Diversity and epidemiology of plant rhabdoviruses

Molecular identification of a putative novel varicosavirus in Agastache rugosa in China

A putative novel virus was identified in Agastache rugosa in China and tentatively named "Agastache rugosa-associated varicosavirus" (ARaVV). The nearly complete genome sequence of ARaVV was obtained through RNA sequencing (RNA-seq) and subsequent RT-PCR. The ARaVV genome consists of two negative-sense single-stranded RNA segments that are 6428 and 3862 nucleotides (nt) in size, respectively. RNA1 encodes a large polymerase (L), and RNA2 encodes a putative nucleocapsid protein (N), protein 2 (P2), and protein 3 (P3). The L protein shared the highest amino acid (aa) sequence identity (51.3%) with Erysimum virus 1 (EryV1, BK061766.1). The N, P2, and P3 shared the highest aa sequence identity (33.1%, 14.0%, and 24.2%) with Leucanthemum virus 1, Raphanus virus 1, and Spinach virus 1, respectively. Phylogenetic analysis based on amino acid sequences of the L protein showed that ARaVV clustered in a clade with the varicosaviruses, indicating that ARaVV is a putative new member of the genus Varicosavirus.

Characterization of Two Novel Viruses Within a Complex Virome from Flowering Ginger in Hawaii

Flowering ginger (Alpinia purpurata) is economically and culturally important in Hawaii. In the past decade, a slow decline syndrome has impacted the production of this crop in the state. RNA sequencing analyses and virus indexing surveys were done on samples collected from four of the Hawaiian Islands. Viral sequences corresponding to six viruses were recovered from transcriptomic data from samples with virus-like symptoms. Canna yellow mottle virus (CaYMV, genus Badnavirus) and two novel viruses, Alpinia vein clearing virus (ApVCV, genus Ampelovirus) and Alpinia vein streaking virus (ApVSV, genus Betanucleorhabdovirus), were found at a moderate incidence in diseased plants. Conversely, three other viruses, including the two potyviruses, banana bract mosaic virus and bean common mosaic virus, and a badnavirus, banana streak GF virus, were also found but at a low incidence. Virus detection in potential insect vectors and transmission assays identified the mealybug Planococcus citri as a vector of CaYMV and ApVCV, whereas the aphid Pentalonia caladii was identified as a vector of the novel ApVSV. Both P. citri and P. caladii are common pests of flowering ginger in Hawaii. Transmission of ApVSV was achieved using P. caladii colonies either established in the laboratory or naturally feeding on infected plants, although no transmission was obtained using viruliferous aphids originally reared on taro (Colocasia esculenta). Our study provides insights into the potential association between viral infections and the observed decline symptoms of flowering ginger in Hawaii. However, more definitive studies are needed to link single or mixed viral infections with decline symptoms.

Genomes of Alphanucleorhabdovirus Physostegiae Isolates from Two Different Cultivar Groups of Solanum melongena

Plant rhabdoviruses cause considerable economic losses and are a threat to the agriculture of Solanaceae plants. Two novel virus isolates belonging to the family Rhabdoviridae are identified by high-throughput sequencing (HTS) in Russian eggplant cultivars grown in the Volga river delta region for the first time. The phylogenetic inference of L protein (polymerase) shows that these virus isolates belong to Alphanucleorhabdovirus physostegia (Physostegia chlorotic mottle virus-PhCMoV), and their minus-sense RNA genomes have the typical gene order 3'-nucleocapsid (N)-X protein (X)-phosphoprotein (P)-Y protein (Y)-matrix protein (M)-glycoprotein (G)-polymerase (L)-5' observed in some plant-infecting alphanucleorhabdoviruses. One of the PhCMoV isolates from the eggplant cultivar Almaz is genetically very similar to the Russian PhCMoV isolate from tomato and grouped in a subclade together with four isolates from Belgium, Germany, the Netherlands, and France. However, another eggplant-infecting isolate from the Russian cultivar Boggart is the most divergent compared with the other 45 virus genomes of European PhCMoV isolates. Thus, our comparative analysis reveals that two virus isolates from Russia may either share a close evolutionary relationship with European isolates or significantly diverge from all known virus isolates. The potential to use the protein sequence comparative analysis of accessory polypeptides, along with the early developed strategy of the nucleotide sequence comparison of the RNA genomes, is shown.

Alpha- and Betagymnorhavirus: two new genera of gymnosperm-infecting viruses in the family Rhabdoviridae, subfamily Betarhabdovirinae

The family Rhabdoviridae includes viruses with a negative-sense RNA genome. This family is divided into four subfamilies, and until recently, the subfamily Betarhabdovirinae, encompassing all plant-associated rhabdoviruses, was further divided into six genera. Here, we report the creation of two new genera within the subfamily Betarhabdovirinae - Alphagymnorhavirus and Betagymnorhavirus - to include recently described gymnosperm-associated viruses. The genus Alphagymnorhavirus includes nine species, while the genus Betagymnorhavirus includes only one species. Phylogenetic analysis indicated that these viruses form two well-supported clades that are clustered with the varicosaviruses, which have bisegmented genomes. In contrast, the 10 viruses included in the newly created genera have the distinctive feature that they have an unsegmented genome encoding five or six proteins. The creation of the genera Alphagymnorhavirus and Betagymnorhavirus has been ratified by the International Committee on Taxonomy of Viruses (ICTV).

RNAi-mediated knockdown of exportin 1 negatively affected ovary development, survival and maize mosaic virus accumulation in its insect vector Peregrinus maidis

Exportin 1 (XPO1) is the major karyopherin-β nuclear receptor mediating the nuclear export of hundreds of proteins and some classes of RNA and regulates several critical processes in the cell, including cell-cycle progression, transcription and translation. Viruses have co-opted XPO1 to promote nucleocytoplasmic transport of viral proteins and RNA. Maize mosaic virus (MMV) is a plant-infecting rhabdovirus transmitted in a circulative propagative manner by the corn planthopper, Peregrinus maidis. MMV replicates in the nucleus of plant and insect hosts, and it remains unknown whether MMV co-opts P. maidis XPO1 (PmXPO1) to complete its life cycle. Because XPO1 plays multiple regulatory roles in cell functions and virus infection, we hypothesized that RNAi-mediated silencing of XPO1 would negatively affect MMV accumulation and insect physiology. Although PmXPO1 expression was not modulated during MMV infection, PmXPO1 knockdown negatively affected MMV accumulation in P. maidis at 12 and 15 days after microinjection. Likewise, PmXPO1 knockdown negatively affected P. maidis survival and reproduction. PmXPO1 exhibited tissue-specific expression patterns with higher expression in the ovaries compared with the guts of adult females. Survival rate was significantly lower for PmXPO1 knockdown females, compared with controls, but no effect was observed for males. PmXPO1 knockdown experiments revealed a role for PmXPO1 in ovary function and egg production. Oviposition and egg hatch on plants were dramatically reduced in females treated with dsRNA PmXPO1. These results suggest that PmXPO1 is a positive regulator of P. maidis reproduction and that it plays a proviral role in the insect vector supporting MMV infection.

