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

The high taxonomic resolution summary network indicated a significantly nested architecture ( = 0.74) with relatively low modularity (modularity index = 0.393, z = 3.307, p = <0.001) with three clusters (Fig. 1a) . The largest cluster (green nodes) included all of the protozoans, acute pathogens, and some FIV Ple genotypes, whilst the remaining two clusters consisted just of FIV Ple genotypes (Fig. 1a) . While the high prevalence FIV Ple genotypes clustered in the largest cluster, the B2, B3 and C2 genotypes clustered separately , and the disconnected C7 was only detected in one pride during the 1980s. The light red cluster is likely to result from the restricted distribution and temporal period in which these genotypes were identified (e.g., the north western region of the SLP in the 1990's). The blue and green clusters, in contrast, included a variety of prides over the full sampling period (with the exception of B2 and B6, which were only detected in the woodlands in the 1980's). Phylogenetically similar genotypes of FIV did not cluster . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 4 1 4 FIV Ple C1 had a higher prevalence (Fig. S6) , C1 had the same overall association profile as FIV Ple C.