Genome sequence and molecular characterization of Homalodisca coagulata virus-1, a novel virus discovered in the glassy-winged sharpshooter (Hemiptera: Cicadellidae)

Diversity of RNA viruses in agricultural insects

Recent advancements in next-generation sequencing (NGS) technology and bioinformatics tools have revealed a vast array of viral diversity in insects, particularly RNA viruses. However, our current understanding of insect RNA viruses has primarily focused on hematophagous insects due to their medical importance, while research on the viromes of agriculturally relevant insects remains limited. This comprehensive review aims to address the gap by providing an overview of the diversity of RNA viruses in agricultural pests and beneficial insects within the agricultural ecosystem. Based on the NCBI Virus Database, over eight hundred RNA viruses belonging to 39 viral families have been reported in more than three hundred agricultural insect species. These viruses are predominantly found in the insect orders of Hymenoptera, Hemiptera, Thysanoptera, Lepidoptera, Diptera, Coleoptera, and Orthoptera. These findings have significantly enriched our understanding of RNA viral diversity in agricultural insects. While further virome investigations are necessary to expand our knowledge to more insect species, it is crucial to explore the biological roles of these identified RNA viruses within insects in future studies. This review also highlights the limitations and challenges for the effective virus discovery through NGS and their potential solutions, which might facilitate for the development of innovative bioinformatic tools in the future.

Broadening the host range and genetic diversity of waikaviruses

Waikaviruses are monopartite, positive sense, single-stranded RNA viruses that cause economically important plant diseases. Despite their importance, waikaviruses are poorly understood and only ten members are currently recognized. The present study on Sequence Read Archive (SRA)-based data-driven virus discovery (DDVD) identified 22 putative new waikaviruses, nearly doubling the number of known waikaviruses, in SRA libraries of diverse plant species, from ferns to trees. Besides, a highly divergent secoviral sequence with distinct genome features was identified in a wheat transcriptome. Other significant findings of the study include identification of a new waikavirus in a library derived from diseased water chestnut sample wherein a caulimovirus was reported, prediction of coiled-coils in hypothetical protein region of waikaviral polyprotein alignment and phylogenetic clustering of tree-infecting waikaviruses. The study not only reiterates the importance of DDVD in unveiling hitherto hidden viral sequences in plant SRA libraries but also deepens our understanding of waikaviral diversity.

Efficient CRISPR/Cas9-mediated genome modification of the glassy-winged sharpshooter Homalodisca vitripennis (Germar)

CRISPR/Cas9 technology enables the extension of genetic techniques into insect pests previously refractory to genetic analysis. We report the establishment of genetic analysis in the glassy-winged sharpshooter (GWSS), Homalodisca vitripennis, which is a significant leafhopper pest of agriculture in California. We use a novel and simple approach of embryo microinjection in situ on the host plant and obtain high frequency mutagenesis, in excess of 55%, of the cinnabar and white eye pigmentation loci. Through pair matings, we obtained 100% transmission of w and cn alleles to the G3 generation and also established that both genes are located on autosomes. Our analysis of wing phenotype revealed an unexpected discovery of the participation of pteridine pigments in wing and wing-vein coloration, indicating a role for these pigments beyond eye color. We used amplicon sequencing to examine the extent of off-target mutagenesis in adults arising from injected eggs, which was found to be negligible or non-existent. Our data show that GWSS can be easily developed as a genetic model system for the Hemiptera, enabling the study of traits that contribute to the success of invasive pests and vectors of plant pathogens. This will facilitate novel genetic control strategies.

Aphis glycines virus 1, a new bicistronic virus with two functional internal ribosome entry sites, is related to a group of unclassified viruses in the Picornavirales

A novel picorna-like virus, provisionally named Aphis glycines virus 1 (ApGlV1) was discovered by high-throughput sequencing of soybean total RNAs and detected in suction trap-collected Aphis glycines. The ApGlV1 genome contains two large ORFs organized similar to those of dicipiviruses in the Picornaviridae where ORFs 1 and 2 encode structural and nonstructural proteins, respectively. Both ORFs are preceded by internal ribosome entry site (IRES) elements. The 5' IRES was more active in dual luciferase activity assays than the IRES in the intergenic region. The ApGlV1 genome was predicted to encode a serine protease instead of a cysteine protease and showed very low aa sequence identities to recognized members of the Picornavirales. In phylogenetic analyses based on capsid protein and RNA-dependent RNA polymerase sequences, ApGlV1 consistently clustered with a group of unclassified bicistronic picorna-like viruses discovered from arthropods and plants that may represent a novel family in the order Picornavirales.

