Diverse Array of New Viral Sequences Identified in Worldwide Populations of the Asian Citrus Psyllid (Diaphorina citri) Using Viral Metagenomics

RNA virus diversity and prevalence in field and laboratory populations of melon fly throughout its distribution

Insects have a rich diversity of RNA viruses that can either cause acute infections or persist in host populations without visible symptoms. The melon fly, Zeugodacus cucurbitae (Tephritidae) causes substantial economic losses through infestation of diverse cucurbit and other crops. Of Indomalayan origin, it is now established in many tropical regions of the world. The virome diversity of Z. cucurbitae is largely unknown across large parts of its distribution, including the Indian subcontinent. We have analysed three transcriptomes each of one field-collected and one laboratory-reared Z. cucurbitae population from Bangalore (India) and discovered genomes of ten putative RNA viruses: two sigmaviruses, one chimbavirus, one cripavirus, one noda-like virus, one nora virus, one orbivirus, one partiti-like virus, one sobemovirus and one toti-like virus. Analysis of the only available host genome of a Hawaiian Z. cucurbitae population did not detect host genome integration of the detected viruses. While all ten viruses were found in the Bangalore field population only seven were detected in the laboratory population, indicating that these seven may cause persistent covert infections. Using virus-specific RNA-dependent RNA polymerase gene primers, we detected nine of the RNA viruses with an overall low variant diversity in some but not all individual flies from four out of five Indian regions. We then screened 39 transcriptomes of Z. cucurbitae laboratory populations from eastern Asia (Guangdong, Hainan, Taiwan) and the Pacific region (Hawaii), and detected seven of the ten virus genomes. We found additional genomes of a picorna-like virus and a negev-like virus. Hawaii as the only tested population from the fly's invasive range only had one virus. Our study provides evidence of new and high RNA virus diversity in Indian populations within the original range of Z. cucurbitae, as well as the presence of persistent covert infections in laboratory populations. It builds the basis for future research of tephritid-associated RNA viruses, including their host effects, epidemiology and application potential in biological control.

Complex interactions among insect viruses-insect vector-arboviruses

Insects are the host or vector of diverse viruses including those that infect vertebrates, plants, and fungi. Insect viruses reside inside their insect hosts and are vertically transmitted from parent to offspring. The insect virus-host relationship is intricate, as these viruses can impact various aspects of insect biology, such as development, reproduction, sex ratios, and immunity. Arthropod-borne viruses (arboviruses) that cause substantial global health or agricultural problems can also be vertically transmitted to insect vector progeny. Multiple infections with insect viruses and arboviruses are common in nature. Such coinfections involve complex interactions, including synergism, dependence, and antagonism. Recent studies have shed light on the influence of insect viruses on the competence of insect vectors for arboviruses. In this review, we focus on the biological effects of insect viruses on the transmission of arboviruses by insects. We also discuss the potential mechanisms by which insect viruses affect the ability of hosts to transmit arboviruses, as well as potential strategies for disease control through manipulation of insect viruses. Analyses of the interactions among insect vectors, insect viruses and arboviruses will provide new opportunities for development of innovative strategies to control arbovirus transmission.

Bactericera cockerelli Picorna-like Virus and Three New Viruses Found Circulating in Populations of Potato/Tomato Psyllids (Bactericera cockerelli)

An investigation of viruses circulating in populations of field and laboratory potato/tomato psyllids (Bactericera cockerelli) was conducted using high-throughput sequencing (HTS) technology and conventional RT-PCR. Three new viruses were discovered: one from the family Tymoviridae and two from the family Solemoviridae. A tymo-like virus sequence represented a nearly complete 6843 nt genome of a virus named Bactericera cockerelli tymo-like virus (BcTLV) that spanned five open reading frames (ORFs) which encoded RNA-dependent RNA polymerase (RdRP), helicase, protease, methyltransferase, and a capsid protein. Phylogenetic analyses placed the RdRP of BcTLV inside a divergent lineage of the viruses from the family Tymoviridae found in insect and plant hosts in a sister clade to the genera Tymovirus, Marafivirus, and Maculavirus. Four solemo-like virus sequences were identified in the HTS outputs, representing two new viruses. One virus found only in field-collected psyllids and named Bactericera cockerelli solemo-like virus 1 (BcSLV-1) had a 5479 nt genome which spanned four ORFs encoding protease and RdRP. Three solemo-like sequences displayed 87.4-99.7% nucleotide sequence identity among themselves, representing variants or strains of the same virus named Bactericera cockerelli solemo-like virus 2 (BcSLV-2). The genome of BcSLV-2 spanned only two ORFs that encoded a protease and an RdRP. Phylogenetic analysis placed the RdRPs of BcSLV-1 and BcSLV-2 in two separate lineages as sister clades to viruses from the genus Sobemovirus found in plant hosts. All three new psyllid viruses were found circulating in psyllids collected from potato fields in southern Idaho along with a previously identified Bactericera cockerelli picorna-like virus. Any possible role of the three viruses in controlling populations of the field psyllids remains to be elucidated.

Detection of Candidatus Liberibacter asiaticus and five viruses in individual Asian citrus psyllid in China

Introduction

Asian citrus psyllid (ACP, Diaphorina citri) is an important transmission vector of "Candidatus Liberibacter asiaticus" (CLas), the causal agent of Huanglongbing (HLB), the most destructive citrus disease in the world. As there are currently no HLB-resistant rootstocks or varieties, the control of ACP is an important way to prevent HLB. Some viruses of insect vectors can be used as genetically engineered materials to control insect vectors.

Methods

To gain knowledge on viruses in ACP in China, the prevalence of five RNA and DNA viruses was successfully determined by optimizing reverse transcription polymerase chain reaction (RT-PCR) in individual adult ACPs. The five ACP-associated viruses were identified as follows: diaphorina citri bunyavirus 2, which was newly identified by high-throughput sequencing in our lab, diaphorina citri reovirus (DcRV), diaphorina citri picorna-like virus (DcPLV), diaphorina citri bunyavirus (DcBV), and diaphorina citri densovirus-like virus (DcDV).

Results

DcPLV was the most prevalent and widespread ACP-associated virus, followed by DcBV, and it was detected in more than 50% of all samples tested. DcPLV was also demonstrated to propagate vertically and found more in salivary glands among different tissues. Approximately 60% of all adult insect samples were co-infected with more than one insect pathogen, including the five ACP-associated viruses and CLas.

Discussion

This is the first time these viruses, including the newly identified ACP-associated virus, have been detected in individual adult ACPs from natural populations in China's five major citrus-producing provinces. These results provide valuable information about the prevalence of ACP-associated viruses in China, some of which have the potential to be used as biocontrol agents. In addition, analysis of the change in prevalence of pathogens in a single insect vector is the basis for understanding the interactions between CLas, ACP, and insect viruses.

Wild lime psyllid Leuronota fagarae Burckhardt (Hemiptera: Psylloidea) picorna-like virus full genome annotation and classification

Picorna-like viruses of the order Picornavirales are a poorly defined group of positive-sense, single-stranded RNA viruses that include numerous pathogens known to infect plants, animals, and insects. A new picorna-like viral species was isolated from the wild lime psyllid (WLP), Leuronota fagarae, in the state of Florida, USA, and labelled: Leuronota fagarae picorna-like virus isolate FL (LfPLV-FL). The virus was found to have homology to a picorna-like virus identified in the Asian Citrus Psyllid (ACP), Diaphorina citri, collected in the state of Florida. Computational analysis of RNA extracts from WLP adult heads identified a 10,006-nucleotide sequence encoding a 2,942 amino acid polyprotein with similar functional domain structure to polyproteins of both Dicistroviridae and Iflaviridae. Sequence comparisons of nucleic acid and amino acid translations of the conserved RNA-dependent RNA polymerase, along with the entire N-terminal nonstructural coding region, provided insight into an evolutionary relationship of LfPLV-FL to insect-infecting iflaviruses. Viruses belonging to the family Iflaviridae encode a polyprotein of around 3000 amino acids in length that is processed post-translationally to produce components necessary for replication. The classification of a novel picorna-like virus in L. fagarae, with evolutionary characteristics similar to picorna-like viruses infecting Bactericera cockerelli and D. citri, provides an opportunity to examine virus host specificity, as well as identify critical components of the virus' genome required for successful transmission, infection, and replication. This bioinformatic classification allows for further insight into a novel virus species, and aids in the research of a closely related virus of the invasive psyllid, D. citri, a major pest of Floridian citriculture. The potential use of viral pathogens as expression vectors to manage the spread D. citri is an area that requires additional research; however, it may bring forth an effective control strategy to reduce the transmission of Candidatus Liberibacter asiaticus (CLas), the causative agent of Huanglongbing (HLB).

