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

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.

Two Novel Iflaviruses Discovered in Bat Samples in Washington State

Arthropods are integral to ecosystem equilibrium, serving as both a food source for insectivores and supporting plant reproduction. Members of the Iflaviridae family in the order Picornavirales are frequently found in RNA sequenced from arthropods, who serve as their hosts. Here we implement a metagenomic deep sequencing approach followed by rapid amplification of cDNA ends (RACE) on viral RNA isolated from wild and captured bat guano in Washington State at two separate time points. From these samples we report the complete genomes of two novel viruses in the family Iflaviridae. The first virus, which we call King virus, is 46% identical by nucleotide to the lethal honeybee virus, deformed wing virus, while the second virus which we call Rolda virus, shares 39% nucleotide identity to deformed wing virus. King and Rolda virus genomes are 10,183 and 8934 nucleotides in length, respectively. Given these iflaviruses were detected in guano from captive bats whose sole food source was the Tenebrio spp. mealworm, we anticipate this invertebrate may be a likely host. Using the NCBI Sequence Read Archive, we found that these two viruses are located in six continents and have been isolated from a variety of arthropod and mammalian specimens.

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.