ICTV Virus Taxonomy Profile: Partitiviridae

Metagenomic analysis evidences a core virome in Anopheles darlingi from three contrasting Colombian ecoregions

Anopheles darlingi is a main malaria vector in the neotropical region, but its viral component is not well studied, especially in the neotropics. This work aimed to analyze the virome in Anopheles darlingi from malaria endemic regions of Colombia. Specimens were collected from the Bajo Cauca, Chocoan Pacific and northwestern Amazonas regions and analyzed using an RNA-Seq approach. Results revealed a variety of RNA viral sequences with homology to those of Insect-Specific Viruses belonging to Rhabdoviridae, Partitiviridae, Metaviridae, Tymoviridae, Phasmaviridae, Totiviridae, Ortervirales and Riboviria. Despite geographical and ecological differences among regions, the An. darlingi viral composition remains consistent in different areas, with a core group of viral operational taxonomic units-vOTUs shared by the populations. Furthermore, diversity analysis uncovered greater dissimilarities in viral sequence among mosquitoes from geographically distant regions, particularly evident between populations located at both sides of the Andes Mountain range. This study provides the first characterization of the metavirome in An. darlingi from Colombia and lays the foundation for future research on the complex interactions among viruses, hosts, and microbiota; it also opens a new line of investigation on the viruses in Anopheles populations of Colombia.

Integrating Sequence- and Structure-Based Similarity Metrics for the Demarcation of Multiple Viral Taxonomic Levels

Viruses exhibit significantly greater diversity than cellular organisms, posing a complex challenge to their taxonomic classification. While primary sequences may diverge considerably, protein functional domains can maintain conserved 3D structures throughout evolution. Consequently, structural homology of viral proteins can reveal deep taxonomic relationships, overcoming limitations inherent in sequence-based methods. In this work, we introduce MPACT (Multimetric Pairwise Comparison Tool), an integrated tool that utilizes both sequence- and structure-based metrics. The program incorporates five metrics: sequence identity, similarity, maximum likelihood distance, TM-score, and 3Di-character similarity. MPACT generates heatmaps and distance trees to visualize viral relationships across multiple levels, enabling users to substantiate viral taxa demarcation. Taxa delineation can be achieved by specifying appropriate score cutoffs for each metric, facilitating the definition of viral groups, and storing their corresponding sequence data. By analyzing diverse viral datasets spanning various levels of divergence, we demonstrate MPACT's capability to reveal viral relationships, even among distantly related taxa. This tool provides a comprehensive approach to assist viral classification, exceeding the current methods by integrating multiple metrics and uncovering deeper evolutionary connections.

Virome analysis of field-collected chilli samples reveals diverse viruses

BACKGROUND

Chilli (Capsicum annuum L.), an important spice crop, is susceptible to diverse viral infections. Traditional detection methods including PCR and its variants had difficulty in identifying the complete spectrum of viruses, especially in mixed infections. High-throughput sequencing (HTS) has emerged as a successful tool for comprehensive virome analyses, enabling the identification of the known and novel viruses in the infected samples. Using HTS, we investigated virome analyses to identify known and novel viruses in chilli.

METHODS

In 2021-22, 19 leaf samples were collected from chili plants in farmer fields in Karnataka, India, showing symptoms such as leaf curling, vein banding, mosaic, mottling, filiform, leathery, dull-colored, and bunchy leaves. Total RNA was extracted, pooled at equimolar concentrations, and subjected to virome profiling. rRNA-depleted RNA was used to prepare mRNA and sRNA libraries, which were sequenced on the Illumina NovaSeq 6000 platform. Bioinformatics tools were used to analyze the sequencing data and identify plant viruses.

RESULTS

Viral disease incidences varied from 26.6 to 47.5% in the farmer fields surveyed. Virome analyses revealed complete/ near-complete genomes of six different viruses: chilli leaf curl virus (ChiLCV), cucumber mosaic virus (CMV), groundnut bud necrosis orthotospovirus (GBNV), pepper cryptic virus-2 (PCV-2), pepper vein yellows virus (PeVYV) and bell pepper alphaendornavirus (BPEV). The viral copy number of ChiLCV was found to be the highest (45.36%) and had the least mutational frequency (SNPs) and was also associated with five satellites. Recombination breakpoints were observed in ChiLCV (coat protein and AC4 regions), CMV RNA2 (2a protein) and PeVYV (P0, P3 and P5 proteins), indicating their origins from intra- and interspecific recombination events. Identified viruses in the pooled RNA sample were confirmed by PCR. Further, novel loop-mediated isothermal amplification (LAMP) diagnostic assays were developed for diagnosing the identified viruses for future use. Among the six viruses identified in chilli, PeVYV and BPEV are the first reports from India.

CONCLUSIONS

This study presents the first virome profiling of chili using HTS and identified known and previously unreported viruses in farmer fields of Karnataka, India. Understanding viral diversity provides insights for developing diagnostic tools and effective management strategies.

Advancing RNA phage biology through meta-omics

Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as important models to understand the principal processes of life, including translation and the genetic code. While RNA phages were generally thought of as rare oddities in nature, meta-omics methods are rapidly changing this simplistic view by studying diverse biomes with unprecedented resolution. Metatranscriptomics dramatically expanded the number of known RNA phages from tens to tens of thousands, revealed their widespread abundance, and discovered several new families of potential RNA phages with largely unknown hosts, biology, and environmental impact. At the same time, (meta)genomic analyses of bacterial hosts are discovering an arsenal of defense systems bacteria employ to protect themselves from predation, whose functions in immunity against RNA phages we are only beginning to understand. Here, I review how meta-omics approaches are advancing the field of RNA phage biology with a focus on the discovery of new RNA phages and how bacteria might fight them.

A Hypovirulence-Associated Partitivirus and Re-Examination of Horizontal Gene Transfer Between Partitiviruses and Cellular Organisms

Previous research has unearthed the integration of the coat protein (CP) gene from alphapartitivirus into plant genomes. Nevertheless, the prevalence of this horizontal gene transfer (HGT) between partitiviruses and cellular organisms remains an enigma. In our investigation, we discovered a novel partitivirus, designated Sclerotinia sclerotiorum alphapartitivirus 1 (SsAPV1), from a hypovirulent strain of Sclerotinia sclerotiorum. Intriguingly, we traced homologs of the SsAPV1 CP to plant genomes, including Helianthus annuus. To delve deeper, we employed the CP and RNA-dependent RNA polymerase (RdRP) sequences of partitiviruses as "bait" to search the NCBI database for similar sequences. Our search unveiled a widespread occurrence of HGT between viruses from all five genera within the family Partitiviridae and other cellular organisms. Notably, numerous CP-like and RdRP-like genes were identified in the genomes of plants, protozoa, animals, fungi, and even, for the first time, in an archaeon. The majority of CP and RdRP genes were integrated into plant and insect genomes, respectively. Furthermore, we detected DNA fragments originating from the SsAPV1 RNA genome in some subcultures of virus-infected strains. It suggested that SsAPV1 RdRP may possesses reverse transcriptase activity, facilitating the integration of viral genes into cellular organism genomes, and this function requires further confirmation. Our study not only offers a hypovirulence-associated partitivirus with implications for fungal disease control but also sheds light on the extensive integration events between partitiviruses and cellular organisms and enhances our comprehension of the origins, evolution, and ecology of partitiviruses, as well as the genome evolution of cellular organisms.

Genomic characterization of a novel gammapartitivirus infecting the phytopathogenic fungus Colletotrichum cliviicola

In this study, we isolated a novel double-stranded RNA (dsRNA) mycovirus from the phytopathogenic fungus Colletotrichum cliviicola, designated as "Colletotrichum cliviicola partitivirus 1" (CcPV1). The complete genome of CcPV1 comprises two dsRNA fragments, referred to as dsRNA1 and dsRNA2, which are 1,756 bp and 1,485 bp in length, respectively. Each dsRNA segment contains an open reading frame (ORF), with the larger ORF1 in dsRNA 1 encoding the viral RNA-dependent RNA polymerase (RdRp) and the smaller ORF2 in dsRNA 2 encoding the capsid protein (CP). Sequence comparisons revealed that the RdRp of CcPV1 shares the highest amino acid sequence identity (76.35%) with the RdRp of Nigrospora sphaerica partitivirus 1 (NsPV1). Phylogenetic analysis based on both RdRp and CP sequences indicated that CcPV1 is a member of the genus Gammapartitivirus of the family Partitiviridae. This is the first report of a gammapartitivirus in C. cliviicola.