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.

Prevalence of Reversed Genome Organizations for Viruses in the Family Iflaviridae, Order Picornavirales

Viruses in the order Picornavirales possess a positive-strand RNA genome that encodes structural proteins (SPs) and nonstructural proteins (NSPs). According to the recent report of the International Committee on Taxonomy of Viruses (ICTV), there are 8 families in Picornavirales, and monopartite picornaviruses in each family exhibit distinct types of genome organizations with rearranged genes coding for SPs and NSPs, namely, TypeI (5'-SPs-NSPs-3') and TypeII (5'-NSPs-SPs-3'). In the present study, 2 iflaviruses with the 2 genome types were unexpectedly identified in a damselfly host species, suggesting that these 2 genome types coexisted in the same host species, and the families of order Picornavirales might be more complex than previously thought. The consequent systematic homologous screening with all the publicly available picornaviruses successfully revealed a considerable number of candidates rearranged genome types of picornaviruses in various families of Picornavirales. Subsequently, phylogenetic trees were reconstructed based on RNA dependent RNA polymerase and coat protein, which evidently confirmed the prevalence of the 10 typeII iflaviruses in the Iflaviridae family. This suggests that genome types may not be relevant to viral taxonomy in this family. However, candidate picornaviruses with reversed genome types in the Secoviridae and Dicistroviridae families require further investigation. All in all, as the number of newly discovered viruses increases, more viruses with non-canonical genome arrangements will be uncovered, which can expand our current knowledge on the genome complexity and evolution of picornaviruses. IMPORTANCE Monopartite viruses in the order Picornavirales exhibit distinct genome arrangement of nonstructural proteins and structural proteins for each of the 8 families. Recent studies indicated that at least 4 ifla-like viruses possessed reversed genome organization in the family Iflaviridae, raising the possibility that this phenomenon may commonly present in different families of picornaviruses. Since we discovered 2 iflaviruses with exchanged structural and nonstructural proteins simultaneously in the damselfly, a systematic screening was subsequently performed for all of the current available picornaviruses (1,543 candidates). The results revealed 10 picornaviruses with reversed genome organization in the family Iflaviridae, implying that this phenomenon might prevalence in the order Picornavirales. These results will contribute to a better understanding for the future study on the genome complexity and taxonomy of picornaviruses.

Discovery of Brassica Yellows Virus and Porcine Reproductive and Respiratory Syndrome Virus in Diaphorina citri and Changes in Virome Due to Infection with 'Ca. L. asiaticus'

Detection of new viruses or new virus hosts is essential for the protection of economically important agroecosystems and human health. Increasingly, metatranscriptomic data are being used to facilitate this process. Such data were obtained from adult Asian citrus psyllids (ACP) (Diaphorina citri Kuwayama) that fed solely on mandarin (Citrus ×aurantium L.) plants grafted with buds infected with 'Candidatus Liberibacter asiaticus' (CLas), a phloem-limited bacterium associated with the severe Asian variant of huanglongbing (HLB), the most destructive disease of citrus. Brassica yellows virus (BrYV), the causative agent of yellowing or leafroll symptoms in brassicaceous plants, and its associated RNA (named as BrYVaRNA) were detected in ACP. In addition, the porcine reproductive and respiratory syndrome virus (PRRSV), which affects pigs and is economically important to pig production, was also found in ACP. These viruses were not detected in insects feeding on plants grafted with CLas-free buds. Changes in the concentrations of insect-specific viruses within the psyllid were caused by coinfection with CLas. IMPORTANCE The cross transmission of pathogenic viruses between different farming systems or plant communities is a major threat to plants and animals and, potentially, human health. The use of metagenomics is an effective approach to discover viruses and vectors. Here, we collected buds from the CLas-infected and CLas-free mandarin (Citrus ×aurantium L. [Rutaceae: Aurantioideae: Aurantieae]) trees from a commercial orchard and grafted them onto CLas-free mandarin plants under laboratory conditions. Through metatranscriptome sequencing, we first identified the Asian citrus psyllids feeding on plants grafted with CLas-infected buds carried the plant pathogen, brassica yellows virus and its associated RNA, and the swine pathogen, porcine reproductive and respiratory syndrome virus. These discoveries indicate that both viruses can be transmitted by grafting and acquired by ACP from CLas+ mandarin seedlings.

Identifying the Gut Virome of Diaphorina citri from Florida Groves

Asian citrus psyllid (Diaphorina citri) transmits the bacterial pathogen Candidatus Liberibacter asiaticus (CLas), the putative causative agent of citrus Huanglongbing disease (HLB). Insect-specific viruses can act against insects as their natural enemies, and recently, several D. citri-associated viruses were discovered. The insect gut plays an important role as not only a pool for diverse microbes but also as a physical barrier to prevent the spread of pathogens such as CLas. However, there is little evidence of the presence of D. citri-associated viruses in the gut and of the interaction between them and CLas. Here, we dissected psyllid guts collected from five growing regions in Florida, and the gut virome was analyzed by high throughput sequencing. Four insect viruses, including D. citri-associated C virus (DcACV), D. citri densovirus (DcDV), D. citri reovirus (DcRV), and D. citri flavi-like virus (DcFLV), were identified, and their presence in the gut, including an additional D. citri cimodo-like virus (DcCLV), were confirmed with PCR-based assays. Microscopic analysis showed that DcFLV infection leads to morphological abnormalities in the nuclear structure in the infected psyllid gut cells. The complex and diverse composition of microbiota in the psyllid gut suggests a possible interaction and dynamics between CLas and the D. citri-associated viruses. Our study identified various D. citri-associated viruses that localized in the psyllid gut and provided more information that helps to evaluate the potential vectors for manipulating CLas in the psyllid gut.

Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses

Bats are important reservoirs for viruses of public health and veterinary concern. Virus studies in Australian bats usually target the families Paramyxoviridae, Coronaviridae and Rhabdoviridae, with little known about their overall virome composition. We used metatranscriptomic sequencing to characterise the faecal virome of grey-headed flying foxes from three colonies in urban/suburban locations from two Australian states. We identified viruses from three mammalian-infecting (Coronaviridae, Caliciviridae, Retroviridae) and one possible mammalian-infecting (Birnaviridae) family. Of particular interest were a novel bat betacoronavirus (subgenus Nobecovirus) and a novel bat sapovirus (Caliciviridae), the first identified in Australian bats, as well as a potentially exogenous retrovirus. The novel betacoronavirus was detected in two sampling locations 1375 km apart and falls in a viral lineage likely with a long association with bats. This study highlights the utility of unbiased sequencing of faecal samples for identifying novel viruses and revealing broad-scale patterns of virus ecology and evolution.

Going Viral: Virus-Based Biological Control Agents for Plant Protection

The most economically important biotic stresses in crop production are caused by fungi, oomycetes, insects, viruses, and bacteria. Often chemical control is still the most commonly used method to manage them. However, the development of resistance in the different pathogens/pests, the putative damage on the natural ecosystem, the toxic residues in the field, and, thus, the contamination of the environment have stimulated the search for saferalternatives such as the use of biological control agents (BCAs). Among BCAs, viruses, a major driver for controlling host populations and evolution, are somewhat underused, mostly because of regulatory hurdles that make the cost of registration of such host-specific BCAs not affordable in comparison with the limited potential market. Here, we provide a comprehensive overview of the state of the art of virus-based BCAs against fungi, bacteria, viruses, and insects, with a specific focus on new approaches that rely on not only the direct biocidal virus component but also the complex ecological interactions between viruses and their hosts that do not necessarily result in direct damage to the host.

