Insect-specific viruses: from discovery to potential translational applications

Insights into the RNA Virome of the Corn Leafhopper Dalbulus maidis, a Major Emergent Threat of Maize in Latin America

The maize leafhopper (Dalbulus maidis) is a significant threat to maize crops in tropical and subtropical regions, causing extensive economic losses. While its ecological interactions and control strategies are well studied, its associated viral diversity remains largely unexplored. Here, we employ high-throughput sequencing data mining to comprehensively characterize the D. maidis RNA virome, revealing novel and diverse RNA viruses. We characterized six new viral members belonging to distinct families, with evolutionary cues of beny-like viruses (Benyviridae), bunya-like viruses (Bunyaviridae) iflaviruses (Iflaviridae), orthomyxo-like viruses (Orthomyxoviridae), and rhabdoviruses (Rhabdoviridae). Phylogenetic analysis of the iflaviruses places them within the genus Iflavirus in affinity with other leafhopper-associated iflaviruses. The five-segmented and highly divergent orthomyxo-like virus showed a relationship with other insect associated orthomyxo-like viruses. The rhabdo virus is related to a leafhopper-associated rhabdo-like virus. Furthermore, the beny-like virus belonged to a cluster of insect-associated beny-like viruses, while the bi-segmented bunya-like virus was related with other bi-segmented insect-associated bunya-like viruses. These results highlight the existence of a complex virome linked to D. maidis and paves the way for future studies investigating the ecological roles, evolutionary dynamics, and potential biocontrol applications of these viruses on the D. maidis-maize pathosystem.

Unleashing Nature's Allies: Comparing the Vertical Transmission Dynamics of Insect-Specific and Vertebrate-Infecting Flaviviruses in Mosquitoes

Insect-specific viruses (ISVs) include viruses that are restricted to the infection of mosquitoes and are spread mostly through transovarial transmission. Despite using a distinct mode of transmission, ISVs are often phylogenetically related to arthropod-borne viruses (arboviruses) that are responsible for human diseases and able to infect both mosquitoes and vertebrates. ISVs can also induce a phenomenon called "superinfection exclusion", whereby a primary ISV infection in an insect inhibits subsequent viral infections of the insect. This has sparked interest in the use of ISVs for the control of pathogenic arboviruses transmitted by mosquitoes. In particular, insect-specific flaviviruses (ISFs) have been shown to inhibit infection of vertebrate-infecting flaviviruses (VIFs) both in vitro and in vivo. This has shown potential as a new and ecologically friendly biological approach to the control of arboviral disease. For this intervention to have lasting impacts for biological control, it is imperative that ISFs are maintained in mosquito populations with high rates of vertical transmission. Therefore, these strategies will need to optimise vertical transmission of ISFs in order to establish persistently infected mosquito lines for sustainable arbovirus control. This review compares recent observations of vertical transmission of arboviral and insect-specific flaviviruses and potential determinants of transovarial transmission rates to understand how the vertical transmission of ISFs may be optimised for effective arboviral control.

The First Isolation of Insect-Specific Alphavirus (Agua Salud alphavirus) in Culex (Melanoconion) Mosquitoes in the Brazilian Amazon

Advances in diagnostic techniques coupled with ongoing environmental changes have resulted in intensified surveillance and monitoring of arbovirus circulation in the Amazon. This increased effort has resulted in increased detection of insect-specific viruses among hematophagous arthropods collected in the field. This study aimed to document the first isolation of Agua Salud alphavirus in mosquitoes collected within the Brazilian Amazon. Arthropods belonging to the family Culicidae were collected within a forest fragment located in the Environmental Protection Area of the metropolitan region of Belem. Subsequently, these specimens were meticulously identified to the species level. Afterward, the collected batches were macerated, and the resulting supernatant was then inoculated into C6/36 and Vero cell cultures to facilitate viral isolation. The presence of arboviruses within the inoculated cell cultures was determined through indirect immunofluorescence analysis. Furthermore, positive supernatant samples underwent nucleotide sequencing to precisely identify the viral strains present. Notably, a batch containing Culex (Melanoconion) mosquitoes was identified to be positive for the genus Alphavirus via indirect immunofluorescence. This study is the first report on insect-specific alphavirus isolation in Brazil and the first-ever description of Agua Salud alphavirus isolation within Amazon Forest remnants.

Highly divergent and diverse viral community infecting sylvatic mosquitoes from Northeast Brazil

Mosquitoes can transmit several pathogenic viruses to humans, but their natural viral community is also composed of a myriad of other viruses such as insect-specific viruses (ISVs) and those that infect symbiotic microorganisms. Besides a growing number of studies investigating the mosquito virome, the majority are focused on few urban species, and relatively little is known about the virome of sylvatic mosquitoes, particularly in high biodiverse biomes such as the Brazilian biomes. Here, we characterized the RNA virome of 10 sylvatic mosquito species from Atlantic forest remains at a sylvatic-urban interface in Northeast Brazil employing a metatranscriptomic approach. A total of 16 viral families were detected. The phylogenetic reconstructions of 14 viral families revealed that the majority of the sequences are putative ISVs. The phylogenetic positioning and, in most cases, the association with a high RNA-dependent RNA polymerase amino acid divergence from other known viruses suggests that the viruses characterized here represent at least 34 new viral species. Therefore, the sylvatic mosquito viral community is predominantly composed of highly divergent viruses highlighting the limited knowledge we still have about the natural virome of mosquitoes in general. Moreover, we found that none of the viruses recovered were shared between the species investigated, and only one showed high identity to a virus detected in a mosquito sampled in Peru, South America. These findings add further in-depth understanding about the interactions and coevolution between mosquitoes and viruses in natural environments.

IMPORTANCE

Mosquitoes are medically important insects as they transmit pathogenic viruses to humans and animals during blood feeding. However, their natural microbiota is also composed of a diverse set of viruses that cause no harm to the insect and other hosts, such as insect-specific viruses. In this study, we characterized the RNA virome of sylvatic mosquitoes from Northeast Brazil using unbiased metatranscriptomic sequencing and in-depth bioinformatic approaches. Our analysis revealed that these mosquitoes species harbor a diverse set of highly divergent viruses, and the majority comprises new viral species. Our findings revealed many new virus lineages characterized for the first time broadening our understanding about the natural interaction between mosquitoes and viruses. Finally, it also provided several complete genomes that warrant further assessment for mosquito and vertebrate host pathogenicity and their potential interference with pathogenic arboviruses.

Genetic Characterization of Two Novel Insect-Infecting Negative-Sense RNA Viruses Identified in a Leaf Beetle, Aulacophora indica

Herbivorous insects harbor a variety of insect-specific viruses (ISVs) some of which are considered to be valuable biological agents for potential applications in biological defense and control strategies. Leaf beetles with chewing mouthparts are particularly known for their capacity to disrupt plant tissue while feeding, often creating openings that can act as entry points for plant pathogens. In this study, we have identified two new negative-sense RNA viruses infecting the leaf beetle Aulacophora indica, an important member of the Chrysomelidae family. These recently discovered viruses belong to the viral families Nyamiviridae and Chuviridae and have been preliminarily named Aulacophora indica nyami-like virus 1 (AINlV1) and Aulacophora indica chu-like virus 1 (AIClV1), respectively. The complete genomic sequences of these viruses were obtained using rapid amplification of cDNA ends (RACE) techniques. Detailed analysis of their genomic structures has confirmed their similarity to other members within their respective families. Furthermore, analysis of virus-derived small interfering RNA (vsiRNA) demonstrated a high abundance and typical vsiRNA pattern of AINlV1 and AIClV1, offering substantial evidence to support their classification as ISVs. This research enhances our understanding of viral diversity within insects.