Global In-Silico Scenario of tRNA Genes and Their Organization in Virus Genomes

Viruses are known to be highly dependent on the host translation machinery for their protein synthesis. However, tRNA genes are occasionally identified in such organisms, and in addition, few of them harbor tRNA gene clusters comprising dozens of genes. Recently, tRNA gene clusters have been shown to occur among the three domains of life. In such a scenario, the viruses could play a role in the dispersion of such structures among these organisms. Thus, in order to reveal the prevalence of tRNA genes as well as tRNA gene clusters in viruses, we performed an unbiased large-scale genome survey. Interestingly, tRNA genes were predicted in ssDNA (single-stranded DNA) and ssRNA (single-stranded RNA) viruses as well in many other dsDNA viruses of families from Caudovirales order. In the latter group, tRNA gene clusters composed of 15 to 37 tRNA genes were characterized, mainly in bacteriophages, enlarging the occurrence of such structures within viruses. These bacteriophages were from hosts that encompass five phyla and 34 genera. This in-silico study presents the current global scenario of tRNA genes and their organization in virus genomes, contributing and opening questions to be explored in further studies concerning the role of the translation apparatus in these organisms.

Pierce's Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model

Xylella fastidiosa is a notorious plant pathogenic bacterium that represents a threat to crops worldwide. Its subspecies, Xylella fastidiosa subsp. fastidiosa is the causal agent of Pierce's disease of grapevines. Pierce's disease has presented a serious challenge for the grapevine industry in the United States and turned into an epidemic in Southern California due to the invasion of the insect vector Homalodisca vitripennis. In an attempt to minimize the effects of Xylella fastidiosa subsp. fastidiosa in vineyards, various studies have been developing and testing strategies to prevent the occurrence of Pierce's disease, i.e., prophylactic strategies. Research has also been undertaken to investigate therapeutic strategies to cure vines infected by Xylella fastidiosa subsp. fastidiosa. This report explicitly reviews all the strategies published to date and specifies their current status. Furthermore, an epidemiological model of Xylella fastidiosa subsp. fastidiosa is proposed and key parameters for the spread of Pierce's disease deciphered in a sensitivity analysis of all model parameters. Based on these results, it is concluded that future studies should prioritize therapeutic strategies, while investments should only be made in prophylactic strategies that have demonstrated promising results in vineyards.

Viral internal ribosomal entry sites: four classes for one goal

To ensure efficient propagation, viruses need to rapidly produce viral proteins after cell entrance. Since viral genomes do not encode any components of the protein biosynthesis machinery, viral proteins must be produced by the host cell. To hi-jack the host cellular translation, viruses use a great variety of distinct strategies. Many single-stranded positive-sensed RNA viruses contain so-called internal ribosome entry sites (IRESs). IRESs are structural RNA motifs that have evolved to specific folds that recruit the host ribosomes on the viral coding sequences in order to synthesize viral proteins. In host canonical translation, recruitment of the translation machinery components is essentially guided by the 5' cap (m⁷ G) of mRNA. In contrast, IRESs are able to promote efficient ribosome assembly internally and in cap-independent manner. IRESs have been categorized into four classes, based on their length, nucleotide sequence, secondary and tertiary structures, as well as their mode of action. Classes I and II require the assistance of cellular auxiliary factors, the eukaryotic intiation factors (eIF), for efficient ribosome assembly. Class III IRESs require only a subset of eIFs whereas Class IV, which are the more compact, can promote translation without any eIFs. Extensive functional and structural investigations of IRESs over the past decades have allowed a better understanding of their mode of action for viral translation. Because viral translation has a pivotal role in the infectious program, IRESs are therefore attractive targets for therapeutic purposes. WIREs RNA 2018, 9:e1458. doi: 10.1002/wrna.1458 This article is categorized under: Translation > Ribosome Structure/Function Translation > Translation Mechanisms RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.