High-quality, chromosome-scale genome assemblies: comparisons of three Diaphorina citri (Asian citrus psyllid) geographic populations

The Asian citrus psyllid, Diaphorina citri, is the insect vector of the causal agent of huanglongbing (HLB), a devastating bacterial disease of commercial citrus. Presently, few genomic resources exist for D. citri. In this study, we utilized PacBio HiFi and chromatin confirmation contact (Hi-C) sequencing to sequence, assemble, and compare three high-quality, chromosome-scale genome assemblies of D. citri collected from California, Taiwan, and Uruguay. Our assemblies had final sizes of 282.67 Mb (California), 282.89 Mb (Taiwan), and 266.67 Mb (Uruguay) assembled into 13 pseudomolecules—a reduction in assembly size of 41–45% compared with previous assemblies which we validated using flow cytometry. We identified the X chromosome in D. citri and annotated each assembly for repetitive elements, protein-coding genes, transfer RNAs, ribosomal RNAs, piwi-interacting RNA clusters, and endogenous viral elements. Between 19,083 and 20,357 protein-coding genes were predicted. Repetitive DNA accounts for 36.87–38.26% of each assembly. Comparative analyses and mitochondrial haplotype networks suggest that Taiwan and Uruguay D. citri are more closely related, while California D. citri are closely related to Florida D. citri. These high-quality, chromosome-scale assemblies provide new genomic resources to researchers to further D. citri and HLB research.

The Diversity of Viral Community in Invasive Fruit Flies (Bactrocera and Zeugodacus) Revealed by Meta-transcriptomics

RNA viruses are extremely diverse and rapidly evolving in various organisms. Our knowledge on viral evolution with interacted hosts in the manner of ecology is still limited. In the agricultural ecosystem, invasive insect species are posing a great threat to sustainable crop production. Among them, fruit flies (Diptera: Tephritidae Bactrocera and Zeugodacus) are destructive to fruits and vegetables, which are also closely related and often share similar ecological niches. Thus, they are ideal models for investigating RNA virome dynamics in host species. Using meta-transcriptomics, we found 39 viral sequences in samples from 12 fly species. These viral species represented the diversity of the viromes including Dicistroviridae, negev-like virus clades, Thika virus clades, Solemoviridae, Narnaviridae, Nodaviridae, Iflaviridae, Orthomyxoviridae, Bunyavirales, Partitiviridae, and Reoviridae. In particular, dicistrovirus, negev-like virus, orthomyxovirus, and orbivirus were common in over four of the fly species, which suggests a positive interaction between fly viromes that exist under the same ecological conditions. For most of the viruses, the virus-derived small RNAs displayed significantly high peaks in 21 nt and were symmetrically distributed throughout the viral genome. These results suggest that infection by these viruses can activate the host's RNAi immunity. Our study provides RNA virome diversity and evidence on their infection activity in ecologically associated invasive fruit fly species, which could help our understanding of interactions between complex species and viruses.

Analysis of Citrus Tristeza Virus Incidences within Asian Citrus Psyllid (Diaphorina citri) Populations in Florida via High-Throughput Sequencing

The destructive citrus disease, Huanglongbing (HLB) or citrus greening, continues to devastate Florida’s citrus industry. A hemipteran insect, the Asian citrus psyllid (ACP), disperses Candidatus Liberibacter asiaticus, one of the putative bacterial pathogens of HLB. This study builds upon ongoing research utilizing high-throughput sequencing to analyze the virome of ACP populations collected from citrus groves throughout Florida. Following the widespread detection of sequences aligning to the genome of citrus tristeza virus (CTV) across consecutive years in the Florida ACP virome, we continued to detect a pervasive amount of CTV in Florida ACPs during subsequent years. Simultaneously, we also detected mixed infections of CTV strains in pooled ACPs from different Florida regions. Predating the HLB epidemic, CTV has been present in Florida for many years and our results confirm its widespread and diverse persistence in Florida citrus groves through a unique lens, the ACP. CTV presence in the ACP likely results from feeding on CTV-infected citrus trees in Florida citrus groves, which may help to understand an overlapping presence of CTV and HLB, both endemic citrus pathosystems in the state, and their role in future integrated pest management strategies.

Novel viral RNA genomes of the vine mealybug Planococcus ficus

The vine mealybug, Planococcus ficus (Signoret, 1875), is the most important insect pest in growing areas of the grapevine Vitis vinifera L. in several countries, including Mexico. In Mexico, Baja California (B.C.) is the region with the highest production of V. vinifera L. grapes for industrial purposes. Recently, the diversity of viruses infecting insects only (insect-specific viruses) has been broadly explored to elucidate further ecological viral-host interactions in many insect species, which in some cases has resulted in the application of virus-based biological control agents for insect pests. However, a survey of the Pl. ficus virome has not been done yet. In the present study, we pooled Pl. ficus individuals collected through different vineyards of Ensenada, B.C., Mexico and analysed them by meta-transcriptomics. Novel nearly complete genomes of five RNA viruses were retrieved. These viruses were related to the Iflaviridae and Reoviridae families, and to the Picornavirales and Tolivirales orders. A new isolate belonging to the Dicistroviridae family was also found. Phylogenetic analyses showed that these putative viral genomes group with viruses having hemipteran (including a mealybug species) or other insect hosts, or with viruses associated with insects. Our results suggest that the identified novel RNA viruses could be insect-specific viruses of Pl. ficus. This work is the first insight into the Pl. ficus virome; it guarantees further studies aimed to characterize those viruses with potential for application in biological control of this economically important insect.

Diaphorina citri flavi-like virus localization, transmission, and association with Candidatus Liberibacter asiaticus in its psyllid host

Huanglongbing is caused by Candidatus Liberibacter asiaticus (CLas) and transmitted by Diaphorina citri. D. citri harbors various insect-specific viruses, including the Diaphorina citri flavi-like virus (DcFLV). The distribution and biological role of DcFLV in its host and the relationship with CLas are unknown. DcFLV was found in various organs of D. citri, including the midgut and salivary glands, where it co-localized with CLas. CLas-infected nymphs had the highest DcFLV titers compared to the infected adults and CLas-free adults and nymphs. DcFLV was vertically transmitted to offspring from female D. citri and was temporarily detected in Citrus macrophylla and grapefruit leaves from greenhouse and field. The incidences of DcFLV and CLas were positively correlated in field-collected D. citri samples, suggesting that DcFLV might be associated with CLas in the vector. These results provide new insights on the interactions between DcFLV, the D. citri, and CLas.

A new picorna-like virus identified in populations of the potato psyllid Bactericera cockerelli

The potato/tomato psyllid Bactericera cockerelli (Hemiptera: Triozidae) is a pest of Solanaceae plants and a vector of the pathogenic bacterium 'Candidatus Liberibacter solanacearum', which is associated with zebra chip disease in potato. This disease is controlled through insecticide treatments, and more environmentally friendly management options are desirable. The objective of this study was to identify viruses present in potato psyllid populations that might be used as biocontrol agents for this insect pest. A new picorna-like virus, tentatively named "Bactericera cockerelli picorna-like virus" (BcPLV), was discovered in B. cockerelli populations maintained in greenhouses, through the use of high-throughput sequencing data and subsequent confirmation by RT-PCR and Sanger sequencing. BcPLV has a positive-sense 9,939-nt RNA genome encoding a single 2,947-aa polyprotein and is related to the Diaphorina citri picorna-like virus (DcPLV) found in Asian citrus psyllid Diaphorina citri populations. Based on their genome organization and the phylogeny of their RNA-dependent RNA polymerase domains, BcPLV and DcPLV together are proposed to comprise a new genus, provisionally named "Psylloidivirus", within the family Iflaviridae.

Preliminary Report on the Acquisition, Persistence, and Potential Transmission of Citrus tristeza virus by Diaphorina citri

Simple Summary

Citrus tristeza virus (CTV) is the causal agent of one of the most serious diseases of citrus and is described to be vectored by several aphid species. There have been no published reports of either acquisition or transmission of CTV by other insects, including phloem-feeding sternorrhynchans. The Asian citrus psyllid Diaphorina citri is an economically important pest since it is the vector of the bacterium associated with Huanglongbing (HLB) in citrus crops. We hereby reported the detection of CTV from field-collected D. citri and estimated the ability of these insects to acquire and transmit the virus. Under controlled conditions, D. citri nymphs were shown to acquire CTV from citrus trees, and the virus persisted in the psyllids for over 15 days. Controlled experiments also suggest that D. citri transmit CTV to healthy citrus plants but not to orange jasmine plants, a favorite host of D. citri. The results indicate D. citri is a potential vector of pathogens for two major citrus diseases: HLB and Citrus tristeza.