RNA editing of genomic neighbors controls antiviral response in fungi

Virus symptom expression involves complex interactions between viruses and their hosts, including antiviral defenses and counter-defenses, many of which are not well understood. This study utilizes Neurospora crassa as a model organism to investigate the role of RNA editing in the fungal antiviral response. We identify two adjacent genes in the genome: the A-to-I RNA-editing enzyme, OTT_1508-like deaminase (old), and its target, zinc fingers adjacent to old (zao). These genes regulate the transcriptional response to viral infection, with old modulating the expression of zao, which functions as a master transcription factor. This regulation contributes to asymptomatic infections by maintaining normal growth and development. However, in RNAi-deficient conditions, the overactivation of these genes leads to severe symptoms, akin to hypersensitive responses observed in plants. Additionally, homologs of zao-old are found as genomic neighbors in various filamentous ascomycetes, suggesting that this RNA-editing system may represent an evolutionarily conserved antiviral mechanism.

Diverse viral communities inhabit the guts of date palm rhinoceros beetles (Oryctes spp.)

Two species of palm tree pests, Oryctes elegans and Oryctes agamemnon (Coleoptera: Scarabaeidae), cause significant damage to date palm trees (Phoenix dactylifera) in many countries in the Middle East. Despite several decades of research and the implementation of numerous control strategies, including mechanical, chemical, regulatory, and biosecurity measures, managing these pests remains challenging. Control of O. rhinoceros in the Pacific using an entomopathogenic virus is a landmark of classical biological control. In this study, we used a transcriptomic approach to examine the virome of populations of two Oryctes species across various regions in southern Iran, with the hope of discovering natural viral pathogens as potential biocontrol agents. Total RNA was extracted from a pool of larval gut samples and sequenced using the Illumina NovaSeq 6000. After analysing the RNA-Seq data, 28 novel virus sequences, including a diverse range of RNA and DNA viruses, were identified. Phylogenetic analyses revealed that these newly discovered viruses are evolutionarily linked with other closely related members in several families, including Partitiviridae, Picobirnaviridae, Totiviridae, Dicistroviridae, Tombusviridae, Nodaviridae, Potyviridae, Endornaviridae, Circoviridae and some unassigned viruses such as Negevirus and Jivivirus. Given the similarity of some of these viruses to plant viruses, and viruses reported from fungi and protists and their unclear host association, we have tentatively named them "Oryctes-associated viruses." This study uncovers the great diversity of viruses in Oryctes species; however, further studies are necessary to determine their natural incidence, geographical distribution, impact on their hosts, and their potential as biological control agents for these significant date palm pests.

In-depth population genetic study of Vitis vinifera ssp. sylvestris from the Black Sea region and its virome

The spread of cultivated grapevine from primary centers of origin is inevitably accompanied by the range expansion of its pathogens, including viruses. A limited number of wild Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi populations have survived in the centers of grapevine domestication and can be used for comprehensive studies. We analyzed 50 grapevines collected in protected areas of the Black Sea region, which belong to the Caucasian domestication center. Based on genotyping of grapevines using simple sequence repeats as DNA markers, we determined the phylogenetic placement of V. vinifera ssp. sylvestris from the Black Sea region compared to cultivated and wild grapevines of the world. Using high-throughput sequencing of total RNA, we obtained the viromes of these grapevines. Ten viruses and one viroid were identified. The most common viruses detected were Vitis cryptic virus, grapevine rupestris stem pitting-associated virus, grapevine Pinot gris virus, and grapevine virus T. Among the economically significant viruses, we identified grapevine leafroll-associated virus 1 and grapevine virus A. A total of 91 complete or nearly complete virus genomes and one viroid genome were assembled, and phylogenetic analysis was performed. Two novel (+) ssRNA viruses were discovered, tentatively named Abrau grapevine-associated virus in the order Hepelivirales and Taurida grapevine-associated virus in the order Picornavirales. It is important to comprehensively consider the phylogeography of both viruses and their plant hosts. This is the first study that simultaneously addresses the population genetics of V. vinifera ssp. sylvestris from the Caucasian domestication center and its viruses.

Discovery of novel mycoviruses from fungi associated with mango leaf spots

Mango (Mangifera indica) is a commercially significant fruit crop cultivated globally. However, leaf spot diseases are common in mango orchards, which severely impact the yield. Mycoviruses hold promise as potential biocontrol agents. To investigate this possibility, fungi were isolated from mango leaf spot lesions, resulting in the identification of six strains that contained double-stranded RNA (dsRNA). Through BLASTx analysis of the NCBI non-redundant database, 27 mycovirus-related contigs were identified, which corresponded to 10 distinct viruses grouped into 8 lineages: Alternaviridae, Chrysoviridae, Partitiviridae, Polymycoviridae, Orthototiviridae, Deltaflexiviridae, Narnaviridae, and Bunyaviricetes. Full genomic sequences of these viruses were characterized and confirmed to be associated with their host fungi. The findings included six novel mycoviruses, three previously unreported viruses discovered in new hosts, and one virus strain. These results highlight the diversity and taxonomy of mycoviruses found in fungi associated with mango leaf spots.

Infection pattern of male-killing viruses alters phenotypes in the tea tortrix moth Homona magnanima

Male-killing is a microbe-induced reproductive manipulation in invertebrates whereby male hosts are eliminated during development. In the tea tortrix moth Homona magnanima, Osugoroshi viruses 1‒3 (OGVs), belonging to Partitiviridae induce male-killing. The infection patterns of OGVs are diverse; however, how the influence of these patterns of host phenotypes remains largely unknown. Using field-collected larvae, we established a OGV1 and OGV3 double-infection line, in addition to a triple-infection line, and examined the dsRNA segments, purified viral proteins, OGV density, and host phenotypes. PCR analysis demonstrated that the triple-infection line lost one dsRNA segment, whereas the double-infection line lost eight segments, including one RNA-dependent RNA polymerase (RdRp) gene. LC-MS analysis revealed three potential structural proteins in the OGVs. Males died at the larval stage in the triple-infection line and at the embryo-larval stage in the double-infection line of OGV1 and OGV3; the RNA load of female parents did not contribute to the developmental stage at which males died. These findings indicate that the pattern of viral infection, rather than viral RNA load transmitted from female parent, controls the stage of development at which male-killing occurs. Furthermore, the duration of the larval stage of the double-infection line was found to be significantly longer than that of the triple-infection line. The shorter duration of the larval stage of the triple-infection line could be advantageous over the double-infection line in maximizing transmission efficiency.

Novel viruses in the families Iflaviridae and Partitiviridae associated with the common eastern firefly Photinus pyralis

Fireflies are iconic insects that are under threat from environmental change. Knowledge of the viral diversity associated with natural firefly populations is important to our understanding of the basic biology of these insects and could be relevant to firefly conservation. We performed metatranscriptome sequencing of the Common Eastern Firefly ( Photinus pyralis) and assembled genomes for two new species of virus in the families Iflaviridae and Partitiviridae. We surveyed multiple individuals for these viruses using PCR, and we showed that both viruses are found at intermediate frequences in a natural population.

A comprehensive RNA virome identified in the oyster Magallana gigas reveals the intricate network of virus sharing between seawater and mollusks

BACKGROUND

As a globally farmed oyster species, Magallana gigas has garnered significant attention due to the contaminated RNA viruses that have caused illness in humans. However, limited knowledge is available on the bioaccumulation status and overall diversity of RNA virome in the M. gigas digestive tissues (DTs). Moreover, there is a lack of understanding regarding the shared community of RNA virome among intertidal mollusks. To address these knowledge gaps, we performed a comprehensive meta-transcriptomic analysis of 173 M. gigas samples from the East China Sea and compared the viral sequences to the meta-transcriptomes of other mollusks and seawater (i.e., the oyster Magallana hongkongensis, bivalves, gastropods, cephalopods, and Yangshan Harbor) through RdRP identification and reads mapping.

RESULTS

Our results indicate that 154 viral RdRPs were confidently identified in the M. gigas DT, with 94% (144/154) showing less than 90% amino acid identity. This indicates the presence of at least 144 putative novel RNA virus species in M. gigas DT. All viruses belonged to the phyla Lenarviricota, Pisuviricota, and Kitrinoviricota, and the marna-like viruses constituted the most diverse assemblage among these newly identified viruses. Furthermore, members of marna-like, picobirna-like, and noda-like virus groups comprise the most prevalent viruses in the M. gigas meta-transcriptome, with 14 RdRP-bearing sequences accounting for at least 1% of the overall aligned reads. M. hongkongensis has been found to harbor the most diverse viruses found in M. gigas, while 37 and 25 newly identified RNA viruses in oysters were discovered in an octopus meta-transcriptome and seawater virome, respectively.