Biological Characterization of Physostegia Chlorotic Mottle Virus, an Emergent Virus Infecting Vegetables in Diversified Production Systems

In 2014, Physostegia chlorotic mottle virus (PhCMoV) was discovered in Austria in Physostegia virginiana. Subsequent collaborative efforts established a link between the virus and severe fruit symptoms on important crops such as tomato, eggplant, and cucumber across nine European countries. Thereafter, specific knowledge gaps, which are crucial to assess the risks PhCMoV can pose for production and how to manage it, needed to be addressed. In this study, the transmission, prevalence, and disease severity of PhCMoV were examined. This investigation led to the identification of PhCMoV presence in a new country, Switzerland. Furthermore, our research indicates that the virus was already present in Europe 30 years ago. Bioassays demonstrated PhCMoV can result in up to 100% tomato yield losses depending on the phenological stage of the plant at the time of infection. PhCMoV was found to naturally infect 12 new host plant species across eight families, extending its host range to 21 plant species across 15 plant families. The study also identified a polyphagous leafhopper (genus Anaceratagallia) as a natural vector of PhCMoV. Overall, PhCMoV was widespread in small-scale diversified vegetable farms in Belgium where tomato is grown in soil under tunnels, occurring in approximately one-third of such farms. However, outbreaks were sporadic and were associated at least once with the cultivation in tomato tunnels of perennial plants that can serve as a reservoir host for the virus and its vector. To further explore this phenomenon and manage the virus, studying the ecology of the vector would be beneficial.

Insect pests and natural enemies associated with lettuce Lactuca sativa L. (Asteraceae) in an aquaponics system

Although food is produced in aquaponics systems worldwide, no information is available on the occurrence of insect pests and natural enemies in aquaponic lettuce, Lactuca sativa L. In this study, a survey was carried out in an aquaponic system combining lettuce with lambari, Astyanax altiparanae (Garutti & Briski), aiming to determine the insect pests and natural enemies associated with this system. We also determined the predominant insect species and the effect of meteorological factors on their populations. Insect abundance was estimated by visual sampling during 13 cultivation cycles, totaling 27 sampling dates. The meteorological factors considered were air temperature and relative humidity, and their effects were determined using the Pearson correlation. The thrips Frankliniella schultzei (Trybom) and Caliothrips phaseoli (Hood) and the aphid Aphis spiraecola (Patch) predominated. Ambient temperature and relative humidity were essential factors affecting C. phaseoli and F. schultzei. The natural enemies found on the lettuce plants were the thrips Franklinothrips vespiformis (Crawford) and Stomatothrips angustipennis (Hood) and the ladybugs Cycloneda sanguinea L., Eriopis connexa (Germar), and Hippodamia convergens (Guérin-Méneville). These results constitute the first step for a lettuce-integrated pest-management program in aquaponics systems.

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.

Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis

BACKGROUND

Viruses have notable effects on agroecosystems, wherein they can adversely affect plant health and cause problems (e.g., increased biosecurity risks and economic losses). However, our knowledge of their diversity and interactions with specific host plants in ecosystems remains limited. To enhance our understanding of the roles that viruses play in agroecosystems, comprehensive analyses of the viromes of a wide range of plants are essential. High-throughput sequencing (HTS) techniques are useful for conducting impartial and unbiased investigations of plant viromes, ultimately forming a basis for generating further biological and ecological insights. This study was conducted to thoroughly characterize the viral community dynamics in individual plants.

RESULTS

An HTS-based virome analysis in conjunction with proximity sampling and a tripartite network analysis were performed to investigate the viral diversity in chunkung (Cnidium officinale) plants. We identified 61 distinct chunkung plant-associated viruses (27 DNA and 34 RNA viruses) from 21 known genera and 6 unclassified genera in 14 known viral families. Notably, 12 persistent viruses (7 DNA and 5 RNA viruses) were exclusive to dwarfed chunkung plants. The detection of viruses from the families Partitiviridae, Picobirnaviridae, and Spinareoviridae only in the dwarfed plants suggested that they may contribute to the observed dwarfism. The co-infection of chunkung by multiple viruses is indicative of a dynamic and interactive viral ecosystem with significant sequence variability and evidence of recombination.

CONCLUSIONS

We revealed the viral community involved in chunkung. Our findings suggest that chunkung serves as a significant reservoir for a variety of plant viruses. Moreover, the co-infection rate of individual plants was unexpectedly high. Future research will need to elucidate the mechanisms enabling several dozen viruses to co-exist in chunkung. Nevertheless, the important insights into the chunkung virome generated in this study may be relevant to developing effective plant viral disease management and control strategies.

The complete genome sequence of a putative novel cytorhabdovirus identified in Chelidonium majus in China

A new cytorhabdovirus, tentatively named "chelidonium yellow mottle associated virus" (CheYMaV), was identified in Chelidonium majus with yellow mottle symptoms by high-throughput sequencing and RT-PCR. Its genome is 12,121 nucleotides in length and contains eight open reading frames (ORFs) in the order 3'-N-P'-P-P3-M-G-P6-L-5'. Amino acid sequence comparisons between the putative proteins of CheYMaV and the corresponding proteins of other cytorhabdoviruses showed that it shares the highest sequence similarity with Trifolium pratense virus A (TpVA, MH982250) and Glehnia littoralis virus 1 (GllV1, BK014304), but with sequence identity values below the species demarcation threshold for cytorhabdoviruses (< 80%). Phylogenetic analysis showed that CheYMaV is most closely related to TpVA and GllV1. CheYMaV should therefore be considered a new member of the genus Cytorhabdovirus. This is the first report of a cytorhabdovirus identified in Chelidonium majus.

Two Novel Betarhabdovirins Infecting Ornamental Plants and the Peculiar Intracellular Behavior of the Cytorhabdovirus in the Liana Aristolochia gibertii

Two novel members of the subfamily Betarhabdovirinae, family Rhabdoviridae, were identified in Brazil. Overall, their genomes have the typical organization 3'-N-P-P3-M-G-L-5' observed in mono-segmented plant-infecting rhabdoviruses. In aristolochia-associated cytorhabdovirus (AaCV), found in the liana aristolochia (Aristolochia gibertii Hook), an additional short orphan ORF encoding a transmembrane helix was detected between P3 and M. The AaCV genome and inferred encoded proteins share the highest identity values, consistently < 60%, with their counterparts of the yerba mate chlorosis-associated virus (Cytorhabdovirus flaviyerbamate). The second virus, false jalap virus (FaJV), was detected in the herbaceous plant false jalap (Mirabilis jalapa L.) and represents together with tomato betanucleorhabdovirus 2, originally found in tomato plants in Slovenia, a tentative new species of the genus Betanucleorhabdovirus. FaJV particles accumulate in the perinuclear space, and electron-lucent viroplasms were observed in the nuclei of the infected cells. Notably, distinct from typical rhabdoviruses, most virions of AaCV were observed to be non-enclosed within membrane-bounded cavities. Instead, they were frequently seen in close association with surfaces of mitochondria or peroxisomes. Unlike FaJV, AaCV was successfully graft-transmitted to healthy plants of three species of the genus Aristolochia, while mechanical and seed transmission proved unsuccessful for both viruses. Data suggest that these viruses belong to two new tentative species within the subfamily Betarhabdovirinae.

Genomic characterization of a novel cytorhabdovirus infecting Ixeris denticulata in China

Ixeris denticulata is a perennial herbal plant with important medical and economic value. In this study, a novel rhabdovirus from I. denticulata with leaf curling and mottle symptoms was identified through next-generation sequencing and molecular cloning approaches. Based on the host species and properties of this virus, it was tentatively named "Ixeris denticulata-associated rhabdovirus" (IdaRV). IdaRV has a negative-sense RNA genome that is 12,705 nucleotides in length and has five open reading frames (ORFs) in the order 3'-nucleoprotein -phosphoprotein -movement protein -matrix protein -large RNA-dependent RNA polymerase-5'. Pairwise sequence comparisons showed that IdaRV had 42.2-53.0% sequence identity to members of the genera Cytorhabdovirus, Varicosavirus, Betanucleorhabdovirus, Gammanucleorhabdovirus, Dichorhavirus, and Alphanucleorhabdovirus in the subfamily Betarhabdovirinae. BLASTp searches indicated that putative products of ORF1, ORF2, ORF3, ORF4, and ORF5 of IdaRV are most closely related to those of rudbeckia virus 1 (RudV1, GenBank accession number ON185810), with 32.1%, 21.3%, 52.4%, 37.6%, and 57.1% amino acid sequence identity, respectively, at the protein level. Phylogenetic analysis showed that IdaRV forms a smaller branch with RudV1, which belongs to the genus Cytorhabdovirus. These results establish IdaRV as a novel rhabdovirus in the genus Cytorhabdovirus of the family Rhabdoviridae.