Metatranscriptomic analysis of common mosquito vector species in the Canadian Prairies

The microbiome plays vital roles in the life history of mosquitoes, including their development, immunity, longevity, and vector competence. Recent advances in sequencing technologies have allowed for detailed exploration into the diverse microorganisms harbored by these medically important insects. Although these meta-studies have cataloged the microbiomes of mosquitoes in several continents, much of the information currently available for North America is limited to the state of California. In this study, we collected >35,000 mosquitoes throughout Manitoba, Canada, over a 3-year period and then harnessed RNA sequencing and targeted reverse transcriptase-PCR to characterize the microbiomes of the eight most pervasive and important vector and pest species. The consensus microbiome of each species was overwhelmingly composed of viruses but also included fungi, bacteria, protozoa, and parasitic invertebrates. The microbial assemblages were heterogeneous between species, even within the same genus. We detected notable pathogens, including the causal agents of Cache Valley Fever, avian malaria, and canine heartworm. The remaining microbiome consisted largely of putatively insect-specific viruses that are not well characterized, including 17 newly discovered viruses from 10 different families. Future research should focus on evaluating the potential application of these viruses in biocontrol, as biomarkers, and/or in disrupting mosquito vectorial capacity. Interestingly, we also detected viruses that naturally infect honeybees and thrips, which were presumably acquired indirectly through nectar foraging behaviors. Overall, we provide the first comprehensive catalog of the microorganisms harbored by the most common and important mosquito vectors and pests in the Canadian Prairies.

IMPORTANCE

Mosquitoes are the most dangerous animals on the planet, responsible for over 800,000 deaths per year globally. This is because they carry and transmit a plethora of human disease-causing microorganisms, such as West Nile virus and the malaria parasite. Recent innovations in nucleic acid sequencing technologies have enabled researchers unparalleled opportunities to characterize the suite of microorganisms harbored by different mosquito species, including the causal agents of disease. In our study, we carried out 3 years of intensive mosquito surveillance in Canada. We collected and characterized the microorganisms harbored by >35,000 mosquitoes, including the identification of the agents of Cache Valley fever, avian malaria, and canine heartworm. We also detected insect-specific viruses and discovered 17 new viruses that have never been reported. This study, which is the first of its kind in Canada and one of only a handful globally, will greatly aid in future infectious disease research.

Discovery of Two Novel Viruses of the Willow-Carrot Aphid, Cavariella aegopodii

The advancement of bioinformatics and sequencing technology has resulted in the identification of an increasing number of new RNA viruses. This study systematically identified the RNA virome of the willow-carrot aphid, Cavariella aegopodii (Hemiptera: Aphididae), using metagenomic sequencing and rapid amplification of cDNA ends (RACE) approaches. C. aegopodii is a sap-sucking insect widely distributed in Europe, Asia, North America, and Australia. The deleterious effects of C. aegopodii on crop growth primarily stem from its feeding activities and its role as a vector for transmitting plant viruses. The virome includes Cavariella aegopodii virga-like virus 1 (CAVLV1) and Cavariella aegopodii iflavirus 1 (CAIV1). Furthermore, the complete genome sequence of CAVLV1 was obtained. Phylogenetically, CAVLV1 is associated with an unclassified branch of the Virgaviridae family and is susceptible to host antiviral RNA interference (RNAi), resulting in the accumulation of a significant number of 22nt virus-derived small interfering RNAs (vsiRNAs). CAIV1, on the other hand, belongs to the Iflaviridae family, with vsiRNAs ranging from 18 to 22 nt. Our findings present a comprehensive analysis of the RNA virome of C. aegopodii for the first time, offering insights that could potentially aid in the future control of the willow-carrot aphid.

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.

Leveraging insect viruses and genetic manipulation for sustainable agricultural pest control

The potential of insect viruses in the biological control of agricultural pests is well-recognized, yet their practical application faces obstacles such as host specificity, variable virulence, and resource scarcity. High-throughput sequencing (HTS) technologies have significantly advanced our capabilities in discovering and identifying new insect viruses, thereby enriching the arsenal for pest management. Concurrently, progress in reverse genetics has facilitated the development of versatile viral expression vectors. These vectors have enhanced the specificity and effectiveness of insect viruses in targeting specific pests, offering a more precise approach to pest control. This review provides a comprehensive examination of the methodologies employed in the identification of insect viruses using HTS. Additionally, it explores the domain of genetically modified insect viruses and their associated challenges in pest management. The adoption of these cutting-edge approaches holds great promise for developing environmentally sustainable and effective pest control solutions. © 2023 Society of Chemical Industry.

Identification and Characterization of Three Novel Solemo-like Viruses in the White-Backed Planthopper, Sogatella furcifera

Agricultural insects play a crucial role in transmitting plant viruses and host a considerable number of insect-specific viruses (ISVs). Among these insects, the white-backed planthoppers (WBPH; Sogatella furcifera, Hemiptera: Delphacidae) are noteworthy rice pests and are responsible for disseminating the southern rice black-streaked dwarf virus (SRBSDV), a significant rice virus. In this study, we analyzed WBPH transcriptome data from public sources and identified three novel viruses. These newly discovered viruses belong to the plant-associated viral family Solemoviridae and were tentatively named Sogatella furcifera solemo-like virus 1-3 (SFSolV1-3). Among them, SFSolV1 exhibited a prevalent existence in different laboratory populations, and its complete genome sequence was obtained using rapid amplification of cDNA ends (RACE) approaches. To investigate the antiviral RNA interference (RNAi) response in WBPH, we conducted an analysis of virus-derived small interfering RNAs (vsiRNAs). The vsiRNAs of SFSolV1 and -2 exhibited typical patterns associated with the host's siRNA-mediated antiviral immunity, with a preference for 21- and 22-nt vsiRNAs derived equally from both the sense and antisense genomic strands. Furthermore, we examined SFSolV1 infection and distribution in WBPH, revealing a significantly higher viral load of SFSolV1 in nymphs' hemolymph compared to other tissues. Additionally, in adult insects, SFSolV1 exhibited higher abundance in male adults than in female adults.

Identification and classification of the genomes of novel microviruses in poultry slaughterhouse

Microviridae is a family of phages with circular ssDNA genomes and they are widely found in various environments and organisms. In this study, virome techniques were employed to explore potential members of Microviridae in a poultry slaughterhouse, leading to the identification of 98 novel and complete microvirus genomes. Using a similarity clustering network classification approach, these viruses were found to belong to at least 6 new subfamilies within Microviridae and 3 higher-level taxonomic units. Genome size, GC content and genome structure of these new taxa showed evident regularities, validating the rationality of our classification method. Our method can divide microviruses into about 45 additional detailed clusters, which may serve as a new standard for classifying Microviridae members. Furthermore, by addressing the scarcity of host information for microviruses, the current study significantly broadened their host range and discovered over 20 possible new hosts, including important pathogenic bacteria such as Helicobacter pylori and Vibrio cholerae, as well as different taxa demonstrated different host specificities. The findings of this study effectively expand the diversity of the Microviridae family, providing new insights for their classification and identification. Additionally, it offers a novel perspective for monitoring and controlling pathogenic microorganisms in poultry slaughterhouse environments.