CONCLUSIONS

The findings provide insights into the cryptic and hitherto unstudied virus-sharing network across the marine food web. Moreover, the viruses identified in oysters have the potential to serve as indicators for identifying the circulation of marine RNA viruses. Video Abstract.

An isolate of human blood-associated partitivirus naturally infects the phytopathogenic fungus Bipolaris maydis

Human blood-associated partitivirus (HuBPV) was first identified through metagenomic analysis of serum samples from two Peruvians, but its natural host remains unknown. Here, we report the detection of an HuBPV strain (HuBPV-Bm) in the phytopathogenic fungus Bipolaris maydis strain HN11 in Hubei Province, China. The dsRNA1 and dsRNA2 of HuBPV-Bm show more than 97.6% and 98.8% nucleotide sequence identity, respectively, to those from the metagenomically discovered HuBPV strain (HuBPV-M). Notably, HuBPV-Bm contains a third dsRNA segment that was not reported for HuBPV-M. All mycelia derived from individual asexual spores of HN11 tested positive for HuBPV-Bm, as did nine out of 293 B. maydis strains collected across Hubei.

Characterization and complete genome sequence of a novel zetapatitivirus from Penicillium exsudans isolate RCEF7900

Penicillium exsudans strain RCEF7900, obtained from leaf litter, was found to harbor two double-stranded RNA (dsRNA) elements, designated as dsRNA1 and dsRNA2, with lengths of 1,816 bp and 1,625 bp, respectively. dsRNA1 encodes a 572-amino-acid RNA-dependent RNA polymerase (RdRp) protein (65.29 kDa), while dsRNA2 encodes a 503-amino-acid coat protein (CP) (56.73 kDa). A BLASTp search indicated that dsRNA1 and dsRNA 2 together constitute the genome of a novel partitivirus, which we have named "Penicillium exsudans partitivirus 1" (PePV1). Phylogenetic analysis based on RdRp amino acid sequences revealed that these genome segments belong to a member of a new species within the proposed genus "Zetapatitivirus" of the family Partitiviridae, with the RdRp showing the most sequence similarity (79.72% identity) to that of Sonifin virus. This is the first report of a zetapatitivirus from P. exsudans, expanding our understanding of mycoviral diversity in this fungal species.

Complete genome sequence of Valeriana jatamansi cryptic virus 1: a novel member of the genus Alphapartitivirus infecting Valeriana jatamansi Jones

A new double-stranded RNA (dsRNA) virus, tentatively named "Valeriana jatamansi cryptic virus 1" (VJCV1, GenBank accession nos. PP482519 and PP482520), was isolated from diseased Valeriana jatamansi Jones plants exhibiting vein-banding in Yunnan. Its complete genome sequence was determined using metatranscriptomic and Sanger sequencing. The genome of VJCV1 consists of two dsRNA of different size, namely dsRNA1 (2,026 bp) and dsRNA2 (1,754 bp), which are predicted to encode an RNA-dependent RNA polymerase (RdRp, 616 aa) with molecular weight of 72.6 kDa and coat protein (CP, 491 aa) with molecular weight of 55.8 kDa, respectively. The non-coding region of dsRNA in VJCV1 is predicted to have a stem-loop structure and a poly(A) tail that are unique to the members of the genus Alphapartitivirus. Multiple sequence alignments showed that the RdRp and CP of VJCV1 shared the highest amino acid sequence identity (86.2% and 56.1%, respectively) with red clover cryptic virus 1 (RCCV1). These values are below the threshold for creating new species within the genus Alphapartitivirus. Phylogenetic analysis based on RdRp and CP sequences showed that VJCV1 clustered independently from members of the genus Alphapartitivirus, with RCCV1 being the closest relative. It is therefore suggested that VJCV1 should be considered a member of a new species of the genus Alphapartitivirus in the family Partitiviridae. This is the first report of a member of the genus Alphapartitivirus infecting a plant of the genus Valeriana.

Metatranscriptomic analysis reveals the diversity of RNA viruses in ticks in Inner Mongolia, China

BACKGROUND

Ticks are widely distributed throughout China and are the second most prevalent pathogen vectors in the world, following only mosquitoes. Tick bites can lead to Lyme disease, forest encephalitis, and other illnesses that may result in death under severe circumstances. Materials and methods: Ticks collected from March 2021 to May 2023 were pooled and used in metatranscriptomic analyses to gain insight into the diversity and distribution of tick-borne viruses in Inner Mongolia. Next-generation sequencing (NGS) outcomes were validated, and viral prevalence across distinct tick species was determined through the application of polymerase chain reaction (PCR) paired with Sanger sequencing.

RESULTS

A total of 20 RNA viruses belonging to at least 8 families, including Chuviridae, Flaviviridae, Solemoviridae, Nairoviridae, Partitiviridae, Phenuiviridae, Rhabdoviridae, and Totiviridae, and to unclassified families were identified by NGS. Five of the identified RNA viruses (Nuomin virus, Yezo virus, tick-borne encephalitis virus, Alongshan virus, and Beiji nairovirus) are considered human pathogens. A potential human pathogen, Mukawa virus, was also among the identified viruses. Ixodes persulcatus carried a significantly greater number of viral species than did Dermacentor nuttalli, Hyalomma marginatum, and Haemaphysalis concinna. The prevalence of coinfection with multiple viruses differed in I. persulcatus from Hinggan League and Hulun Buir, and Beiji nairovirus was the codominant virus species.

CONCLUSIONS

There is a remarkable diversity of RNA viruses harboured by ticks in Inner Mongolia, with variations observed in the distribution of these tick-borne viruses across different regions and tick hosts.

Mycoviruses from Aspergillus fungi involved in fermentation of dried bonito

Fungi are exploited for fermentation of foods such as cheese, Japanese sake, and soy sauce. However, the diversity of viruses that infect fungi involved in food fermentation is poorly understood. Fermented dried bonito ("katsuobushi") is one of the most important processed marine products in Japan. Fungi involved in katsuobushi fermentation are called katsuobushi molds, and Aspergillus spp. have been reported to be dominant on the surface of katsuobushi during fermentation. Because various mycoviruses have been found in members of the genus Aspergillus, we hypothesized that katsuobushi molds are also infected with mycoviruses. Here, we describe seven novel mycoviruses belonging to six families (Chrysoviridae, Fusariviridae, Mitoviridae, Partitiviridae, Polymycoviridae, and Pseudototiviridae) from isolated katsuobushi molds (Aspergillus chevalieri and A. sulphureus) detected by fragmented and primer-ligated double-stranded RNA sequencing. Aspergillus chevalieri fusarivirus 1 has a unique bi-segmented genome, whereas other known fusariviruses have a single genomic segment. Phenotypic comparison between the parental A. chevalieri strain infected with Aspergillus chevalieri polymycovirus 1 (AchPmV1) and isogenic AchPmV1-free isolates indicated that AchPmV1 inhibits the early growth of the host. This study reveals the diversity of mycoviruses that infect katsuobushi molds, and provides insight into the effect of mycoviruses on fungi involved in fermentation.

Dothistroma septosporum and Dothistroma pini, the causal agents of Dothistroma needle blight, are infected by multiple viruses

Dothistroma septosporum and Dothistroma pini are severe foliar pathogens of conifers. They infect a broad spectrum of hosts (mainly Pinus spp.), causing chlorosis, defoliation of needles, and eventually the death of pine trees in extreme cases. Mycoviruses represent a novel and innovative avenue for controlling pathogens. To search for possible viruses hosted by Dothistroma spp. we screened a subset of isolates (20 strains of D. septosporum and one D. pini) originating from the Czech Republic, Slovenia, Italy, Austria and Ireland for viral dsRNA segments. Only five of them showed the presence of dsRNA segments. A total of 21 fungal isolates were prepared for total RNA extractions. RNA samples were pooled, and two separate RNA libraries were constructed for stranded total RNA sequencing. RNA-Seq data processing, pairwise sequence comparisons (PASC) and phylogenetic analyses revealed the presence of thirteen novel putative viruses with varying genome types: seven negative-sense single-stranded RNA viruses, including six bunya-like viruses and one new member of the order Mononegavirales; three positive-sense single-stranded RNA viruses, two of which are similar to those of the family Narnaviridae, while the genome of the third correspond to those of the family Gammaflexiviridae; and three double-stranded RNA viruses, comprising two novel members of the family Chrysoviridae and a potentially new species of gammapartitivirus. The results were confirmed with RT-PCR screening that the fungal pathogens hosted all the viruses and showed that particular fungal strains harbour multiple virus infections and that they are transmitted vertically. In this study, we described the narnavirus infecting D. pini. To our knowledge, this is the first virus discovered in D. pini.