Virion Structure of Black Queen Cell Virus, a Common Honeybee Pathogen

Viral diseases are a major threat to honeybee (Apis mellifera) populations worldwide and therefore an important factor in reliable crop pollination and food security. Black queen cell virus (BQCV) is the etiological agent of a fatal disease of honeybee queen larvae and pupae. The virus belongs to the genus Triatovirus from the family Dicistroviridae, which is part of the order Picornavirales. Here we present a crystal structure of BQCV determined to a resolution of 3.4 Å. The virion is formed by 60 copies of each of the major capsid proteins VP1, VP2, and VP3; however, there is no density corresponding to a 75-residue-long minor capsid protein VP4 encoded by the BQCV genome. We show that the VP4 subunits are present in the crystallized virions that are infectious. This aspect of the BQCV virion is similar to that of the previously characterized triatoma virus and supports the recent establishment of the separate genus Triatovirus within the family Dicistroviridae. The C terminus of VP1 and CD loops of capsid proteins VP1 and VP3 of BQCV form 34-Å-tall finger-like protrusions at the virion surface. The protrusions are larger than those of related dicistroviruses.

IMPORTANCE The western honeybee is the most important pollinator of all, and it is required to sustain the agricultural production and biodiversity of wild flowering plants. However, honeybee populations worldwide are suffering from virus infections that cause colony losses. One of the most common, and least known, honeybee pathogens is black queen cell virus (BQCV), which at high titers causes queen larvae and pupae to turn black and die. Here we present the three-dimensional virion structure of BQCV, determined by X-ray crystallography. The structure of BQCV reveals large protrusions on the virion surface. Capsid protein VP1 of BQCV does not contain a hydrophobic pocket. Therefore, the BQCV virion structure provides evidence that capsid-binding antiviral compounds that can prevent the replication of vertebrate picornaviruses may be ineffective against honeybee virus infections.

Sequence polymorphism in an insect RNA virus field population: A snapshot from a single point in space and time reveals stochastic differences among and within individual hosts

Population structure of Homalodisca coagulata Virus-1 (HoCV-1) among and within field-collected insects sampled from a single point in space and time was examined. Polymorphism in complete consensus sequences among single-insect isolates was dominated by synonymous substitutions. The mutant spectrum of the C2 helicase region within each single-insect isolate was unique and dominated by nonsynonymous singletons. Bootstrapping was used to correct the within-isolate nonsynonymous:synonymous arithmetic ratio (N:S) for RT-PCR error, yielding an N:S value ~one log-unit greater than that of consensus sequences. Probability of all possible single-base substitutions for the C2 region predicted N:S values within 95% confidence limits of the corrected within-isolate N:S when the only constraint imposed was viral polymerase error bias for transitions over transversions. These results indicate that bottlenecks coupled with strong negative/purifying selection drive consensus sequences toward neutral sequence space, and that most polymorphism within single-insect isolates is composed of newly-minted mutations sampled prior to selection.

Propagation of Homalodisca coagulata virus-01 via Homalodisca vitripennis cell culture

The glassy-winged sharpshooter (Homalodisca vitripennis) is a highly vagile and polyphagous insect found throughout the southwestern United States. These insects are the predominant vectors of Xylella fastidiosa (X. fastidiosa), a xylem-limited bacterium that is the causal agent of Pierce's disease (PD) of grapevine. Pierce's disease is economically damaging; thus, H. vitripennis have become a target for pathogen management strategies. A dicistrovirus identified as Homalodisca coagulata virus-01 (HoCV-01) has been associated with an increased mortality in H. vitripennis populations. Because a host cell is required for HoCV-01 replication, cell culture provides a uniform environment for targeted replication that is logistically and economically valuable for biopesticide production. In this study, a system for large-scale propagation of H. vitripennis cells via tissue culture was developed, providing a viral replication mechanism. HoCV-01 was extracted from whole body insects and used to inoculate cultured H. vitripennis cells at varying levels. The culture medium was removed every 24 hr for 168 hr, RNA extracted and analyzed with qRT-PCR. Cells were stained with trypan blue and counted to quantify cell survivability using light microscopy. Whole virus particles were extracted up to 96 hr after infection, which was the time point determined to be before total cell culture collapse occurred. Cells were also subjected to fluorescent staining and viewed using confocal microscopy to investigate viral activity on F-actin attachment and nuclei integrity. The conclusion of this study is that H. vitripennis cells are capable of being cultured and used for mass production of HoCV-01 at a suitable level to allow production of a biopesticide.