Identification and characterization of a novel Cytorhabdovirus associated with goji berry (Lycium barbarum L.) crinkle disease

Goji berry (Lycium barbarum L.) is a traditional Chinese herbal medicinal plant that is extensively cultivated in the arid and semiarid regions of northwest China. In this study, a novel cytorhabdovirus, tentatively named "goji cytorhabdovirus A (GCVA)," was identified from the goji berry plant exhibiting leaf crinkle symptoms through high-throughput sequencing (HTS). GCVA contains a linear, negative sense single-stranded RNA genome of 14,812 nucleotides and encodes six open reading frames in the order of 3' leader-N-P-P4-M-G-L-5' trailer. The genome of GCVA shares the highest nucleotide (nt) identity of 65.80% (16% query coverage) with yerba mate virus A (YmVA) (NC_076472). The N and L proteins also share low amino acid (aa) identities (<35.42 and < 41.23%, respectively) with known cytorhabdoviruses. Typical features of the viruses in the genus Cytorhabdovirus include a highly conserved consensus sequence in the intergenic regions and extensive complementation of the 5' non-coding trailer and the 3' leader. These features were also found in GCVA. These data in combination with a phylogenetic analysis that was based on the aa sequences of the N and L proteins support the proposal that GCVA is a new species in the genus Cytorhabdovirus.

Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses

Cytorhabdoviruses (genus Cytorhabdovirus, family Rhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genus Cytorhabdovirus have unsegmented single-stranded negative-sense RNA genomes (ca. 10-16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 93 novel viruses with genetic and evolutionary cues of cytorhabdoviruses. Strikingly, five unprecedented viruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the family Rhabdoviridae, and they should be classified in a novel genus within this family for which we suggest the name "Trirhavirus". Interestingly, the nucleocapsid and polymerase were the only typical rhabdoviral proteins encoded by those tri-segmented viruses, whereas in three of them, a protein similar to the emaravirus (family Fimoviridae) silencing suppressor was found, while the other predicted proteins had no matches in any sequence databases. Genetic distance and evolutionary insights suggest that all these novel viruses may represent members of novel species. Phylogenetic analyses, of both novel and previously classified plant rhabdoviruses, provide compelling support for the division of the genus Cytorhabdovirus into three distinct genera. This proposed reclassification not only enhances our understanding of the evolutionary dynamics within this group of plant rhabdoviruses but also illuminates the remarkable genomic diversity they encompass. This study not only represents a significant expansion of the genomics of cytorhabdoviruses that will enable future research on the evolutionary peculiarity of this genus but also shows the plasticity in the rhabdovirus genome organization with the discovery of tri-segmented members with a unique evolutionary trajectory.

Rescue of the first alphanucleorhabdovirus entirely from cloned complementary DNA: An efficient vector for systemic expression of foreign genes in maize and insect vectors

Recent reverse genetics technologies have enabled genetic manipulation of plant negative-strand RNA virus (NSR) genomes. Here, we report construction of an infectious clone for the maize-infecting Alphanucleorhabdovirus maydis, the first efficient NSR vector for maize. The full-length infectious clone was established using agrobacterium-mediated delivery of full-length maize mosaic virus (MMV) antigenomic RNA and the viral core proteins (nucleoprotein N, phosphoprotein P, and RNA-directed RNA polymerase L) required for viral transcription and replication into Nicotiana benthamiana. Insertion of intron 2 ST-LS1 into the viral L gene increased stability of the infectious clone in Escherichia coli and Agrobacterium tumefaciens. To monitor virus infection in vivo, a green fluorescent protein (GFP) gene was inserted in between the N and P gene junctions to generate recombinant MMV-GFP. Complementary DNA (cDNA) clones of MMV-wild type (WT) and MMV-GFP replicated in single cells of agroinfiltrated N. benthamiana. Uniform systemic infection and high GFP expression were observed in maize inoculated with extracts of the infiltrated N. benthamiana leaves. Insect vectors supported virus infection when inoculated via feeding on infected maize or microinjection. Both MMV-WT and MMV-GFP were efficiently transmitted to maize by planthopper vectors. The GFP reporter gene was stable in the virus genome and expression remained high over three cycles of transmission in plants and insects. The MMV infectious clone will be a versatile tool for expression of proteins of interest in maize and cross-kingdom studies of virus replication in plant and insect hosts.

Identification, molecular characterization and phylogenetic analysis of a novel nucleorhabdovirus infecting Paris polyphylla var. yunnanensis

A novel betanucleorhabdovirus infecting Paris polyphylla var. yunnanensis, tentatively named Paris yunnanensis rhabdovirus 1 (PyRV1), was recently identified in Yunnan Province, China. The infected plants showed vein clearing and leaf crinkle at early stage of infection, followed by leaf yellowing and necrosis. Enveloped bacilliform particles were observed using electron microscopy. The virus was mechanically transmissible to Nicotiana bethamiana and N. glutinosa. The complete genome of PyRV1 consists of 13,509 nucleotides, the organization of which was typical of rhabdoviruses, containing six open reading frames encoding proteins N-P-P3-M-G-L on the anti-sense strand, separated by conserved intergenic regions and flanked by complementary 3'-leader and 5'-trailer sequences. The genome of PyRV1 shared highest nucleotide sequence identity (55.1%) with Sonchus yellow net virus (SYNV), and the N, P, P3, M, G, and L proteins showed 56.9%, 37.2%, 38.4%, 41.8%, 56.7%, and 49.4% amino acid sequence identities with respective proteins of SYNV, suggesting RyRV1 belongs to a new species of the genus Betanucleorhabdovirus.

Complete genome sequence of cnidium virus 2, a novel cytorhabdovirus isolated from Cnidium officinale in South Korea

High-throughput sequencing identified a cytorhabdovirus, tentatively named "cnidium virus 2" (CnV2), in Cnidium officinale, and Sanger sequencing confirmed the genome sequence. CnV2 is 13,527 nucleotides in length and contains seven open reading frames in the order 3'-N-P-3-4-M-G-L-5', separated by intergenic regions. The full-length nucleotide sequence of CnV2 shares 19.4-53.8% identity with other known cytorhabdovirus genome sequences. The N, P, P3, M, G, and L proteins share 15.8-66.7%, 11-64.3%, 11.1-80.5%, 10.8-75.3%, 12.3-72.1%, and 20-72.7% amino acid sequence identity, respectively, with the cognate deduced protein sequences from known cytorhabdoviruses. CnV2 is related to other members of the genus Cytorhabdovirus, with sambucus virus 1 being the closest relative. Thus, CnV2 should be classified as a new member in the genus Cytorhabdovirus of the family Rhabdoviridae.