Detection and discovery of plant viruses in Disporopsis through high-throughput sequencing

Background

Disporopsis, a member of the Liliaceae family and a perennial herb, is predominantly cultivated in southwestern and southeastern China. Its rhizome, referred to as Zhugenqi, serves as a traditional Chinese medicinal herb for the treatment of bone injuries. However, viral diseases have emerged as a significant challenge in the cultivation of Disporopsis.

Objective

The aim of this study was to identify and characterize viruses present in diseased samples of Disporopsis spp. using high-throughput sequencing (HTS) and reverse transcription-polymerase chain reaction (RT-PCR) to enhance the understanding of the virome associated with Disporopsis and to inform diagnostic and control strategies for viral diseases in this plant.

Methods

Diseased samples of Disporopsis spp. were subjected to HTS and RT-PCR for virus identification. A total of five viruses were detected, including three novel viruses and two known viruses. The novel viruses were provisionally named Disporopsis chlorotic stripe virus (DCSV), Disporopsis pernyi-associated partitivirus (DaPTV), and Disporopsis pernyi-associated lispi-like virus (DaLV). Sequence identity and phylogenetic analyses were performed to confirm the novelty and taxonomic placement of these viruses.

Results

DCSV exhibited polyprotein sequence identities ranging from 47.6% to 83.6% with other potyviruses, with the highest identity (83.6%) shared with Polygonatum kingianum virus 5 (PKgV5). DaLV shared an amino acid sequence identity of 34.59% with maize suscal virus (MSV), and DaPTV shared an identity of 76.18-85.10% with Paris alphapartitivirus (ParAPV). Phylogenetic analyses supported the potential classification of the three novel viruses as new members of their respective genera. Two isolates of polygonatum mosaic-associated virus 1 (PMaV1) were identified in Disporopsis for the first time, showing divergences of 96.33% and 98.86% from existing isolates. RT-PCR analysis of 67 Disporopsis field samples collected from four cities in China revealed that more than half of the samples tested positive for at least one of the five viruses. PMaV1 and DaLV were the most prevalent, detected in 22 and 34 out of the 67 samples, respectively. Other viruses were detected at low rates and/or had limited distribution.

Conclusion

This study provides insights into the virome infecting Disporopsis and offers valuable information for the diagnosis and control of viral diseases in this plant. The identification of five viruses, including three potential new members of their respective genera, contributes to the understanding of the viral threats to Disporopsis cultivation.

Molecular characterization of a novel partitivirus with four segments isolated from Fusarium solani, the causal agent of citrus root rot

We report here the identification of a dsRNA virus, obtained from Fusarium solani strain Newher-7, tentatively named F. solani partitivirus 3 (FsPV3). It consists of four dsRNA segments (dsRNA1-4) with lengths of 1961, 1900, 1830 and 1830 bp, respectively. Sequence analysis showed that dsRNA1 encodes an RNA-dependent RNA polymerase (RdRp), dsRNA2 encodes a capsid protein (CP), dsRNA3 encodes a hypothetical protein of unknown function and dsRNA4 encodes two hypothetical proteins of unknown function. Amino acid sequence comparisons showed that the RdRp of FsPV3 is most similar to that of Hulunbuir Parti tick virus 1. In contrast, the CP of FsPV3, as well as the hypothetical protein encoded by ORF3 of dsRNA3, was most similar to cognate proteins encoded by Colletotrichum-associated partitivirus 2. However, the two hypothetical proteins encoded by dsRNA4 showed no significant similarity to the available sequences in the National Center for Biotechnology Information database and encoded no apparent conserved domains. Phylogenetic analysis of the RdRp and CP showed that FsPV3 clustered together with other species in the genus Alphapartitivirus. Given that proteins encoded by FsPV3 are not sufficiently highly homologous to a single known virus and that it encodes two novel proteins, we suggest that FsPV3 should be regarded as a new member of the genus Alphapartitivirus in the family Partitiviridae. This is the first report of FsPV3 infecting F. solani.

Disclosing the virome of Aedes, Anopheles and Culex female mosquitoes, Alto Pantanal of Mato Grosso, Brazil, 2019

Using Illumina NextSeq sequencing and bioinformatics, we identified and characterized thirty-three viral sequences of unsegmented and multipartite viral families in Aedes spp., Culex sp. and Anopheles darlingi female mosquito pools from Porto São Luiz and Pirizal, Alto Pantanal. Seventeen sequences belong to unsegmented viral families, twelve represent putative novel insect-specific viruses (ISVs) within families Chuviridae (3/33; partial genomes) and coding-complete sequences of Xinmoviridae (1/33), Rhabdoviridae (2/33) and Metaviridae (6/33); and five coding-complete sequences of already-known ISVs. Notably, two putative novel rhabdoviruses, Corixo rhabdovirus 1 and 2, were phylogenetically related to Coxipo dielmovirus, but separated from other Alpharhabdovirinae genera, sharing Anopheles spp. as host. Regarding multipartite families, sixteen segments of different putative novel viruses were identified (13 coding-complete segments) within Durnavirales (4/33), Elliovirales (1/33), Hareavirales (3/33) and Reovirales (8/33) orders. Overall, this study describes twenty-eight (28/33) putative novel ISVs and five (5/33) already described viruses using metagenomics approach.

Molecular characterization of a novel gammapartitivirus infecting the fungus Nigrospora oryzae

Here, we identified a new mycovirus infecting the phytopathogenic fungus Nigrospora oryzae, which we have designated "Nigrospora oryzae partitivirus 2" (NoPV2). The genome of NoPV2 consists of two dsRNA segments (dsRNA 1 and dsRNA 2), measuring 1771 and 1440 bp in length, respectively. dsRNA 1 and dsRNA 2 each contain a single open reading frame (ORF) that encodes the RNA-dependent RNA polymerase (RdRp) and capsid protein (CP), respectively. A BLASTp search showed that the RdRp of NoPV2 had significant sequence similarity to the RdRps of other partitiviruses, including Nigrospora sphaerica partitivirus 1 (75.61% identity) and Magnaporthe oryzae partitivirus 1 (67.53% identity). Phylogenetic analysis revealed that NoPV2 is a new member of the genus Gammapartitivirus in the family Partitiviridae. This study provides important information for understanding the diversity of mycoviruses in N. oryzae.

The Expanding Mycovirome of Aspergilli

Mycoviruses are viruses that infect fungi and are widespread across all major fungal taxa, exhibiting great biological diversity. Since their discovery in the 1960s, researchers have observed a myriad of fungal phenotypes altered due to mycoviral infection. In this review, we examine the nuanced world of mycoviruses in the context of the medically and agriculturally important fungal genus, Aspergillus. The advent of RNA sequencing has revealed a previous underestimate of viral prevalence in fungi, in particular linear single-stranded RNA viruses, and here we outline the diverse viral families known to date that contain mycoviruses infecting Aspergillus. Furthermore, we describe these novel mycoviruses, highlighting those with peculiar genome structures, such as a split RNA dependent RNA polymerase gene. Next, we delineate notable mycovirus-mediated phenotypes in Aspergillus, in particular reporting on observations of mycoviruses that affect their fungal host's virulence and explore how this may relate to virus-mediated decreased stress tolerance. Furthermore, mycovirus effects on microbial competition and antifungal resistance are discussed. The factors that influence the manifestation of these phenotypes, such as temperature, fungal life stage, and infection with multiple viruses, among others, are also evaluated. In addition, we attempt to elucidate the molecular mechanisms that underpin these phenotypes, examining how mycoviruses can be targets, triggers, and even suppressors of RNA silencing and how this can affect fungal gene expression and phenotypes. Finally, we highlight the potential therapeutic applications of mycoviruses and how, in an approach analogous to bacteriophage therapy, their ability to produce hypovirulence in Aspergillus might be used to attenuate invasive aspergillosis infections in humans.

