Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units

Abstract

Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae.

Pathological findings in the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides), with special emphasis on infectious and zoonotic agents in Northern Germany

“…Obtained reads were analysed by BLASTN and BLASTX with a bioinformatics virus discovery pipeline using standard parameters as previously described [58]. The European Nucleotide Archive Study accession number of this study is PRJEB19187, with secondary study accession number ERP021170.…”

Investigation into diseases in free-ranging ring-necked pheasants (Phasianus colchicus) in northwestern Germany during population decline with special reference to infectious pathogens

“…The investigation was performed on frozen brain and liver tissue of one pheasant with a lymphohistiocytic hepatitis and a periocular dermatitis and on periocular skin of another pheasant presenting with periocular dermatitis and conjunctivitis. Obtained reads were analyzed by blastN and blastX analysis (Schurch et al 2014).…”

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses

“…De novo assemblies of MG data alone usually result in a large fraction of reads that are unmappable to the assembled contigs and therefore remain unused, thereby leading to suboptimal data usage [43, 58–60]. Previous studies have assembled sets of unmappable reads iteratively to successfully obtain additional contigs, leading to an overall increase in the number of predicted genes, which in turn results in improved data usage [43, 58–60].…”

“…Previous studies have assembled sets of unmappable reads iteratively to successfully obtain additional contigs, leading to an overall increase in the number of predicted genes, which in turn results in improved data usage [43, 58–60]. Therefore, IMP uses an iterative assembly strategy to maximize NGS read usage.…”