Figure - available from: Microbial Ecology
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Functions encode in the viral regions originating the nrEVEs. A Pie chart of the viral functions assigned to the tephritid nrEVEs. B Distribution of the viral functions within each viral family. The total number of nrEVEs per viral family is displayed on the right of the bar graph. C and D nrEVEs distribution across a representative viral genome. The genomic structure of a representative member of Partitiviridae (C) and Rhabdoviridae (D) is shown in the upper panel. Boxes represent the viral ORFs, and viral functions are indicated in capital letters: N (capsid), G (Glycoprotein), L (RNA-dependent RNA polymerase), P (uncharacterized). Best blastx hits shared by different nrEVEs are shown. nrEVEs are displayed according to their length and mapping position on the representative viral genome
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A wide variety of insect-specific non-retroviral RNA viruses specifically infect insects. During viral infection, fragments of viral sequences can integrate into the host genomes creating non-retroviral endogenous viral elements (nrEVEs). Although the exact function of nrEVEs is so far unknown, some studies suggest that nrEVEs may interfere with vi...
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The respiratory syncytial virus (RSV) polymerase is a multifunctional RNA-dependent RNA polymerase composed of the large (L) protein and the phosphoprotein (P). It transcribes the RNA genome into ten viral mRNAs and replicates full-length viral genomic and antigenomic RNAs¹. The RSV polymerase initiates RNA synthesis by binding to the conserved 3′-...
Citations
... However, this approach initially restricts the search to few hallmark genes, which are not universally present in viruses and relies on the presence of enough viral-like sequences in the datasets to be clustered within current software limitations (Edgar, 2010;Li and Godzik, 2006). As other dipteran models such as Ceratitis capitata (Hernández-Pelegrín et al., 2024 and Drosophila spp. (Webster et al., 2016), host more viruses than BSF, this calls for a more comprehensive search of BSF datasets and for a broadened exploration of BSF from different sources. ...
Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (Hermetia illucens, BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the orders Ghabrivirales and Bunyavirales, as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. A high-throughput pipeline allowed the simultaneous investigation of 203 next generation sequencing datasets. This revealed the presence of seven viruses belonging to the families Dicistroviridae, Iflaviridae, Rhabdoviridae, Solinviviridae, Inseviridae, Lebotiviridae, and an unclassified Bunyavirales. Here we describe five viruses, which were detected in BSF from multiple origins, outlining the diversity of naturally occurring viruses associated with BSF colonies. As this viral community may also include BSF pathogens, we developed molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.
... The hit length ranged from 308 to 998 bp, and the pairwise identity ranged from 25.30 to 35.20% [16]. In dipterans, with the exception of the Aedes mosquito genome, in which more than 200 nrEVEs have been identified, a low number of integrated viral sequences have been described (0-1 in Drosophila melanogaster, 1 in Phlebotomus papatasi, 7 in Musca domestica, 5 in tephritid fruit flies, 1-3 in species of Culicidae and Anopheles) [66]. In tephritid fruit flies, the most abundant nrEVEs reported are Rhabdoviridaederived EVEs, and this was also found for mosquitos [66,67]. ...
... In dipterans, with the exception of the Aedes mosquito genome, in which more than 200 nrEVEs have been identified, a low number of integrated viral sequences have been described (0-1 in Drosophila melanogaster, 1 in Phlebotomus papatasi, 7 in Musca domestica, 5 in tephritid fruit flies, 1-3 in species of Culicidae and Anopheles) [66]. In tephritid fruit flies, the most abundant nrEVEs reported are Rhabdoviridaederived EVEs, and this was also found for mosquitos [66,67]. Nevertheless, we consider that an in-depth analysis of nrEVEs in arbovirus vectors is needed and that generating high-quality genome assemblies will be key. ...
... Additionally, it is important to notice that viruses responsible for an existing nrEVE come from ancient viruses or might have undergone significant mutations over time. In that sense, viral query selection and filtering parameters are important parameters that need to be tuned in for the identification of nrEVEs [66]. ...
Background
Advancing our knowledge of vector species genomes is a key step in our battle against the spread of diseases. Biting midges of the genus Culicoides are vectors of arboviruses that significantly affect livestock worldwide. Culicoides stellifer is a suspected vector with a wide range distribution in North America, for which cryptic diversity has been described.