Nucleotide and dinucleotide preference of segmented viruses are shaped more by segment: In case study of tomato spotted wilt virus

Several studies have showed that the nucleotide and dinucleotide composition of viruses possibly follows their host species or protein coding region. Nevertheless, the influence of viral segment on viral nucleotide and dinucleotide composition is still unknown. Here, we explored through tomato spotted wilt virus (TSWV), a segmented virus that seriously threatens the production of tomatoes all over the world. Through nucleotide composition analysis, we found the same over-representation of A across all viral segments at the first and second codon position, but it exhibited distinct in segments at the third codon position. Interestingly, the protein coding regions which encoded by the same or different segments exhibit obvious distinct nucleotide preference. Then, we found that the dinucleotides UpG and CpU were overrepresented and the dinucleotides UpA, CpG and GpU were underrepresented, not only in the complete genomic sequences, but also in different segments, protein coding regions and host species. Notably, 100% of the data investigated here were predicted to the correct viral segment and protein coding region, despite the fact that only 67% of the data analyzed here were predicted to the correct viral host species. In conclusion, in case study of TSWV, nucleotide composition and dinucleotide preference of segment viruses are more strongly dependent on segment and protein coding region than on host species. This research provides a novel perspective on the molecular evolutionary mechanisms of TSWV and provides reference for future research on genetic diversity of segmented viruses.

The Virome of Cocoa Fermentation-Associated Microorganisms

Theobroma cacao plantations are of significant economic importance worldwide, primarily for chocolate production. During the harvest and processing of cocoa beans, they are subjected to fermentation either by microorganisms present in the environment (spontaneous fermentation) or the addition of starter cultures, with different strains directly contributing distinct flavor and color characteristics to the beans. In addition to fungi and bacteria, viruses are ubiquitous and can affect the quality of the fermentation process by infecting fermenting organisms, destabilizing microbial diversity, and consequently affecting fermentation quality. Therefore, in this study, we explored publicly available metatranscriptomic libraries of cocoa bean fermentation in Limon Province, Costa Rica, looking for viruses associated with fermenting microorganisms. Libraries were derived from the same sample at different time points: 7, 20, and 68 h of fermentation, corresponding to yeast- and lactic acid bacteria-driven phases. Using a comprehensive pipeline, we identified 68 viral sequences that could be assigned to 62 new viral species and 6 known viruses distributed among at least nine families, with particular abundance of elements from the Lenarviricota phylum. Interestingly, 44 of these sequences were specifically associated with ssRNA phages (Fiersviridae) and mostly fungi-infecting viral families (Botourmiaviridae, Narnaviridae, and Mitoviridae). Of note, viruses from those families show a complex evolutionary relationship, transitioning from infecting bacteria to infecting fungi. We also identified 10 and 3 viruses classified within the Totiviridae and Nodaviridae families, respectively. The quantification of the virus-derived RNAs shows a general pattern of decline, similar to the dynamic profile of some microorganism genera during the fermentation process. Unexpectedly, we identified narnavirus-related elements that showed similarity to segmented viral species. By exploring the molecular characteristics of these viral sequences and applying Hidden Markov Models, we were capable of associating these additional segments with a specific taxon. In summary, our study elucidates the complex virome associated with the microbial consortia engaged in cocoa bean fermentation that could contribute to organism/strain selection, altering metabolite production and, consequently, affecting the sensory characteristics of cocoa beans.

Discovery of Novel Viruses in Culicoides Biting Midges in Chihuahua, Mexico

Biting midges (Culicoides) are vectors of many pathogens of medical and veterinary importance, but their viromes are poorly characterized compared to certain other hematophagous arthropods, e.g., mosquitoes and ticks. The goal of this study was to use metagenomics to identify viruses in Culicoides from Mexico. A total of 457 adult midges were collected in Chihuahua, northern Mexico, in 2020 and 2021, and all were identified as female Culicoides reevesi. The midges were sorted into five pools and homogenized. An aliquot of each homogenate was subjected to polyethylene glycol precipitation to enrich for virions, then total RNA was extracted and analyzed by unbiased high-throughput sequencing. We identified six novel viruses that are characteristic of viruses from five families (Nodaviridae, Partitiviridae, Solemoviridae, Tombusviridae, and Totiviridae) and one novel virus that is too divergent from all classified viruses to be assigned to an established family. The newly discovered viruses are phylogenetically distinct from their closest known relatives, and their minimal infection rates in female C. reevesi range from 0.22 to 1.09. No previously known viruses were detected, presumably because viral metagenomics had never before been used to study Culicoides from the Western Hemisphere. To conclude, we discovered multiple novel viruses in C. reevesi from Mexico, expanding our knowledge of arthropod viral diversity and evolution.

Metatranscriptomic Sequencing of Sheath Blight-Associated Isolates of Rhizoctonia solani Revealed Multi-Infection by Diverse Groups of RNA Viruses

Rice sheath blight, caused by the soil-borne fungus Rhizoctonia solani (teleomorph: Thanatephorus cucumeris, Basidiomycota), is one of the most devastating phytopathogenic fungal diseases and causes yield loss. Here, we report on a very high prevalence (100%) of potential virus-associated double-stranded RNA (dsRNA) elements for a collection of 39 fungal strains of R. solani from the rice sheath blight samples from at least four major rice-growing areas in the Philippines and a reference isolate from the International Rice Research Institute, showing different colony phenotypes. Their dsRNA profiles suggested the presence of multiple viral infections among these Philippine R. solani populations. Using next-generation sequencing, the viral sequences of the three representative R. solani strains (Ilo-Rs-6, Tar-Rs-3, and Tar-Rs-5) from different rice-growing areas revealed the presence of at least 36 viruses or virus-like agents, with the Tar-Rs-3 strain harboring the largest number of viruses (at least 20 in total). These mycoviruses or their candidates are believed to have single-stranded RNA or dsRNA genomes and they belong to or are associated with the orders Martellivirales, Hepelivirales, Durnavirales, Cryppavirales, Ourlivirales, and Ghabrivirales based on their coding-complete RNA-dependent RNA polymerase sequences. The complete genome sequences of two novel RNA viruses belonging to the proposed family Phlegiviridae and family Mitoviridae were determined.

A novel betapartitivirus isolated from Cordyceps militaris, an edible-medicinal mushroom

In this study, we identified a novel partitivirus, named "Cordyceps militaris partitivirus 1" (CmPV1), in Cordyceps militaris strain RCEF7506. The complete genome of CmPV1 comprises two segments, dsRNA1 and dsRNA2, each encoding a single protein. dsRNA1 (2,206 bp) encodes an RNA-dependent RNA polymerase (RdRp), and dsRNA2 (2,256 bp) encodes a coat protein (CP). Sequence analysis revealed that dsRNA1 has the highest similarity to that of Bipolaris maydis partitivirus 2 (BmPV2), whereas dsRNA2 shows the highest similarity to human blood-associated partitivirus (HuBPV). Phylogenetic analysis based on RdRp sequences suggests that CmPV1 is a new member of the genus Betapartitivirus of the family Partitiviridae. This is the first documentation of a betapartitivirus infecting the entomopathogenic fungus C. militaris.

Known and novel viruses in Belgian honey bees: yearly differences, spatial clustering, and associations with overwintering loss

In recent years, managed honey bee colonies have been suffering from an increasing number of biotic and abiotic stressors, resulting in numerous losses of colonies worldwide. A pan-European study, EPILOBEE, estimated the colony loss in Belgium to be 32.4% in 2012 and 14.8% in 2013. In the current study, absolute viral loads of four known honey bee viruses (DWV-A, DWV-B, AmFV, and BMLV) and three novel putative honey bee viruses (Apis orthomyxovirus 1, apthili virus, and apparli virus) were determined in 300 Flemish honey bee samples, and associations with winter survival were determined. This revealed that, in addition to the known influence of DWV-A and DWV-B on colony health, one of the newly described viruses (apthili virus) shows a strong yearly difference and is also associated with winter survival. Furthermore, all scrutinized viruses revealed significant spatial clustering patterns, implying that despite the limited surface area of Flanders, local virus transmission is paramount. The vast majority of samples were positive for at least one of the seven investigated viruses, and up to 20% of samples were positive for at least one of the three novel viruses. One of those three, Apis orthomyxovirus 1, was shown to be a genuine honey bee-infecting virus, able to infect all developmental stages of the honey bee, as well as the Varroa destructor mite. These results shed light on the most prevalent viruses in Belgium and their roles in the winter survival of honey bee colonies.

IMPORTANCE

The western honey bee (Apis mellifera) is a highly effective pollinator of flowering plants, including many crops, which gives honey bees an outstanding importance both ecologically and economically. Alarmingly high annual loss rates of managed honey bee colonies are a growing concern for beekeepers and scientists and have prompted a significant research effort toward bee health. Several detrimental factors have been identified, such as varroa mite infestation and disease from various bacterial and viral agents, but annual differences are often not elucidated. In this study, we utilize the viral metagenomic survey of the EPILOBEE project, a European research program for bee health, to elaborate on the most abundant bee viruses of Flanders. We complement the existing metagenomic data with absolute viral loads and their spatial and temporal distributions. Furthermore, we identify Apis orthomyxovirus 1 as a potentially emerging pathogen, as we find evidence for its active replication honey bees.

