RNA virome diversity and Wolbachia infection in individual Drosophila simulans flies

Experimental assessment of 3D-printed traps and chemical attractants for the collection of wild Drosophila melanogaster

Drosophila melanogaster, the common fruit fly, has been instrumental to our understanding of evolution, genetics and disease. There are benefits to studying these flies in the wild, including assessment of their naturally occurring microbiota. To facilitate efforts to catch wild D. melanogaster, we designed two fly traps and evaluated several candidate attractants. The first trap utilized a stable food substrate that can be used to catch live flies to establish new lab colonies. The second trap was designed to be reusable and easy to ship to enable the collection of flies over time from diverse locations. We evaluated several chemical attractants derived from banana and from marula fruit, which is the proposed ancestral food host of D. melanogaster. We found that wild flies were preferentially attracted to banana-based odorants over marula-derived ones. Overall, these traps and attractants represent an inexpensive and simple option for the collection of wild D. melanogaster and related species for sampling or colony establishment.

Candidate DNA and RNA viruses of Drosophila suzukii from Canada and Germany, and their interactions with Wolbachia

Some species of insects harbour strains of the endosymbiotic bacteria Wolbachia that do not cause obvious reproductive manipulations, and so it is unclear why they persist in host populations. There is some evidence that some of these endosymbionts may provide their hosts with protection against viruses, which would help to explain their persistence, but few studies have explored associations between Wolbachia and naturally occurring, common viruses in natural populations. Here, we asked whether individuals of the invasive vinegar fly Drosophila suzukii infected with the wSuz strain of Wolbachia were less likely to be infected by naturally occurring viruses in its invaded range, in western North America and in Europe. First, using next-generation sequencing, we conducted a virome survey of adult and larval D. suzukii in British Columbia, Canada, finding eight candidate RNA viruses and two candidate DNA viruses; all but one have not been reported previously. Only the previously described Teise virus, an RNA virus, was abundant in our virome survey. We then screened individual flies from British Columbia and Germany for Teise virus and Wolbachia. Wolbachia-infected D. suzukii from the field were not less likely to be infected by Teise virus. Overall, our results do not provide conclusive evidence that wSuz provides strong protection for D. suzukii against viruses that are common in natural populations. However, the other viruses that we discovered in this study deserve further characterization in terms of their pathogenicity to D. suzukii and the frequency and dynamics of infection in wild populations.

Sequencing RNA from old, dried specimens reveals past viromes and properties of long-surviving RNA

Recovery of virus sequences from old samples provides an opportunity to study virus evolution and reconstruct historic virus-host interactions. Studies of old virus sequences have mainly relied on DNA or on RNA from fixed or frozen samples. The millions of specimens in natural history museums represent a potential treasure trove of old virus sequences, but it is not clear how well RNA survives in old samples. We experimentally assessed the stability of RNA in insects stored dry at room temperature over 72 weeks. Although RNA molecules grew fragmented, RNA yields remained surprisingly constant. RT-qPCR of host and virus RNA showed minimal differences between dried and frozen specimens. To assess RNA survival in much older samples we acquired Drosophila specimens from North American entomological collections. We recovered sequences from known and novel viruses including several coding complete virus genomes from a fly collected in 1908. We found that the virome of D. melanogaster has changed little over the past century. Galbut virus, the most prevalent virus infection in contemporary D. melanogaster, was also the most common in historic samples. Finally, we investigated the genomic and physical features of surviving RNA. RNA that survived was fragmented, chemically damaged, and preferentially double stranded or contained in ribonucleoprotein complexes. This showed that RNA - especially certain types of RNA - can survive in biological specimens over extended periods in the absence of fixation or freezing and confirms the utility of dried specimens to provide a clearer understanding of virus evolution.