Structure of the Triatoma virus capsid

The members of the Dicistroviridae family are non-enveloped positive-sense single-stranded RNA (+ssRNA) viruses pathogenic to beneficial arthropods as well as insect pests of medical importance. Triatoma virus (TrV), a member of this family, infects several species of triatomine insects (popularly named kissing bugs), which are vectors for human trypanosomiasis, more commonly known as Chagas disease. The potential use of dicistroviruses as biological control agents has drawn considerable attention in the past decade, and several viruses of this family have been identified, with their targets covering honey bees, aphids and field crickets, among others. Here, the crystal structure of the TrV capsid at 2.5 Å resolution is reported, showing that as expected it is very similar to that of Cricket paralysis virus (CrPV). Nevertheless, a number of distinguishing structural features support the introduction of a new genus (Triatovirus; type species TrV) under the Dicistroviridae family. The most striking differences are the absence of icosahedrally ordered VP4 within the infectious particle and the presence of prominent projections that surround the fivefold axis. Furthermore, the structure identifies a second putative autoproteolytic DDF motif in protein VP3, in addition to the conserved one in VP1 which is believed to be responsible for VP0 cleavage during capsid maturation. The potential meaning of these new findings is discussed.

Small RNA populations for two unrelated viruses exhibit different biases in strand polarity and proximity to terminal sequences in the insect host Homalodisca vitripennis

Next generation sequence analyses were used to assess virus-derived small RNA (vsRNA) profiles for Homalodisca coagulata virus-1 (HoCV-1), family Dicistroviridae, and Homalodisca vitripennis reovirus (HoVRV), family Reoviridae, from virus-infected H. vitripennis, the glassy-winged sharpshooter. The vsRNA reads were mapped against the monopartite genome of HoCV-1 and all 12 genome segments of HoVRV, and 21nt vsRNAs were most common. However, strikingly contrasting patterns for the HoCV-1 and HoVRV genomic RNAs were observed. The majority of HoCV-1 vsRNAs mapped to the genomic positive-strand RNA and, although minor hotspots were observed, vsRNAs mapped across the entire genomic RNA. In contrast, HoVRV vsRNAs mapped to both positive and negative-sense strands for all genome segments, but different genomic segments showed distinct hotspots. The HoVRV vsRNAs were more common for 5' and 3' regions of HoVRV regions of all segments. These data suggest that taxonomically different viruses in the same host offer different targets for RNA-antiviral defense.

Pathogenicity and complete genome sequence analysis of the mud crab dicistrovirus-1

A virus with a particle diameter of approximately 30 nm and no envelope was purified from diseased mud crab, Scylla paramamosain and it was demonstrated to be pathogenic to mud crab. The complete nucleotide sequence analysis indicated that its genome was a single molecule of linear positive-sense ssRNA with a length of 10,415 nucleotides, excluding the 3'poly (A) tail. It consisted of two open reading frames (ORF) separated by an intergenic region (IGR) and flanked by a 5'untranslated region (5'-UTR) and a 3'untranslated region (3'-UTR). The 5'-ORF encode five putative non-structural proteins, including BIR (Baculovirus Inhibitor of Apoptosis Protein Repeat), helicase, VPg (the genome-linked viral protein), 3C-like protease and RdRP (RNA-dependent RNA polymerase), while the 3'-ORF encode the structural protein precursors. This genome organization was consistent with the typical organization of dicistrovirus and the virus was designated as mud crab dicistrovirus-1 (MCDV-1). The results of the phylogenetic analysis of the putative structural protein precursor suggest that MCDV-1 has a closer genetic relationship with Taura syndrome virus (TSV) than do other dicistroviruses and that MCDV-1 is a new member of the family Dicistroviridae and assigned into the genus Aparavirus.

Metatranscriptomics and pyrosequencing facilitate discovery of potential viral natural enemies of the invasive Caribbean crazy ant, Nylanderia pubens

BACKGROUND

Nylanderia pubens (Forel) is an invasive ant species that in recent years has developed into a serious nuisance problem in the Caribbean and United States. A rapidly expanding range, explosive localized population growth, and control difficulties have elevated this ant to pest status. Professional entomologists and the pest control industry in the United States are urgently trying to understand its biology and develop effective control methods. Currently, no known biological-based control agents are available for use in controlling N. pubens.

METHODOLOGY AND PRINCIPAL FINDINGS

Metagenomics and pyrosequencing techniques were employed to examine the transcriptome of field-collected N. pubens colonies in an effort to identify virus infections with potential to serve as control agents against this pest ant. Pyrosequencing (454-platform) of a non-normalized N. pubens expression library generated 1,306,177 raw sequence reads comprising 450 Mbp. Assembly resulted in generation of 59,017 non-redundant sequences, including 27,348 contigs and 31,669 singlets. BLAST analysis of these non-redundant sequences identified 51 of potential viral origin. Additional analyses winnowed this list of potential viruses to three that appear to replicate in N. pubens.