Transfection of entomopathogenic Metarhizium species with a mycovirus confers hypervirulence against two lepidopteran pests

Although most known viruses infecting fungi pathogenic to higher eukaryotes are asymptomatic or reduce the virulence of their host fungi, those that confer hypervirulence to entomopathogenic fungus still need to be explored. Here, we identified and studied a novel mycovirus in Metarhizium flavoviride, isolated from small brown planthopper (Laodelphax striatellus). Based on molecular analysis, we tentatively designated the mycovirus as Metarhizium flavoviride partitivirus 1 (MfPV1), a species in genus Gammapartitivirus, family Partitiviridae. MfPV1 has two double-stranded RNAs as its genome, 1,775 and 1,575 bp in size respectively, encapsidated in isometric particles. When we transfected commercial strains of Metarhizium anisopliae and Metarhizium pingshaense with MfPV1, conidiation was significantly enhanced (t test; P-value < 0. 01), and the significantly higher mortality rates of the larvae of diamondback moth (Plutella xylostella) and fall armyworm (Spodoptera frugiperda), two important lepidopteran pests were found in virus-transfected strains (ANOVA; P-value < 0.05). Transcriptomic analysis showed that transcript levels of pathogenesis-related genes in MfPV1-infected M. anisopliae were obviously altered, suggesting increased production of metarhizium adhesin-like protein, hydrolyzed protein, and destruxin synthetase. Further studies are required to elucidate the mechanism whereby MfPV1 enhances the expression of pathogenesis-related genes and virulence of Metarhizium to lepidopteran pests. This study presents experimental evidence that the transfection of other entomopathogenic fungal species with a mycovirus can confer significant hypervirulence and provides a good example that mycoviruses could be used as a synergistic agent to enhance the biocontrol activity of entomopathogenic fungi.

Replication of single viruses across the kingdoms, Fungi, Plantae, and Animalia

It is extremely rare that a single virus crosses host barriers across multiple kingdoms. Based on phylogenetic and paleovirological analyses, it has previously been hypothesized that single members of the family Partitiviridae could cross multiple kingdoms. Partitiviridae accommodates members characterized by their simple bisegmented double-stranded RNA genome; asymptomatic infections of host organisms; the absence of an extracellular route for entry in nature; and collectively broad host range. Herein, we show the replicability of single fungal partitiviruses in three kingdoms of host organisms: Fungi, Plantae, and Animalia. Betapartitiviruses of the phytopathogenic fungusRosellinia necatrix could replicate in protoplasts of the carrot (Daucus carota), Nicotiana benthamiana and Nicotiana tabacum, in some cases reaching a level detectable by agarose gel electrophoresis. Moreover, betapartitiviruses showed more robust replication than the tested alphapartitiviruses. One of the fungal betapartitiviruses, RnPV18, could persistently and stably infect carrot plants regenerated from virion-transfected protoplasts. Both alpha- and betapartitiviruses, although with different host preference, could replicate in two insect cell lines derived from the fall armyworm Spodoptera frugiperda and the fruit fly Drosophila melanogaster. Our results indicate the replicability of single partitiviruses in members of three kingdoms and provide insights into virus adaptation, host jumping, and evolution.

A Novel Cryptic Virus Isolated from Galphimia spp. in Mexico

Galphimia spp. is a plant employed in traditional medicine in Mexico because of its anxiolytic and sedative effects. Viruses have been associated with different alterations in plants, although asymptomatic agents (i.e., cryptic viruses) are also known. High-throughput sequencing (HTS) allows for the detection of pathogenic and non-pathogenic viral agents in plants, including potential novel viruses. The aim of this study was to investigate the presence of viral agents in two populations of Galphimia spp. by HTS. Sequencing was conducted on an Illumina NextSeq 550 platform, and a putative novel virus was identified. Two contigs showed homology to partitiviruses, and these encoded the RNA-dependent RNA polymerase and coat protein. These proteins showed the highest identities with orthologs in the recently discovered Vitis cryptic virus. A phylogenetic analysis of both RNAs showed that the new virus clusters into the monophyletic genus Deltapartitivirus along with other plant-infecting viruses. The result of the HTS analysis was validated by conventional RT-PCR and Sanger sequencing. A novel virus was discovered in a symptomless Galphimia spp. plant and tentatively named the Galphimia cryptic virus (GCV). This is the first virus discovered in medicinal plants in Mexico.

Discovery of novel RNA viruses through analysis of fungi-associated next-generation sequencing data

BACKGROUND

Like all other species, fungi are susceptible to infection by viruses. The diversity of fungal viruses has been rapidly expanding in recent years due to the availability of advanced sequencing technologies. However, compared to other virome studies, the research on fungi-associated viruses remains limited.

RESULTS

In this study, we downloaded and analyzed over 200 public datasets from approximately 40 different Bioprojects to explore potential fungal-associated viral dark matter. A total of 12 novel viral sequences were identified, all of which are RNA viruses, with lengths ranging from 1,769 to 9,516 nucleotides. The amino acid sequence identity of all these viruses with any known virus is below 70%. Through phylogenetic analysis, these RNA viruses were classified into different orders or families, such as Mitoviridae, Benyviridae, Botourmiaviridae, Deltaflexiviridae, Mymonaviridae, Bunyavirales, and Partitiviridae. It is possible that these sequences represent new taxa at the level of family, genus, or species. Furthermore, a co-evolution analysis indicated that the evolutionary history of these viruses within their groups is largely driven by cross-species transmission events.

CONCLUSIONS

These findings are of significant importance for understanding the diversity, evolution, and relationships between genome structure and function of fungal viruses. However, further investigation is needed to study their interactions.

Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts

The RNA virus family Picobirnaviridae has traditionally been associated with the gastrointestinal systems of terrestrial mammals and birds, with the majority of viruses detected in animal stool samples. Metatranscriptomic studies of vertebrates, invertebrates, microbial communities, and environmental samples have resulted in an enormous expansion of the genomic and phylogenetic diversity of this family. Yet picobirnaviruses remain poorly classified, with only one genus and three species formally ratified by the International Committee of Virus Taxonomy. Additionally, an inability to culture picobirnaviruses in a laboratory setting or isolate them in animal tissue samples, combined with the presence of bacterial genetic motifs in their genomes, suggests that these viruses may represent RNA bacteriophage rather than being associated with animal infection. Utilising a data set of 2,286 picobirnaviruses sourced from mammals, birds, reptiles, fish, invertebrates, microbial communities, and environmental samples, we identified seven consistent phylogenetic clusters likely representing Picobirnavirus genera that we tentatively name 'Alpha-', 'Beta-', 'Gamma-', 'Delta-', 'Epsilon-', 'Zeta-', and 'Etapicobirnavirus'. A statistical analysis of topological congruence between virus-host phylogenies revealed more frequent cross-species transmission than any other RNA virus family. In addition, bacterial ribosomal binding site motifs were more enriched in Picobirnavirus genomes than in the two groups of established RNA bacteriophage-the Leviviricetes and Cystoviridae. Overall, our findings support the hypothesis that the Picobirnaviridae have bacterial hosts and provide a lower-level taxonomic classification for this highly diverse and ubiquitous family of RNA viruses.

Characterization of a novel gammapartitivirus infecting the phytopathogenic fungus Pyricularia oryzae

In this study, we identified a novel double-strand RNA (dsRNA) mycovirus in Pyricularia oryzae, designated "Magnaporthe oryzae partitivirus 4" (MoPV4). The genome of MoPV4 consists of a dsRNA-1 segment encoding an RNA-dependent RNA polymerase (RdRP) and a dsRNA-2 segment encoding a capsid protein (CP). Phylogenetic analysis indicated that MoPV4 belongs to the genus Gammapartitivirus within family Partitiviridae. The particles of MoPV4 are isometric with a diameter of about 32.4 nm. Three-dimensional structure predictions indicated that the RdRP of MoPV4 forms a classical right-handed conformation, while the CP has a reclining-V shape.

