Total infectome investigation of diphtheritic stomatitis in yellow-eyed penguins (<i>Megadyptes antipodes</i>) reveals a novel and abundant megrivirus

<p dir="ltr">First identified in 2002, diphtheritic stomatitis (DS) is a devastating disease affecting yellow-eyed penguins (<i>Megadyptes antipodes</i>, or hoiho in te reo Māori). The disease is associated with oral lesions in chicks and has caused significant morbidity and mortality. DS is widespread among yellow-eyed penguin chicks on mainland New Zealand yet appears to be absent from the subantarctic population. <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/corynebacterium" target="_blank"><i>Corynebacterium</i></a> spp. have previously been suspected as causative agents yet, due to inconsistent cultures and inconclusive <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/pathogenicity" target="_blank">pathogenicity</a>, their role in DS is unclear. Herein, we used a metatranscriptomic approach to identify potential causative agents of DS by revealing the presence and abundance of all viruses, bacteria, fungi and <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/protozoa" target="_blank">protozoa</a> - together, the infectome. Oral and cloacal swab samples were collected from presymptomatic, symptomatic and recovered chicks along with a control group of healthy adults. Two novel viruses from the <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/picornaviridae" target="_blank"><i>Picornaviridae</i></a> were identified, one of which - yellow-eyed penguin megrivirus – was highly abundant in chicks irrespective of health status but not detected in healthy adults. Tissue from biopsied oral lesions also tested positive for the novel megrivirus upon <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/polymerase-chain-reaction" target="_blank">PCR</a>. We found no overall clustering among bacteria, protozoa and fungi communities at the genus level across samples, although <i>Paraclostridium bifermentans</i> was significantly more abundant in oral microbiota of symptomatic chicks compared to other groups. The detection of a novel and highly abundant megrivirus has sparked a new line of inquiry to investigate its potential association with DS.</p>