Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System

• Published in: Viruses Vol. 15; no. 6; p. 1399
• Main Authors: Fomsgaard, Anna S., Tahas, Stamatios A., Spiess, Katja, Polacek, Charlotta, Fonager, Jannik, Belsham, Graham J.
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 20.06.2023; MDPI
• Subjects: Animal health; Animals; Avian leukosis; Avian leukosis virus; Capra hircus; Chickens - genetics; Choloepus didactylus; cross-species transmission; Denmark; Deoxyribonucleic acid; disease control; DNA; DNA sequencing; DNA viruses; DNA Viruses - genetics; Elephantid betaherpesvirus 1; Elephas maximus; enzootic diseases; field detection; Gallus gallus; Genomes; Head & neck cancer; Health aspects; Herpes viruses; Herpesviridae - genetics; High-Throughput Nucleotide Sequencing - methods; Humans; human–animal interface; Identification and classification; Leukosis; Life sciences; Mammals; metagenomic sequencing; Metagenomics; Metagenomics - methods; Methods; nanopore sequencing; neoplasms; Next-generation sequencing; nose; Nucleotide sequencing; Pathogens; point-of-care test (POCT); protocols; RNA; RNA viruses; Surveillance; Viruses; Zoo animals; Zoonoses; Zoos; Denmark; United States > US; Switzerland; Germany; metagenomic sequencing; cross-species transmission; human–animal interface; nanopore sequencing; field detection; point-of-care test (POCT)
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v15061399

Metagenomic next-generation sequencing (mNGS) is receiving increased attention for the detection of new viruses and infections occurring at the human–animal interface. The ability to actively transport and relocate this technology enables in situ virus identification, which could reduce response time and enhance disease management. In a previous study, we developed a straightforward mNGS procedure that greatly enhances the detection of RNA and DNA viruses in human clinical samples. In this study, we improved the mNGS protocol with transportable battery-driven equipment for the portable, non-targeted detection of RNA and DNA viruses in animals from a large zoological facility, to simulate a field setting for point-of-incidence virus detection. From the resulting metagenomic data, we detected 13 vertebrate viruses from four major virus groups: (+)ssRNA, (+)ssRNA-RT, dsDNA and (+)ssDNA, including avian leukosis virus in domestic chickens (Gallus gallus), enzootic nasal tumour virus in goats (Capra hircus) and several small, circular, Rep-encoding, ssDNA (CRESS DNA) viruses in several mammal species. More significantly, we demonstrate that the mNGS method is able to detect potentially lethal animal viruses, such as elephant endotheliotropic herpesvirus in Asian elephants (Elephas maximus) and the newly described human-associated gemykibivirus 2, a human-to-animal cross-species virus, in a Linnaeus two-toed sloth (Choloepus didactylus) and its enclosure, for the first time.