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.

RNA Viruses Are Prevalent and Active Tenants of the Predatory Mite Phytoseiulus persimilis (Acari: Phytoseiidae)

Many arthropod species harbor a diverse range of viruses. While much is known about pathogenic viruses of some economically important insects and arthropods involved in disease transmission, viruses associated with mites have rarely been studied. The main objective of this study was to characterize the virome of Phytoseiulus persimilis (Phytoseiidae), a predatory mite commercially used worldwide for the biological control of the key pest Tetranychus urticae (Tetranichidae). A combination of de novo transcriptome assembly and virion sequencing, revealed that RNA viruses are highly prevalent and active tenants of commercial populations of P. persimilis, comprising on average 9% of the mite's total mRNA. Seventeen RNA viruses dominated the mite's virome (i.e., were highly transcribed) with over half (n = 10) belonging to the order Picornavirales, + ssRNA viruses that infect a large range of hosts, including arthropods. Screening of the 17 dominant virus sequences in P. persimilis and T. urticae revealed that three viruses (two Picornavirales of the families Iflaviridae and Dicistroviridae, and one unclassified Riboviria) are unique to P. persimilis and three others (two unclassified Picornavirales and one unclassified Riboviria) are present in both mite species. Most of the sequences were related to viruses previously documented in economically important arthropods, while others have rarely been documented before in arthropods. These findings demonstrate that P. persimilis, like many other arthropods, harbors a diverse RNA virome, which might affect the mite's physiology and consequently its efficiency as a biological control agent.

The identification and genetic characteristics of Quang Binh virus from field-captured Culex tritaeniorhynchus (Diptera: Culicidae) from Guizhou Province, China

BACKGROUND

Mosquitoes carry a variety of viruses that can cause disease in humans, animals and livestock. Surveys for viruses carried by wild mosquitoes can significantly contribute to surveillance efforts and early detection systems. In addition to mosquito-borne viruses, mosquitoes harbor many insect-specific viruses (ISVs). Quang Binh virus (QBV) is one such example, categorized as an ISV within the Flavivirus genus (family Flaviviridae). QBV has been specifically documented in Vietnam and China, with reports limited to several mosquito species.

METHODS

The homogenate obtained from female mosquitoes was cultured on C6/36 (Aedes albopictus) and BHK-21 (baby hamster kidney) cell lines. Positive cultures were identified by reverse transcription-polymerase chain reaction (RT‒PCR) with taxon- or species-specific primers. Next-generation sequencing was employed to sequence the complete genomes of the identified positive samples. Subsequently, phylogenetic, gene homology, molecular evolutionary and genetic variation analyses were conducted.

RESULT

In 2021, a total of 32,177 adult female mosquitoes were collected from 15 counties in Guizhou Province, China. The predominant mosquito species identified were Culex tritaeniorhynchus, Armigeres subalbatus and Anopheles sinensis. Among the collected mosquitoes, three positive cultures were obtained from Cx. tritaeniorhynchus pools, revealing the presence of Quang Binh virus (QBV) RNA sequences. Phylogenetic analysis indicated that the three Guizhou isolates, along with the prototype isolate from Vietnam, formed distinct branches. These branches were primarily closely related to other QBV isolates reported in China. Comparative analysis revealed a high degree of nucleotide and amino acid homology between the Guizhou isolates and both Vietnamese and other indigenous Chinese isolates. Additionally, nonsynonymous single-nucleotide variants (SNVs) were observed in these strains compared to the QBV prototype strain.

CONCLUSION

This study represents the first report of QBV presences in Cx. tritaeniorhynchus mosquitoes in Guizhou Province, China. Phylogenetic tree analysis showed that the three Guizhou isolates were most closely related to the QBV genes found in China. In addition, the study of the genetic characteristics and variation of this virus provided a deeper understanding of QBV and enriched the baseline data of these insect-specific flaviviruses (ISFVs).

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.

Distribution and prevalence of viral genomes in Italian populations of the invasive brown marmorated stink bug Halyomorpha halys

Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species that causes significant agricultural losses, especially to orchard fruits, vegetables, herbaceous and ornamental plants. It is also a nuisance pest that seeks shelter in indoor spaces during the winter months. Harnessing the H. halys virome can result in new environmentally sustainable approaches to contain its populations and its relatated agricultural damages. In this study, RNA-Seq data were used to explore the virome associated to ten field populations collected in the Lombardy region in Northern Italy. We identified six complete viral genomes, three of which were previously unknown, belonging to the orders Reovirales, Articulavirales, Ghabrivirales, Durnavirales, and Picornavirales. The prevalence of the six viruses was evaluated by Real-time reverse transcription-quantitative PCR on eighty individuals. Halyomorpha halys ifla-like virus 2 turned out to be the most geographically widespread virus, as it was found in more than 50% of the analyzed insects and in nine out of the ten sampling locations. Moreover, in some individuals, this iflavirus was found in association with each of the other viruses in various combinations that involved up to four viruses. Further studies on such virus-virus interactions and their relationships with the insect host may open the possibility to exploit these naturally occurring viruses as specific and targeted biocontrol agents of H. halys.

Shotgun Metagenomic Sequencing Reveals Virome Composition of Mosquitoes from a Transition Ecosystem of North-Northeast Brazil

A wide diversity of pathogenic mosquito-borne viruses circulate in the Brazilian Amazon, and the intense deforestation can contribute to the spread of these viruses. In this context, this study aimed to investigate the viral diversity in mosquitoes of the genera Aedes, Culex, Haemagogus, and Sabethes from a transition area between the Amazon, Cerrado, and Caatinga biomes in Brazil. Metagenomic high-throughput sequencing was used to characterize the virome of 20 mosquito pools. A total of 15 virus-like genomes were identified, comprising species genomically close to insect-specific viruses of the families Iflaviridae, Metaviridae, Lispiviridae, Rhabdoviridae, Xinmoviridae, and Parvoviridae and species of plant viruses of the families Solemoviridae, Virgaviridae, and Partitiviridae. However, sequences of viruses associated with human and animal diseases were not detected. Most of the recovered genomes were divergent from those previously described. These findings reveal that there are a large number of unknown viruses to be explored in the middle-north of Brazil.

Methods of crop improvement and applications towards fortifying food security

Agriculture has supported human life from the beginning of civilization, despite a plethora of biotic (pests, pathogens) and abiotic (drought, cold) stressors being exerted on the global food demand. In the past 50 years, the enhanced understanding of cellular and molecular mechanisms in plants has led to novel innovations in biotechnology, resulting in the introduction of desired genes/traits through plant genetic engineering. Targeted genome editing technologies such as Zinc-Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) have emerged as powerful tools for crop improvement. This new CRISPR technology is proving to be an efficient and straightforward process with low cost. It possesses applicability across most plant species, targets multiple genes, and is being used to engineer plant metabolic pathways to create resistance to pathogens and abiotic stressors. These novel genome editing (GE) technologies are poised to meet the UN's sustainable development goals of "zero hunger" and "good human health and wellbeing." These technologies could be more efficient in developing transgenic crops and aid in speeding up the regulatory approvals and risk assessments conducted by the US Departments of Agriculture (USDA), Food and Drug Administration (FDA), and Environmental Protection Agency (EPA).