Role of Plant Virus Movement Proteins in Suppression of Host RNAi Defense

One of the systems of plant defense against viral infection is RNA silencing, or RNA interference (RNAi), in which small RNAs derived from viral genomic RNAs and/or mRNAs serve as guides to target an Argonaute nuclease (AGO) to virus-specific RNAs. Complementary base pairing between the small interfering RNA incorporated into the AGO-based protein complex and viral RNA results in the target cleavage or translational repression. As a counter-defensive strategy, viruses have evolved to acquire viral silencing suppressors (VSRs) to inhibit the host plant RNAi pathway. Plant virus VSR proteins use multiple mechanisms to inhibit silencing. VSRs are often multifunctional proteins that perform additional functions in the virus infection cycle, particularly, cell-to-cell movement, genome encapsidation, or replication. This paper summarizes the available data on the proteins with dual VSR/movement protein activity used by plant viruses of nine orders to override the protective silencing response and reviews the different molecular mechanisms employed by these proteins to suppress RNAi.

Complete genome sequence of daphne virus 1, a novel cytorhabdovirus infecting Daphne odora

A novel cytorhabdovirus was identified in Daphne odora in South Korea using high-throughput sequencing. The virus, tentatively named "daphne virus 1" (DV1), has a full-length genome sequence of 13,206 nucleotides with a genome organization comparable to that of unsegmented plant rhabdoviruses and contains seven antisense putative genes in the order 3'-leader-N-P'-P-P3-M-G-L-5'-trailer. The coding region of the genome is flanked by a 3' leader and a 5' trailer sequence, 261 and 151 nucleotides long, respectively. The DV1 genome shares 33.74%-57.44% nucleotide sequence identity with other cytorhabdoviruses. The DV1-encoded proteins share the highest amino acid sequence identity with homologues from Asclepias syriaca virus 1. Phylogenetic analysis showed that DV1 clustered with representative cytorhabdoviruses. We propose classifying DV1 in a new species within the genus Cytorhabdovirus, family Rhabdoviridae.

In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

BACKGROUND

In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data.

RESULTS

Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments.

CONCLUSIONS

We showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases and would serve as baseline for further post-discovery characterization studies. Video Abstract.

Identification and molecular characterization of a novel cytorhabdovirus from rose plants (Rosa chinensis Jacq.)

A novel negative-sense single-stranded RNA virus, tentatively named "rose-associated cytorhabdovirus" (RaCV), was identified by high-throughput sequencing. RaCV is 16,067 nucleotides in length and contains eight open reading frames (ORFs 1-8) encoding a nucleocapsid protein (N), a putative phosphoprotein (P), a putative P3 protein (P3), a putative P4 protein (P4), a putative matrix protein (M), a glycoprotein (G), a putative P7 protein (P7), and an RNA-dependent RNA polymerase (L), respectively. The coding genes are flanked by a 3' leader sequence (228 nt) and a 5' trailer sequence (251 nt) and are separated by conserved intergenic junctions (3'-AUUCUUUUUG(N)nCUN-5'). Phylogenetic analysis showed that RaCV clustered with yerba mate virus A (YmVA) within the cytorhabdovirus clade, and it exhibited low a degree of nt sequence similarity (<40% identity) to other rhabdoviruses. Amino acid sequence comparisons between the putative proteins of RaCV and the corresponding proteins of other cytorhabdoviruses showed that the sequence identity levels were far below the species demarcation cutoff of 80% for cytorhabdoviruses. These results suggest that RaCV should be classified as a new member of the genus Cytorhabdovirus.

A Novel, Divergent Member of the Rhabdoviridae Family Infects Strawberry

Strawberry (Fragaria × ananassa) is the most important berry crop worldwide and viruses pose a constant threat to the industry. In this communication, we describe a novel virus in the family Rhabdoviridae referred to as strawberry virus 3 (StrV-3). The virus does not show significant homology when compared with recognized rhabdoviruses and, therefore, the establishment of a new genus should be considered. A triplex reverse-transcription PCR test was developed and successfully employed in a survey of the National Clonal Germplasm Repository Fragaria collection. A CRISPR-Cas-based protocol was also developed and shown to detect the virus in as little as 1 fg of total RNA, a protocol to be used in the detection of the virus in candidate G1 plants. The strawberry aphid (Chaetosiphon fragaefolii) was evaluated-alas, unsuccessfully-as a potential vector of the virus. This work broadens our understanding of the family Rhabdoviridae and assists in the quest of releasing plant material free of viruses.

Discovery of a Closterovirus Infecting Jujube Plants Grown at Aksu Area in Xinjiang of China

Chinese jujube (Ziziphus jujuba Mill.) is a widely grown fruit crop at Aksu in Xinjiang Uygur Autonomous Region of China. Viral disease-like symptoms are common on jujube plants. Here, for the first time, we report a virus tentatively named persimmon ampelovirus jujube isolate (PAmpV-Ju) infecting jujube plants. The virus was identified using high-throughput sequencing from a jujube plant (ID: AKS15) and molecularly related to viruses in the family Closteroviridae. The genomic sequences of two PAmpV-Ju variants named AKS15-20 and AKS15-17 were determined by RT-PCR amplifications. The genome structure of PAmpV-Ju was identical to that of a recently reported persimmon ampelovirus (PAmpV) and consisted of seven open reading frames. The genomes of AKS15-20 and AKS15-17 shared 83.7% nt identity with each other, and the highest nt sequence identity of 79% with two variants of PAmpV. The incidence of PAmpV-Ju on Aksu jujube plants was evaluated by RT-PCR assays. The phylogenetic analysis of amplified partial sequences coding for polymerase, HSP70h, and CP revealed two phylogenetic clades represented by AKS15-20 and AKS15-17. Our study provides important evidence for understanding viruses infecting jujube plants and establishing efficient measures to prevent virus spread.

The physical interactome between Peregrinus maidis proteins and the maize mosaic virus glycoprotein provides insights into the cellular biology of a rhabdovirus in the insect vector

Rhabdovirus glycoproteins (G) serve multifunctional roles in virus entry, assembly, and exit from animal cells. We hypothesize that maize mosaic virus (MMV) G is required for invasion, infection, and spread in Peregrinus maidis, the planthopper vector. Using a membrane-based yeast two-hybrid assay, we identified 107 P. maidis proteins that physically interacted with MMV G, of which approximately 53% matched proteins with known functions including endocytosis, vesicle-mediated transport, protein synthesis and turnover, nuclear export, metabolism and host defense. Physical interaction networks among conserved proteins indicated a possible cellular coordination of processes associated with MMV G translation, protein folding and trafficking. Non-annotated proteins contained predicted functional sites, including a diverse array of ligand binding sites. Cyclophilin A and apolipophorin III co-immunoprecipitated with MMV G, and each showed different patterns of localization with G in insect cells. This study describes the first protein interactome for a rhabdovirus spike protein and insect vector.

Isolation of a novel rhabdovirus and detection of multiple novel viral sequences in Culex species mosquitoes in the United States

To increase our understanding of the diversity of the mosquito virome, 6956 mosquitoes of five species (Culex erraticus, Culex pipiens, Culex restuans, Culex tarsalis, and Culex territans) collected in Iowa in the United States in 2017 and 2020 were assayed for novel viruses by performing polyethylene glycol precipitation, virus isolation in cell culture, and unbiased high-throughput sequencing. A novel virus, provisionally named "Walnut Creek virus", was isolated from Cx. tarsalis, and its genomic sequence and organization are characteristic of viruses in the genus Hapavirus (family Rhabdoviridae). Replication of Walnut Creek virus occurred in avian, mammalian, and mosquito, but not tick, cell lines. A novel virus was also isolated from Cx. restuans, and partial genome sequencing revealed that it is distantly related to an unclassified virus of the genus Phytoreovirus (family Sedoreoviridae). Two recognized viruses were also isolated: Culex Y virus (family Birnaviridae) and Houston virus (family Mesoniviridae). We also identified sequences of eight novel viruses from six families (Amalgaviridae, Birnaviridae, Partitiviridae, Sedoreoviridae, Tombusviridae, and Totiviridae), two viruses that do not belong to any established families, and many previously recognized viruses. In summary, we provide evidence of multiple novel and recognized viruses in Culex spp. mosquitoes in the United States.