Metagenomic sequencing reveals viral diversity of mosquitoes from Shandong Province, China

Mosquitoes carry a large number of known and unknown viruses, some of which could cause serious diseases in humans or animals. Metagenomic sequencing for mosquito viromes is crucial for understanding the evolutionary history of viruses and preventing emerging mosquito-borne diseases. We collected 1,598 mosquitoes belonging to four species from five counties in Shandong Province, China in 2021. They were grouped by species and sampling locations and subjected to metagenomic next-generation sequencing for the analysis of the viromes. A total of 233,317,352 sequencing reads were classified into 30 viral families and an unclassified group. Comparative analysis showed that mosquitoes in Shandong Province generally possessed host-specific virome. We detected mosquito-borne viruses including Japanese encephalitis virus, Getah virus, and Kadipiro virus in Culex tritaeniorhynchus and Anopheles sinensis samples. Phylogenetic analysis showed that these pathogenic viruses may have existed in mosquitoes in Shandong Province for a long time. Meanwhile, we identified 22 novel viruses belonging to seven families and the genus Negevirus. Our study comprehensively described the viromes of several common mosquito species in Shandong Province, China, and demonstrated the major role of host species in shaping mosquito viromes. Furthermore, the metagenomic data provided valuable epidemiological information on multiple mosquito-borne viruses, highlighting the potential risk of infection transmission.

IMPORTANCE

Mosquitoes are known as the source of various pathogens for humans and animals. Culex tritaeniorhynchus, Armigeres subalbatus, and Anopheles sinensis have been found to transmit the Getah virus, which has recently caused increasing infections in China. Cx. tritaeniorhynchus and Culex pipiens are the main vectors of Japanese encephalitis virus and have caused epidemics of Japanese encephalitis in China in past decades. These mosquitoes are widely present in Shandong Province, China, leading to a great threat to public health and the breeding industry. This study provided a comprehensive insight into the viromes of several common mosquito species in Shandong Province, China. The metagenomic sequencing data revealed the risks of multiple pathogenic mosquito-borne viruses, including Japanese encephalitis virus, Getah virus, and Kadipiro virus, which are of great importance for preventing emerging viral epidemics.

Transcriptome Analysis Reveals a Diverse Range of Novel Viruses in Australian Sugarcane Soldier Fly (Inopus flavus) Larvae

In Australia, Soldier flies (Inopus spp.) are economically significant pests of sugarcane that currently lack a viable management strategy. Despite various research efforts, the mechanisms underlying the damage caused by soldier fly larvae remain poorly understood. Our study aims to explore whether this damage is associated with the transmission of plant viruses during larval feeding. We also explore the larval transcriptome to identify any entomopathogenic viruses with the potential to be used as biocontrol agents in future pest management programs. Seven novel virus sequences are identified and characterised using de novo assembly of RNA-Seq data obtained from salivary glands of larvae. The novel virus sequences belong to different virus families and are tentatively named SF-associated anphevirus (SFaAV), SF-associated orthomyxo-like virus (SFaOV), SF-associated narna-like virus (SFaNV), SF-associated partiti-like virus (SFaPV), SF-associated toti-like virus (SFaTV-1 and SFaTV-2) and SF-associated densovirus (SFaDV). These newly identified viruses are more likely insect-associated viruses, as phylogenetic analyses show that they cluster with other insect-specific viruses. Small RNA analysis indicates prominent peaks at both 21 nt and 26-29 nt, suggesting the activation of host siRNA and piwiRNA pathways. Our study helps to improve understanding of the virome of soldier flies and could identify insect viruses for deployment in novel pest management strategies.

Complete genome sequence of a novel partitivirus with a dsRNA3 segment, isolated from Fusarium commune strain CP-SX-3 causing strawberry root rot

A novel partitivirus, Fusarium commune partitivirus 1 (FcoPV1), was identified in Fusarium commune strain CP-SX-3 isolated from diseased roots of strawberry with symptoms of root rot. The complete genome of FcoPV1 comprises three double-stranded RNAs (dsRNAs): dsRNA1 (1,825 nt), dsRNA2 (1,592 nt), and dsRNA3 (1,421 nt). dsRNA1 contains a single open reading frame (ORF1) encoding an RNA-dependent RNA polymerase (RdRp), and dsRNA2 contains a single ORF (ORF2) encoding a coat protein (CP). dsRNA3 is a possible satellite RNA that does not appear to encode a known protein. BLASTp analysis revealed that RdRp (86.59%) and CP (74.13%) encoded by the two ORFs (ORF1 and ORF2) had the highest sequence similarity to their counterparts in Fusarium equiseti partitivirus 1 (FePV1). Phylogenetic analysis based on the complete amino acid sequence of RdRp suggested that FcoPV1 should be considered a member of a new species in the proposed genus "Zetapartitivirus" within the family Partitiviridae. To the best of our knowledge, this is the first report of a zetapartitivirus infecting phytopathogenic F. commune.

Characterization of the RNA Mycovirome Associated with Grapevine Fungal Pathogens: Analysis of Mycovirus Distribution and Their Genetic Variability within a Collection of Botryosphaeriaceae Isolates

Botryosphaeriaceae are fungi involved in the decay of various woody species, including the grapevine, leading to significant production losses. This fungal family is largely ubiquitous, and seven species of Botryosphaeriaceae have been identified in French vineyards, with variable levels of aggressiveness, both in vitro and in planta. Mycoviruses can impact the life traits of their fungal hosts, including aggressiveness, and are one of the factors influencing fungal pathogenicity. In this study, the RNA mycovirome of fifteen Botryosphaeriaceae isolates was characterized through the high-throughput sequencing of double-stranded RNA preparations from the respective samples. Eight mycoviruses were detected, including three potential novel species in the Narnaviridae family, as well as in the proposed Mycobunyaviridae and Fusagraviridae families. A large collection of Botryosphaeriaceae isolates was screened using RT-PCR assays specific for 20 Botryosphaeriaceae-infecting mycoviruses. Among the mycoviruses detected, some appeared to be specialists within a single host species, while others infected isolates belonging to multiple Botryosphaeriaceae species. This screening allowed us to conclude that one-third of the Botryosphaeriaceae isolates were infected by at least one mycovirus, and a significant proportion of isolates (43.5%) were found to be coinfected by several viruses, with very complex RNA mycoviromes for some N. parvum isolates.

Virome profiling of fig wasps (Ceratosolen spp.) reveals virus diversity spanning four realms

We investigated the virome of agaonid fig wasps (Ceratosolen spp.) inside syconia ("fruits") of various Ficus trees fed upon by frugivores such as pteropodid bats in Sub-Saharan Africa. This virome includes representatives of viral families spanning four realms and includes near-complete genome sequences of three novel viruses and fragments of five additional potentially novel viruses evolutionarily associated with insects, fungi, plants, and vertebrates. Our study provides evidence that frugivorous animals are exposed to a plethora of viruses by coincidental consumption of fig wasps, which are obligate pollinators of figs worldwide.

Complete genome sequence of a novel gammapartitivirus from Penicillium oxalicum RCEF7482

Penicillium oxalicum, an important biocontrol fungus in China, has been a subject of extensive study due to its role in combating various pathogenic fungi. Despite the prevalence of mycoviruses with double-stranded (ds) RNA genomes in filamentous fungi, there has been no screening of mycoviruses in P. oxalicum. In this report, we describe the identification and characterization of a novel dsRNA virus isolated from P. oxalicum, designated as "Penicillium oxalicum partitivirus 1" (PoPV1). The genome of PoPV1 consists of two dsRNA segments, dsRNA1 (1,770 bp) and dsRNA2 (1,584 bp), each containing a single open reading frame (ORF): ORF1 and ORF2. Comparative analysis revealed that the RdRp and CP amino acid sequences of PoPV1 share the highest identity (89.18% and 73.97%, respectively) with those of Penicillium aurantiogriseum partitivirus 1 (PaPV1). Motif analysis based on RdRp amino acid sequences places PoPV1 in the genus Gammapartitivirus within the family Partitiviridae, with a distinctive motif VI (R/KV/ILGDD). Phylogenetic analysis further established a close relationship of PoPV1 to PaPV1, forming a unique clade among the gammapartitiviruses. Consequently, we propose that Penicillium oxalicum partitivirus 1 represents a new species in the genus Gammapartitivirus. This is the first report of a dsRNA virus in P. oxalicum.

Mixed infection of ITPase-encoding potyvirid and secovirid in Mercurialis perennis: evidences for a convergent euphorbia-specific viral counterstrike

BACKGROUND

In cellular organisms, inosine triphosphate pyrophosphatases (ITPases) prevent the incorporation of mutagenic deaminated purines into nucleic acids. These enzymes have also been detected in the genomes of several plant RNA viruses infecting two euphorbia species. In particular, two ipomoviruses produce replicase-associated ITPases to cope with high concentration of non-canonical nucleotides found in cassava tissues.

