Viral metagenomics as an emerging and powerful tool in veterinary medicine

Abstract

New diseases continue to emerge in both human and animal populations, and the importance of animals, as reservoirs for viruses that can cause zoonoses are evident. Thus, an increased knowledge of the viral flora in animals, both in healthy and diseased individuals, is important both for animal and human health. Viral metagenomics is a culture-independent approach that is used to investigate the complete viral genetic populations of a sample. This review describes and discusses the different possible steps of a viral metagenomic study utilizing sequence-independent amplification, high-throughput sequencing, and bioinformatics to identify viruses. With this technology, multiple viruses can be detected simultaneously and novel and highly divergent viruses can be discovered and genetically characterized for the first time. This review also briefly discusses the applications of viral metagenomics in veterinary science and lists some of the viruses discovered within this field.

Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples

“…Viral metagenomics approaches can provide insights into the composition and structure of environmental viral communities (Edwards and Rohwer, 2005) and are being increasingly used for viral discovery in diseased humans or animals Bibby, 2013;Blomstrom, 2011;Delwart, 2007;Tang and Chiu, 2010). The applied protocols usually start with a virion enrichment step such as (ultra)centrifugation, polyethylene glycol (PEG) precipitation, (ultra)filtration, chloroform treatment, or nuclease treatment (Thurber et al, 2009).…”

Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

“…In particular, viral genomes are so small that a large amount of viral particles must be obtained from air samples to be amplified, quantified, and sequenced. Furthermore, the absence of conserved genes and high genetic variation also make it difficult apply PCR assays to viral populations (5). Thus, there have been no previous metagenomic analyses of atmospheric viral ecology because great challenges are involved in determining the biodiversity and composition of airborne viruses.…”

Infectious diseases of Antarctic penguins: current status and future threats

“…Coupled with this could be an adoption of microbial metagenomic approaches (''the functional and sequence-based analysis of the collective microbial genomes contained in an environmental sample,' ' Riesenfeld et al 2004) for not only ''pathogen discovery'' but also to determine the ''normal background microflora'' in conjunction with disease (serological) surveillance (Blomström 2011). This approach would allow the detection and identification of nonindigenous microbes from the endemic microbial taxa already in the Antarctic Treaty area (Cowan et al 2011).…”

“…This approach would allow the detection and identification of nonindigenous microbes from the endemic microbial taxa already in the Antarctic Treaty area (Cowan et al 2011). With the capability to detect potentially all infectious agents present in biological or environmental samples (Mokili et al 2012), such an approach has obvious advantages over more traditional diagnostics (e.g., the ability to detect fastidious organisms that are unculturable; Riesenfeld et al 2004;Blomström 2011;Lipkin 2013;Belák et al 2013). This approach has already been successfully applied to studies ranging from ''discovering'' the viral etiologies in polar bear encephalitis (Szentiks et al 2014) and a mortality event in captive California sea lions (Zalophus californianus; Ng et al 2009), to a study of a freshwater lake on Livingston Island, Antarctica, revealing much higher than expected microbial diversity (López-Bueno et al 2009).…”