Results
With just one specimen of C. stellifer, we assembled and annotated the nuclear and mitochondrial genome using the ultra-low input DNA PacBio protocol. The genome assembly is 119 Mb in length with a contig N50 value of 479.3 kb, contains 11% repeat sequences and 18,895 annotated protein-coding genes. To further elucidate the role of this species as a vector, we provide genomic evidence of a non-retroviral endogenous viral element integrated into the genome that corresponds to rhabdovirus nucleocapsid proteins, the same family as the vesicular stomatitis virus.
Conclusions
This genomic information will pave the way for future investigations into this species’s putative vector role. We also demonstrate the practicability of completing genomic studies in small dipterans using single specimens preserved in ethanol as well as introduce a workflow for data analysis that considers the challenges of insect genome assembly.
... : bioRxiv preprint enough viral-like sequences in the datasets to be clustered within current software limitations (Edgar, 2010;Li and Godzik, 2006). Other dipteran models such as Ceratitis capitata (Hernández-Pelegrín et al., 2024 and Drosophila spp. (Webster et al., 2016), host fairly diverse viromes compared to BSF. ...
Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the orders Ghabrivirales and Bunyavirales , as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. In this study, we describe five newly discovered viruses from the families Dicistroviridae , Iflaviridae , Rhabdoviridae , Solinviviridae , and Inseviridae . These viruses were detected in BSF from multiple origins, outlining a diversity of naturally occurring viruses associated with BSF. This viral community may also include BSF pathogens. The growing list of viruses found in BSF allowed the development of molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.
... Moreover, few studies in Aedes mosquitoes have unravelled the antiviral role of certain nrEVEs, which is mediated by the Piwi-interacting RNA pathway (Blair, 2019;Suzuki et al., 2020;Tassetto et al., 2019). nrEVEs have been extensively studied in insects of health relevance as disease vector mosquitoes or insect pests (Crava et al., 2021;Hernández-Pelegrín et al., 2023b;Palatini et al., 2017;Pischedda et al., 2019;Russo et al., 2019;Whitfield et al., 2017). Instead, the presence and distribution of nrEVEs in the genomes of insect species reared for biocontrol purposes remains unexplored. ...
... Second, RNA viruses could influence the effectiveness of biocontrol by altering the predatory behaviour of O. laevigatus. In this line, infection with certain ISVs enhances the parasitism performance of parasitic wasps (Coffman et al., 2020;Hernández-Pelegrín et al., 2023b;Roossinck & Bazán, 2017). Third, field conditions may enhance the effect of RNA viruses on the host, in comparison to the controlled conditions encountered in the laboratory. ...
... However, the detection of complete virus genomes in the fly transcriptomes, as well as the detection of some of these in our laboratory population, in isolation from the field environment, indicates that they may be persistently maintained in this fly species, and hence constitute active infections, or, alternatively, be linked to gut microbes or the laboratory food source (cucumber and yeast). Furthermore we tested for any potential integration of viruses in the host genome as they have been described for C. capitata (Hernández-Pelegrín et al., 2024). For this the assembled virus sequences found in this study were mapped against the genome assembly of the USDA-PBARC (Hawaii) Z. cucurbitae laboratory population (NCBI GenBank assembly: GCA_000806345.1, GCA_028554715.1, GCA_028554725.2) using the CLC genomics workbench 22 (CLC Bio.) (Sim and Geib, 2017). ...
Background
Advancing our knowledge of vector species genomes is a key step in our battle against the spread of diseases. Biting midges of the genus Culicoides are vectors of arboviruses that significantly affect livestock worldwide. Culicoides stellifer is a suspected vector with a wide range distribution in North America, for which cryptic diversity has been described.
Results
With just one specimen of C. stellifer, we assembled and annotated both a high-quality nuclear and a mitochondrial genome using the ultra-low input DNA PacBio protocol. The genome assembly is 119 Mb in length with a contig N50 value of 479.3 kb, contains 11% repeat sequences and 18,895 annotated protein-coding genes. To further elucidate the role of this species as a vector, we provide genomic evidence of a non-retroviral endogenous viral element integrated into the genome that corresponds to rhabdovirus nucleocapsid proteins, the same family as the Vesicular Stomatitis Virus.
Conclusions
This genomic information will pave the way for future investigations into this species's putative vector role. We also demonstrate the practicability of completing genomic studies in small dipterans using single specimens preserved in ethanol as well as introduce a workflow for data analysis that considers the challenges of insect genome assembly.