METHOD

Using high-throughput RNA sequencing on the wild euphorbia species Mercurialis perennis, two new members of the families Potyviridae and Secoviridae were identified. Both viruses encode for a putative ITPase, and were found in mixed infection with a new partitivirid. Following biological and genomic characterization of these viruses, the origin and function of the phytoviral ITPases were investigated.

RESULTS

While the potyvirid was shown to be pathogenic, the secovirid and partitivirid could not be transmitted. The secovirid was found belonging to a proposed new Comovirinae genus tentatively named "Mercomovirus", which also accommodates other viruses identified through transcriptome mining, and for which an asymptomatic pollen-associated lifestyle is suspected. Homology and phylogenetic analyses inferred that the ITPases encoded by the potyvirid and secovirid were likely acquired through independent horizontal gene transfer events, forming lineages distinct from the enzymes found in cassava ipomoviruses. Possible origins from cellular organisms are discussed for these proteins. In parallel, the endogenous ITPase of M. perennis was predicted to encode for a C-terminal nuclear localization signal, which appears to be conserved among the ITPases of euphorbias but absent in other plant families. This subcellular localization is in line with the idea that nucleic acids remain protected in the nucleus, while deaminated nucleotides accumulate in the cytoplasm where they act as antiviral molecules.

CONCLUSION

Three new RNA viruses infecting M. perennis are described, two of which encoding for ITPases. These enzymes have distinct origins, and are likely required by viruses to circumvent high level of cytoplasmic non-canonical nucleotides. This putative plant defense mechanism has emerged early in the evolution of euphorbias, and seems to specifically target certain groups of RNA viruses infecting perennial hosts.

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.

Considerations in engineering viral vectors for genome editing in plants

Plant viruses have been engineered to express proteins and induce gene silencing for decades. Recently, plant viruses have also been used to deliver components into plant cells for genome editing, a technique called virus-induced genome editing (VIGE). Although more than a dozen plant viruses have been engineered into VIGE vectors and VIGE has been successfully accomplished in some plant species, application of VIGE to crops that are difficult to tissue culture and/or have low regeneration efficiency is still tough. This paper discusses factors to consider for an ideal VIGE vector, including insertion capacity for foreign DNA, vertical transmission ability, expression level of the target gene, stability of foreign DNA insertion, and biosafety. We also proposed a step-by-step schedule for excavating the suitable viral vector for VIGE.

The Viromes of Six Ecosystem Service Provider Parasitoid Wasps

Parasitoid wasps are fundamental insects for the biological control of agricultural pests. Despite the importance of wasps as natural enemies for more sustainable and healthy agriculture, the factors that could impact their species richness, abundance, and fitness, such as viral diseases, remain almost unexplored. Parasitoid wasps have been studied with regard to the endogenization of viral elements and the transmission of endogenous viral proteins that facilitate parasitism. However, circulating viruses are poorly characterized. Here, RNA viromes of six parasitoid wasp species are studied using public libraries of next-generation sequencing through an integrative bioinformatics pipeline. Our analyses led to the identification of 18 viruses classified into 10 families (Iflaviridae, Endornaviridae, Mitoviridae, Partitiviridae, Virgaviridae, Rhabdoviridae, Chuviridae, Orthomyxoviridae, Xinmoviridae, and Narnaviridae) and into the Bunyavirales order. Of these, 16 elements were described for the first time. We also found a known virus previously identified on a wasp prey which suggests viral transmission between the insects. Altogether, our results highlight the importance of virus surveillance in wasps as its service disruption can affect ecology, agriculture and pest management, impacting the economy and threatening human food security.

Grapevine Virome of the Don Ampelographic Collection in Russia Has Concealed Five Novel Viruses

In this study, an analysis of the virome of 51 grapevines from the Don ampelographic collection named after Ya. I. Potapenko (Russia) was performed using high-throughput sequencing of total RNA. A total of 20 previously described grapevine viruses and 4 viroids were identified. The most detected were grapevine rupestris stem pitting-associated virus (98%), hop stunt viroid (98%), grapevine Pinot gris virus (96%), grapevine yellow speckle viroid 1 (94%), and grapevine fleck virus (GFkV, 80%). Among the economically significant viruses, the most present were grapevine leafroll-associated virus 3 (37%), grapevine virus A (24%), and grapevine leafroll-associated virus 1 (16%). For the first time in Russia, a grapevine-associated tymo-like virus (78%) was detected. After a bioinformatics analysis, 123 complete or nearly complete viral genomes and 64 complete viroid genomes were assembled. An analysis of the phylogenetic relationships with reported global isolates was performed. We discovered and characterized the genomes of five novel grapevine viruses: bipartite dsRNA grapevine alphapartitivirus (genus Alphapartitivirus, family Partitiviridae), bipartite (+) ssRNA grapevine secovirus (genus Fabavirus, family Secoviridae) and three (+) ssRNA grapevine umbra-like viruses 2, -3, -4 (which phylogenetically occupy an intermediate position between representatives of the genus Umbravirus and umbravirus-like associated RNAs).

Neolamarckia cadamba hosts a putative novel deltapartitivirus: a revelation by transcriptome data-mining

Neolamarckia cadamba (Roxb.) Bosser is a medicinally important, fast-growing, timber-yielding tree species. In the present study, the virome of N. cadamba was explored using the publicly available N. cadamba transcriptome datasets and a putative novel virus, tentatively named as cadamba cryptic virus 1 (CdbCV1), was identified. CdbCV1 contained two genome segments, each coding for a single protein. CdbCV1 RNA1 (1564 nt) encoded for an RNA dependent RNA polymerase (RdRp) protein while CdbCV1 RNA2 (1492 nt) encoded for a coat protein (CP). Phylogenetic and sequence similarity analyses revealed the relatedness of CdbCV1 to pepper cryptic virus 1 and pittosporum cryptic virus 1. Based on the species demarcation criteria, genome organization and phylogeny, CdbCV1 can be regarded a new member of the genus Deltapartitivirus.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-023-00845-8.

Identification and nucleotide sequencing of a novel partitivirus derived from Rhizoctonia solani AG-4 HG III isolate A14

Rhizoctonia solani is a widely disseminated phytopathogen that is found in the soil and is capable of harming many important species of crops. Here, analysis of the R. solani AG-4 HG III strain A14 led to the identification of a novel mycovirus assigned the tentative name "Rhizoctonia solani partitivirus A14" (RsPV-A14), which was subjected to sequencing and associated analyses. This approach revealed that RsPV-A14 harbored two dsRNA segments, 2022 bp (dsRNA1) and 1905 bp (dsRNA2) in length. dsRNA1 was found to contain a single open reading frame (ORF1) that codes for a 622-amino-acid protein with conserved RNA-dependent RNA polymerase (RdRp) motifs, and dsRNA2 was found to contain an ORF (ORF2) that is predicted to code for a 558-amino-acid capsid protein (CP). BLASTp analysis using the putative RdRp of RsPV-A14 showed sequence similarity to partitiviruses, including Rosellinia necatrix partitivirus 7 (50.53% identity), an unclassified partitivirus. Phylogenetic analysis based on RdRp protein sequences suggested that RsPV-A14 is a novel member of the family Partitiviridae.

Molecular and biological characterization of a partitivirus from Paecilomyces variotii

Paeciliomyces variotii is a thermo-tolerant, ubiquitous fungus commonly found in food products, indoor environments, soil and clinical samples. It is a well-known biocontrol agent used against phytopathogenic fungi and its metabolites have many industrial applications. Rare reports of P. variotii-related human infections have been found in the medical literature. In this study, we report for the first time the infection of P. variotii isolated from a soil sample collected in a rice field with a double-stranded RNA virus, Paeciliomyces variotii partitivirus 1 (PvPV-1) in the family Partitiviridae. P. variotii harboured icosahedral virus particles 30 nm in diameter with two dsRNA segments 1758 and 1356 bp long. Both dsRNA1 and dsRNA2 have a single open reading frame encoding proteins of 63 and 40 kDa, respectively. These proteins have significant similarity to the RNA-dependent RNA polymerase and capsid protein encoded by the genomic segments of several viruses from the family Partitiviridae. Phylogenetic analysis revealed that PvPV-1 belongs to the family Partitiviridae but in an unclassified group/genus, tentatively nominated Zetapartitivirus. PvPV-1 was found to increase the growth rate of the host fungus, as indicated by time course experiments performed on a range of different media for virus-infected and virus-free isogenic lines. Further, dual-culture assays performed for both isogenic lines confirmed the antagonistic potential of P. variotii against other phytopathogenic fungi. The findings of this study assist us in understanding P. variotii as a potential biocontrol agent, together with plant-fungus-virus interactions.