Journal Articles

Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915

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    Land Use Change and Infectious Disease Emergence
    (John Wiley and Sons, Inc on behalf of the American Geophysical Union, 2025-06-01) Rulli MC; D’Odorico P; Galli N; John RS; Muylaert RL; Santini M; Hayman DTS
    Major infectious diseases threatening human health are transmitted to people from animals or by arthropod vectors such as insects. In recent decades, disease outbreaks have become more common, especially in tropical regions, including new and emerging infections that were previously undetected or unknown. Even though there is growing awareness that altering natural habitats can lead to disease outbreaks, the link between land use change and emerging diseases is still often overlooked and poorly understood. Land use change typically destroys natural habitat and alters landscape composition and configuration, thus altering wildlife population dynamics, including those of pathogen hosts, domesticated (often intermediary) hosts, infectious agents, and their vectors. Moreover, land use changes provide opportunities for human exposure to direct contact with wildlife, livestock, and disease-carrying vectors, thereby increasing pathogen spillover from animals to humans. Here we explore the nexus between human health and land use change, highlighting multiple pathways linking emerging disease outbreaks and deforestation, forest fragmentation, urbanization, agricultural expansion, intensified farming systems, and concentrated livestock production. We connect direct and underlying drivers of land use change to human health outcomes related to infectious disease emergence. Despite growing evidence of land-use induced spillover, strategies to reduce the risks of emerging diseases are often absent from discussions on sustainable food systems and land management. A “One Health” perspective—integrating human, animal, and environmental health—provides a critical yet often-overlooked dimension for understanding the health impacts of land use change.
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    Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads.
    (Frontiers Media S.A., 2023-08-10) Yang Z; Guarracino A; Biggs PJ; Black MA; Ismail N; Wold JR; Merriman TR; Prins P; Garrison E; de Ligt J; Hane J
    Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes of the same species. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants as a graph structure that includes all types of variations. In this study, we present a practical bioinformatics pipeline that employs the PanGenome Graph Builder and the Variation Graph toolkit to build pangenomes from assembled genomes, align whole genome sequencing data and call variants against a graph reference. The pangenome graph enables the identification of structural variants, rearrangements, and small variants (e.g., single nucleotide polymorphisms and insertions/deletions) simultaneously. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves mapping rates and variant calling for both simulated and real datasets of the pathogen Neisseria meningitidis. Overall, pangenome graphs offer a promising approach for comparative genomics and comprehensive genetic variation analysis in infectious disease. Moreover, this innovative pipeline, leveraging pangenome graphs, can bridge variant analysis, genome assembly, population genetics, and evolutionary biology, expanding the reach of genomic understanding and applications.