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

We used qPCR for identification of nucleotides for feline immunodeficiency virus (FIV Ple ) and the protozoan pathogens in this study (Table 1) . Three distinct subtypes of FIV Ple co-circulate in . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 lions in the Serengeti (Troyer et al. 2005 (Troyer et al. , 2011 Antunes et al. 2008 ) and thus subtype specific qPCR was performed (see Troyer et al. 2004 Troyer et al. , 2005 for qPCR protocols). The resultant 300 base pair sequences from the pol gene were aligned and assigned to 21 operational taxonomic units/genotypes based on a 95% molecular similarity threshold (see Fountain-Jones et al. 2017 for details). Lions also commonly get chronically infected by a rich protozoan fauna including Babesia and Hepatazoon genera. We developed quantitative PCR protocols using density gel gradient electrophoresis to identify each protozoan species (see Munson et al. 2008) .