Agua Salud Alphavirus Infection, Dissemination and Transmission in Aedes aegypti Mosquitoes

Mosquitoes are competent vectors for many important arthropod-borne viruses (arboviruses). In addition to arboviruses, insect-specific viruses (ISV) have also been discovered in mosquitoes. ISVs are viruses that replicate in insect hosts but are unable to infect and replicate in vertebrates. They have been shown to interfere with arbovirus replication in some cases. Despite the increase in studies on ISV-arbovirus interactions, ISV interactions with their hosts and how they are maintained in nature are still not well understood. In the present study, we investigated the infection and dissemination of the Agua Salud alphavirus (ASALV) in the important mosquito vector Aedes aegypti through different infection routes (per oral infection, intrathoracic injection) and its transmission. We show here that ASALV infects the female Ae. aegypti and replicates when mosquitoes are infected intrathoracically or orally. ASALV disseminated to different tissues, including the midgut, salivary glands and ovaries. However, we observed a higher virus load in the brain than in the salivary glands and carcasses, suggesting a tropism towards brain tissues. Our results show that ASALV is transmitted horizontally during adult and larval stages, although we did not observe vertical transmission. Understanding ISV infection and dissemination dynamics in Ae. aegypti and their transmission routes could help the use of ISVs as an arbovirus control strategy in the future.

Spodoptera litura larvae are attracted by HvAV-3h-infected S. litura larvae-damaged pepper leaves

BACKGROUND

Herbivore-induced plant volatiles (HIPVs) are important self-defense outputs of pepper plants to resist insect pests. Ascoviruses are pathogenic to the larvae of most lepidopteran vegetable pests. However, whether Heliothis virescens ascovirus 3h (HvAV-3h)-infected Spodoptera litura larvae can change pepper leaf HIPVs is not well understood.

RESULTS

Spodoptera litura larvae preferred S. litura-infested leaves, and this preference was stronger with longer duration of S. litura infestation. In addition, S. litura larvae significantly chose pepper leaves damaged by HvAV-3h-infected S. litura over the healthy pepper leaves. Results also showed that S. litura larvae preferred leaves mechanically damaged and treated with oral secretions from HvAV-3h infected-S. litura larvae in a simulation test. We captured the volatiles emitted by leaves under six treatments. Results showed that the volatile profile changed with the different treatments. Testing of volatile blends, prepared to the proportion released showed that the blend from simulated HvAV-3h-infected S. litura larvae-damaged plants was the most attractive to S. litura larvae. Further, we also found that some of the compounds significantly attracted S. litura larvae at specific concentrations.

CONCLUSION

HvAV-3h-infected S. litura can alter the release of HIPVs in pepper plants and thus become more attractive to S. litura larvae. We speculate that this may be due to alterations in the concentration of some compounds (such as geranylacetone and prohydrojasmon) affecting the behavior of S. litura larvae. © 2023 Society of Chemical Industry.

Metatranscriptomic Sequencing Reveals Host Species as an Important Factor Shaping the Mosquito Virome

Mosquitoes are important vector hosts for numerous viral pathogens and harbor a large number of mosquito-specific viruses as well as human-infecting viruses. Previous studies have mainly focused on the discovery of mosquito viruses, and our understanding of major ecological factors associated with virome structure in mosquitoes remains limited. We utilized metatranscriptomic sequencing to characterize the viromes of five mosquito species sampled across eight locations in Yunnan Province, China. This revealed the presence of 52 viral species, of which 19 were novel, belonging to 15 viral families/clades. Of particular note was Culex hepacivirus 1, clustering within the avian clade of hepaciviruses. Notably, both the viromic diversity and abundance of Aedes genus mosquitoes were significantly higher than those of the Culex genus, while Aedes albopictus mosquitoes harbored a higher diversity than Aedes aegypti mosquitoes. Our findings thus point to discernible differences in viromic structure between mosquito genera and even between mosquito species within the same genus. Importantly, such differences were not attributable to differences in sampling between geographical location. Our study also revealed the ubiquitous presence of the endosymbiont bacterium Wolbachia, with the genetic diversity and abundance also varying between mosquito species. In conclusion, our results suggested that the mosquito host species play an important role in shaping the virome's structure. IMPORTANCE This study revealed the huge capability of mosquitoes in harboring a rich diversity of RNA viruses, although relevant studies have characterized the intensively unparalleled diversity of RNA viruses previously. Furthermore, our findings showed discernible differences not only in viromic structure between mosquito genera and even between mosquito species within the same genus but also in the genetic diversity and abundance of Wolbachia between different mosquito populations. These findings emphasize the importance of host genetic background in shaping the virome composition of mosquitoes.

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.

Identification, characterization and prevalence in southern China of a new iflavirus in the leafhopper Recilia dorsalis (Hemiptera: Cicadellidae)

The leafhopper Recilia dorsalis (Hemiptera: Cicadellidae) is not only a significant pest in agriculture but also an important vector involved in transmitting numerous pathogens that are known to cause economic losses by affecting rice crops. Here, a new iflavirus was discovered in the leafhopper R. dorsalis by employing a transcriptomic approach. The complete viral genome was determined to be 10,711 nucleotides (nt) in length and contains a single open reading frame (ORF) encoding a putative polyprotein comprised of 3,161 amino acids (aa), which is flanked by 5' and 3' untranslated regions. The full viral genome nt and the deduced polyprotein aa sequence showed the highest similarity (71.6% and 77.8%, respectively) with Langfang leafhopper iflavirus. Phylogenetic analysis based on the RdRp domain indicated that the isolated virus, which we have tentatively named Recilia dorsalis iflavirus 2 (RdIV2), is clustered with the members of the family Iflaviridae. Moreover, the results of our surveys indicate that RdIV2 predominates in southwestern Guangdong and southeastern Guangxi, China, and was absent in the other three species of leafhoppers; Nephotettix cincticeps, N. virescens and N. nigropictus. Notably, R. dorsalis was found to be co-infected with RdIV2 and rice stripe mosaic virus (RSMV; a well-known rice-infecting virus vectored by R. dorsalis) in rice fields, although the co-infection rate is low.

An RNA Virome Analysis of the Pink-Winged Grasshopper Atractomorpha sinensis

A large number of RNA viruses have been discovered in most insect orders using high-throughput sequencing (HTS) and advanced bioinformatics methods. In this study, an RNA virome of the grasshopper was systematically identified in Atractomorpha sinensis (Orthoptera: Pyrgomorphidae), an important agricultural pest known as the pink-winged grasshopper. These insect viruses were classified as the nege-like virus, iflavirus, ollusvirus, and chu-like virus using HTS and phylogenetic analyses. Meanwhile, the full sequences of four novel RNA viruses were obtained with RACE and named Atractomorpha sinensis nege-like virus 1 (ASNV1), Atractomorpha sinensis iflavirus 1 (ASIV1), Atractomorpha sinensis ollusvirus 1 (ASOV1), and Atractomorpha sinensis chu-like virus 1 (ASCV1), respectively. Moreover, the analysis of virus-derived small interfering RNAs showed that most of the RNA viruses were targeted by the host antiviral RNA interference pathway. Moreover, our results provide a comprehensive analysis on the RNA virome of A. sinensis.