CONCLUSIONS

Pyrosequencing the transcriptome of field-collected samples of N. pubens has identified at least three sequences that are likely of viral origin and, in which, N. pubens serves as host. In addition, the N. pubens transcriptome provides a genetic resource for the scientific community which is especially important at this early stage of developing a knowledgebase for this new pest.

Reovirus genomes from plant-feeding insects represent a newly discovered lineage within the family Reoviridae

A complex set of double-stranded RNAs (dsRNAs) was isolated from threecornered alfalfa hopper (Spissistilus festinus), a plant-feeding hemipteran pest. A subset of these dsRNAs constitute the genome of a new reovirus, provisionally designated Spissistilus festinus reovirus (SpFRV). SpFRV was present in threecornered alfalfa hopper populations in the San Joaquin Valley of California, with incidence ranging from 10% to 60% in 24 of 25 sample sets analyzed. The 10 dsRNA segments of SpFRV were completely sequenced and shown to share conserved terminal sequences (5'-AGAGA and CGAUGUUGU-3') of the positive-sense strand that are distinct from known species of the family Reoviridae. Comparisons of the RNA directed RNA polymerase (RdRp) indicated SpFRV is most closely related (39.1% amino acid identity) to another new reovirus infecting the angulate leafhopper (Acinopterus angulatus) and provisionally designated Acinopterus angulatus reovirus (AcARV). The RdRp of both viruses was distantly related to Raspberry latent virus RdRp at 27.0% (SpFRV) and 30.0% (AcARV) or Rice ragged stunt virus RdRp at 26.2% (SpFRV) and 29.0% (AcARV) amino acid identity. RdRp phylogeny confirmed that SpFRV and AcARV are sister taxa sharing a most recent common ancestor. SpFRV segment 6 encodes a protein containing two NTP binding motifs that are conserved in homologs of reoviruses in the subfamily Spinareovirinae. The protein encoded by SpFRV segment 4 was identified as a guanylyltransferase homolog. SpFRV segments 1, 3, and 10 encode homologs of reovirus structural proteins. No homologs were identified for proteins encoded by SpFRV segments 5, 7, 8, and 9. Collectively, the low level of sequence identity with other reoviruses, similar segment terminal sequences, RdRp phylogeny, and host taxa indicate that SpFRV and AcARV may be considered members of a proposed new genus of the family Reoviridae (subfamily Spinareovirinae), with SpFRV assigned as the type species.

Next generation sequencing technologies for insect virus discovery

Insects are commonly infected with multiple viruses including those that cause sublethal, asymptomatic, and latent infections. Traditional methods for virus isolation typically lack the sensitivity required for detection of such viruses that are present at low abundance. In this respect, next generation sequencing technologies have revolutionized methods for the discovery and identification of new viruses from insects. Here we review both traditional and modern methods for virus discovery, and outline analysis of transcriptome and small RNA data for identification of viral sequences. We will introduce methods for de novo assembly of viral sequences, identification of potential viral sequences from BLAST data, and bioinformatics for generating full-length or near full-length viral genome sequences. We will also discuss implications of the ubiquity of viruses in insects and in insect cell lines. All of the methods described in this article can also apply to the discovery of viruses in other organisms.

In vivo functional analysis of the Dicistroviridae intergenic region internal ribosome entry sites

Some viral and cellular messages use an alternative mechanism to initiate protein synthesis that involves internal recruitment of the ribosome to an internal ribosome entry site (IRES). The Dicistroviridae intergenic regions (IGR) have been studied as model IRESs to understand the mechanism of IRES-mediated translation. In this study, the in vivo activity of IGR IRESs were compared. Our analysis demonstrates that Class I and II IGR IRESs have comparable translation efficiency in yeast and that Class II is significantly more active in mammalian cells. Furthermore, while Class II IGR IRES activity was enhanced in yeast grown at a higher temperature, temperature did not affect IGR IRES activity in mammalian cells. This suggests that Class II IRESs may not function optimally with yeast ribosomes. Examination of chimeric IGR IRESs, established that the IRES strength and temperature sensitivity are mediated by the ribosome binding domain. In addition, the sequence of the first translated codon is also an important determinant of IRES activity. Our findings provide us with a comprehensive overview of IGR IRES activities and allow us to begin to understand the differences between Classes I and II IGR IRESs.

