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

Author:

Fomsgaard Anna S.12,Tahas Stamatios A.3,Spiess Katja1,Polacek Charlotta1,Fonager Jannik1,Belsham Graham J.2ORCID

Affiliation:

1. Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark

2. Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark

3. Copenhagen Zoo, Roskildevej 38, 2000 Frederiksberg, Denmark

Abstract

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.

Funder

European Union’s Horizon 2020 Research and Innovation program

Publisher

MDPI AG

Subject

Virology,Infectious Diseases

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