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

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.

INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance

“…This impact is well reflected in several works, namely in the rapid identification and characterization of emerging viral threats [ 8 ], in national [ 9 , 83 , 84 ] and local [ 85 , 86 ] outbreak tracking, and in research studies in viral evolution [ 87 , 88 ], which ultimately contributed to strengthening the integration of the genomics pathogen surveillance in public health decision-making towards infectious diseases’ prevention and control. Moreover, coupled with a portable metagenomic virus detection wet-lab protocol [ 21 ], the newly developed TELEVIR bioinformatics component could be successfully tested in proof-of-concept studies conducted by TELEVIR consortium members, under very different conditions ( https://onehealthejp.eu/projects/emerging-threats/jrp-tele-vir ) [ 20 ]. These exercises in a real context not only provided a good complement to the multiple tests performed during the TELEVIR pipeline development, benchmarking, and final refinement, but also introduced it as a bioinformatics resource of reference among several Public Health and Veterinary institutes across Europe.…”

“…The early detection, characterization, and surveillance of viruses is an urgent need at a global level in the light of the continuous emergence of viral threats, as recently observed in SARS-CoV-2 and MPXV epidemics. In this context, on behalf of the EU-funded TELEVIR project, in addition to the development of wet-lab protocols for virus metagenomic detection using ONT sequencing (addressed in Fomsgaard et al, 2023)[ 21 ], we built on an existing INSaFLU platform [ 19 ] to deploy a freely accessible and user-oriented “start-to-end” bioinformatics framework for viral metagenomic detection and routine genomic surveillance: the upgraded INSaFLU-TELEVIR platform ( https://insaflu.insa.pt ) [ 22 ]. The present report describes: i) the development, benchmarking, and implementation of a novel virus detection module (TELEVIR), from reads and quality control to the identification of both RNA and DNA viruses; ii) the improvement and adaptation of the “surveillance-oriented” platform components to handle “multi-technology” sequence data (ONT, Illumina, and Ion Torrent) of “any” virus, from reads to quality control, mutations detection, consensus generation, alignments, genotyping (through Nextclade and pangolin), “genotype-phenotype” screening (through incorporation and standalone release of “algn2pheno” for mutation screening), phylogenetics, integrative phylogeographical and temporal analysis (through incorporation of Nextstrain).…”

“…In order to catch up with this technological revolution, and aiming to increase the capacity of laboratories with fewer resources, we have previously developed INSaFLU [ 19 ], an open and innovative web-based bioinformatics platform for virus NGS data analysis. On behalf of the One Health European Joint Programme (OHEJP) TELEVIR ( https://onehealthejp.eu/projects/emerging-threats/jrp-tele-vir ) [ 20 ] project, along with the development of wet-lab protocols [ 21 ], and also as a response to public health threats (namely, the COVID-19 pandemic and the multi-country mpox outbreak), we expanded its genomic surveillance component and developed a brand new module (TELEVIR) for viral metagenomic identification. In this study, we present the upgraded INSaFLU-TELEVIR platform ( https://insaflu.insa.pt/ ) [ 22 ], a free, versatile, and user-oriented “start-to-end” pan-viral bioinformatics framework aiming at facilitating or strengthening the laboratories capacity building in genomic epidemiology and public and animal health bioinformatics towards an enhanced and global surveillance of viral threats.…”