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ABSTRACT Metagenomics is a powerful tool for characterising viruses, with broad applications across diverse disciplines, from understanding the ecology and evolutionary history of viruses to identifying causative agents of emerging outbreaks with unknown aetiology. Additionally, metagenomic data contains valuable information about the amount of virus present within samples. However, we have yet to leverage metagenomics to assess viral load, which is a key epidemiological parameter. To effectively use sequencing outputs to inform transmission, we need to understand the relationship between read depth and viral load across a diverse set of viruses. Here, using target enrichment sequencing, we investigated the detection and recovery of virus genomes by spiking known concentrations of DNA and RNA viruses into wild rodent faecal samples. In total, 15 experimental replicates were sequenced with target enrichment sequencing and compared to shotgun sequencing of the same background samples. Target enriched sequencing recovered all spike-in viruses at every concentration (10², 10³, and 10⁵± 1 log genome copies) and showed a log-linear relationship between spike-in concentration and mean read depth. Background viruses (includingKobuvirusandCardiovirus) were recovered consistently across all biological and technical replicates, but genome coverage was variable between virus genera and likely reflected the composition of target enrichment probe panel. Overall, our study highlights the strengths and weaknesses of using commercially available panels to quantify and characterise wildlife viromes, and underscores the importance of probe panel design for accurately interpreting coverage and read depth. To advance the use of metagenomics for understanding virus transmission, further research will be needed to elucidate how sequencing strategy (e.g. library depth, pooling), virome composition, and probe design influence viral read counts and genome coverage. 

Abstract Substantial global attention is focused on how to reduce the risk of future pandemics. Reducing this risk requires investment in prevention, preparedness, and response. Although preparedness and response have received significant focus, prevention, especially the prevention of zoonotic spillover, remains largely absent from global conversations. This oversight is due in part to the lack of a clear definition of prevention and lack of guidance on how to achieve it. To address this gap, we elucidate the mechanisms linking environmental change and zoonotic spillover using spillover of viruses from bats as a case study. We identify ecological interventions that can disrupt these spillover mechanisms and propose policy frameworks for their implementation. Recognizing that pandemics originate in ecological systems, we advocate for integrating ecological approaches alongside biomedical approaches in a comprehensive and balanced pandemic prevention strategy. 

Community Food Strategies provides guidance and tools to local food networks in North Carolina to empower the creation of equitable policy change at all levels. Their vision is the realization of an equitable food system that improves the quality of life for all. In Davidson County, the recently formed Local Food Network, created under the guidance of Community Food Strategies, is working to create a more equitable and sustainable food system and is evaluating how best to apply their resources toward this end. The county is largely rural, and rural areas tend to have lower food access. Two cities, Lexington and Thomasville, have experienced economic depression over the past three decades with the exodus of furniture manufacturing overseas and as such, both cities have communities that suffer from poverty and food insecurity issues. In this research, we use visual analytics and spatial analysis to build a survey and analysis of local food availability for the county. Visual analytics is increasingly being applied to applications like this to increase understanding of large datasets and improve decision making. This research provides a base analysis for the Local Food Network to present the state of the local food system to potential partners who can help create policies that will increase equity and availability of food to everyone in the county. 

Pathogen spillover between different host species is the trigger for many infectious disease outbreaks and emergence events, and ecosystem boundary areas have been suggested as spatial hotspots of spillover. This hypothesis is largely based on suspected higher rates of zoonotic disease spillover and emergence in fragmented landscapes and other areas where humans live in close vicinity to wildlife. For example, Ebola virus outbreaks have been linked to contacts between humans and infected wildlife at the rural-forest border, and spillover of yellow fever via mosquito vectors happens at the interface between forest and human settlements. Because spillover involves complex interactions between multiple species and is difficult to observe directly, empirical studies are scarce, particularly those that quantify underlying mechanisms. In this review, we identify and explore potential ecological mechanisms affecting spillover of pathogens (and parasites in general) at ecosystem boundaries. We borrow the concept of ‘permeability’ from animal movement ecology as a measure of the likelihood that hosts and parasites are present in an ecosystem boundary region. We then discuss how different mechanisms operating at the levels of organisms and ecosystems might affect permeability and spillover. This review is a step towards developing a general theory of cross-species parasite spillover across ecosystem boundaries with the eventual aim of improving predictions of spillover risk in heterogeneous landscapes. This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.