Mixed Infection of Blackcurrant with a Novel Cytorhabdovirus and Black Currant-Associated Nucleorhabdovirus

A virome screen was performed on a new breeding line, KB1, of blackcurrant. Rhabdovirus-like particles were observed by electron microscopy in ultrathin sections of flower stalks, and the complete genome sequence of a novel virus, provisionally named blackcurrant rhabdovirus 2 (BCRV2), was determined and verified using high-throughput sequencing. The genomic organization of BCRV2 was characteristic of cytorhabdoviruses (family Rhabdoviridae) and included seven genes: 3 ́- N-P´-P-P3-M-G-L -5 ́. BLASTP analysis revealed that the putative L protein had the highest amino acid sequence identity (75 %) with strawberry virus 2. BCRV2 was detected in Cryptomyzusgaleopsidis, but efficient transmission by this aphid was not confirmed. Of note, we observed coinfection of the KB1 line with blackcurrant-associated rhabdovirus (BCaRV) by RT-PCR. This is likely the first evidence of the presence of a cyto- and a nucleorhabdovirus in a single host.

Genome Characterization and Pathogenicity of Two New Hyptis pectinata Viruses Transmitted by Distinct Insect Vectors

Two newly described viruses belonging to distinct families, Rhabdoviridae and Geminiviridae, were discovered co-infecting Hyptis pectinata from a tropical dry forest of Ecuador. The negative-sense RNA genome of the rhabdovirus, tentatively named Hyptis latent virus (HpLV), comprises 13,765 nucleotides with seven open reading frames separated by the conserved intergenic region 3'-AAUUAUUUUGAU-5'. Sequence analyses showed identities as high as 56% for the polymerase and 38% for the nucleocapsid to members of the genus Cytorhabdovirus. Efficient transmission of HpLV was mediated by the pea aphid (Acyrthosiphon pisum) in a persistent replicative manner. The single-stranded DNA genome of the virus tentatively named Hyptis golden mosaic virus (HpGMV) shared homology with members of the genus Begomovirus with bipartite genomes. The DNA-A component consists of 2,716 nucleotides (nt), whereas the DNA-B component contains 2,666 nt. Pairwise alignments using the complete genomic sequence of DNA-A of HpGMV and closest relatives showed identities below the cutoff (<91% shared nt) established by the ICTV as species demarcation, indicating that HpGMV should be classified in a distinct begomovirus species. Transmission experiments confirmed that the whitefly Bemisia tabaci Middle East-Asia Minor 1 (MEAM1) is a vector of HpGMV.

Identification, Characterization, and Detection of a Novel Strawberry Cytorhabdovirus

In 2020, a novel agent was discovered in strawberry, a rhabdovirus closely related to lettuce necrotic yellows virus. The new virus, named strawberry virus 2 (StrV-2), was discovered in an accession of the Fragaria virus collection of the National Clonal Germplasm Repository (NCGR), and for this reason, it was studied in-depth. The complete StrV-2 genome was obtained and investigated in silico. Transmission was assessed using two aphid species whereas a multiplex RT-PCR test targeting plant and virus genes was developed and used to screen the NCGR Fragaria virus collection.

Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses

The genus Varicosavirus is one of six genera of plant-infecting rhabdoviruses. Varicosaviruses have non-enveloped, flexuous, rod-shaped virions and a negative-sense, single-stranded RNA genome. A distinguishing feature of varicosaviruses, which is shared with dichorhaviruses, is a bi-segmented genome. Before 2017, a sole varicosavirus was known and characterized, and then two more varicosaviruses were identified through high-throughput sequencing in 2017 and 2018. More recently, the number of known varicosaviruses has substantially increased in concert with the extensive use of high-throughput sequencing platforms and data mining approaches. The novel varicosaviruses have revealed not only sequence diversity, but also plasticity in terms of genome architecture, including a virus with a tentatively unsegmented genome. Here, we report the discovery of 45 novel varicosavirus genomes which were identified in publicly available metatranscriptomic data. The identification, assembly, and curation of the raw Sequence Read Archive reads has resulted in 39 viral genome sequences with full-length coding regions and 6 with nearly complete coding regions. The highlights of the obtained sequences include eight varicosaviruses with unsegmented genomes, which are linked to a phylogenetic clade associated with gymnosperms. These findings have resulted in the most complete phylogeny of varicosaviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant rhabdoviruses. Thus, the extensive use of sequence data mining for virus discovery has allowed us to unlock of the hidden genetic diversity of varicosaviruses, the largely neglected plant rhabdoviruses.

Expanding the environmental virome: Infection profile in a native rainforest tree species

Agroforestry systems (AFS) for cocoa production combine traditional land-use practices with local biodiversity conservation, resulting in both ecological and agricultural benefits. The cacao-cabruca AFS model is widely implemented in regions of the Brazilian Atlantic Forest. Carpotroche brasiliensis (Raddi) A. Gray (Achariaceae) is a tree found in cabruca landscapes that is often used for reforestation and biotechnological applications. Despite its importance, we still lack information about viruses circulating in C. brasiliensis, particularly considering the possibility of spillover that could affect cocoa production. In our study, we analyzed the Carpotroche brasiliensis virome from Atlantic Forest and cacao-cabruca AFS regions using metatranscriptomics from several vegetative and reproductive organs. Our results revealed a diverse virome detecting near-complete or partial coding sequences of single- and double-stranded DNA and RNA viruses classified into at least six families (Botourmiaviridae, Bromoviridae, Caulimoviridae, Genomoviridae, Mitoviridae, and Rhabdoviridae) plus unclassified elements. We described with high confidence the near-complete and the partial genomes of two tentative novel viruses: Carpotroche-associated ilarvirus and Carpotroche-associated genomovirus, respectively. Interestingly, we also described sequences likely derived from a rhabdovirus, which could represent a novel member of the genus Gammanucleorhabdovirus. We observed higher viral diversity in cacao-cabruca AFS and reproductive organs of C. brasiliensis with preferential tropism to fruits, which could directly affect production. Altogether, our results provide data to better understand the virome in this unexplored agroecological interface, such as cacao-cabruca AFS and forest ecosystem, providing information on the aspects of virus–plant interactions.

Complete genome sequence of a putative novel cytorhabdovirus isolated from Rudbeckia sp

Through high-throughput RNA sequencing, we discovered a putative new cytorhabdovirus in the seeds of Rudbeckia sp., which we have tentatively named "rudbeckia virus 1" (RudV1). Its complete 12,502-nt genomic sequence contains five open reading frames (ORFs): ORF1 (putative nucleocapsid protein, N), ORF2 (putative phosphoprotein, P), ORF3 (putative cell-to-cell movement protein, P3), ORF4 (putative matrix protein, M), and ORF5 (putative RNA-dependent RNA polymerase, L). BLASTp searches showed that ORF1, ORF3, ORF4, and ORF5 of RudV1 are most closely related to the corresponding proteins of Tagetes erecta virus 1 (a putative member of the genus Cytorhabdovirus) with 33.87% (88% query coverage), 55.98% (89% query coverage), 35.33% (94% query coverage), and 57.75% (98% query coverage) sequence identity at the amino acid level, respectively. Phylogenetic analysis and pairwise comparisons indicated that RudV1 is a novel member of the genus Cytorhabdovirus within the family Rhabdoviridae.

