced the mycelial growth rate of P. pulmonarius. The OMSV-infected strain demonstrated abnormal performance including twisted mushrooms or irregular edge of the cap as well as reduced yield of fruiting bodies in P. pulmonarius, compared to the OMSV-free strain. This study is the first report on the infection and pathogenicity of OMSV to the new host P. pulmonarius. The data from this study therefore suggest that OMSV is a potential threat to P. pulmonarius.

Fungal Viruses Unveiled: A Comprehensive Review of Mycoviruses

Mycoviruses (viruses of fungi) are ubiquitous throughout the fungal kingdom and are currently classified into 23 viral families and the genus botybirnavirus by the International Committee on the Taxonomy of Viruses (ICTV). The primary focus of mycoviral research has been on mycoviruses that infect plant pathogenic fungi, due to the ability of some to reduce the virulence of their host and thus act as potential biocontrol against these fungi. However, mycoviruses lack extracellular transmission mechanisms and rely on intercellular transmission through the hyphal anastomosis, which impedes successful transmission between different fungal strains. This review provides a comprehensive overview of mycoviruses, including their origins, host range, taxonomic classification into families, effects on their fungal counterparts, and the techniques employed in their discovery. The application of mycoviruses as biocontrol agents of plant pathogenic fungi is also discussed.

Identification of novel RNA mycoviruses from wild mushroom isolates in Japan

The characterization of viruses from environmental samples could aid in our understanding of their ecological significance and potential for biotechnological exploitation. While there has been much focus on pathogenic fungi or commercially cultivated mushrooms, attention to viruses from wild Basidiomycota mushrooms is lacking. Therefore, in this study, we conducted viral screening of fungal mycelia isolated from wild basidiocarps using agarose gel electrophoresis (AGE) and fragmented and primer-ligated dsRNA sequencing (FLDS). Among the 51 isolates, seven isolates were detected with virus-like bands during the initial screening with AGE, but only five isolates were detected with viruses after long-term storage. Using the FLDS method, we obtained seven viral genome sequences, including five double-stranded RNA (dsRNA) viruses belonging to Partitiviridae and Curvulaviridae, one positive-sense single-stranded RNA (ssRNA) virus belonging to Endornaviridae and one negative-sense ssRNA virus belonging to Tulasviridae (Bunyavirales). All viruses characterized in this study are novel species. These findings greatly expanded our knowledge of the diversity of RNA viruses from environmental samples.

Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle

Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.

2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Novel and diverse mycoviruses co-infecting a single strain of the phytopathogenic fungus Alternaria dianthicola

Alternaria dianthicola is a pathogenic fungus that causes serious leaf or flower blight on some medicinal plants worldwide. In this study, multiple dsRNA bands in the range of 1.2-10 kbp were found in a Alternaria dianthus strain HNSZ-1, and eleven full-length cDNA sequences of these dsRNA were obtained by high-throughput sequencing, RT-PCR detection and conventional Sanger sequencing. Homology search and phylogenetic analyses indicated that the strain HNSZ-1 was infected by at least nine mycoviruses. Among the nine, five viruses were confirmed to represent novel viruses in the families Hypoviridae, Totiviridae, Mymonaviridae and a provisional family Ambiguiviridae. Virus elimination and horizontal transmission indicated that the (-) ssRNA virus, AdNSRV1, might be associated with the slow growth and irregular colony phenotype of the host fungus. As far as we know, this is the first report for virome characterization of A. dianthus, which might provide important insights for screening of mycovirus for biological control and for studying of the interactions between viruses or viruses and their host.

Diversity of mycoviruses in edible fungi

Mycoviruses (fungal viruses) are widespread in all major taxonomic groups of fungi. Although most mycovirus infections are latent, some mycoviruses, such as La France isometric virus, mushroom virus X, and oyster mushroom spherical virus, can cause severe diseases in edible fungi and lead to significant production losses. Recently, deep sequencing has been employed as a powerful research tool to identify new mycoviruses and to enhance our understanding of virus diversity and evolution. An increasing number of novel mycoviruses that can infect edible fungi have been reported, including double-stranded (ds) RNA, positive-sense ( +)ssRNA, and negative-sense (-)ssRNA viruses. To date, approximately 60 mycoviruses have been reported in edible fungi. In this review, we summarize the recent advances in the diversity and evolution of mycoviruses that can infect edible fungi. We also discuss mycovirus transmission, co-infections, and genetic variations, as well as the methods used to detect and control of mycoviruses in edible fungi, and provide insights for future research on mushroom viral diseases.

The complete genome sequence of a novel mycovirus in the plant-pathogenic fungus Exobasidium gracile

The plant-pathogenic fungus Exobasidium gracile belongs to the basidiomycetous genus Exobasidium and causes leaf abnormalities in Camellia oleifera. Here, we report a novel mycovirus from E. gracile strain Z-2, called "Exobasidium gracile zybavirus 2" (EgZV2), which is related phylogenetically to a member of the genus Zybavirus in the family Amalgaviridae. Like those of other zybaviruses, the EgZV2 genome has two large open reading frames (ORFs) encoding an unknown protein and an RNA-dependent RNA polymerase (RdRp), respectively. In addition, we found a conserved +1 programmed ribosomal frameshifting (PRF) motif (UUUCGG) between ORF1 and ORF2 in EgZV2.

