Isolation of a natural DNA virus ofDrosophila melanogaster, and characterisation of host resistance and immune responses

Abstract

Drosophila melanogaster has played a key role in our understanding of invertebrate immunity.However, both functional and evolutionary studies of host-virus interaction in this model have been limited by a dearth of native Drosophila virus isolates. In particular, despite a long history of virus research, DNA viruses of D. melanogaster have only recently been described, and none have been available for experimental study. Here, we report the isolation and comprehensive characterisation of Kallithea virus, a large double-stranded DNA virus, and the first DNA virus to have been reported from wild populations of D. melanogaster. We find that Kallithea virus infection is costly for adult flies, reaching high titres in both sexes and reducing survival in males, and movement and late fecundity in females. Using the Drosophila Genetic Reference Panel we quantify host genetic variance for virus-induced mortality and viral titre, and identify candidate host genes that may underlie this variation, including Cdc42-interacting protein 4.Using full transcriptome sequencing of infected males and females, we examine the transcriptional response of flies to Kallithea virus infection, and find differential regulation of male-biased genes, and genes involved in innate immune pathways, cuticle development, chorion production, and serine endopeptidase activity. This work establishes Kallithea Virus as a new tractable model to study the natural relationship between D. melanogaster and DNA viruses, and we hope it will serve as a basis for future studies of immune responses to DNA viruses in insects.

Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells

“…In order to detect the source of these unmapped reads, we extracted unmapped reads, and assembled them into contigs using CAP3 (Huang and Madan 1999). We then used the assembled contigs to query the nr database using BLASTn (Altschul et al 1990), and identified dsDNA nudivirus Tomelloso (Palmer et al 2018) as the source. We then extended this search genome-wide, by identifying somatic clusters of reads with unmapped mates and assembling their mates as described above, but found no other instances of viral integration in other samples.…”

“…3d). That we detect the involvement of TEs in so many of the structural variants in Notch highlights the role that TE sequences may play in influencing somatic mutation, as well as underscoring the complexity of mutations inactivating a model tumour-suppressor locus.In addition to detecting TE presence at breakpoints, we identified breakpoints at reads whose mates mapped to the double-stranded DNA (dsDNA) nudivirus Tomelloso in one sample (P31;(Palmer et al 2018). The breakpoint read orientation was consistent with a ~100 kb fragment of viral DNA integrated into the Drosophila genome as part of a complex rearrangement(Fig.…”

Natural Variation in Resistance to Virus Infection in Dipteran Insects

“…This depends on recognition of virus-associated molecular patterns, and on other infection-derived cues such as host manipulation or damage (reviewed in [ 4 ]). As in mammals, NF-κB and JAK-STAT pathways help coordinate these inducible responses, and a subset of upstream signaling pathway regulators are often differentially expressed during infection with different viruses [ 21 , 71 , 72 , 106 , 107 ]. In Drosophila , the Toll and Imd pathways are antiviral against a broad panel of RNA viruses.…”

“…An exemplar of this trend is an analysis of JAK-STAT responsive genes vir-1 and TotM , which show an almost mutually exclusive expression pattern in response to a panel of viruses, whereby vir-1 is strongly induced in response to CrPV, DCV, and FHV, while TotM is induced after SINV, VSV, or DXV infection [ 21 ]. Neither gene is strongly upregulated in response to the DNA viruses IIV6 or Kallithea virus [ 21 , 107 ]. Likewise, the heatshock pathway is induced in vivo in response to DCV and CrPV, but not IIV6 [ 72 ].…”

Dissecting the genetic architecture of a stepwise infection process

“…In the fly, for example, resistance to infection by the sigma virus has long been shown to be influenced by a single locus of large effect, as measured by the binary response of exposed animals to a CO 2 paralysis test (Bangham, Knott, Kim, Young, & Jiggins, ; Bangham, Obbard, Kim, Haddrill, & Jiggins, ; Cogni et al, ; Magwire et al, ). Including more diverse phenotypes, however, such as changes in longevity, fecundity or virus titre (and also exploring new pathogens), is beginning to uncover many more minor effect loci (Cogni et al, ; Howick & Lazzaro, ; Palmer, Medd, Beard, & Obbard, ; Wang, Lu, & St Leger, ; but see Martins et al, ). Thus, the prediction that a host's susceptibility to infection may have a different genetic architecture to other complex traits need not apply to all components of disease, but rather, as shown here, to the very specific step that defines whether or not a pathogen has the ability to infect a host.…”