Plant-feeding insects harbor double-stranded RNA viruses encoding a novel proline-alanine rich protein and a polymerase distantly related to that of fungal viruses

Novel double-stranded RNAs (approximately 8 kbp) were isolated from threecornered alfalfa hopper (Spissistilus festinus) and beet leafhopper (Circulifer tenellus), two plant-feeding hemipteran insect pests. The two new viruses, designated Spissistilus festinus virus 1 (SpFV1) and Circulifer tenellus virus 1 (CiTV1), do not appear to be encapsidated in conventional virions and shared a genome organization similar to that of several unclassified fungal viruses. SpFV1 and CiTVl encode a proline-alanine rich protein (PArp) and an RNA-directed RNA polymerase (RdRp). Expression of the 3'-proximal RdRp ORF appears to result from -1 translational frameshifting of the PArp ORF. Phylogenetic analysis of the RdRp indicated that SpFV1 and CiTV1 were most closely related to each other and the unclassified plant virus Cucurbit yellows associated virus, and more distantly related to the unclassified fungal dsRNA viruses Phlebiopsis gigantea virus 2 and Fusarium graminearum virus 3.

Discovery and effects of Texas Solenopsis invicta virus [SINV-1 (TX5)] on red imported fire ant populations

Solenopsis invicta Buren (Hymenoptera: Formicidae), the red imported fire ant is native to South America but has invaded areas of the southeastern US, and parts of Southern California. The S. invicta virus-1 (SINV-1) is a positive sense, single-stranded RNA picorna-like virus that only affects Solenopsis species. The virus can infect all caste members and developmental stages. Infection of SINV-1 can result in colony collapse in less than 3 months under laboratory conditions. This study screened S. invicta colonies from Texas for the presence of SINV through Reverse Transcriptase PCR (RT-PCR). Positive samples were genetically characterized by direct sequencing and compared with known picorna-like viruses. SINV-1 was detected in ant colonies from Smith and Henderson TX counties. Amino acid sequence comparison of SINV-1 (TX5) ORF2 region showed homologies of 96% with SINV-1, 97% with SINV-1A, 17.6% with SINV-2, and 20.7% with SINV-3. In addition, SINV-1 (TX5) was compared to 18 other Dicistroviridae viruses. Ant-infecting viruses may provide new approaches to suppressing these important economic pests.

Data mining cDNAs reveals three new single stranded RNA viruses in Nasonia (Hymenoptera: Pteromalidae)

We report three novel small RNA viruses uncovered from cDNA libraries from parasitoid wasps in the genus Nasonia. The genome of this kind of virus is a positive-sense single-stranded RNA with a 3' poly(A), which facilitates cloning from cDNAs. Two of the viruses, NvitV-1 and NvitV-2, possess a RNA-dependent RNA polymerase that associates them with the family Iflaviridae of the order Picornavirales. A third virus, NvitV-3, is most similar to the Nora virus from Drosophila. A reverse transcription-PCR method developed for NvitV-1 indicates that it is a persistent commensal infection of Nasonia.

Characterization of a Taura syndrome virus isolate originating from the 2004 Texas epizootic in cultured shrimp

A comprehensive investigation of the Taura syndrome virus (TSV) isolate that caused epizootics in shrimp farms in Texas in 2004 (Texas isolate) revealed that this virus was more virulent in laboratory bioassays than the TSV reference isolate, Hawaii 1994, causing severe symptom development and rapid mortality. Histopathology of moribund animals demonstrated epithelial necrosis within the stomach, appendages, general body cuticle and gills, and the surviving animals demonstrated moderate to numerous lymphoid organ spheroids. Purified virions showed icosahedral morphology, with a diameter of 31 nm. Comparative genome analysis showed that the Texas isolate is more closely related to TSV isolates from Thailand and China than to the Hawaii isolate. The predicted tertiary structures of the inhibition of apoptosis protein (IAP) and protease domains of the Texas isolate are very similar to those of the Hawaii isolate. However, the RNA-dependent RNA polymerase (RdRp) of the Texas isolate has significant structural differences from the Hawaii isolate due to point mutation(s) in the RdRp gene. Changes in the RdRp tertiary structure might contribute to the replication fidelity, virulence and ecological adaptability of the Texas isolate.

