Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool.

The response of the global virus genomics community to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant advances made towards the 'real-time' generation and sharing of SARS-CoV-2 genomic data. The rapid growth in virus genome data production has necessitated the development of new analytical methods that can deal with orders of magnitude of more genomes than previously available. Here, we present and describe Phylogenetic Assignment of Named Global Outbreak Lineages (pangolin), a computational tool that has been developed to assign the most likely lineage to a given SARS-CoV-2 genome sequence according to the Pango dynamic lineage nomenclature scheme. To date, nearly two million virus genomes have been submitted to the web-application implementation of pangolin, which has facilitated the SARS-CoV-2 genomic epidemiology and provided researchers with access to actionable information about the pandemic's transmission lineages.

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

Drosophila melanogaster has played a key role in our understanding of invertebrate immunity. However, both functional and evolutionary studies of host-virus interaction in Drosophila have been limited by a dearth of native 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 disproportionately 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 describe differential regulation of virus-responsive genes. This work establishes Kallithea virus as a new tractable model to study the natural interaction 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.

The virome of Drosophila suzukii, an invasive pest of soft fruit.

Drosophila suzukii (Matsumura) is one of the most damaging and costly pests to invade temperate horticultural regions in recent history. Conventional control of this pest is challenging, and an environmentally benign microbial biopesticide is highly desirable. A thorough exploration of the pathogens infecting this pest is not only the first step on the road to the development of an effective biopesticide, but also provides a valuable comparative dataset for the study of viruses in the model family Drosophilidae. Here we use a metatransciptomic approach to identify viruses infecting this fly in both its native (Japanese) and invasive (British and French) ranges. We describe eighteen new RNA viruses, including members of the Picornavirales, Mononegavirales, Bunyavirales, Chuviruses, Nodaviridae, Tombusviridae, Reoviridae, and Nidovirales, and discuss their phylogenetic relationships with previously known viruses. We also detect 18 previously described viruses of other Drosophila species that appear to be associated with D. suzukii in the wild.

An evaluation of three predatory mite species for the control of greenhouse whitefly (Trialeurodes vaporariorum).

BACKGROUND: Within integrated pest control programmes, the use of high mite inoculations to control hot spots of whitefly is desirable for many growers. In this experiment, two species of predatory mites established as commercial biological control agents, Typhlodromips montdorensis and Amblyseius swirskii (Acari: Phytoseiidae), were compared with another, more recently introduced species, Amblydromalus limonicus, for their ability to control dense populations of greenhouse whitefly (Trialeurodes vaporariorum) on cucumber plants (Cucumis sativus). RESULTS: Mite formulation type had a significant effect on the number of mites found on plants, but this did not correspond to increased whitefly control. Plots treated with A. limonicus or T. montdorensis, applied as loose product, had significantly reduced whitefly populations throughout the trial. Analysis showed that no species was observed more often on leaves with higher whitefly densities than on those with lower densities. CONCLUSION: No species was clearly identified as a suitable candidate for treatment of high-density whitefly colonies, but results suggest the highest level of predation in A. limonicus. Strategies for the effective use of these predatory mite species in control programmes are discussed.