Genomics of respiratory pathogens responsible for mortality in wild chimpanzees from Tai National Park, Ivory Coast

Respiratory disease is among the main causes of death in endangered great apes. Common human respiratory viruses and the bacterium Streptococcus pneumoniae have often been identified as causative agents of lethal outbreaks. However, our knowledge of these pathogens in wild great apes remains sparse. Here we applied hybridization capture coupled with next generation sequencing to retrieve full viral genomes and pneumococcal virulence factors from faecal samples collected during five distinct outbreaks in the human-habituated Tai chimpanzee community. By assembling 33 complete viral genomes and 4 distinct constellations of pneumococcal virulence factors, we provide genomic insights into respiratory pathogen emergence and transmission in a wild chimpanzee population.