The Characterization of Three Novel Insect-Specific Viruses Discovered in the Bean Bug, Riptortus pedestris

Insect-specific virus (ISV) is one of the most promising agents for the biological control of insects, which is abundantly distributed in hematophagous insects. However, few ISVs have been reported in Riptortus pedestris (Fabricius), one of the major pests threatening soybeans and causing great losses in yield and quality. In this work, field Riptortus pedestris was collected from six soybean-producing regions in China, and their virome was analyzed with the metatranscriptomic approach. Altogether, seven new insect RNA viruses were identified, three of which had complete RNA-dependent RNA polymerase (RdRp) and nearly full-length genome sequences, which were named Riptortus pedestris alphadrosrha-like virus 1 (RpALv1), Riptortus pedestris alphadrosrha-like virus 2 (RpALv2) and Riptortus pedestris almendra-like virus (RiALv). The three identified novel ISVs belonged to the family Rhabdoviridae, and phylogenetic tree analysis indicated that they were clustered into new distinct clades. Interestingly, the analysis of virus-derived small-interfering RNAs (vsiRNAs) indicated that only RiALv-derived siRNAs exhibited 22 nt length preference, whereas no clear 21 or 22 nt peaks were observed for RpALv1 and RpALv2, suggesting the complexity of siRNA-based antiviral immunity in R. pedestris. In conclusion, this study contributes to a better understanding of the microenvironment in R. pedestris and provides viral information for the development of potential soybean insect-specific biocontrol agents.

Aedes aegypti and Ae. albopictus microbiome/virome: new strategies for controlling arboviral transmission?

Aedes aegypti and Aedes albopictus are the main vectors of highly pathogenic viruses for humans, such as dengue (DENV), chikungunya (CHIKV), and Zika (ZIKV), which cause febrile, hemorrhagic, and neurological diseases and remain a major threat to global public health. The high ecological plasticity, opportunistic feeding patterns, and versatility in the use of urban and natural breeding sites of these vectors have favored their dispersal and adaptation in tropical, subtropical, and even temperate zones. Due to the lack of available treatments and vaccines, mosquito population control is the most effective way to prevent arboviral diseases. Resident microorganisms play a crucial role in host fitness by preventing or enhancing its vectorial ability to transmit viral pathogens. High-throughput sequencing and metagenomic analyses have advanced our understanding of the composition and functionality of the microbiota of Aedes spp. Interestingly, shotgun metagenomics studies have established that mosquito vectors harbor a highly conserved virome composed of insect-specific viruses (ISV). Although ISVs are not infectious to vertebrates, they can alter different phases of the arboviral cycle, interfering with transmission to the human host. Therefore, this review focuses on the description of Ae. aegypti and Ae. albopictus as vectors susceptible to infection by viral pathogens, highlighting the role of the microbiota-virome in vectorial competence and its potential in control strategies for new emerging and re-emerging arboviruses.

Local-scale virome depiction in Medellín, Colombia, supports significant differences between Aedes aegypti and Aedes albopictus

Aedes spp. comprise the primary group of mosquitoes that transmit arboviruses such as dengue, Zika, and chikungunya viruses to humans, and thus these insects pose a significant burden on public health worldwide. Advancements in next-generation sequencing and metagenomics have expanded our knowledge on the richness of RNA viruses harbored by arthropods such as Ae. aegypti and Ae. albopictus. Increasing evidence suggests that vector competence can be modified by the microbiome (comprising both bacteriome and virome) of mosquitoes present in endemic zones. Using an RNA-seq-based metataxonomic approach, this study determined the virome structure, Wolbachia presence and mitochondrial diversity of field-caught Ae. aegypti and Ae. albopictus mosquitoes in Medellín, Colombia, a municipality with a high incidence of mosquito-transmitted arboviruses. The two species are sympatric, but their core viromes differed considerably in richness, diversity, and abundance; although the community of viral species identified was large and complex, the viromes were dominated by few virus species. BLAST searches of assembled contigs suggested that at least 17 virus species (16 of which are insect-specific viruses [ISVs]) infect the Ae. aegypti population. Dengue virus 3 was detected in one sample and it was the only pathogenic virus detected. In Ae. albopictus, up to 11 ISVs and one plant virus were detected. Therefore, the virome composition appears to be species-specific. The bacterial endosymbiont Wolbachia was identified in all Ae. albopictus samples and in some Ae. aegypti samples collected after 2017. The presence of Wolbachia sp. in Ae. aegypti was not related to significant changes in the richness, diversity, or abundance of this mosquito’s virome, although it was related to an increase in the abundance of Aedes aegypti To virus 2 (Metaviridae). The mitochondrial diversity of these mosquitoes suggested that the Ae. aegypti population underwent a change that started in the second half of 2017, which coincides with the release of Wolbachia-infected mosquitoes in Medellín, indicating that the population of wMel-infected mosquitoes released has introduced new alleles into the wild Ae. aegypti population of Medellín. However, additional studies are required on the dispersal speed and intergenerational stability of wMel in Medellín and nearby areas as well as on the introgression of genetic variants in the native mosquito population.

Characterization of Two Novel Insect-Specific Viruses Discovered in the Green Leafhopper, Cicadella viridis

Simple Summary

Insect-specific viruses (ISVs) have gained increasing attention for their potential use as biological agents. In this study, the full genomes of two ISVs (Cicadella viridis iflavirus 1, CvIfV1; Cicadella viridis nido-like virus 1, CvNiLV1) were revealed in green leafhoppers, using metatranscriptome, RT-PCR, and RACE approaches, respectively. CvIfV1 is a member of iflavirus and has a typical iflavirus genome organization. An antiviral RNA interference (RNAi) was triggered when host insects were challenged with CvIfV1, which resulted in an abundant accumulation of 21-nt virus-derived siRNAs (vsiRNAs). CvNiLV1 clusters are within a distinct unclassified clade of viruses in the order Nidovirales, and evolutionary related with viruses that infect vertebrate hosts. CvNiLV1 was also targeted by the host antiviral RNAi pathway, and generated the 21-nt vsiRNAs with a strong A/U bias in the 5′-terminal. Our study provided valuable information on ISVs in leafhoppers, and might prove useful in pest management.