Genomic characterization of soybean blotchy mosaic virus, a cytorhabdovirus from South Africa

Samples showing blotchy mottle symptoms were collected from soybeans in North-West province, South Africa. The assembly of high-throughput sequencing data from three samples yielded contigs of 13,426 to 13,435nt, which represent the first complete genome sequences of soybean blotchy mosaic virus (SbBMV). SbBMV shows a typical cytorhabdovirus gene organization (3'-N-P-P3-M-G-L-5'), with each putative gene product being most similar, but with only 49.1-71.1% sequence identity, to those of cucurbit cytorhabdovirus 1. Given the species demarcation thresholds for rhabdoviruses, SbBMV is thus a distinct member of the genus Cytorhabdovirus.

Diversity of the virome associated with alfalfa (Medicago sativa L.) in the U.S. Pacific Northwest

Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage legumes in the world. It is currently the third most valuable field crop in the United States with an estimated value of over $9.3 billion. Alfalfa productivity is limited by various infectious diseases that can reduce forage yield and quality and shorten stand life. The crop can frequently be infected with a diverse array of pathogens and other organisms that have distinct life cycles, biology, and mode of action. Among them are many coinfecting viruses, that greatly contribute to the heterogeneity of within-host pathogenic communities, representing a ubiquitous and abundant background for all other host–pathogen interactions. Regrettably, the impact of viral diseases, their role in alfalfa health and involvement in the severity of multi-pathogen infections are often underestimated and not well understood. As high-throughput sequencing approaches have been developed, opportunities to delve into these complex interactions can be realized. In this work, we have characterized a diversity of viral populations in several commercial alfalfa production fields located in the U.S. Pacific Northwest. At least 45 distinct viruses have been identified in all alfalfa samples. Among them some were known to infect the crop prior to this study, and others were designated as emerging, novel and viruses integrated into the alfalfa genome. Known viruses included alfalfa mosaic virus, pea streak virus and bean leafroll virus, while among emerging and novel agents were alfalfa virus S, cherry virus Trakiya, several rhabdoviruses and others. Additional biological and impact studies will be needed to determine if newly identified viruses, especially those that have not been reported from alfalfa before, should be considered pathogens of this crop.

Complete genome sequence of a novel cytorhabdovirus infecting elderberry (Sambucus nigra L.) in the Czech Republic

The genus Cytorhabdovirus includes plant viruses with an unsegmented, single-stranded, negative-sense RNA genome that infect various plant hosts. In this work, we report the detection of a new cytorhabdovirus infecting elderberry (Sambucus nigra L.). Total RNA was purified from infected leaves and, after ribodepletion, sequenced using an Illumina system. The RNA genome of viral isolate B15 is 12,622 nucleotides (nt) long, and that of isolate B42 is 12,621 nt long. A nearly complete sequence (12,592 nt) was also obtained for a third isolate (B160). The RNA genomes of all three isolates showed an organisation typical of cytorhabdoviruses, harbouring all six of the expected genes (3´ N-P-P3-M-G-L 5´), separated by intergenic regions. These isolates were closely related to each other (99.5-99.6% nt sequence identity) and showed the highest overall similarity to trichosanthes associated rhabdovirus 1 (63.5% identity) and Wuhan insect virus 5 (58% identity), and similar results were obtained when comparing individual coding sequences or proteins. Phylogenetic analysis confirmed that this elderberry virus, for which we propose the name "sambucus virus 1" belongs to the genus Cytorhabdovirus and fulfils the criteria to represent a novel species.

Polyamine-metabolizing enzymes are activated to promote the proper assembly of rice stripe mosaic virus in insect vectors

Both viruses and host cells compete for intracellular polyamines for efficient propagation. Currently, how the key polyamine-metabolizing enzymes, including ornithine decarboxylase 1 (ODC1) and its antizyme 1 (OAZ1), are activated to co-ordinate viral propagation and polyamine biosynthesis remains unknown. Here, we report that the matrix protein of rice stripe mosaic virus (RSMV), a cytorhabdovirus, directly hijacks OAZ1 to ensure the proper assembly of rigid bacilliform non-enveloped virions in leafhopper vector. Viral matrix protein effectively competes with ODC1 to bind to OAZ1, and thus, the ability of OAZ1 to target and mediate the degradation of ODC1 is significantly inhibited during viral propagation, which finally promotes polyamines production. Thus, OAZ1 and ODC1 are activated to synergistically promote viral persistent propagation and polyamine biosynthesis in viruliferous vectors. Our data suggest that it is a novel mechanism for rhabdovirus to exploit OAZ1 for facilitating viral assembly.

Complete genome sequence of cnidium virus 1, a novel betanucleorhabdovirus infecting Cnidium officinale

The complete genomic sequence of a plant rhabdovirus that was identified in Cnidium officinale in Yeongyang-dun, South Korea, is reported here. The virus, tentatively named "cnidium virus 1" (CnV1), has a negative-sense RNA genome of ~ 14 kb, and its organization most closely resembles that of unsegmented plant rhabdoviruses, containing six antisense open reading frames (ORFs) in the order 3'-N-P-P3-M-G-L-5'. Intergenic regions containing conserved sequences separate the genes. The genome of CnV1 is 37.8-56% identical in its complete nucleotide sequence to betanucleorhabdoviruses and other related rhabdoviruses. Therefore, based on the sequence similarity criteria for species demarcation, its genome organization, and its phylogenetic position, CnV1 should be classified as a new member of the genus Betanucleorhabdovirus in the family Rhabdoviridae. CnV1 is the first rhabdovirus found in C. officinale.

Transmission and Pathogenicity of Papaya Virus E: Insights from an Experimental Papaya Orchard

A study was conducted to investigate epidemiological aspects of papaya virus E (PpVE), a cytorhabdovirus commonly found in papaya (Carica papaya L.) plantings in Ecuador. Besides papaya, PpVE was found in three Fabaceae weeds, including Rhynchosia minima, Centrosema plumieri, and Macroptilium lathyroides, the latter being the species with the highest virus prevalence. Greenhouse experiments showed that in M. lathyroides, single infections of PpVE induce only mild leaf mosaic, whereas in mixed infections with cowpea severe mosaic virus, PpVE contributes to severe mosaic. In papaya, PpVE did not induce noticeable symptoms in single or mixed infections with papaya ringspot virus. Transmission experiments confirmed that whiteflies (Bemisia tabaci) transmit PpVE in a semipersistent, nonpropagative manner.

Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes

The genus Cilevirus groups enveloped single-stranded (+) RNA virus members of the family Kitaviridae, order Martellivirales. Proteins P15, scarcely conserved polypeptides encoded by cileviruses, have no apparent homologs in public databases. Accordingly, the open reading frames (ORFs) p15, located at the 5'-end of the viral RNA2 molecules, are considered orphan genes (ORFans). In this study, we have delved into ORFs p15 and the relatively poorly understood biochemical properties of the proteins P15 to posit their importance for viruses across the genus and theorize on their origin. We detected that the ORFs p15 are under purifying selection and that, in some viral strains, the use of synonymous codons is biased, which might be a sign of adaptation to their plant hosts. Despite the high amino acid sequence divergence, proteins P15 show the conserved motif [FY]-L-x(3)-[FL]-H-x-x-[LIV]-S-C-x-C-x(2)-C-x-G-x-C, which occurs exclusively in members of this protein family. Proteins P15 also show a common predicted 3D structure that resembles the helical scaffold of the protein ORF49 encoded by radinoviruses and the phosphoprotein C-terminal domain of mononegavirids. Based on the 3D structural similarities of P15, we suggest elements of common ancestry, conserved functionality, and relevant amino acid residues. We conclude by postulating a plausible evolutionary trajectory of ORFans p15 and the 5'-end of the RNA2 of cileviruses considering both protein fold superpositions and comparative genomic analyses with the closest kitaviruses, negeviruses, nege/kita-like viruses, and unrelated viruses that share the ecological niches of cileviruses.