Abstract

Citrus tristeza virus (CTV) is one of the most important citrus tree viruses: a graft-transmissible virus that can be vectored by several aphid species. Diaphorina citri is the insect vector of “Candidatus Liberibacter spp.”, a bacterium associated with citrus Huanglongbing (HLB). However, no detailed description of the relationship between CTV and D. citri has been reported. In this study, D. citri adults collected from CTV-infected “Shatangju” mandarin, “Newhall” sweet orange, and “fingered citron” trees in different orchards yielded CTV-positive rates of 40%, 65%, and 95%, respectively, upon detection by conventional PCR. Illumina HiSeq sequencing followed by de novo assembly recovered the primary full CTV genome from the RNA of 30 D. citri adults sampled from CTV-positive citrus plants. Molting and adult emergence did not affect the presence or titers of CTV within the D. citri; however, the persistence of CTV in psyllids varied among different host plant species. Groups of 10 D. citri (from a population 85% CTV-positive) were shown to potentially transmit CTV to two citrus species, “Shatangju” mandarin and “Eureka” lemon, yielding 58.33% and 83.33% CTV-positive plants, respectively. No transmission of CTV to orange jasmine plants occurred. Thus, this study reports on the ability of D. citri to acquire and transmit CTV, making D. citri as a vector of two important citrus pathogens, warranting further attention and investigation.

Complexity and local specificity of the virome associated with tospovirus-transmitting thrips species

Frankliniella occidentalis (western flower thrips=WFT) and Thrips tabaci (onion thrips=OT) are insect species that greatly impact horticultural crops through direct damage and their efficient vectoring of tomato spotted wilt virus and iris yellow spot virus. In this study we collected thrips of these species from 12 field populations in various regions in Italy. We also included one field population of Neohydatothrips variabilis (soybean thrips=ST) from the U.S.A. Total RNAseq from high-throughput sequencing (HTS) was used to assemble the virome and then we assigned putative viral contigs to each thrips sample by qRT-PCR. Excluding plant and fungal viruses, we were able to identify 61 viral segments, corresponding to 41 viruses: 14 were assigned to WFT, 17 to OT, one from ST and 9 viruses could not be assigned to any species based on our stringent criteria. All these viruses are putative representative of new species (with only the exception of a sobemo-like virus that is 100% identical to a virus recently characterized in ST) and some belong to new higher-ranking taxa. These additions to the viral phylogeny suggest previously undescribed evolutionary niches. Most of the Baltimore's classes of RNA viruses were present (positive- and minus- strand and dsRNA viruses), but only one DNA virus was identified in our collection. Repeated sampling in a subset of locations in 2019 and 2020 and further virus characterization in a subset of four thrips populations maintained in laboratory allowed us to provide evidence of a locally persistent thrips core virome that characterizes each population. IMPORTANCE Harnessing the insect microbiome can result in new approaches to contain their populations or the damage they cause vectoring viruses of medical, veterinary, or agricultural importance. Persistent insect viruses are a neglected component of their microbiota. Here for the first time, we characterize the virome associated with the two model systems for tospovirus-transmitting thrips species, of utmost importance for the direct and indirect damage they cause to a number of different crops. The thrips virome here characterized includes several novel viruses, that in some cases reveal previously undescribed clades. More importantly, some of the viruses we describe are part of a core virome that is specific and consistently present in distinct geographical locations monitored over the years, hinting at a possible mutualistic symbiotic relationship with their host.

Novel RNA Viruses from the Transcriptome of Pheromone Glands in the Pink Bollworm Moth, Pectinophora gossypiella

Simple Summary

The pink bollworm, Pectinophora gossypiella (Lepidoptera: Gelechiidae), is a major pest of cotton. In this study, we analyzed the mRNA from pheromone glands of two populations in Israel. We found several virus sequences that were the same in these populations. We identified these viruses based on high-throughput sequencing data and analysis of the assembled transcripts. Through analysis of the sequences, we identified several unique viral sequences representing possible novel viral species. Two of the viral sequences were found in relatively high abundance in pheromone glands. One of the virus sequences was also found through analysis of previous transcriptome sequencing data from the midgut of pink bollworm larvae. This is the first report of these unique viral sequences found in the pink bollworm, and these viruses could be developed to help control this pest around the world, but more research is needed to determine their utility as biological control agents.

Abstract

In this study, we analyzed the transcriptome obtained from the pheromone gland isolated from two Israeli populations of the pink bollworm Pectinophora gossypiella to identify viral sequences. The lab population and the field samples carried the same viral sequences. We discovered four novel viruses: two positive-sense single-stranded RNA viruses, Pectinophora gossypiella virus 1 (PecgV1, a virus of Iflaviridae) and Pectinophora gossypiella virus 4 (PecgV4, unclassified), and two negative-sense single-stranded RNA viruses, Pectinophora gossypiella virus 2 (PecgV2, a virus of Phasmaviridae) and Pectinophora gossypiella virus 3 (PecgV3, a virus of Phenuiviridae). In addition, sequences derived from two negative-sense single-stranded RNA viruses that belong to Mononegavirales were found in the data. Analysis of previous transcriptome sequencing data derived from the midgut of pink bollworm larvae of a USA population only identified PecgV1, but no other viruses. High viral sequence coverages of PecgV1 and PecgV4 were observed in both field and lab populations. This is the first report of viral sequences discovered from the pink bollworm. Results from this investigation suggest that the pink bollworm harbors multiple viruses. Further investigation of the viral pathogens may help to develop novel pest management strategies for control of the pink bollworm.

Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses

Soybean thrips (Neohydatothrips variabilis) are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, the metatranscriptome of soybean thrips, collected by the Midwest Suction Trap Network during 2018, was analyzed. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified. The novel viruses were predicted to have positive-sense RNA, negative-stranded RNA, double-stranded RNA, and single-stranded DNA genomes. The assembled sequences included 100 contigs that represented at least 95% coverage of a virus genome or genome segment. Sequences represented 12 previously described arthropod viruses including eight viruses reported from Hubei Province in China, and 12 plant virus sequences of which six have been previously described. The presence of diverse populations of plant viruses within soybean thrips suggests they feed on and acquire viruses from multiple host plant species that could be transmitted to soybean. Assessment of the virome of soybean thrips provides, for the first time, information on the diversity of viruses present in thrips.

Insects' potential: Understanding the functional role of their gut microbiome

The study of insect-associated microbial communities is a field of great importance in agriculture, principally because of the role insects play as pests. In addition, there is a recent focus on the potential of the insect gut microbiome in areas such as biotechnology, given some microorganisms produce molecules with biotechnological and industrial applications, and also in biomedicine, since some bacteria and fungi are a reservoir of antibiotic resistance genes (ARGs). To date, most studies aiming to characterize the role of the gut microbiome of insects have been based on high-throughput sequencing of the 16S rRNA gene and/or metagenomics. However, recently functional approaches such as metatranscriptomics, metaproteomics and metabolomics have also been employed. Besides providing knowledge about the taxonomic distribution of microbial populations, these techniques also reveal their functional and metabolic capabilities. This information is essential to gain a better understanding of the role played by microbes comprising the microbial communities in their hosts, as well as to indicate their possible exploitation. This review provides an overview of how far we have come in characterizing insect gut functionality through omics, as well as the challenges and future perspectives in this field.

