Obtaining a complete good-quality sequence and annotation for the long double-stranded DNA genome of the African swine fever virus (ASFV) from next-generation sequencing (NGS) technology has proven difficult, despite the increasing availability of reference genome sequences and the increasing affordability of NGS. A gap analysis conducted by the global African swine fever research alliance (GARA) partners identified that a standardized, automatic pipeline for NGS analysis was urgently needed, particularly for new outbreak strains. Whilst there are several diagnostic and research labs worldwide that collect isolates of the ASFV from outbreaks, many do not have the capability to analyze, annotate, and format NGS data from outbreaks for submission to NCBI, and some publicly available ASFV genomes have missing or incorrect annotations. We developed an automated, standardized pipeline for the analysis of NGS reads that directly provides users with assemblies and annotations formatted for their submission to NCBI. This pipeline is freely available on GitHub and has been tested through the GARA partners by examining two previously sequenced ASFV genomes; this study also aimed to assess the accuracy and limitations of two strategies present within the pipeline: reference-based (Illumina reads) and de novo assembly (Illumina and Nanopore reads) strategies.

African swine fever virus (ASFV) is a highly stable DNA virus showing little genetic variation among genomes. This genetic stability has often posed challenges in tracking variants and identifying potential transmission chains as ASFV spreads into new regions. While mutations within individual sequenced genes are infrequent, the application of whole‐genome sequencing enables the identification of neutral and functional mutations across the entire genome, contributing to a deeper understanding of ASFV evolution and epidemiology. In this study, we sequenced whole genomes from 25 ASFV positive samples collected from Vietnam, Timor‐Leste and Papua New Guinea (PNG). We classified mutations across ASFV genes and non‐coding regions, while identifying mutations that may act as candidates for geographic‐based population genetic structuring. Overall, ASFV samples showed >99.8% genetic similarity to the Georgia 2007 isolate reference genome. Nonetheless, emergent genetic clusters rooted in geographic location were apparent. Multiple nonsynonymous mutations were found in sequenced genomes, often unique to ASFV collected within only one studied country. Of the observed mutations, four were found within genes of known function ( E199L , CP80R , B962L and B602L ), with the latter ( B602L ) being a novel mutation within a known targeted marker gene for conventional genotyping of the virus. This work highlights the benefits of incorporating whole‐genome sequencing into ongoing ASFV surveillance to better reflect the natural population genetic structuring within the species as it has spread across the Asia–Pacific region. Additionally, this work highlights the value of whole‐genome sequencing as a tool for actively monitoring emergent variants displaying functional divergence in key genes associated with ASFV proliferation and host selection.

The capacity of species to tolerate physical stressors is critical in a world of increasing environmental instability, however, past selective environments should dramatically impact on future stress tolerance, particularly in isolated populations. Through stabilising selection, long-term environmental stasis may reduce physiological tolerance, creating an evolutionary legacy where populations are less fit if environments change. Few empirical studies have investigated this evolutionary legacy of past selection, and of particular interest whether stabilising selection in a benign environment reduces stress tolerance in natural systems. Here we use multiple populations of salt-lake invertebrates (Coxiella striata, Austrochiltonia subtenuis) with either stable or fluctuating environmental histories to investigate the relationship between stabilising selection and environmental stress resistance. Tolerance to both salinity and temperature stress were examined in invertebrate populations from lakes with long-term (decadal) stable environments and compared with populations from lakes with extreme salinity variations. Individuals from stable environments demonstrated significantly lower survival under both increasing salinity and temperature stresses when compared with environmentally unstable populations. Our results support the hypothesis that the evolutionary legacy from stabilising selection in constant environments leads to reduced stress tolerance. This finding demonstrates that under an increasingly variable climate, the evolutionary legacies of populations will be critical for future survival and adaptation.

Genetic sampling from European honeybee (Apis mellifera) hives is a promising repository of terrestrial environmental nucleic acids (eNA) from a range of taxonomic sources. eNA samples from honeybee hives can be used to monitor environments via vegetation assessments and plant pathogen detection, while simultaneously assessing honeybee hive health through the identification of honeybee pests and pathogens. However, there is still limited comparison across the different types of hive samples commonly used for biomonitoring. There is also a need for less invasive sampling methods to facilitate adoption of hive eNA surveillance at scale. The aim of this study was to compare the effectiveness of using non-invasive swabbing of hive entrances with common sample types collected from honeybee hives (honey, pollen, and bees) for eNA detection of various taxa. Using a DNA metabarcoding approach for bacteria (16S), animal (COI), fungi (ITS1), and plant (ITS2) identification, and metatranscriptomic sequencing for virus detection, swabbing was found to provide comparable or better detection of taxa compared with more invasive sampling methods. Swabs were most informative for identifying bacterial and fungal communities, while plant detections were similar between swabs and honey samples. Detection of RNA viral diversity was highest in honey samples, however, swabs also showed good recovery of plant and insect viruses. A minimum of two swab replicates was recommended to increase taxa yield for DNA metabarcoding. Our study suggests that swabbing of hive entrances is a highly effective biomonitoring method for non-invasively collecting hive eNA and delivering comprehensive surveillance for animal, plant and microbial communities in the environment.

Insect-specific viruses (ISVs) are integral components of mosquito viromes, influencing virus evolution, vector competence, and arbovirus ecology. Papua Ne