Abstract

Insect-specific viruses (ISV) are one of the most promising agents for the biological control of insects. The green leafhopper, Cicadella viridis (Linnaeus), is an significant pest in agriculture, and causes economic losses to fruit trees, willows, and field crops. As a representative species of the large family Cicadellidae, ISVs in C. viridis have never been studied, to date. In this study, the full genome sequences of two ISVs, named Cicadella viridis iflavirus1 (CvIfV1), and Cicadella viridis nido-like virus 1 (CvNiLV1), were revealed using a metatranscriptomic approach. A homology search and phylogenetic analysis indicated that CvIfV1 is a new member in the family Iflaviridae (genus Iflavirus) with a typical iflavirus genome organization, whereas CvNiLV1 belongs to the unclassified clade/family of the order Nidovirales. In addition, analysis of virus-derived small interfering RNAs (vsiRNAs) was performed to investigate the antiviral RNA interference (RNAi) response of C. viridis. The vsiRNAs exhibit typical patterns produced by host siRNA-mediated antiviral immunity, including a preference of 21-nt vsiRNAs derived equally from the sense and antisense genomic strands, and a strong A/U bias in the 5′-terminus of the viral genomes. Our study provides valuable information for ISVs in leafhoppers for the first time, which might prove useful in the control of C. viridis in future.

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.

Exploring Virome Diversity in Public Data in South America as an Approach for Detecting Viral Sources From Potentially Emerging Viruses

The South American continent presents a great diversity of biomes, whose ecosystems are constantly threatened by the expansion of human activity. The emergence and re-emergence of viral populations with impact on the human population and ecosystem have shown increases in the last decades. In deference to the growing accumulation of genomic data, we explore the potential of South American-related public databases to detect signals that contribute to virosphere research. Therefore, our study aims to investigate public databases with emphasis on the surveillance of viruses with medical and ecological relevance. Herein, we profiled 120 "sequence read archives" metagenomes from 19 independent projects from the last decade. In a coarse view, our analyses identified only 0.38% of the total number of sequences from viruses, showing a higher proportion of RNA viruses. The metagenomes with the most important viral sequences in the analyzed environmental models were 1) aquatic samples from the Amazon River, 2) sewage from Brasilia, and 3) soil from the state of São Paulo, while the models of animal transmission were detected in mosquitoes from Rio Janeiro and Bats from Amazonia. Also, the classification of viral signals into operational taxonomic units (OTUs) (family) allowed us to infer from metadata a probable host range in the virome detected in each sample analyzed. Further, several motifs and viral sequences are related to specific viruses with emergence potential from Togaviridae, Arenaviridae, and Flaviviridae families. In this context, the exploration of public databases allowed us to evaluate the scope and informative capacity of sequences from third-party public databases and to detect signals related to viruses of clinical or environmental importance, which allowed us to infer traits associated with probable transmission routes or signals of ecological disequilibrium. The evaluation of our results showed that in most cases the size and type of the reference database, the percentage of guanine-cytosine (GC), and the length of the query sequences greatly influence the taxonomic classification of the sequences. In sum, our findings describe how the exploration of public genomic data can be exploited as an approach for epidemiological surveillance and the understanding of the virosphere.

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.

Identification of Phasi Charoen-Like Phasivirus in Field Collected Aedes aegypti from Karnataka State, India

Background: A wide range of insect-specific viruses (ISVs) have been reported worldwide. There are no studies from India that have reported ISVs. The current study describes the identification of Phasi Charoen-like virus (PCLV) from Aedes aegypti mosquito-pools from six districts of Karnataka state, India. Materials and Methods: During the Chikungunya virus (CHIKV) outbreak in the Bangalore Urban district in 2019, using conventional PCR, it was found that both human and mosquito samples were positive for CHIKV. For retrieve the complete genome sequence, mosquito samples were subjected to next generation sequencing (NGS) analysis and PCLV was also found. During 2019, as part of a vector-borne disease surveillance, we received 50 mosquito pool samples from 6 districts of the state, all of them were subjected to NGS to identify PCLV. Results: The A. aegypti mosquito-pools samples were subjected to the NGS platform that led to identification of an ISV, PCLV. PCLV was identified in 26 A. aegypti mosquito-pools collected from 6 districts. We also found mixed infection of PCLV with the Dengue virus (DENV; genotypes 1 and 3) and CHIKV from five pools. The nucleotide identity for the L gene of Indian PCLV sequences ranged between 97.1% and 98.3% in comparison with the Thailand sequences. Conclusions: To the best of our knowledge, this is the first report of PCLV dual infection with DENV and CHIKV in India. The present study confirms the presence of PCLV in A. aegypti mosquitoes from Karnataka state. The study adds India in the global geographical distribution of PCLV.

Partial Genome Sequence of a Novel Reo-Like Virus Detected in Asian Citrus Psyllid (Diaphorina citri) Populations from Florida Citrus Groves

This report describes the partial (nearly complete) genome sequence of a novel reo-like virus tentatively named Diaphorina citri Cimodo-like virus. This putative virus has 10 double-stranded RNA segments and was detected in Asian citrus psyllid (Diaphorina citri) populations collected from Florida commercial citrus groves.

Genetic lineage characterization and spatiotemporal dynamics of classical insect-specific flaviviruses: outcomes and limitations

The genus Flavivirus incorporates bona fide arboviruses, as well as others viruses with restricted replication in insect cells. Among the latter, a large monophyletic cluster of viruses, known as cISF (classical insect-specific flaviviruses), has been sampled in many species of mosquitoes collected over a large geographic range. In this study, we investigated nucleotide and protein sequences with a suite of molecular characterization approaches including genetic distance, Shannon entropy, selective pressure analysis, polymorphism identification, principal coordinate analysis, likelihood mapping, phylodynamic reconstruction, and spatiotemporal dispersal, to further characterize this diverse group of insect-viruses. The different lineages and sub-lineages of viral sequences presented low sequence diversity and entropy (though some displayed lineage-specific polymorphisms), did not show evidence of frequent recombination and evolved under strong purifying selection. Moreover, the reconstruction of the evolutionary history and spatiotemporal dispersal was highly impacted by overall low signals of sequence divergence throughout time but suggested that cISF distribution in space and time is dynamic and may be dependent on human activities, including commercial trading and traveling.

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.

Integrated Analysis of microRNA and mRNA Transcriptome Reveals the Molecular Mechanism of Solanum lycopersicum Response to Bemisia tabaci and Tomato chlorosis virus

Tomato chlorosis virus (ToCV), is one of the most devastating cultivated tomato viruses, seriously threatened the growth of crops worldwide. As the vector of ToCV, the whitefly Bemisia tabaci Mediterranean (MED) is mainly responsible for the rapid spread of ToCV. The current understanding of tomato plant responses to this virus and B. tabaci is very limited. To understand the molecular mechanism of the interaction between tomato, ToCV and B. tabaci, we adopted a next-generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed under the infection of B. tabaci and ToCV in tomato plants. Our data revealed that 6199 mRNAs were significantly regulated, and the differentially expressed genes were most significantly associated with the plant-pathogen interaction, the MAPK signaling pathway, the glyoxylate, and the carbon fixation in photosynthetic organisms and photosynthesis related proteins. Concomitantly, 242 differentially expressed miRNAs were detected, including novel putative miRNAs. Sly-miR159, sly-miR9471b-3p, and sly-miR162 were the most expressed miRNAs in each sample compare to control group. Moreover, we compared the similarities and differences of gene expression in tomato plant caused by infection or co-infection of B. tabaci and ToCV. Taken together, the analysis reported in this article lays a solid foundation for further research on the interaction between tomato, ToCV and B. tabaci, and provide evidence for the identification of potential key genes that influences virus transmission in tomato plants.

