viral metagenomics

I am very happy to present you a summary of the paper “Beyond research: a primer for considerations on using viral metagenomics in the field and clinic” to which our CEO, Fiona Nielsen, is a co-author. The paper by Hall et al discusses the issues arising when considering metagenomics sequencing for critical applications in the field or clinical applications.

viral metagenomics

What is metagenomics?

Usually researchers obtain genetic material (e.g. DNA) from a single source – from an individual patient, isolated plant, fungus, bacteria, virus, etc. But in reality, there are many situations in which myriads of different organisms are present together and it is impossible to isolate their DNA individually. Examples include plants, fungi, and bacteria living in soil or water in a certain area, gut flora living in the human digestive tract, different viruses that affect animals and plants etc.

Metagenomics studies genetic material obtained directly from environmental samples, allowing one to identify all species present in the sample at once. This makes metagenomics a very powerful diagnostic tool, and clinical laboratories are about to start using it.

But before it takes off, there are several serious issues that need to be sorted out.

Hall and collaborators highlight some of the most important problems that can arise:

1. Revealing unexpected information.

If someone is tested to diagnose a cough, but happens to be HIV positive – what do you do? Although this might not be directly related to the current disease, it is very important and very sensitive information. Health specialists should be informed about this possibility and instructed about their actions: what they should and should not tell the patient.

2. Breaching data sharing regulations.

When it comes to samples derived from humans (e.g. faecal samples that are used to identify which bacteria live in the gut), there is a risk of identification of the individual, leading to a potential privacy breach. Normally, human genomic data are protected by special regulations but these do not yet exist for clinical metagenomics.

To summarise, before clinical metagenomics can really step into clinical practice, all uncertainties and potential problems should be considered and broadly discussed. Researchers and policy makers must unite their efforts and produce a set of regulations protecting all interested parties.

Reference: Hall, Draper, Nielsen, and Dutilh (2015) “Beyond research: a primer for considerations on using viral metagenomics in the field and clinic“, Frontiers in Microbiology.