Discovery of Culex pipiens associated tunisia virus: a new ssRNA(+) virus representing a new insect associated virus family

Diverse viral communities inhabit the guts of date palm rhinoceros beetles (Oryctes spp.)

Two species of palm tree pests, Oryctes elegans and Oryctes agamemnon (Coleoptera: Scarabaeidae), cause significant damage to date palm trees (Phoenix dactylifera) in many countries in the Middle East. Despite several decades of research and the implementation of numerous control strategies, including mechanical, chemical, regulatory, and biosecurity measures, managing these pests remains challenging. Control of O. rhinoceros in the Pacific using an entomopathogenic virus is a landmark of classical biological control. In this study, we used a transcriptomic approach to examine the virome of populations of two Oryctes species across various regions in southern Iran, with the hope of discovering natural viral pathogens as potential biocontrol agents. Total RNA was extracted from a pool of larval gut samples and sequenced using the Illumina NovaSeq 6000. After analysing the RNA-Seq data, 28 novel virus sequences, including a diverse range of RNA and DNA viruses, were identified. Phylogenetic analyses revealed that these newly discovered viruses are evolutionarily linked with other closely related members in several families, including Partitiviridae, Picobirnaviridae, Totiviridae, Dicistroviridae, Tombusviridae, Nodaviridae, Potyviridae, Endornaviridae, Circoviridae and some unassigned viruses such as Negevirus and Jivivirus. Given the similarity of some of these viruses to plant viruses, and viruses reported from fungi and protists and their unclear host association, we have tentatively named them "Oryctes-associated viruses." This study uncovers the great diversity of viruses in Oryctes species; however, further studies are necessary to determine their natural incidence, geographical distribution, impact on their hosts, and their potential as biological control agents for these significant date palm pests.

Disclosing the virome of Aedes, Anopheles and Culex female mosquitoes, Alto Pantanal of Mato Grosso, Brazil, 2019

Using Illumina NextSeq sequencing and bioinformatics, we identified and characterized thirty-three viral sequences of unsegmented and multipartite viral families in Aedes spp., Culex sp. and Anopheles darlingi female mosquito pools from Porto São Luiz and Pirizal, Alto Pantanal. Seventeen sequences belong to unsegmented viral families, twelve represent putative novel insect-specific viruses (ISVs) within families Chuviridae (3/33; partial genomes) and coding-complete sequences of Xinmoviridae (1/33), Rhabdoviridae (2/33) and Metaviridae (6/33); and five coding-complete sequences of already-known ISVs. Notably, two putative novel rhabdoviruses, Corixo rhabdovirus 1 and 2, were phylogenetically related to Coxipo dielmovirus, but separated from other Alpharhabdovirinae genera, sharing Anopheles spp. as host. Regarding multipartite families, sixteen segments of different putative novel viruses were identified (13 coding-complete segments) within Durnavirales (4/33), Elliovirales (1/33), Hareavirales (3/33) and Reovirales (8/33) orders. Overall, this study describes twenty-eight (28/33) putative novel ISVs and five (5/33) already described viruses using metagenomics approach.

Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity

Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Here, using a meta-transcriptomic approach, we determined the viromes of 2,438 individual mosquitoes (81 species), spanning ~4,000 km along latitudes and longitudes in China. From these data we identified 393 viral species associated with mosquitoes, including 7 (putative) species of arthropod-borne viruses (that is, arboviruses). We identified potential mosquito species and geographic hotspots of viral diversity and arbovirus occurrence, and demonstrated that the composition of individual mosquito viromes was strongly associated with host phylogeny. Our data revealed a large number of viruses shared among mosquito species or genera, enhancing our understanding of the host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, perhaps reflecting long-distance mosquito dispersal. Together, these results greatly expand the known mosquito virome, linked viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the biogeography and diversity of viruses in insect vectors.

Identification and characterization of two closely related virga-like viruses latently infecting rubber trees (Hevea brasiliensis)

A novel virga-like virus, provisionally named Rubber tree latent virus 2 (RTLV2), was identified from rubber tree (Hevea brasiliensis). It is a close relative of the previously reported Rubber tree latent virus 1 (RTLV1). The complete genomes of RTLV1 and RTLV2 were sequenced and comparatively analyzed in terms of genome organization, putative gene products and phylogenetic relationship. Both RTLV1 and RTLV2 have positive-sense single-stranded RNA genomes that encode seven open reading frames (ORFs), forming a similar genomic layout. In phylogenetic analyses based on replicase and coat protein amino acid sequences, RTLV1 and RTLV2 were clustered with unclassified virga-like viruses. They are distinct from currently recognized plant virus families. RTLV1 and RTLV2 can be distinguished from members of Virgaviridae by the presence of a putative coat protein duplex and a poly(A) tail at the 3'-terminus. The authenticity of RTLV1 and RTLV2 as infectious viruses was confirmed through field investigations and transmissibility assays. In conclusion, RTLV1 and RTLV2 represent a novel plant virus group that does not readily fit into current virus families.

Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses

Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Using a meta-transcriptomic approach, we analysed the virome of 2,438 individual mosquitos (79 species), spanning ~4000 km along latitudes and longitudes in China. From these data we identified 393 core viral species associated with mosquitos, including seven (putative) arbovirus species. We identified potential species and geographic hotspots of viral richness and arbovirus occurrence, and demonstrated that host phylogeny had a strong impact on the composition of individual mosquito viromes. Our data revealed a large number of viruses shared among mosquito species or genera, expanding our knowledge of host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, possibly facilitated by long-distance mosquito migrations. Together, our results greatly expand the known mosquito virome, linked the viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the ecology of viruses of insect vectors.

Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics

Several aspects of mosquito ecology that are important for vectored disease transmission and control have been difficult to measure at epidemiologically important scales in the field. In particular, the ability to describe mosquito population structure and movement rates has been hindered by difficulty in quantifying fine-scale genetic variation among populations. The mosquito virome represents a possible avenue for quantifying population structure and movement rates across multiple spatial scales. Mosquito viromes contain a diversity of viruses, including several insect-specific viruses (ISVs) and "core" viruses that have high prevalence across populations. To date, virome studies have focused on viral discovery and have only recently begun examining viral ecology. While nonpathogenic ISVs may be of little public health relevance themselves, they provide a possible route for quantifying mosquito population structure and dynamics. For example, vertically transmitted viruses could behave as a rapidly evolving extension of the host's genome. It should be possible to apply established analytical methods to appropriate viral phylogenies and incidence data to generate novel approaches for estimating mosquito population structure and dispersal over epidemiologically relevant timescales. By studying the virome through the lens of spatial and genomic epidemiology, it may be possible to investigate otherwise cryptic aspects of mosquito ecology. A better understanding of mosquito population structure and dynamics are key for understanding mosquito-borne disease ecology and methods based on ISVs could provide a powerful tool for informing mosquito control programs.

Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

Endornaviruses are capsidless linear (+) ssRNA viruses in the family Endornaviridae. In this study, Scelrotinia sclerotiorum endornavirus 11 (SsEV11), a novel endornavirus infecting hypovirulent Sclerotinia sclerotiorum strain XY79, was identified and cloned using virome sequencing analysis and rapid amplification of cDNA ends (RACE) techniques. The full-length genome of SsEV11 is 11906 nt in length with a large ORF, which encodes a large polyprotein of 3928 amino acid residues, containing a viral methyltransferase domain, a cysteine-rich region, a putative DEADc, a viral helicase domain, and an RNA-dependent RNA polymerase (RdRp) 2 domain. The 5' and 3' untranslated regions (UTR) are 31 nt and 90 nt, respectively. According to the BLAST result of the nucleotide sequence, SsEV11 shows the highest identity (45%) with Sclerotinia minor endornavirus 1 (SmEV1). Phylogenetic analysis based on amino acid sequence of RdRp demonstrated that SsEV11 clusters to endornavirus and has a close relationship with Betaendornavirus. Phylogenetic analysis based on the sequence of endornaviral RdRp domain indicated that there were three large clusters in the phylogenetic tree. Combining the results of alignment analysis, Cluster I at least has five subclusters including typical members of Alphaendornavirus and many unclassified endornaviruses that isolated from fungi, oomycetes, algae, and insects; Cluster II also has five subclusters including typical members of Betaendornavirus, SsEV11, and other unclassified viruses that infected fungi; Cluster III includes many endorna-like viruses that infect nematodes, mites, and insects. Viruses in Cluster I and Cluster II are close to each other and relatively distant to those in Cluster III. Our study characterized a novel betaendornavirus, SsEV11, infected fungal pathogen S. sclerotiorum, and suggested that notable phylogenetic diverse exists in endornaviruses. In addition, at least, one novel genus, Gammaendornavirus, should be established to accommodate those endorna-like viruses in Cluster III.