A novel Actinidia cytorhabdovirus characterized using genomic and viral protein interaction features

A novel cytorhabdovirus, tentatively named Actinidia virus D (AcVD), was identified from kiwifruit (Actinidia chinensis) in China using high-throughput sequencing technology. The genome of AcVD consists of 13,589 nucleotides and is organized into seven open reading frames (ORFs) in its antisense strand, coding for proteins in the order N-P-P3-M-G-P6-L. The ORFs were flanked by a 3' leader sequence and a 5' trailer sequence and are separated by conserved intergenic junctions. The genome sequence of AcVD was 44.6%-51.5% identical to those of reported cytorhabdoviruses. The proteins encoded by AcVD shared the highest sequence identities, ranging from 27.3% (P6) to 44.5% (L), with the respective proteins encoded by reported cytorhabdoviruses. Phylogenetic analysis revealed that AcVD clustered together with the cytorhabdovirus Wuhan insect virus 4. The subcellular locations of the viral proteins N, P, P3, M, G, and P6 in epidermal cells of Nicotiana benthamiana leaves were determined. The M protein of AcVD uniquely formed filament structures and was associated with microtubules. Bimolecular fluorescence complementation assays showed that three proteins, N, P, and M, self-interact, protein N plays a role in the formation of cytoplasm viroplasm, and protein M recruits N, P, P3, and G to microtubules. In addition, numerous paired proteins interact in the nucleus. This study presents the first evidence of a cytorhabdovirus infecting kiwifruit plants and full location and interaction maps to gain insight into viral protein functions.

Complete genome sequence of a novel varicosavirus infecting tall morning glory (Ipomoea purpurea)

A novel varicosa-like virus was identified in a tall morning glory (Ipomoea purpurea) plant by high-throughput sequencing and tentatively named "morning glory varicosavirus" (MGVV). The complete genome of MGVV contains two segments of negative-sense single-stranded RNA of 6409 (RNA1) and 5288 (RNA2) nucleotides. RNA1 encodes a 224.3-kDa large protein (224K), and RNA2 encodes four putative proteins of 48.6 kDa (49K), 46.4 kDa (46K), 35.7 kDa (36K), and 36.8 kDa (37K), respectively. The 224K and 49K proteins show amino acid sequence similarity to the large protein (39.4%) and the 49K protein (22.6%), respectively, of red clover-associated varicosavirus, and the 36K protein shares 19.6% amino acid sequence similarity with protein 3 of lettuce big-vein associated virus. The 46K and 37K proteins share no significant sequence similarity to known functional viral sequences. Phylogenetic analysis based on the large protein of MGVV and other rhabdoviruses showed that MGVV clustered with the varicosaviruses. These analyses indicate that MGVV is a novel member of the genus Varicosavirus in the family Rhabdoviridae.

Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here, we report the discovery of 27 novel rhabdovirus genomes associated with 25 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3000 plant and insect transcriptomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using known plant rhabdovirus sequences as the query. The identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses and seven to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provided additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrated that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy.

Efficient translation of Eggplant mottled dwarf nucleorhabdovirus N and X genes requires both 5' and 3' UTRs

Background

Circularization of RNA mediated by association of translation factors and RNA elements in 5′ and 3′ UTRs is a common feature for translation control in eukaryotes. There is no information about translation in plant rhabdoviruses and little information is known in animal rhabdoviruses.

Methods

The role of 5′ and 3′ UTRs in two genes of EMDV in translation were studied using luciferase constructs and RNA structures of these sequences were analyzed by SHAPE and Inline probing.

Results

We have found that efficient translation of N and X mRNAs of nucleorhabdovirus Eggplant mottled dwarf virus (EMDV) requires elements present in both 5′ and 3′ UTRs. Luciferase reporter constructs containing precise 5′ and 3′ UTRs of the N and X genes had substantially higher translational activity compared with constructs containing only the 5′ or 3′ UTR. The 3′UTR of carmovirus Turnip crinkle virus, which contains a well-characterized cap-independent translation enhancer, was unable to complement the lack of EMDV 3′ UTR. Addition of cap analog to luciferase constructs containing the UTRs of the N gene did not restore translation, and translation of the reporter construct in the absence of the 5′ cap was higher than the capped construct. No RNA-RNA interactions between 5′ and 3′ UTRs were detected by EMSA or in-line cleavage structural assays. Deletion of 11 nucleotides from the 3′ terminus negated the synergistic activity of the 3′UTR.

Conclusions

The results with RNA-RNA interaction suggesting that translational synergy between the UTRs may utilize alternative means. Mutation analysis in 3′UTR suggesting that the polyadenylation signal sequence contained in this location may play a critical role in translation.

Mining of the water hyssop (Bacopa monnieri) transcriptome reveals genome sequences of two putative novel rhabdoviruses and a solendovirus

The genomes of three putative novel viruses, tentatively named "Bacopa monnieri virus 1" (BmV1), "Bacopa monnieri virus 2" (BmV2), and "Bacopa monnieri virus 3" (BmV3) were identified in the transcriptome dataset of a medicinally important herb - water hyssop (Bacopa monnieri (L.) Wettst.). The BmV1 and BmV2 genomes resemble those of plant rhabdoviruses. The 13.3-kb-long BmV1 genome contains eight antisense ORFs in the order 3' l-N-P2'-P-P3-M-G-P6-L-t 5', with P2' ORF overlapping with P, while the 13.2-kb BmV2 genome contains six interspersed ORFs in the antisense orientation (3' l-N-P-P3-M-G-L-t 5'). The 8-kb BmV3 genome possesses five overlapping ORFs, with ORFs 2 to 5 being similar to those of solendoviruses. Based on genome organization, sequence similarity, and phylogeny, BmV1, BmV2, and BmV3 can be regarded as new members of the genera Cytorhabdovirus, Betanucleorhabdovirus, and Solendovirus, respectively.

Joá yellow blotch-associated virus, a new alphanucleorhabdovirus from a wild solanaceous plant in Brazil

We identified a novel plant rhabdovirus infecting native joá (Solanum aculeatissimum) plants in Brazil. Infected plants showed yellow blotches on the leaves, and typical enveloped bacilliform rhabdovirus particles associated with the nucleus were seen in thin sections by electron microscopy. The virus could be graft-transmitted to healthy joá and tomato plants but was not mechanically transmissible. RT-PCR using degenerate plant rhabdovirus L gene primers yielded an amplicon from extracted total RNA, the sequence of which was similar to those of alphanucleorhabdoviruses. Based on close sequence matches, especially with the type member potato yellow dwarf virus (PYDV), we adopted a degenerate-primer-walking strategy towards both genome ends. The complete genome of joá yellow blotch-associated virus (JYBaV) is comprised of 12,965 nucleotides, is less than 75% identical to that of its closest relative PYDV, and clusters with PYDV and other alphanucleorhabdoviruses in L protein phylogenetic trees, suggesting that it should be taxonomically classified in a new species in the genus Alphanucleorhabdovirus, family Rhabdoviridae. The genome organization of JYBaV is typical of the 'PYDV-like' subgroup of alphanucleorhabdoviruses, with seven genes (N-X-P-Y-M-G-L) separated by conserved intergenic regions and flanked by partly complementary 3' leader and 5' trailer regions.