Endogenous Viral Element-Derived Piwi-Interacting RNAs (piRNAs) Are Not Required for Production of Ping-Pong-Dependent piRNAs from Diaphorina citri Densovirus

Piwi-interacting RNAs (piRNAs) are a class of small RNAs primarily responsible for silencing transposons in the animal germ line. The ping-pong cycle, the posttranscriptional silencing branch of the piRNA pathway, relies on piRNAs produced from endogenous transposon remnants to direct cleavage of transposon RNA via association with Piwi-family Argonaute proteins. In some mosquito species and mosquito-derived cell lines expressing a functionally expanded group of Piwi-family Argonaute proteins, both RNA and DNA viruses are targeted by piRNAs in a manner thought to involve direct processing of exogenous viral RNA into piRNAs. Whether viruses are targeted by piRNAs in nonmosquito species is unknown. Partial integrations of DNA and nonretroviral RNA virus genomes, termed endogenous viral elements (EVEs), are abundant in arthropod genomes and often produce piRNAs that are speculated to target cognate viruses through the ping-pong cycle. Here, we describe a Diaphorina citri densovirus (DcDV)-derived EVE in the genome of Diaphorina citri We found that this EVE gives rise to DcDV-specific primary piRNAs and is unevenly distributed among D. citri populations. Unexpectedly, we found that DcDV is targeted by ping-pong-dependent virus-derived piRNAs (vpiRNAs) in D. citri lacking the DcDV-derived EVE, while four naturally infecting RNA viruses of D. citri are not targeted by vpiRNAs. Furthermore, a recombinant Cricket paralysis virus containing a portion of the DcDV genome corresponding to the DcDV-derived EVE was not targeted by vpiRNAs during infection in D. citri harboring the EVE. These results demonstrate that viruses can be targeted by piRNAs in a nonmosquito species independently of endogenous piRNAs.IMPORTANCE Small RNAs serve as specificity determinants of antiviral responses in insects. Piwi-interacting RNAs (piRNAs) are a class of small RNAs found in animals, and their primary role is to direct antitransposon responses. These responses require endogenous piRNAs complementary to transposon RNA. Additionally, piRNAs have been shown to target RNA and DNA viruses in some mosquito species. In contrast to transposons, targeting of viruses by the piRNA pathway in these mosquito species does not require endogenous piRNAs. Here, we show that piRNAs target a DNA virus, but not RNA viruses, in an agricultural insect pest. We found that targeting of this DNA virus did not require endogenous piRNAs and that endogenous piRNAs did not mediate targeting of an RNA virus with which they shared complementary sequence. Our results highlight differences between mosquitoes and our experimental system and raise the possibility that DNA viruses may be targeted by piRNAs in other species.

Citrus Psorosis Virus: Current Insights on a Still Poorly Understood Ophiovirus

Citrus psorosis was reported for the first time in Florida in 1896 and was confirmed as a graft-transmissible disease in 1934. Citrus psorosis virus (CPsV) is the presumed causal agent of this disease. It is considered as a type species of the genus Ophiovirus, within the family Aspiviridae. CPsV genome is a negative single-stranded RNA (-ssRNA) with three segments. It has a coat protein (CP) of 48 kDa and its particles are non-enveloped with naked filamentous nucleocapsids existing as either circular open structures or collapsed pseudo-linear forms. Numerous rapid and sensitive immuno-enzymatic and molecular-based detection methods specific to CPsV are available. CPsV occurrence in key citrus growing regions across the world has been spurred the establishment of the earliest eradication and virus-free budwood programs. Despite these efforts, CPsV remains a common and serious challenge in several countries and causes a range of symptoms depending on the isolate, the cultivar, and the environment. CPsV can be transmitted mechanically to some herbaceous hosts and back to citrus. Although CPsV was confirmed to be seedborne, the seed transmission is not efficient. CPsV natural spread has been increasing based on both CPsV surveys detection and specific CPsV symptoms monitoring. However, trials to ensure its transmission by a soil-inhabiting fungus and one aphid species have been unsuccessful. Psorosis disease control is achieved using CPsV-free buds for new plantations, launching budwood certification and indexing programs, and establishing a quarantine system for the introduction of new varieties. The use of natural resistance to control CPsV is very challenging. Transgenic resistance to at least some CPsV isolates is now possible in at least some sweet orange varieties and constitutes a promising biotechnological alternative to control CPsV. This paper provides an overview of the most remarkable achievements in CPsV research that could improve the understanding of the disease and lead the development of better control strategies.

The RNA Virome and Its Dynamics in an Invasive Fruit Fly, Bactrocera dorsalis, Imply Interactions Between Host and Viruses

The oriental fruit fly, Bactrocera dorsalis (Hendel), is an important invasive agricultural insect pest with a wide host range, and has spread around the world over the last century. This evolutionary trait may have arisen primarily from interactions between B. dorsalis and other invertebrates that share the same ecological niches. The invasive behavior of B. dorsalis also frequently exposes them to diverse species of viruses. Thereby, RNA viromes may be useful microbial markers to understand the ecological evolution of B. dorsalis as well as to investigate virus-host interactions. Here, we reported eight novel RNA viruses in B. dorsalis of a lab colony, including four positive-strand RNA viruses, two negative-strand RNA viruses, and two double-stranded RNA viruses using high-throughput sequencing technology. Analysis of the virus-derived small RNAs suggested that most of these viruses may be active and trigger the host antiviral RNAi responses. The viruses were also detected in various geographical populations of B. dorsalis, implying that there is a strong association between the viromes and host. In addition, these viruses infected specific fly tissues, predominately the central nervous system and gut. Furthermore, we explored the dynamics of the viruses when hosts were exposed to short- or long-term stressors, which showed that titers of some viruses were responsively altered in the stressed B. dorsalis. The discovery of these viruses may enrich our understanding of the species diversity of RNA viruses and also provide information on viruses in association with host adaptation in insects.

Diaphorina citri reovirus is most closely related to fijiviruses

The Asian citrus psyllid, Diaphorina citri Kuwayama, is an important insect vector of Candidatus Liberibacter asiaticus, the causal agent of Huanglongbing, which is the most destructive disease of citrus worldwide. Sequences for putative Diaphorina citri reovirus (DcRV) were identified from some worldwide populations of D. citri. Here, field surveys indicated that the virus was common in D. citri populations from Hawaii and Fuzhou of PR China. Electron microscopy showed that DcRV virions possessed a typical reovirus-like morphology. The U. S. and Chinese DcRV isolates both showed 10 segments of double-stranded RNA sharing >96% nucleotide sequence identity, and encoding 11 deduced proteins. All genome segments contained conserved 5' and 3' terminal nucleotide sequences and inverted repeats that are hallmarks of reovirus sequence. Phylogenetic analysis showed that DcRV may be considered a new species of the genus Fijivirus sharing a most recent common ancestor with the insect-specific fijivirus Nilaparvata lugens reovirus.

New Viral Sequences Identified in the Flavescence Dorée Phytoplasma Vector Scaphoideus titanus

(1) Background: The leafhopper Scaphoideus titanus is the primary vector of Flavescence dorée phytoplasma (FDp) in European vineyards. Flavescence dorée is one of the most severely damaging diseases of Vitis vinifera and, consequently, a major threat to grape and wine production in several European countries. Control measures are compulsory, but they mainly involve large-scale insecticide treatments, with detrimental impacts on the environment. One possible solution is to exploit the largely unexplored genetic diversity of viruses infecting S. titanus as highly specific and environmentally benign tools for biological control. (2) Methods: A metatranscriptomic approach was adopted to identify viruses that may infect individuals caught in the wild in both its native (United States) and invasive (Europe) areas. Reverse transcription PCR was used to confirm their presence in RNA pools and explore their prevalence. (3) Results: We described nine new RNA viruses, including members of “Picorna-Calici”, “Permutotetra”, “Bunya-Arena”, “Reo”, “Partiti-Picobirna”, “Luteo-Sobemo” and “Toti-Chryso” clades. A marked difference in the diversity and abundance of the viral species was observed between the USA population and the European ones. (4) Conclusions: This work represents the first survey to assess the viral community of a phytoplasma insect vector. The possibility to exploit these naturally occurring viruses as specific and targeted biocontrol agents of S. titanus could be the answer to increasing demand for a more sustainable viticulture.

RNA virome screening in diverse but ecologically related citrus pests reveals potential virus-host interactions

As an evergreen ecosystem, citrus orchards have specialized pest species and stable ecological homeostasis; thus, they provide an ideal model for investigating RNA viromes in diverse but ecologically related species. For this purpose, we collected specialized citrus pests from three classes of invertebrates, Insecta, Arachnida, and Gastropoda and we constructed two kinds of libraries (RNA and small RNA) for the pests by deep sequencing. In total, six virus-derived sequences were identified, including four Picornavirales, one Jingchuvirales and one Nidovirales. The picornavirus-derived small RNAs showed significant small RNA peaks and symmetric distribution patterns along the genome, which suggests these viruses infected the hosts and triggered host antiviral immunity RNA interference. Screening of virus-derived sequences in multiple species of citrus pests (n = 10 per species) showed that Eotetranychus kankitus picorna-like virus and Tetranychus urticae mivirus may be present in multiple pests. Our investigation in citrus pests confirmed that RNA viruses revealed by metagenomics could impact host immunity (e.g. RNAi). An approach with parallel deep sequencing of RNAs and small RNAs is useful not only for viral discoveries but also for understanding virus-host interactions of ecologically related but divergent pest species.