Dicistroviruses

Dicistroviruses are members of a recently defined and rapidly growing family of picornavirus-like RNA viruses called the Dicistroviridae. Dicistroviruses are pathogenic to beneficial arthropods such as honey bees and shrimp and to insect pests of medical and agricultural importance. Our understanding of these viruses is uneven. We present highly advanced studies of the virus particle structure, remarkable mechanisms of internal ribosome entry in translation of viral RNA, and the use of dicistroviruses to study the insect immune system. However, little is known about dicistrovirus RNA replication mechanisms or gene function, except by comparison with picornaviruses. The recent construction of infectious clones of dicistrovirus genomes may fill these gaps in knowledge. We discuss economically important diseases caused by dicistroviruses. Future research may lead to protection of beneficial arthropods from dicistroviruses and to application of dicistroviruses as biopesticides targeting pestiferous insects.

Medium for development of bee cell cultures (Apis mellifera: Hymenoptera: Apidae)

A media for the production of cell cultures from hymenopteran species such as honey bee, Apis mellifera L. (Hymenoptera: Apidae) was developed. Multiple bee cell cultures were produced when using bee larvae and pupae as starting material and modified Hert-Hunter 70 media. Cell culture systems for bees solves an impasse that has hindered efforts to isolate and screen pathogens which may be influencing or causing colony collapse disorder of bees. Multiple life stages of maturing larvae to early pupae were used to successfully establish cell cultures from the tissues of the head, thorax, and abdomen. Multiple cell types were observed which included free-floating suspensions, fibroblast-like, and epithelia-like monolayers. The final culture medium, WH2, was originally developed for hemipterans, Asian citrus psyllid, Diaphorina citri, and leafhopper, Homalodisca vitripennis cell cultures but has been shown to work for a diverse range of insect species such as bees. Bee cell cultures had various doubling times at 21-23 degrees C ranging from 9-15 d. Deformed wing virus was detected in the primary explanted tissues, which tested negative by rt-PCR for Israeli acute paralysis virus (IAPV), Kashmir bee virus, acute bee paralysis virus, and black queen cell virus. Culture inoculation with IAPV from an isolate from Florida field samples, was detectable in cell cultures after two subcultures. Cell culture from hymenoptera species, such as bees, greatly advances the approaches available to the field of study on colony collapse disorders.

Behavioral model for Homalodisca vitripennis (Hemiptera: Cicadellidae): optimization of host plant utilization and management implications

The glassy-winged sharpshooter, Homalodisca vitripennis (Germar), (Hemiptera: Cicadellidae), is a xylophagous leafhopper native to the southeastern United States and northern Mexico, with recent introductions into California, Arizona, French Polynesia, and Hawaii. It is a primary vector of the xylem-limited bacterium, Xylella fastidiosa Wells et al., the causative agent of Pierce's disease of grape, citrus variegated chlorosis, phony peach, and numerous leaf scorch diseases. H. vitripennis uses several hundred species of host plants for feeding, development, and reproduction. Variation in host utilization allows H. vitripennis to respond to diurnal and seasonal changes in its nutrient-poor food source, xylem fluid, as well as changing nutritional requirements of each leafhopper developmental stage. Here we provide a conceptual model that integrates behavior, life history strategies, and their associated risks with the nutritional requirements of adult and nymphal stages of H. vitripennis. The model is a useful heuristic tool that explains patterns of host plant use, describes insect behavior and ecology, suggests new associations among the ecological components, and most importantly, identifies and supports the development of suppression strategies for X. fastidiosa aimed at reducing vector populations through habitat manipulation.

Functional analysis of structural motifs in dicistroviruses

The family Dicistroviridae is composed of positive-stranded RNA viruses which have monopartite genomes. These viruses carry genome-linked virus proteins (VPg) and poly (A) tails. The 5' untranslated region (UTR) is approximately 500 nucleotides and contains an internal ribosome entry site (IRES). These features resemble those of vertebrate picornaviruses, but dicistroviruses have other distinct characteristics. Picornaviruses have a single large open reading frame (ORF) encoding the capsid proteins at the 5'-end and the replicases at the 3'-end. In contrast, dicistroviruses have two nonoverlapping ORFs. The 5'-proximal ORF encodes the replicases and the 3'-proximal ORF encodes the capsid proteins. Usually, positive-stranded viruses which have capsid protein genes in the 3' part of the genome produce subgenomic RNA for synthesis of the capsid proteins, because abundant quantities of the capsid proteins are required for the viral replication cycle. In dicistroviruses, translation of the capsid proteins is controlled by an additional IRES. This IRES is located in the intergenic region (IGR) between the replicase and capsid coding regions, and mediates the initiation of translation for the capsid proteins. The IGR-IRES has a multiple stem-loop structure containing three pseudoknots. We describe the characteristics of dicistroviruses, including the RNA elements and viral proteins.

