A Metagenomic Investigation into Apteryx rowi Dermatosis Identifies Multiple Novel Viruses and a Highly Abundant Nematode

Abstract

Sporadic cases of dermatosis have been reported in wild Ōkarito Rowi (Apteryx rowi), a species of brown kiwi, for over a decade. The disease exhibits distinctive features, including lesions, lichenification, and feather loss. Swab samples and full-thickness skin biopsies were collected during a survey of affected kiwi in 2023 for a metatranscriptome-based, total infectome investigation to identify any possible microbial agents associated with the disease. Our approach identified novel viruses as well as a species of nematode in high relative abundance. We found a highly abundant hepacivirus within the Flaviviridae, but only in some mild cases of dermatitis across all sample types, and in both active and chronic infections. In addition, we found a significant shift in the taxonomic composition of the nonviral microbiome within severe chronic dermatitis cases, particularly an increased abundance of transcripts from a Eucoleus sp. parasitic. Although determining the primary cause of disease in critically endangered wildlife such as Rowi remains challenging, our detection of novel and highly abundant microorganisms opens new lines of inquiry to investigate their potential association with dermatosis in this nationally iconic species.