The Detection and Surveillance of Asian Citrus Psyllid (Diaphorina citri)-Associated Viruses in Florida Citrus Groves

The plant pathogenic bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent of the citrus disease Huanglongbing (HLB), and its insect vector, the Asian citrus psyllid (ACP; Diaphorina citri), have been devastating the Florida citrus industry. To restore the competitive production presence of Florida in the worldwide citrus market, effective and sustainable control of HLB and the ACP needs to be identified. As alternatives for resistance-inducing insecticides, viruses are currently being considered for biological control of the ACP. To identify possible biological control candidates, we conducted one of the most comprehensive surveys of natural ACP populations in major citrus production regions spanning 21 counties in Florida. By optimizing PCRs and RT-PCRs, we were able to successfully detect and monitor the prevalence of five previously identified ACP-associated RNA and DNA viruses throughout Florida citrus groves, which include: Diaphorina citri-associated C virus (DcACV), Diaphorina citri flavi-like virus (DcFLV), Diaphorina citri densovirus (DcDNV), Diaphorina citri reovirus (DcRV), and Diaphorina citri picorna-like virus (DcPLV). Adult and nymph ACP populations from 21 of Florida's major citrus-producing counties were collected each month during approximately 18 consecutive months. RNA extracts used for these viral screens were also regionally combined and subjected to High Throughput Sequencing (HTS) to reveal a more comprehensive picture of known and unknown viruses in Florida ACP populations. We discovered that DcACV was the most prevalent ACP-associated virus throughout nymph and adult ACP populations in Florida, detected in more than 60% of all samples tested, followed by DcPLV and DcFLV. HTS allowed us to identify a novel ACP-associated reo-like virus and a picorna-like virus. The putative reo-like virus, tentatively named Diaphorina citri cimodo-like virus, was later surveyed and detected back in seasonal adult and nymph ACP samples collected in Florida during this study. HTS generated data also revealed that the most abundant virus in Florida ACP populations was Citrus tristeza virus (CTV), which is not an ACP-associated virus, suggesting persistent presence of CTV infection in citrus throughout Florida groves. Collectively, information obtained from our study may be able to help guide the direction of biotechnological pest control efforts involving a number of viruses that were detected for the first time in Florida ACP populations, including two newly identified ACP-associated viruses.

Diaphorina citri densovirus is a persistently infecting virus with a hybrid genome organization and unique transcription strategy

Diaphorina citri densovirus (DcDV) is an ambisense densovirus with a 5071 nt genome. Phylogenetic analysis places DcDV in an intermediate position between those in the Ambidensovirus and Iteradensovirus genera, a finding that is consistent with the observation that DcDV possesses an Iteradensoviris-like non-structural (NS) protein-gene cassette, but a capsid-protein (VP) gene cassette resembling those of other ambisense densoviruses. DcDV is maternally transmitted to 100 % of the progeny of infected female Diaphorina citri, and the progeny of infected females carry DcDV as a persistent infection without outward phenotypic effects. We were unable to infect naïve individuals by oral inoculation, however low levels of transient viral replication are detected following intrathoracic injection of DcDV virions into uninfected D. citri insects. Transcript mapping indicates that DcDV produces one transcript each from the NS and VP gene cassettes and that these transcripts are polyadenylated at internal sites to produce a ~2.2 kb transcript encoding the NS proteins and a ~2.4 kb transcript encoding the VP proteins. Additionally, we found that transcriptional readthrough leads to the production of longer non-canonical transcripts from both genomic strands.

Topical dsRNA delivery induces gene silencing and mortality in the pea aphid

BACKGROUND

With the growing number of available aphid genomes and transcriptomes, an efficient and easy-to-adapt tool for gene function study is urgently required. RNA interference (RNAi), as a post-transcriptional gene silencing mechanism, is important as a research tool for determining gene functions and has potential as a novel insect control strategy. However, these applications have been hampered by the lack of effective dsRNA delivery approaches in aphids.

RESULTS

Here, we developed a convenient and efficient dsRNA delivery method, topical RNAi, in aphids. An investigation of its dose and time-dependent RNAi efficiencies revealed that with as little as 60 ng dsRNA per adult pea aphid (Acyrthosiphon pisum), the indicator gene, Aphunchback, could be significantly silenced within 2 h of exposure. The method was further validated by successfully silencing other different genes, and it was also efficient toward two other aphid species, Aphis citricidus and Myzus persicae. Furthermore, a noticeable mortality was also observed in pea aphids using topical RNAi-mediated gene silencing, within 4 days post-dsRNA application for four out of seven tested genes.

CONCLUSION

Compared with the currently used dsRNA delivery methods in aphids, microinjection and ingestion, topical RNAi is time- and cost-effective, which could greatly influence RNAi-based gene functional studies and potential candidate gene selection for developing RNAi-based aphid control strategies in the future. © 2019 Society of Chemical Industry.

The Probing Behavior Component of Disease Transmission in Insect-Transmitted Bacterial Plant Pathogens

Insects can be effective vectors of plant diseases and this may result in billions of dollars in lost agricultural productivity. New, emerging or introduced diseases will continue to cause extensive damage in afflicted areas. Understanding how the vector acquires the pathogen and inoculates new hosts is critical in developing effective management strategies. Management may be an insecticide applied to kill the vector or a host plant resistance mechanism to make the host plant less suitable for the vector. In either case, the tactic must act before the insect performs the key behavior(s) resulting in either acquisition or transmission. This requires knowledge of the timing of behaviors the insect uses to probe the plant and commence ingestion. These behaviors are visualized using electropenetrography (EPG), wherein the plant and insect become part of an electrical circuit. With the tools to define specific steps in the probing process, we can understand the timing of acquisition and inoculation. With that understanding comes the potential for more relevant testing of management strategies, through insecticides or host plant resistance. The primary example will be Candidatus Liberibacter asiaticus transmitted by Diaphorina citri Kuwayama in the citrus agroecosystem, with additional examples used as appropriate.

A Nonstructural Protein Responsible for Viral Spread of a Novel Insect Reovirus Provides a Safe Channel for Biparental Virus Transmission to Progeny

The Asian citrus psyllid, Diaphorina citri Kuwayama, is an important pest in the worldwide citrus industry. It is the vector of “Candidatus Liberibacter asiaticus,” the bacterial pathogen of Huanglongbing, which is currently considered the most destructive disease of citrus worldwide. DcRV was previously identified based on metagenomics surveys for virus discovery. Here, we found that this novel and persistent insect reovirus took advantage of a virus-encoded nonstructural protein, P10, for efficient vertical transmission from parents to progeny. P10 assembled into a virion-packaging tubular structure and was associated with oocytes of female D. citri and sperm of males. Consistent with this, knockdown of P10 for either male or female D. citri insects inhibited DcRV transmission to offspring. This tubular strategy for viral spread and biparental transmission might serve as a target for controlling viral vertical transmission and population expansion.

Diaphorina citri reovirus (DcRV) was previously identified based on metagenomics surveys for virus discovery. Here, we demonstrated that DcRV induces persistent infection in its psyllid host, Diaphorina citri. DcRV was efficiently vertically passed to offspring in a biparental manner. Transmission electron microscopic and immunological analyses showed that the DcRV-encoded nonstructural protein P10 assembled into a virion-packaging tubular structure which is associated with the spread of DcRV throughout the bodies of D. citri insects. P10 tubules containing virions were associated with oocytes of female and sperm of male D. citri insects, suggesting a role in the highly efficient biparental transmission of DcRV. Knocking down P10 by RNA interference for males reduced the percentage of DcRV-infected progeny and for females reduced the viral accumulation in progeny. These results, for the first time, show that a nonstructural protein of a novel insect reovirus provides a safe and pivotal channel for virus spread and biparental transmission to progeny.