Infectious genomic RNA of Rhopalosiphum padi virus transcribed in vitro from a full-length cDNA clone

Availability of a cloned genome from which infectious RNA can be transcribed is essential for investigating RNA virus molecular mechanisms. To date, no such clones have been reported for the Dicistroviridae, an emerging family of invertebrate viruses. Previously we demonstrated baculovirus-driven expression of a cloned Rhopalosiphum padi virus (RhPV; Dicistroviridae) genome that was infectious to aphids, and we identified a cell line (GWSS-Z10) from the glassy-winged sharpshooter, that supports RhPV replication. Here we report that RNA transcribed from a full-length cDNA clone is infectious. Transfection of GWSS-Z10 cells with the RhPV transcript resulted in cytopathic effects, ultrastructural changes, and accumulation of progeny virions, consistent with virus infection. Virions from transcript-infected cells were infectious in aphids. This infectious transcript of a cloned RhPV genome provides a valuable tool, and a more tractable system without interference from baculovirus infection, for investigating replication and pathogenesis of dicistroviruses.

Isolation and characterization of Israeli acute paralysis virus, a dicistrovirus affecting honeybees in Israel: evidence for diversity due to intra- and inter-species recombination

We report the isolation, purification, genome-sequencing and characterization of a picorna-like virus from dead bees in Israel. Sequence analysis indicated that IAPV (Israeli acute paralysis virus) is a distinct dicistrovirus. It is most homologous to Kashmir bee virus and acute bee paralysis virus. The virus carries a 9487 nt RNA genome in positive orientation, with two open reading frames separated by an intergenic region, and its coat comprises four major proteins, the sizes of which suggest alternate processing of the polyprotein. IAPV virions also carry shorter, defective-interfering (DI)-like RNAs. Some of these RNAs are recombinants of different segments of IAPV RNA, some are recombinants of IAPV RNA and RNA from another dicistrovirus, and yet others are recombinants of IAPV and non-viral RNAs. In several of the DI-like RNAs, a sense-oriented fragment has recombined with its complement, forming hairpins and stem–loop structures. In previous reports, we have shown that potyviral and IAPV sequences are integrated into the genome of their respective hosts. The dynamics of information exchange between virus and host and the possible resistance-engendering mechanisms are discussed.

Prevalence and natural host range of Homalodisca coagulata virus-1 (HoCV-1)

Transmission electron microscopy was used to confirm the presence of picorna-like virus particles presumed to be Homalodisca coagulata virus-1 (HoCV-1) in the midgut region of adult glassy-winged sharpshooters (GWSS). In addition, we offer a reverse transcription polymerase chain reaction (RT-PCR) assay for the detection of this virus with a sensitivity of approximately 95 genome equivalents. A survey employing this assay in conjunction with GWSS samples collected throughout the United States including California, Hawaii, Florida Georgia, and the Carolinas revealed a fairly widespread pattern of distribution, although potentially restricted to temperate regions, areas with elevated host densities, or to populations of a common origin. The virus was found to naturally infect adults regardless of host plant and was not specific to a particular lifestage or sex. Examination of alternate leafhopper species further demonstrated that, although infection is not ubiquitous to all sharpshooter genera, HoCV-1 is not limited to Homalodisca vitripennis (=H. coagulata).

A baculovirus-expressed dicistrovirus that is infectious to aphids

Detailed investigation of virus replication is facilitated by the construction of a full-length infectious clone of the viral genome. To date, this has not been achieved for members of the family Dicistroviridae. Here we demonstrate the construction of a baculovirus that expresses a dicistrovirus that is infectious in its natural host. We inserted a full-length cDNA clone of the genomic RNA of the dicistrovirus Rhopalosiphum padi virus (RhPV) into a baculovirus expression vector. Virus particles containing RhPV RNA accumulated in the nuclei of baculovirus-infected Sf21 cells expressing the recombinant RhPV clone. These virus particles were infectious in R. padi, a ubiquitous aphid vector of major cereal viruses. The recombinant virus was transmitted efficiently between aphids, despite the presence of 119 and 210 vector-derived bases that were stably maintained at the 5' and 3' ends, respectively, of the RhPV genome. The maintenance of such a nonviral sequence was surprising considering that most RNA viruses tolerate few nonviral bases beyond their natural termini. The use of a baculovirus to express a small RNA virus opens avenues for investigating replication of dicistroviruses and may allow large-scale production of these viruses for use as biopesticides.