Molecular characterization of a novel cytorhabdovirus associated with chrysanthemum yellow dwarf disease

Deep-sequencing analysis of a chrysanthemum plant with yellow dwarf symptoms led to the discovery of a novel putative cytorhabdovirus, here tentatively named "chrysanthemum yellow dwarf associated virus" (CYDaV). Its negative-sense single-stranded RNA genome comprises 14,086 nucleotides and contains eight open reading frames in the order 3' leader-N-P'-P-P3-M-G-P6-L-5' trailer. CYDaV shares moderate sequence similarity (< 54.2% nucleotide and 51% amino acid sequence identity) with its cytorhabdovirus counterparts in cognate genes. Phylogenetic analysis showed that CYDaV clustered with strong support with alfalfa dwarf virus, raspberry vein chlorosis virus, and strawberry crinkle virus. These findings suggest that CYDaV should be considered a novel member of the genus Cytorhabdovirus, family Rhabdoviridae.

Identification and characterization of a novel rhabdovirus in green rice leafhopper, Nephotettix cincticeps

The family Rhabdoviridae is one of the most ecological diverse groups of RNA viruses, with remarkable genome complexity and wide host range. Rhabdoviruses are discovered in many insect species, and insects, such as midges, mosquitoes, aphids and leafhoppers, act as crucial vectors for rhabdovirus transmission. Here, a novel rhabdovirus was identified in green rice leafhopper, Nephotettix cincticeps (Hemiptera: Cicadellidae), a common virus vector on rice. This virus was named as Nephotettix cincticeps negative-stranded RNA virus-1 (NcNSRV-1). The genome of NcNSRV-1 is 12,361 nucleotides in length, flanked by untranslated 3' leader and 5' trailer. The anti-sense viral genome consists of five major structural protein genes (N, P, M, G and L), which shares a typical architecture with the family Rhabdoviridae. An additional gene, P6, is interposed between G and L genes. NcNSRV-1 is phylogenetically clustered with the unclassified rhabdoviruses isolated from insects and exhibits low sequence identities with other viruses. The transcription regulatory sequences in NcNSRV-1 gene junctions were determined, revealing a unique transcription initiation sequence. In view of the phylogeny, sequence identity and genome organization, NcNSRV-1 is likely to be an insect rhabdovirus. Field surveys showed NcNSRV-1 was prevalent in the rice field populations of N. cincticeps in China.

Rose virus R, a cytorhabdovirus infecting rose

RNA was extracted from 'Hugh Dickson' rose leaves displaying virus-like symptoms in Maryland, USA. Using high-throughput sequencing, we identified a new virus, tentatively named "rose virus R". This virus has a negative-sense, single-stranded RNA genome and exhibits genomic features of a rhabdovirus, including a genome organization of 3'-N-P-P3-M-G-P6-L-5' and a gene junction region consensus sequence 3'-AUUUAUUUUGACUCUA-5'. Rose virus R is phylogenetically related to cytorhabdoviruses, and the nucleotide and amino acid sequences of rose virus R and related cytorhabdoviruses have diverged considerably, suggesting that rose virus R should be classified as a member of a novel species in the genus Cytorhabdovirus.

Population Genomics of Plant Viruses: The Ecology and Evolution of Virus Emergence

The genomics era has revolutionized studies of adaptive evolution by monitoring large numbers of loci throughout the genomes of many individuals. Ideally, the investigation of emergence in plant viruses requires examining the population dynamics of both virus and host, their interactions with each other, with other organisms and the abiotic environment. Genetic mechanisms that affect demographic processes are now being studied with high-throughput technologies, traditional genetics methods, and new computational tools for big-data. In this review, we discuss the utility of these approaches to monitor and detect changes in virus populations within cells and individuals, and over wider areas across species and communities of ecosystems. The advent of genomics in virology has fostered a multidisciplinary approach to tackling disease risk. The ability to make sense of the information now generated in this integrated setting is by far the most substantial obstacle to the ultimate goal of plant virology to minimize the threats to food security posed by disease. To achieve this goal, it is imperative to understand and forecast how populations respond to future changes in complex natural systems.

Dichorhaviruses Movement Protein and Nucleoprotein Form a Protein Complex That May Be Required for Virus Spread and Interacts in vivo With Viral Movement-Related Cilevirus Proteins

Brevipalpus-transmitted viruses (BTVs) belong to the genera Dichorhavirus and Cilevirus and are the main causal agents of the citrus leprosis (CL) disease. In this report, we explored aspects related to the movement mechanism mediated by dichorhaviruses movement proteins (MPs) and the homologous and heterologous interactions among viral proteins related to the movement of citrus leprosis-associated viruses. The membrane-spanning property and topology analysis of the nucleocapsid (N) and MP proteins from two dichorhaviruses revealed that the MPs are proteins tightly associated with the cell membrane, exposing their N- and C-termini to the cytoplasm and the inner part of the nucleus, whereas the N proteins are not membrane-associated. Subcellular localization analysis revealed the presence of dichorhavirus MPs at the cell surface and in the nucleus, while the phosphoproteins (P) were located exclusively in the nucleus and the N proteins in both the cytoplasm and the nucleus. Co-expression analysis with the MP, P, and N proteins showed an interaction network formed between them. We highlight the MP capability to partially redistribute the previously reported N-P core complex, redirecting a portion of the N from the nucleus to the plasmodesmata at the cell periphery, which indicates not only that the MP might guide the intracellular trafficking of the viral infective complex but also that the N protein may be associated with the cell-to-cell movement mechanism of dichorhaviruses. The movement functionality of these MPs was analyzed by using three movement-defective infectious systems. Also, the MP capacity to generate tubular structures on the protoplast surface by ectopic expression was analyzed. Finally, we evaluated the in vivo protein–protein interaction networks between the dichorhavirus MP and/or N proteins with the heterologous cilevirus movement components, which suggest a broad spectrum of interactions, highlighting those among capsid proteins (CP), MPs, and Ns from citrus leprosis-associated viruses. These data may aid in understanding the mixed infection process naturally observed in the field caused by distinct BTVs.

Transmission of the Bean-Associated Cytorhabdovirus by the Whitefly Bemisia tabaci MEAM1

The knowledge of genomic data of new plant viruses is increasing exponentially; however, some aspects of their biology, such as vectors and host range, remain mostly unknown. This information is crucial for the understanding of virus–plant interactions, control strategies, and mechanisms to prevent outbreaks. Typically, rhabdoviruses infect monocot and dicot plants and are vectored in nature by hemipteran sap-sucking insects, including aphids, leafhoppers, and planthoppers. However, several strains of a potentially whitefly-transmitted virus, papaya cytorhabdovirus, were recently described: (i) bean-associated cytorhabdovirus (BaCV) in Brazil, (ii) papaya virus E (PpVE) in Ecuador, and (iii) citrus-associated rhabdovirus (CiaRV) in China. Here, we examine the potential of the Bemisia tabaci Middle East-Asia Minor 1 (MEAM1) to transmit BaCV, its morphological and cytopathological characteristics, and assess the incidence of BaCV across bean producing areas in Brazil. Our results show that BaCV is efficiently transmitted, in experimental conditions, by B. tabaci MEAM1 to bean cultivars, and with lower efficiency to cowpea and soybean. Moreover, we detected BaCV RNA in viruliferous whiteflies but we were unable to visualize viral particles or viroplasm in the whitefly tissues. BaCV could not be singly isolated for pathogenicity tests, identification of the induced symptoms, and the transmission assay. BaCV was detected in five out of the seven states in Brazil included in our study, suggesting that it is widely distributed throughout bean producing areas in the country. This is the first report of a whitefly-transmitted rhabdovirus.