Molecular Surveillance for Known and Novel Pathogens in Humboldt Penguins (Spheniscus humboldti) in Peru, 2009-18

The Humboldt Penguin (Spheniscus humboldti) is an IUCN Vulnerable species endemic to the Humboldt Current on the western coast of South America. Infectious disease is an inadequately understood potential threat to this species. To assess for the occurrence and prevalence of potential pathogens, conventional and quantitative PCR assays were conducted for 23 viral and bacterial targets in cloacal and tracheal swabs from adult penguins (n=224) sampled from 2009 to 2018 in a Peruvian breeding colony. Adenoviruses, circoviruses, herpesviruses, and Mycoplasma spp. were detected. Adenoviruses were detected at low prevalence (1%). Two circoviruses were detected: one circovirus with high homology to porcine circovirus 2 (overall positivity 14% of sampled individuals) and another apparently novel circovirus (12%). Spheniscid alphaherpesvirus 1 (overall positivity 3%) and penguin herpesvirus 1 (1%) were detected at low prevalence. Positivity to Mycoplasma gallisepticum was 26%. Various other Mycoplasma spp. were also detected (overall positivity 10%). Gallid herpesvirus 1, psittacine herpesvirus 1, psittacine circovirus, avian polyomavirus 1, avipoxviruses, coronaviruses, orthoreoviruses, Chlamydophila pneumoniae, Chlamydophila psittaci, Mycoplasma synoviae, and Salmonella enterica (serovars Typhimurium, Enteriditis, Pullorum, and Gallisepticum) were not detected. This study contributes to existing knowledge of the prevalence of potential pathogens in Humboldt Penguins. Further work is needed to characterize the epidemiology and health significance of detected pathogens, particularly circoviruses and Mycoplasma species.