Uncovering the genetic diversity within the Aedes notoscriptus virome and isolation of new viruses from this highly urbanised and invasive mosquito

The Australian backyard mosquito, Aedes notoscriptus, is a highly urbanised pest species that has invaded New Zealand and the USA. Importantly, Ae. notoscriptus has been implicated as a vector of Ross River virus, a common and arthritogenic arbovirus in Australia, and is a laboratory vector of numerous other pathogenic viruses, including West Nile, yellow fever, and Zika viruses. To further explore live viruses harboured by field populations of Ae. notoscriptus and, more specifically, assess the genetic diversity of its virome, we processed 495 pools, comprising a total of 6,674 female Ae. notoscriptus collected across fifteen suburbs in Brisbane, Australia, between January 2018 and May 2019. Nine virus isolates were recovered and characterised by metagenomic sequencing and phylogenetics. The principal viral family represented was Flaviviridae. Known viruses belonging to the genera Flavivirus, Orbivirus, Mesonivirus, and Nelorpivirus were identified together with two novel virus species, including a divergent Thogoto-like orthomyxovirus and an insect-specific flavivirus. Among these, we recovered three Stratford virus (STRV) isolates and an isolate of Wongorr virus (WGRV), which for these viral species is unprecedented for the geographical area of Brisbane. Thus, the documented geographical distribution of STRV and WGRV, both known for their respective medical and veterinary importance, has now been expanded to include this major urban centre. Phylogenies of the remaining five viruses, namely, Casuarina, Ngewotan, the novel Thogoto-like virus, and two new flavivirus species, suggested they are insect-specific viruses. None of these viruses have been previously associated with Ae. notoscriptus or been reported in Brisbane. These findings exemplify the rich genetic diversity and viral abundance within the Ae. notoscriptus virome and further highlight this species as a vector of concern with the potential to transmit viruses impacting human or animal health. Considering it is a common pest and vector in residential areas and is expanding its global distribution, ongoing surveillance, and ecological study of Ae. notoscriptus, together with mapping of its virome and phenotypic characterisation of isolated viruses, is clearly warranted. Immanently, these initiatives are essential for future understanding of both the mosquito virome and the evolution of individual viral species.

Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay

Mosquitoes are major infectious disease-carrying vectors. Assessment of current and future risks associated with the mosquito population requires knowledge of the full repertoire of pathogens they carry, including novel viruses, as well as their blood meal sources. Unbiased metatranscriptomic sequencing of individual mosquitoes offers a straightforward, rapid, and quantitative means to acquire this information. Here, we profile 148 diverse wild-caught mosquitoes collected in California and detect sequences from eukaryotes, prokaryotes, 24 known and 46 novel viral species. Importantly, sequencing individuals greatly enhanced the value of the biological information obtained. It allowed us to (a) speciate host mosquito, (b) compute the prevalence of each microbe and recognize a high frequency of viral co-infections, (c) associate animal pathogens with specific blood meal sources, and (d) apply simple co-occurrence methods to recover previously undetected components of highly prevalent segmented viruses. In the context of emerging diseases, where knowledge about vectors, pathogens, and reservoirs is lacking, the approaches described here can provide actionable information for public health surveillance and intervention decisions.

Global evaluation of taxonomic relationships and admixture within the Culex pipiens complex of mosquitoes

BACKGROUND

Within the Culex pipiens mosquito complex, there are six contemporarily recognized taxa: Cx. quinquefasciatus, Cx. pipiens f. pipiens, Cx. pipiens f. molestus, Cx. pipiens pallens, Cx. australicus and Cx. globocoxitus. Many phylogenetic aspects within this complex have eluded resolution, such as the relationship of the two Australian endemic taxa to the other four members, as well as the evolutionary origins and taxonomic status of Cx. pipiens pallens and Cx. pipiens f. molestus. Ultimately, insights into lineage relationships within the complex will facilitate a better understanding of differential disease transmission by these mosquitoes. To this end, we have combined publicly available data with our own sequencing efforts to examine these questions.

RESULTS

We found that the two Australian endemic complex members, Cx. australicus and Cx. globocoxitus, comprise a monophyletic group, are genetically distinct, and are most closely related to the cosmopolitan Cx. quinquefasciatus. Our results also show that Cx. pipiens pallens is genetically distinct, but may have arisen from past hybridization. Lastly, we observed complicated patterns of genetic differentiation within and between Cx. pipiens f. pipiens and Cx. pipiens f. molestus.