Metatranscriptomic analysis identifies different viral-like sequences in two neotropical Mansoniini mosquito species

Mosquitoes interact with a wide range of viruses including both arboviruses and insect-specific viruses. This study aimed to characterize the RNA viruses that are interacting with Mansonia wilsoni and Coquillettidia hermanoi mosquito species. The total RNA extracted from mosquito pools were sequenced on a Ion torrent platform. Viral contigs were identified against viral databases and their evolutionary relationship were reconstructed. We identified a total of 107 viral sequences, 11 of which were assigned as endogenous viral elements, and at least six known viral families were identified. Phylogenetic reconstructions were performed for 4 viral families. All Mansoniini viruses investigated through phylogenetic analysis are closely related to insect-specific viruses found in other mosquito species although with considerable divergence at the amino acid level, suggesting that we have detected new viral lineages. This study enhanced our understanding about the virome of two sylvatic Mansoniini mosquitoes.

Diversity and infectivity of the RNA virome among different cryptic species of an agriculturally important insect vector: whitefly Bemisia tabaci

A large number of insect-specific viruses (ISVs) have recently been discovered, mostly from hematophagous insect vectors because of their medical importance, but little attention has been paid to important plant virus vectors such as the whitefly Bemisia tabaci, which exists as a complex of cryptic species. Public SRA datasets of B. tabaci and newly generated transcriptomes of three Chinese populations are here comprehensively investigated to characterize the whitefly viromes of different cryptic species. Twenty novel ISVs were confidently identified, mostly associated with a particular cryptic species while different cryptic species harbored one or more core ISVs. Microinjection experiments showed that some ISVs might cross-infect between the two invasive whitefly cryptic species, Middle East Asia Minor 1 (MEAM1) and Mediterranean (MED), but others appeared to have a more restricted host range, reflecting the possibility of distinct long-term coevolution of these ISVs and whitefly hosts. Moreover, analysis of the profiles of virus-derived small-interfering RNAs indicated that some of the ISVs can successfully replicate in whitefly and the antiviral RNAi pathway of B. tabaci is actively involved in response to ISV infections. Our study provides a comprehensive analysis of the RNA virome, the distinct relationships and cross-cryptic species infectivity of ISVs in an agriculturally important insect vector.

Interkingdom Gut Microbiome and Resistome of the Cockroach Blattella germanica

Cockroaches are intriguing animals with two coexisting symbiotic systems, an endosymbiont in the fat body, involved in nitrogen metabolism, and a gut microbiome whose diversity, complexity, role, and developmental dynamics have not been fully elucidated. In this work, we present a metagenomic approach to study Blattella germanica populations not treated, treated with kanamycin, and recovered after treatment, both naturally and by adding feces to the diet, with the aim of better understanding the structure and function of its gut microbiome along the development as well as the characterization of its resistome.IMPORTANCE For the first time, we analyze the interkingdom hindgut microbiome of this species, including bacteria, fungi, archaea, and viruses. Network analysis reveals putative cooperation between core bacteria that could be key for ecosystem equilibrium. We also show how antibiotic treatments alter microbiota diversity and function, while both features are restored after one untreated generation. Combining data from B. germanica treated with three antibiotics, we have characterized this species' resistome. It includes genes involved in resistance to several broad-spectrum antibiotics frequently used in the clinic. The presence of genetic elements involved in DNA mobilization indicates that they can be transferred among microbiota partners. Therefore, cockroaches can be considered reservoirs of antibiotic resistance genes (ARGs) and potential transmission vectors.

Mosquito antiviral immune pathways

Mosquitoes are vectors of a large number of viral pathogens. In recent years, increased urbanization and climate change has expanded the range of many vector mosquitoes. The lack of effective medical interventions has made the control of mosquito-borne viral diseases very difficult. Understanding the interactions between the mosquito immune system and viruses is critical if we are to develop effective control strategies against these diseases. Mosquitoes harbor multiple conserved immune pathways that curb invading viral pathogens. Despite the conservation of these pathways, the activation and intensity of the mosquito immune response varies with the mosquito species, tissue, and the infecting virus. This article reviews major conserved antiviral immune pathways in vector mosquitoes, their interactions with invading viral pathogens, and how these interactions restrict or promote infection of these medically important viruses.

A Novel Iflavirus Was Discovered in Green Rice Leafhopper Nephotettix cincticeps and Its Proliferation Was Inhibited by Infection of Rice Dwarf Virus

The green rice leafhopper, Nephotettix cincticeps (Hemiptera: Cicadellidae), is a key insect vector transmitting rice dwarf virus (RDV) that causes rice dwarf disease. We discovered a novel iflavirus from the transcriptomes of N. cincticeps and named it as Nephotettix cincticeps positive-stranded RNA virus-1 (NcPSRV-1). The viral genome consists of 10,524 nucleotides excluding the poly(A) tail and contains one predicted open reading frame encoding a polyprotein of 3,192 amino acids, flanked by 5' and 3' untranslated regions. NcPSRV-1 has a typical iflavirus genome arrangement and is clustered with the members of the family Iflaviridae in the phylogenetic analysis. NcPSRV-1 was detected in all tested tissues and life stages of N. cincticeps and could be transmitted horizontally and vertically. Moreover, NcPSRV-1 had high prevalence in the laboratory populations and was widely spread in field populations of N. cincticeps. NcPSRV-1 could also infect the two-striped leafhopper, Nephotettix apicalis, at a 3.33% infection rate, but was absent in the zigzag leafhopper, Recilia dorsalis, and rice Oryza sativa variety TN1. The infection of RDV altered the viral load and infection rate of NcPSRV-1 in N. cincticeps, for which it seems that RDV has an antagonistic effect on NcPSRV-1 infection in the host.

Detection of Cell-Fusing Agent virus across ecologically diverse populations of Aedes aegypti on the Caribbean island of Saint Lucia

Background. Outbreaks of mosquito-borne arboviral diseases including dengue virus (DENV), Zika virus (ZIKV), yellow fever virus (YFV) and chikungunya virus (CHIKV) have recently occurred in the Caribbean. The geographical range of the principal vectors responsible for transmission, Aedes (Ae.) aegypti and Ae. albopictus are increasing and greater mosquito surveillance is needed in the Caribbean given international tourism is so prominent. The island of Saint Lucia has seen outbreaks of DENV and CHIKV in the past five years but vector surveillance has been limited with the last studies dating back to the late 1970s. Natural disasters have changed the landscape of Saint Lucia and the island has gone through significant urbanisation. Methods. In this study, we conducted an entomological survey of Ae. aegypti and Ae. albopictus distribution across the island and analysed environmental parameters associated with the presence of these species in addition to screening for medically important arboviruses and other flaviviruses. Results. Although we collected Ae. aegypti across a range of sites across the island, no Ae. albopictus were collected despite traps being placed in diverse ecological settings. The number of Ae. aegypti collected was significantly associated with higher elevation, and semi-urban settings yielded female mosquito counts per trap-day that were five-fold lower than urban settings. Screening for arboviruses revealed a high prevalence of cell-fusing agent virus (CFAV). Conclusions. Outbreaks of arboviruses transmitted by Ae. aegypti and Ae. albopictus have a history of occurring in small tropical islands and Saint Lucia is particularly vulnerable given the limited resources available to undertake vector control and manage outbreaks. Surveillance strategies can identify risk areas for predicting future outbreaks. Further research is needed to determine the diversity of current mosquito species, investigate insect-specific viruses, as well as pathogenic arboviruses, and this should also be extended to the neighbouring smaller Caribbean islands.