Complete nucleotide sequence of a novel mycovirus infecting Rhizoctonia fumigata AG-Ba isolate C-314 Baishi

The complete nucleotide sequence of a novel mycovirus, designated as "Rhizoctonia fumigata bipartite virus 1" (RfBV1), from Rhizoctonia fumigata AG-Ba isolate C-314 Baishi was determined. The genome of RfBV1 is composed of two double-stranded RNAs (dsRNA). dsRNA-1 (2311 bp) contains one open reading frame (ORF), which codes for the putative RNA-dependent RNA polymerase (RdRp) of the virus. dsRNA-2 (1690 bp) contains one ORF, which encodes a putative protein whose function is unknown. Phylogenetic analysis indicated that the RdRp of RfBV1 clustered with several unassigned bipartite viruses belonging to the CThTV-like viruses group, but not the family Amalgaviridae or Partitiviridae. Our study suggests that RfBV1 is a novel mycovirus related to the CThTV-like viruses.

Molecular characterization of three novel mycoviruses in the plant pathogenic fungus Exobasidium

The plant pathogen Exobasidium gracile, which belongs to the basidiomycetous genus Exobasidium, can lead to swollen and thicker leaves of C. oleifera. To our knowledge, there have been no reports of mycoviruses infecting Exobasidium gracile. This study characterized three mycoviruses coinfecting the plant pathogen Exobasidium gracile strain Z-1. Based on phylogenetic and genomic analyses, E. gracile strain Z-1 was infected two putative Totiviruses designated Exobasidium gracile Totivirus 1 (EgTV1) and Exobasidium gracile Totivirus 2 (EgTV2) and a putative Zybavirus of the family Amalgaviridae defined Exobasidium gracile Zybavirus 1 (EgZV1). Similar to the genomic organization of other Totiviruses, the EgTV1 and EgTV2 genomes are composed of one dsRNA segment that exhibits two large ORFs encoding a CP (capsid protein) and an RdRp (RNA-dependent RNA polymerase), respectively. Moreover, EgTV1 and EgTV2 genomes with a candidate -1 slippery heptamer sequence were discovered between CP and RdRp, respectively. Similar to other Zybaviruses of the family Amalgaviridae, the EgZV1 genome is composed of one dsRNA segment that contains two large ORFs encoding an unknown protein and an RdRp. In addition, the EgZV1 genome has a candidate +1 slippery heptamer sequence between an unknown protein and RdRp.

Assessment of mycoviral diversity in Pakistani fungal isolates revealed infection by 11 novel viruses of a single strain of Fusarium mangiferae isolate SP1

An extensive screening survey was conducted on Pakistani filamentous fungal isolates for the identification of viral infections. A total of 396 fungal samples were screened, of which 36 isolates were found double-stranded (ds) RNA positive with an overall frequency of 9% when analysed by a classical dsRNA isolation method. One of 36 dsRNA-positive strains, strain SP1 of a plant pathogenic fungus Fusarium mangiferae, was subjected to virome analysis. Next-generation sequencing and subsequent completion of the entire genome sequencing by a classical Sanger sequencing method showed the SP1 strain to be co-infected by 11 distinct viruses, at least seven of which should be described as new taxa at the species level according to the ICTV (International Committee on Taxonomy of Viruses) species demarcation criteria. The newly identified F. mangiferae viruses (FmVs) include two partitivirids, one betapartitivirus (FmPV1) and one gammapartitivirus (FmPV2); six mitovirids, three unuamitovirus (FmMV2, FmMV4, FmMV6), one duamitovirus (FmMV5), and two unclassified mitovirids (FmMV1, FmMV3); and three botourmiavirids, two magoulivirus (FmBOV1, FmBOV3) and one scleroulivirus (FmBOV2). The number of coinfecting viruses is among the largest ones of fungal coinfections. Their molecular features are thoroughly described here. This represents the first large virus survey in the Indian sub-continent.

Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems

Thanks to the development of HTS technologies, a vast amount of genetic information on the virosphere of temperate forests has been gained in the last seven years. To estimate the qualitative/quantitative impact of HTS on forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of HTS methods is extremely significant for forest virology. Reviewed data on viral presence in holobionts allowed us a first attempt to address the role of virome in holobionts. Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont; symbiotic microbiota and pathogens engage in a permanent interplay, which influences the host. Through virus–virus interplays synergistic or antagonistic relations may evolve, which may drastically affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protection based on endophytes and mycovirus biocontrol agents. The current analysis is conceived in light of the prospect that novel viruses may initiate an emergent infectious disease and that measures for the avoidance of future outbreaks in forests should be considered.

Armillaria root rot fungi host single-stranded RNA viruses

Species of Armillaria are distributed globally and include some of the most important pathogens of forest and ornamental trees. Some of them form large long-living clones that are considered as one of the largest organisms on earth and are capable of long-range spore-mediated transfer as well as vegetative spread by drought-resistant hyphal cords called rhizomorphs. However, the virus community infecting these species has remained unknown. In this study we used dsRNA screening and high-throughput sequencing to search for possible virus infections in a collection of Armillaria isolates representing three different species: Armillaria mellea from South Africa, A. borealis from Finland and Russia (Siberia) and A. cepistipes from Finland. Our analysis revealed the presence of both negative-sense RNA viruses and positive-sense RNA viruses, while no dsRNA viruses were detected. The viruses included putative new members of virus families Mymonaviridae, Botourmiaviridae and Virgaviridae and members of a recently discovered virus group tentatively named "ambiviruses" with ambisense bicistronic genomic organization. We demonstrated that Armillaria isolates can be cured of viruses by thermal treatment, which enables the examination of virus effects on host growth and phenotype using isogenic virus-infected and virus-free strains.