CONCLUSIONS

Two Australian endemic Culex taxa, Cx. australicus and Cx. globocoxitus, belong within the Cx. pipiens complex, but have a relatively older evolutionary origin. They likely diverged from Cx. quinquefasciatus after its colonization of Australia. The taxon Cx. pipiens pallens is a distinct evolutionary entity that likely arose from past hybridization between Cx. quinquefasciatus and Cx. pipiens f. pipiens/Cx. pipiens f. molestus. Our results do not suggest it derives from ongoing hybridization. Finally, genetic differentiation within the Cx. pipiens f. pipiens and Cx. pipiens f. molestus samples suggests that they collectively form two separate geographic clades, one in North America and one in Europe and the Mediterranean. This may indicate that the Cx. pipiens f. molestus form has two distinct origins, arising from Cx. pipiens f. pipiens in each region. However, ongoing genetic exchange within and between these taxa have obscured their evolutionary histories, and could also explain the absence of monophyly among our samples. Overall, this work suggests many avenues that warrant further investigation.

Sensitivity and specificity of metatranscriptomics as an arbovirus surveillance tool

The ability to identify all the viruses within a sample makes metatranscriptomic sequencing an attractive tool to screen mosquitoes for arboviruses. Practical application of this technique, however, requires a clear understanding of its analytical sensitivity and specificity. To assess this, five dilutions (1:1, 1:20, 1:400, 1:8,000 and 1:160,000) of Ross River virus (RRV) and Umatilla virus (UMAV) isolates were spiked into subsamples of a pool of 100 Culex australicus mosquitoes. The 1:1 dilution represented the viral load of one RRV-infected mosquito in a pool of 100 mosquitoes. The subsamples underwent nucleic acid extraction, mosquito-specific ribosomal RNA depletion, and Illumina HiSeq sequencing. The viral load of the subsamples was also measured using reverse transcription droplet digital PCR (RT-ddPCR) and quantitative PCR (RT-qPCR). Metatranscriptomic sequencing detected both RRV and UMAV in the 1:1, 1:20 and 1:400 subsamples. A high specificity was achieved, with 100% of RRV and 99.6% of UMAV assembled contigs correctly identified. Metatranscriptomic sequencing was not as sensitive as RT-qPCR or RT-ddPCR; however, it recovered whole genome information and detected 19 other viruses, including four first detections for Australia. These findings will assist arbovirus surveillance programs in utilising metatranscriptomics in routine surveillance activities to enhance arbovirus detection.

Viruses in the Invasive Hornet Vespa velutina

The Asian yellow-legged hornet Vespa velutina nigrithorax, a major predator of honeybees, is spreading in Europe in part due to a lack of efficient control methods. In this study, as a first step to identify biological control agents, we characterized viral RNA sequences present in asymptomatic or symptomatic hornets. Among 19 detected viruses, the honey bee virus Deformed wing virus-B was predominant in all the samples, particularly in muscles from the symptomatic hornet, suggesting a putative cause of the deformed wing symptom. Interestingly, two new viruses closely related to Acyrthosiphon pisumvirus and Himetobi Pvirus and viruses typically associated with honey bees, Acute bee paralysis virus and Black queen cell virus, were detected in the brain and muscles, and may correspond to the circulation and possible replication forms of these viruses in the hornet. Aphid lethal paralysis virus, Bee Macula-like virus, and Moku virus, which are known to infect honey bees, were also identified in the gut virus metagenome of hornets. Therefore, our study underlined the urgent need to study the host range of these newly discovered viruses in hornets to determine whether they represent a new threat for honey bees or a hope for the biocontrol of V. velutina.

A Divergent Strain of Culex pipiens-Associated Tunisia Virus in the Malaria Vector Anopheles epiroticus

Here, we report the draft genome sequence of a divergent strain of Culex pipiens-associated Tunisia virus (CpATV) identified in the malaria vector Anopheles epiroticus (CpATV-AnE). CpATV-AnE expands the reference virus sequence, introducing an extended replicase with novel virga-like domains. Our results suggest that the host range of CpATV includes Anopheles sp. mosquitoes.

Insect-specific viruses: from discovery to potential translational applications

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

Investigating the viral ecology of global bee communities with high-throughput metagenomics

Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 4 continents and Oceania. We developed a novel pipeline to rapidly and inexpensively screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and filtering to identify contigs specifically corresponding to viral sequences. We identified sequences for (+)ssRNA, (−)ssRNA, dsRNA, and ssDNA viruses. Overall, we found 127 contigs corresponding to novel viruses (i.e. previously not observed in bees), with 27 represented by >0.1% of the reads in a given sample, and 7 contained an RdRp or replicase sequence which could be used for robust phylogenetic analysis. This study provides a sequence-independent pipeline for viral metagenomics analysis, and greatly expands our understanding of the diversity of viruses found in bee communities.