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Front Microbiol. 2015 Mar 25;6:224. doi: 10.3389/fmicb.2015.00224. eCollection 2015.

Beyond research: a primer for considerations on using viral metagenomics in the field and clinic.

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Institute of Environmental Science and Research, National Centre for Biosecurity and Infectious Disease, Upper Hutt New Zealand.
Ministry for Primary Industries Animal Health Laboratory, National Centre for Biosecurity and Infectious Disease, Upper Hutt New Zealand.
DNAdigest, Future Business Centre, Cambridge UK.
Theoretical Biology and Bioinformatics, Utrecht University, Utrecht Netherlands ; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen Netherlands ; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro Brazil.


Powered by recent advances in next-generation sequencing technologies, metagenomics has already unveiled vast microbial biodiversity in a range of environments, and is increasingly being applied in clinics for difficult-to-diagnose cases. It can be tempting to suggest that metagenomics could be used as a "universal test" for all pathogens without the need to conduct lengthy serial testing using specific assays. While this is an exciting prospect, there are issues that need to be addressed before metagenomic methods can be applied with rigor as a diagnostic tool, including the potential for incidental findings, unforeseen consequences for trade and regulatory authorities, privacy and cultural issues, data sharing, and appropriate reporting of results to end-users. These issues will require consideration and discussion across a range of disciplines, with inclusion of scientists, ethicists, clinicians, diagnosticians, health practitioners, and ultimately the public. Here, we provide a primer for consideration on some of these issues.


biomarkers; data interpretation; diagnostic tools; ethics; incidental findings; medical; metagenomics; viral metagenomics

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