IMPORTANCE The Asian citrus psyllid, Diaphorina citri Kuwayama, is an important pest in the worldwide citrus industry. It is the vector of “Candidatus Liberibacter asiaticus,” the bacterial pathogen of Huanglongbing, which is currently considered the most destructive disease of citrus worldwide. DcRV was previously identified based on metagenomics surveys for virus discovery. Here, we found that this novel and persistent insect reovirus took advantage of a virus-encoded nonstructural protein, P10, for efficient vertical transmission from parents to progeny. P10 assembled into a virion-packaging tubular structure and was associated with oocytes of female D. citri and sperm of males. Consistent with this, knockdown of P10 for either male or female D. citri insects inhibited DcRV transmission to offspring. This tubular strategy for viral spread and biparental transmission might serve as a target for controlling viral vertical transmission and population expansion.

Genome organization and molecular characterization of the three Formica exsecta viruses-FeV1, FeV2 and FeV4

We present the genome organization and molecular characterization of the three Formica exsecta viruses, along with ORF predictions, and functional annotation of genes. The Formica exsecta virus-4 (FeV4; GenBank ID: MF287670) is a newly discovered negative-sense single-stranded RNA virus representing the first identified member of order Mononegavirales in ants, whereas the Formica exsecta virus-1 (FeV1; GenBank ID: KF500001), and the Formica exsecta virus-2 (FeV2; GenBank ID: KF500002) are positive single-stranded RNA viruses initially identified (but not characterized) in our earlier study. The new virus FeV4 was found by re-analyzing data from a study published earlier. The Formica exsecta virus-4 genome is 9,866 bp in size, with an overall G + C content of 44.92%, and containing five predicted open reading frames (ORFs). Our bioinformatics analysis indicates that gaps are absent and the ORFs are complete, which based on our comparative genomics analysis suggests that the genomes are complete. Following the characterization, we validate virus infection for FeV1, FeV2 and FeV4 for the first time in field-collected worker ants. Some colonies were infected by multiple viruses, and the viruses were observed to infect all castes, and multiple life stages of workers and queens. Finally, highly similar viruses were expressed in adult workers and queens of six other Formica species: F. fusca, F. pressilabris, F. pratensis, F. aquilonia, F. truncorum and F. cinerea. This research indicates that viruses can be shared between ant species, but further studies on viral transmission are needed to understand viral infection pathways.

Insect-specific viruses: from discovery to potential translational applications

Over the past decade the scientific community has experienced a new age of virus discovery in arthropods in general, and in insects in particular. Next generation sequencing and advanced bioinformatics tools have provided new insights about insect viromes and viral evolution. In this review, we discuss some high-throughput sequencing technologies used to discover viruses in insects and the challenges raised in data interpretations. Additionally, the discovery of these novel viruses that are considered as insect-specific viruses (ISVs) has gained increasing attention in their potential use as biological agents. As example, we show how the ISV Nhumirim virus was used to reduce West Nile virus transmission when co-infecting the mosquito vector. We also discuss new translational opportunities of using ISVs to limit insect vector competence by using them to interfere with pathogen acquisition, to directly target the insect vector or to confer pathogen resistance by the insect vector.

Metagenomic analysis of Varroa-free Australian honey bees (Apis mellifera) shows a diverse Picornavirales virome

The viral landscape of the honey bee (Apismellifera) has changed as a consequence of the global spread of the parasitic mite Varroa destructor and accompanying virulent strains of the iflavirus deformed wing virus (DWV), which the mite vectors. The presence of DWV in honey bee populations is known to influence the occurrence of other viruses, suggesting that the current known virome of A. mellifera may be undercharacterized. Here we tested this hypothesis by examining the honey bee virome in Australia, which is uniquely free of parasitic mites or DWV. Using a high-throughput sequencing (HTS) approach, we examined the RNA virome from nine pools of A. mellifera across Australia. In addition to previously reported honey bee viruses, several other insect viruses were detected, including strains related to aphid lethal paralysis virus (ALPV) and Rhopalosiphum padi virus (RhPV), which have recently been identified as infecting honey bees in the USA, as well as several other viruses recently found in Drosophila spp. A further 42 putative novel insect virus genomes spanning the order Picornavirales were assembled, which significantly increases the known viral diversity in A. mellifera. Among these novel genomes, we identified several that were similar (but different) to key A. mellifera viruses, such as DWV, that warrant further investigation. We propose that A. mellifera may be preferentially infected with viruses of the order Picornavirales and that a diverse population of these viruses may be representative of a Varroa-free landscape.

Absence of deformed wing virus and Varroa destructor in Australia provides unique perspectives on honeybee viral landscapes and colony losses

Honeybee (Apis mellifera) health is threatened globally by the complex interaction of multiple stressors, including the parasitic mite Varroa destructor and a number of pathogenic viruses. Australia provides a unique opportunity to study this pathogenic viral landscape in the absence of V. destructor. We analysed 1,240A. mellifera colonies across Australia by reverse transcription-polymerase chain reaction (RT-PCR) and next-generation sequencing (NGS). Five viruses were prevalent: black queen cell virus (BQCV), sacbrood virus (SBV), Israeli acute paralysis virus (IAPV) and the Lake Sinai viruses (LSV1 and LSV2), of which the latter three were detected for the first time in Australia. We also showed several viruses were absent in our sampling, including deformed wing virus (DWV) and slow bee paralysis virus (SBPV). Our findings highlight that viruses can be highly prevalent in A. mellifera populations independently of V. destructor. Placing these results in an international context, our results support the hypothesis that the co-pathogenic interaction of V. destructor and DWV is a key driver of increased colony losses, but additional stressors such as pesticides, poor nutrition, etc. may enable more severe and frequent colony losses to occur.

drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes

Background: Virus discovery using high-throughput next-generation sequencing has become more commonplace. However, although analysis of deep next-generation sequencing data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data.

Results: This manuscript presents a pipeline, drVM (detect and reconstruct known viral genomes from metagenomes), for rapid viral read identification, genus-level read partition, read normalization, de novo assembly, sequence annotation, and coverage profiling. The first two procedures and sequence annotation rely on known viral genomes as a reference database. drVM was validated via the analysis of over 300 sequencing runs generated by Illumina and Ion Torrent platforms to provide complete viral genome assemblies for a variety of virus types including DNA viruses, RNA viruses, and retroviruses. drVM is available for free download at: https://sourceforge.net/projects/sb2nhri/files/drVM/ and is also assembled as a Docker container, an Amazon machine image, and a virtual machine to facilitate seamless deployment.

Conclusions: drVM was compared with other viral detection tools to demonstrate its merits in terms of viral genome completeness and reduced computation time. This substantiates the platform's potential to produce prompt and accurate viral genome sequences from clinical samples.

Deep Sequencing Analysis of RNAs from Citrus Plants Grown in a Citrus Sudden Death-Affected Area Reveals Diverse Known and Putative Novel Viruses

Citrus sudden death (CSD) has caused the death of approximately four million orange trees in a very important citrus region in Brazil. Although its etiology is still not completely clear, symptoms and distribution of affected plants indicate a viral disease. In a search for viruses associated with CSD, we have performed a comparative high-throughput sequencing analysis of the transcriptome and small RNAs from CSD-symptomatic and -asymptomatic plants using the Illumina platform. The data revealed mixed infections that included Citrus tristeza virus (CTV) as the most predominant virus, followed by the Citrus sudden death-associated virus (CSDaV), Citrus endogenous pararetrovirus (CitPRV) and two putative novel viruses tentatively named Citrus jingmen-like virus (CJLV), and Citrus virga-like virus (CVLV). The deep sequencing analyses were sensitive enough to differentiate two genotypes of both viruses previously associated with CSD-affected plants: CTV and CSDaV. Our data also showed a putative association of the CSD-symptomatic plants with a specific CSDaV genotype and a likely association with CitPRV as well, whereas the two putative novel viruses showed to be more associated with CSD-asymptomatic plants. This is the first high-throughput sequencing-based study of the viral sequences present in CSD-affected citrus plants, and generated valuable information for further CSD studies.