Highly divergent CRESS DNA and picorna-like viruses associated with bleached thalli of the green seaweed Ulva

Marine macroalgae (seaweeds) are important primary producers and foundation species in coastal ecosystems around the world. Seaweeds currently contribute to an estimated 51% of the global mariculture production, with a long-term growth rate of 6% per year, and an estimated market value of more than US$11.3 billion. Viral infections could have a substantial impact on the ecology and aquaculture of seaweeds, but surprisingly little is known about virus diversity in macroalgal hosts. Using metagenomic sequencing, we characterized viral communities associated with healthy and bleached specimens of the commercially important green seaweed Ulva. We identified 20 putative new and divergent viruses, of which the majority belonged to the Circular Rep-Encoding Single-Stranded (CRESS) DNA viruses [single-stranded (ss)DNA genomes], Durnavirales [double-stranded (ds)RNA], and Picornavirales (ssRNA). Other newly identified RNA viruses were related to the Ghabrivirales, the Mitoviridae, and the Tombusviridae. Bleached Ulva samples contained particularly high viral read numbers. While reads matching assembled CRESS DNA viruses and picorna-like viruses were nearly absent from the healthy Ulva samples (confirmed by qPCR), they were very abundant in the bleached specimens. Therefore, bleaching in Ulva could be caused by one or a combination of the identified viruses but may also be the result of another causative agent or abiotic stress, with the viruses simply proliferating in already unhealthy seaweed tissue. This study highlights how little we know about the diversity and ecology of seaweed viruses, especially in relation to the health and diseases of the algal host, and emphasizes the need to better characterize the algal virosphere. IMPORTANCE Green seaweeds of the genus Ulva are considered a model system to study microbial interactions with the algal host. Remarkably little is known, however, about viral communities associated with green seaweeds, especially in relation to the health of the host. In this study, we characterized the viral communities associated with healthy and bleached Ulva. Our findings revealed the presence of 20 putative novel viruses associated with Ulva, encompassing both DNA and RNA viruses. The majority of these viruses were found to be especially abundant in bleached Ulva specimens. This is the first step toward understanding the role of viruses in the ecology and aquaculture of this green seaweed.

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.

Isolation of a novel rhabdovirus and detection of multiple novel viral sequences in Culex species mosquitoes in the United States

To increase our understanding of the diversity of the mosquito virome, 6956 mosquitoes of five species (Culex erraticus, Culex pipiens, Culex restuans, Culex tarsalis, and Culex territans) collected in Iowa in the United States in 2017 and 2020 were assayed for novel viruses by performing polyethylene glycol precipitation, virus isolation in cell culture, and unbiased high-throughput sequencing. A novel virus, provisionally named "Walnut Creek virus", was isolated from Cx. tarsalis, and its genomic sequence and organization are characteristic of viruses in the genus Hapavirus (family Rhabdoviridae). Replication of Walnut Creek virus occurred in avian, mammalian, and mosquito, but not tick, cell lines. A novel virus was also isolated from Cx. restuans, and partial genome sequencing revealed that it is distantly related to an unclassified virus of the genus Phytoreovirus (family Sedoreoviridae). Two recognized viruses were also isolated: Culex Y virus (family Birnaviridae) and Houston virus (family Mesoniviridae). We also identified sequences of eight novel viruses from six families (Amalgaviridae, Birnaviridae, Partitiviridae, Sedoreoviridae, Tombusviridae, and Totiviridae), two viruses that do not belong to any established families, and many previously recognized viruses. In summary, we provide evidence of multiple novel and recognized viruses in Culex spp. mosquitoes in the United States.

Wolbachia reduces virus infection in a natural population of Drosophila

Wolbachia is a maternally transmitted bacterial symbiont that is estimated to infect approximately half of arthropod species. In the laboratory it can increase the resistance of insects to viral infection, but its effect on viruses in nature is unknown. Here we report that in a natural population of Drosophila melanogaster, individuals that are infected with Wolbachia are less likely to be infected by viruses. By characterising the virome by metagenomic sequencing and then testing individual flies for infection, we found the protective effect of Wolbachia was virus-specific, with the prevalence of infection being up to 15% greater in Wolbachia-free flies. The antiviral effects of Wolbachia may contribute to its extraordinary ecological success, and in nature the symbiont may be an important component of the antiviral defences of insects.