Chronic infections can shape epidemic exposure: Pathogen co-occurrence networks in the Serengeti lions

Nicholas M. Fountain-Jones; Craig Packer; Maude Jacquot; F. Guillaume Blanchet; Karen Terio; Meggan E. Craft

Here we demonstrate non-random pathogen interactions infecting wild African lions, with both facilitative and competitive associations detected between chronic and acute pathogens across different spatiotemporal scales. We found that whilst there was minimal structure in the summary co-occurrence network (Fig. 1a) , we uncovered structure after accounting for scale and controlling for potentially confounding environmental and host variables (Fig. 2) . The particular chronic pathogen an individual is infected by as a cub may have consequences for which acute pathogen the individual is infected with later in life (Fig. 3) . Moreover, we detected strong relationships between chronic pathogens across scales, and these associations may have . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/370841 doi: bioRxiv preprint 1 5 consequences for lion health. We emphasize that the approach used here can start to untangle pathogen infra-community relationships and identify potential chronic-acute interactions in wild populations. These can then be compared with knowledge of pathogen pathogenesis and validated in-vitro in a laboratory setting. Whilst clinical or laboratory studies of co-infection in lions are rare, the associations we found have clear precedence in similar pathogens co-infecting humans. Our results not only provide new insights on disease dynamics in the Serengeti lions but also provide a valuable framework for exploring pathogen co-occurrence networks and infracommunity dynamics across taxonomic and spatial scales.