Search for: All records

Abstract Galbut virus is a remarkably successful virus of the model organism Drosophila melanogaster. The ease of capturing galbut virus–infected wild flies presents an opportunity to study persistent virus–host interactions. To better understand galbut virus diversity, evolution, and genotype–phenotype relationships, we screened 957 flies collected from 13 locations across the USA. Galbut virus was detected in every population, and overall, 75% of flies tested positive. We selected 149 flies for shotgun RNA sequencing and recovered 368 coding-complete or near-complete sequences of galbut virus and its likely satellite, chaq virus. Galbut virus sequences clustered phylogenetically into three major clades. Two clades, termed melA and melB, comprised mainly viruses infecting D. melanogaster, while the third, simA, included D. simulans-infecting viruses. Between-clade pairwise nucleotide identity was as low as 75%, but diversity within clades was low. Geography partly explained phylogenetic clustering: some sequences from the same location were identical or nearly identical, while others were spread throughout trees. Several genotype–phenotype associations emerged, including higher average RNA levels in melA infections and an exclusive association of chaq virus with melA and simA infections. Coinfection was detected in 11% of samples and did not require complete sets of all three galbut virus segments. Coinfection is a prerequisite of reassortment, and there was evidence of reassortment involving all segments and chaq virus. However, reassortment did not occur between clades, despite coinfection, indicating that clades are reproductively isolated. Galbut virus RNA 3 sequences exhibited more involvement in coinfection, greater diversity, and stronger evidence of diversifying selection than the other segments, consistent with a possible role in host modulation. These findings corroborated the ecological success of galbut virus and reveal the need for experiments to uncover the mechanisms underlying reassortment incompatibility and clade-specific phenotypes. 

ABSTRACT 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 wildD. 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 ofD. 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 wildD. melanogasterand related species for sampling or colony establishment. 

ABSTRACT Whole-genome sequencing was performed for aPlanococcus sp. isolate. This bacterium was of interest because of its vibrant orange pigmentation. 

ABSTRACT 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 acquiredDrosophilaspecimens 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 ofD. melanogasterhas changed little over the past century. Galbut virus, the most prevalent virus infection in contemporaryD. 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. 

ABSTRACT A whole genome sequence of aPaenibacillussp. bacterium isolated from soil in Fort Collins, Colorado was obtained. This bacterium was of particular interest due to its antibiotic potential against Gram-positive pathogen surrogates. 

Galbut virus (family Partitiviridae) infects Drosophila melanogaster and can be transmitted vertically from infected mothers or infected fathers with near perfect efficiency. This form of super-Mendelian inheritance should drive infection to 100% prevalence, and indeed, galbut virus is ubiquitous in wild D. melanogaster populations. However, on average, only about 60% of individual flies are infected. One possible explanation for this is that a subset of flies are resistant to infection. Although galbut virus-infected flies appear healthy, infection may be sufficiently costly to drive selection for resistant hosts, thereby decreasing overall prevalence. To test this hypothesis, we quantified a variety of fitness-related traits in galbut virus-infected flies from two lines from the Drosophila Genetic Reference Panel (DGRP). Galbut virus-infected flies had no difference in average lifespan and total offspring production compared to their uninfected counterparts. Galbut virus-infected DGRP-517 flies pupated and eclosed faster than their uninfected counterparts. Some galbut virus-infected flies exhibited altered sensitivity to viral, bacterial, and fungal pathogens. The microbiome composition of flies was not measurably perturbed by galbut virus infection. Differences in phenotype attributable to galbut virus infection varied as a function of fly sex and DGRP strain, and differences attributable to infection status were dwarfed by larger differences attributable to strain and sex. Thus, galbut virus infection does produce measurable phenotypic changes, with changes being minor, offsetting, and possibly net-negative. 

Virology has largely focused on viruses that are pathogenic to humans or to the other species that we care most about. There is no doubt that this has been a worthwhile investment. But many transformative advances have been made through the in-depth study of relatively obscure viruses that do not appear on lists of prioritized pathogens. In this review, I highlight the benefits that can accrue from the study of viruses and hosts off the beaten track. I take stock of viral sequence diversity across host taxa as an estimate of the bias that exists in our understanding of host-virus interactions. I describe the gains that have been made through the metagenomic discovery of thousands of new viruses in previously unsampled hosts as well as the limitations of metagenomic surveys. I conclude by suggesting that the study of viruses that naturally infect existing and emerging model organisms represents an opportunity to push virology forward in useful and hard to predict ways.