Protocols for Investigating the Host-tissue Distribution, Transmission-mode, and Effect on the Host Fitness of a Densovirus in the Cotton Bollworm

Many novel viruses have been discovered in animal hosts using next-generation sequencing technologies. Previously, we reported a mutualistic virus, Helicoverpa armigera densovirus (HaDV2), in a lepidopteran species, the cotton bollworm, Helicoverpa armigera (Hubner). Here, we describe the protocols that are currently used to study the effect of HaDV2 on its host. First, we establish a HaDV2-free cotton bollworm colony from a single breeding pair. Then, we orally inoculate some neonate larval offspring with HaDV2-containing filtered liquid to produce two colonies with the same genetic background: one HaDV2-infected, the other uninfected. A protocol to compare life table parameters (e.g., larval, pupal, and adult periods and fecundity) between the HaDV2-infected and -uninfected individuals is also presented, as are the protocols for determining the host-tissue distribution and transmission efficiency of HaDV2. These protocols would also be suitable for investigating the effects of other orally transmitted viruses on their insect hosts, lepidopteran hosts in particular.

Unexpected differences in the population genetics of phasmavirids (Bunyavirales) from subarctic ponds

Little is known of the evolution of RNA viruses in aquatic systems. Here, we assess the genetic connectivity of two bunyaviruses (Kigluaik phantom orthophasmavirus or KIGV and Nome phantom orthophasmavirus or NOMV) with zooplanktonic hosts from subarctic ponds. We expected weak genetic structure among populations as the hosts (phantom midges) have a terrestrial winged dispersal stage. To test whether their respective viruses mirror this structure, we collected and analyzed population datasets from 21 subarctic freshwater ponds and obtained sequences from all four genes in the viral genomes. Prevalence averaged 66 per cent for 514 host specimens and was not significantly different between recently formed thaw ponds and glacial ponds. Unexpectedly, KIGV from older ponds showed pronounced haplotype divergence with little evidence of genetic connectivity. However, KIGV populations from recent thaw ponds appeared to be represented by a closely related haplotype group, perhaps indicating a genotypic dispersal bias. Unlike KIGV, NOMV had modest structure and diversity in recently formed thaw ponds. For each virus, we found elevated genetic diversity relative to the host, but similar population structures to the host. Our results suggest that non-random processes such as virus-host interactions, genotypic bias, and habitat effects differ among polar aquatic RNA viruses.

Unbiased RNA Shotgun Metagenomics in Social and Solitary Wild Bees Detects Associations with Eukaryote Parasites and New Viruses

The diversity of eukaryote organisms and viruses associated with wild bees remains poorly characterized in contrast to the well-documented pathosphere of the western honey bee, Apis mellifera. Using a deliberate RNA shotgun metagenomic sequencing strategy in combination with a dedicated bioinformatics workflow, we identified the (micro-)organisms and viruses associated with two bumble bee hosts, Bombus terrestris and Bombus pascuorum, and two solitary bee hosts, Osmia cornuta and Andrena vaga. Ion Torrent semiconductor sequencing generated approximately 3.8 million high quality reads. The most significant eukaryote associations were two protozoan, Apicystis bombi and Crithidia bombi, and one nematode parasite Sphaerularia bombi in bumble bees. The trypanosome protozoan C. bombi was also found in the solitary bee O. cornuta. Next to the identification of three honey bee viruses Black queen cell virus, Sacbrood virus and Varroa destructor virus-1 and four plant viruses, we describe two novel RNA viruses Scaldis River bee virus (SRBV) and Ganda bee virus (GABV) based on their partial genomic sequences. The novel viruses belong to the class of negative-sense RNA viruses, SRBV is related to the order Mononegavirales whereas GABV is related to the family Bunyaviridae. The potential biological role of both viruses in bees is discussed in the context of recent advances in the field of arthropod viruses. Further, fragmentary sequence evidence for other undescribed viruses is presented, among which a nudivirus in O. cornuta and an unclassified virus related to Chronic bee paralysis virus in B. terrestris. Our findings extend the current knowledge of wild bee parasites in general and addsto the growing evidence of unexplored arthropod viruses in valuable insects.

Application of Genomics for Understanding Plant Virus-Insect Vector Interactions and Insect Vector Control

The relationships between plant viruses and their vectors have evolved over the millennia, and yet, studies on viruses began <150 years ago and investigations into the virus and vector interactions even more recently. The advent of next generation sequencing, including rapid genome and transcriptome analysis, methods for evaluation of small RNAs, and the related disciplines of proteomics and metabolomics offer a significant shift in the ability to elucidate molecular mechanisms involved in virus infection and transmission by insect vectors. Genomic technologies offer an unprecedented opportunity to examine the response of insect vectors to the presence of ingested viruses through gene expression changes and altered biochemical pathways. This review focuses on the interactions between viruses and their whitefly or thrips vectors and on potential applications of genomics-driven control of the insect vectors. Recent studies have evaluated gene expression in vectors during feeding on plants infected with begomoviruses, criniviruses, and tospoviruses, which exhibit very different types of virus-vector interactions. These studies demonstrate the advantages of genomics and the potential complementary studies that rapidly advance our understanding of the biology of virus transmission by insect vectors and offer additional opportunities to design novel genetic strategies to manage insect vectors and the viruses they transmit.

Vector-Borne Bacterial Plant Pathogens: Interactions with Hemipteran Insects and Plants

Hemipteran insects are devastating pests of crops due to their wide host range, rapid reproduction, and ability to transmit numerous plant-infecting pathogens as vectors. While the field of plant-virus-vector interactions has flourished in recent years, plant-bacteria-vector interactions remain poorly understood. Leafhoppers and psyllids are by far the most important vectors of bacterial pathogens, yet there are still significant gaps in our understanding of their feeding behavior, salivary secretions, and plant responses as compared to important viral vectors, such as whiteflies and aphids. Even with an incomplete understanding of plant-bacteria-vector interactions, some common themes have emerged: (1) all known vector-borne bacteria share the ability to propagate in the plant and insect host; (2) particular hemipteran families appear to be incapable of transmitting vector-borne bacteria; (3) all known vector-borne bacteria have highly reduced genomes and coding capacity, resulting in host-dependence; and (4) vector-borne bacteria encode proteins that are essential for colonization of specific hosts, though only a few types of proteins have been investigated. Here, we review the current knowledge on important vector-borne bacterial pathogens, including Xylella fastidiosa, Spiroplasma spp., Liberibacter spp., and 'Candidatus Phytoplasma spp.'. We then highlight recent approaches used in the study of vector-borne bacteria. Finally, we discuss the application of this knowledge for control and future directions that will need to be addressed in the field of vector-plant-bacteria interactions.

Complete Genome Sequence of a Putative Densovirus of the Asian Citrus Psyllid, Diaphorina citri

Here, we report the complete genome sequence of a putative densovirus of the Asian citrus psyllid, Diaphorina citri. Diaphorina citri densovirus (DcDNV) was originally identified through metagenomics, and here, we obtained the complete nucleotide sequence using PCR-based approaches. Phylogenetic analysis places DcDNV between viruses of the Ambidensovirus and Iteradensovirus genera.

Complete Genome Sequence of Diaphorina citri-associated C virus, a Novel Putative RNA Virus of the Asian Citrus Psyllid, Diaphorina citri

We present here the complete nucleotide sequence and genome organization of a novel putative RNA virus identified in field populations of the Asian citrus psyllid, Diaphorina citri, through sequencing of the transcriptome followed by reverse transcription-PCR (RT-PCR). We tentatively named this virus Diaphorina citri-associated C virus (DcACV). DcACV is an unclassified positive-sense RNA virus.

Twenty-Five New Viruses Associated with the Drosophilidae (Diptera)

Drosophila melanogaster is an important laboratory model for studies of antiviral immunity in invertebrates, and Drosophila species provide a valuable system to study virus host range and host switching. Here, we use metagenomic RNA sequencing of about 1600 adult flies to discover 25 new RNA viruses associated with six different drosophilid hosts in the wild. We also provide a comprehensive listing of viruses previously reported from the Drosophilidae. The new viruses include Iflaviruses, Rhabdoviruses, Nodaviruses, and Reoviruses, and members of unclassified lineages distantly related to Negeviruses, Sobemoviruses, Poleroviruses, Flaviviridae, and Tombusviridae. Among these are close relatives of Drosophila X virus and Flock House virus, which we find in association with wild Drosophila immigrans. These two viruses are widely used in experimental studies but have not been previously reported to naturally infect Drosophila. Although we detect no new DNA viruses, in D. immigrans and Drosophila obscura, we identify sequences very closely related to Armadillidium vulgare iridescent virus (Invertebrate iridescent virus 31), bringing the total number of DNA viruses found in the Drosophilidae to three.