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.

In and Outs of Chuviridae Endogenous Viral Elements: Origin of a Potentially New Retrovirus and Signature of Ancient and Ongoing Arms Race in Mosquito Genomes

BACKGROUND

Endogenous viral elements (EVEs) are sequences of viral origin integrated into the host genome. EVEs have been characterized in various insect genomes, including mosquitoes. A large EVE content has been found in Aedes aegypti and Aedes albopictus genomes among which a recently described Chuviridae viral family is of particular interest, owing to the abundance of EVEs derived from it, the discrepancy among the chuvirus endogenized gene regions and the frequent association with retrotransposons from the BEL-Pao superfamily. In order to better understand the endogenization process of chuviruses and the association between chuvirus glycoproteins and BEL-Pao retrotransposons, we performed a comparative genomics and evolutionary analysis of chuvirus-derived EVEs found in 37 mosquito genomes.

RESULTS

We identified 428 EVEs belonging to the Chuviridae family confirming the wide discrepancy among the chuvirus genomic regions endogenized: 409 glycoproteins, 18 RNA-dependent RNA polymerases and one nucleoprotein region. Most of the glycoproteins (263 out of 409) are associated specifically with retroelements from the Pao family. Focusing only on well-assembled Pao retroelement copies, we estimated that 263 out of 379 Pao elements are associated with chuvirus-derived glycoproteins. Seventy-three potentially active Pao copies were found to contain glycoproteins into their LTR boundaries. Thirteen out of these were classified as complete and likely autonomous copies, with a full LTR structure and protein domains. We also found 116 Pao copies with no trace of glycoproteins and 37 solo glycoproteins. All potential autonomous Pao copies, contained highly similar LTRs, suggesting a recent/current activity of these elements in the mosquito genomes.

CONCLUSION

Evolutionary analysis revealed that most of the glycoproteins found are likely derived from a single or few glycoprotein endogenization events associated with a recombination event with a Pao ancestral element. A potential functional Pao-chuvirus hybrid (named Anakin) emerged and the glycoprotein was further replicated through retrotransposition. However, a number of solo glycoproteins, not associated with Pao elements, can be found in some mosquito genomes suggesting that these glycoproteins were likely domesticated by the host genome and may participate in an antiviral defense mechanism against both chuvirus and Anakin retrovirus.

Understanding the Mechanisms Underlying Host Restriction of Insect-Specific Viruses

Arthropod-borne viruses contribute significantly to global mortality and morbidity in humans and animals. These viruses are mainly transmitted between susceptible vertebrate hosts by hematophagous arthropod vectors, especially mosquitoes. Recently, there has been substantial attention for a novel group of viruses, referred to as insect-specific viruses (ISVs) which are exclusively maintained in mosquito populations. Recent discoveries of novel insect-specific viruses over the past years generated a great interest not only in their potential use as vaccine and diagnostic platforms but also as novel biological control agents due to their ability to modulate arbovirus transmission. While arboviruses infect both vertebrate and invertebrate hosts, the replication of insect-specific viruses is restricted in vertebrates at multiple stages of virus replication. The vertebrate restriction factors include the genetic elements of ISVs (structural and non-structural genes and the untranslated terminal regions), vertebrate host factors (agonists and antagonists), and the temperature-dependent microenvironment. A better understanding of these bottlenecks is thus warranted. In this review, we explore these factors and the complex interplay between ISVs and their hosts contributing to this host restriction phenomenon.

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.

Detection of a novel insect-specific flavivirus across ecologically diverse populations of Aedes aegypti on the Caribbean island of Saint Lucia

Background. Outbreaks of mosquito-borne arboviral diseases including dengue virus (DENV), Zika virus (ZIKV), yellow fever virus (YFV) and chikungunya virus (CHIKV) have recently occurred in the Caribbean. The geographical range of the principle vectors responsible for transmission, Aedes (Ae.) aegypti and Ae. albopictus is increasing and greater mosquito surveillance is needed in the Caribbean given international tourism is so prominent. The island of Saint Lucia has seen outbreaks of DENV and CHIKV in the past five years but vector surveillance has been limited with the last studies dating back to the late 1970s. Natural disasters have changed the landscape of Saint Lucia and the island has gone through significant urbanisation. Methods. In this study, we conducted an entomological survey of Ae. aegypti and Ae. albopictus distribution across the island and analysed environmental parameters associated with the presence of these species in addition to screening for medically important arboviruses and other flaviviruses. Results. Although we collected Ae. aegypti across a range of sites across the island, no Ae. albopictus were collected despite traps being placed in diverse ecological settings. The number of Ae. aegypti collected was significantly associated with higher elevation, and semi-urban settings yielded female mosquito counts per trap-day that were five-fold lower than urban settings. Screening for arboviruses revealed a high prevalence of a novel insect-specific flavivirus closely related to cell fusing agent virus (CFAV). Conclusions. Outbreaks of arboviruses transmitted by Ae. aegypti and Ae. albopictus have a history of occurring in small tropical islands and Saint Lucia is particularly vulnerable given the limited resources available to undertake vector control and manage outbreaks. Surveillance strategies can identify risk areas for predicting future outbreaks and further research is needed to determine the diversity of current mosquito species and this should be extended to the neighbouring smaller Caribbean islands.

Mosquito-borne viruses, insect-specific flaviviruses (family Flaviviridae, genus Flavivirus), Banna virus (family Reoviridae, genus Seadornavirus), Bogor virus (unassigned member of family Permutotetraviridae), and alphamesoniviruses 2 and 3 (family Mesoniviridae, genus Alphamesonivirus) isolated from Indonesian mosquitoes

Mosquitoes transmit many kinds of arboviruses (arthropod-borne viruses), and numerous arboviral diseases have become serious problems in Indonesia. In this study, we conducted surveillance of mosquito-borne viruses at several sites in Indonesia during 2016-2018 for risk assessment of arbovirus infection and analysis of virus biodiversity in mosquito populations. We collected 10,015 mosquitoes comprising at least 11 species from 4 genera. Major collected mosquito species were Culex quinquefasciatus, Aedes albopictus, Culex tritaeniorhynchus, Aedes aegypti, and Armigeres subalbatus. The collected mosquitoes were divided into 285 pools and used for virus isolation using two mammalian cell lines, Vero and BHK-21, and one mosquito cell line, C6/36. Seventy-two pools showed clear cytopathic effects only in C6/36 cells. Using RT-PCR and next-generation sequencing approaches, these isolates were identified as insect flaviviruses (family Flaviviridae, genus Flavivirus), Banna virus (family Reoviridae, genus Seadornavirus), new permutotetravirus (designed as Bogor virus) (family Permutotetraviridae, genus Alphapermutotetravirus), and alphamesoniviruses 2 and 3 (family Mesoniviridae, genus Alphamesonivirus). We believed that this large surveillance of mosquitoes and mosquito-borne viruses provides basic information for the prevention and control of emerging and re-emerging arboviral diseases.