Metagenomic sequencing to diagnose infectious diseases

An article published in Genome Medicine reports the ability to detect viruses in clinical samples using a nanopore sequencer. The senior author of the work tells more in this blog.

I first heard about the Oxford Nanopore MinIONTM sequencer two years ago. It was being billed as the ‘future of sequencing’. My immediate thoughts were that a pocket-sized, USB-powered, real-time sequencer would be ideal for field-ready applications.

Metagenomic sequencing

In particular, this technology should be perfectly suited for infectious disease outbreaks such as Ebola, where rapid diagnosis is needed both for managing the patient and containing spread of the disease.

However, we didn’t actually get our hands on a MinIONTM sequencer until September of 2014. Even worse, the first couple of flow cells that we analyzed yielded no usable data at all, as the platform was still at a very early stage. It was not until January of this year that we had a successful sequencing run and were off to the races.

Our approach to diagnosing infectious diseases is called metagenomic sequencing. The general idea is that we sequence all of the nucleic acid – DNA and RNA – in clinical samples and analyze the data using computational software to find the proverbial ‘needle in the haystack’.

We search for the generally <0.1% of sequence reads that may correspond to a virus that may be causing the illness, whether it be Ebola or influenza. This is in contrast to other groups and commercial laboratories, which typically sequence using primers or probes that specifically target individual pathogens.

Our article published inGenome Medicine presents a ‘proof-of-concept’ study on leveraging MinION nanopore sequencing to metagenomically detect viruses in clinical samples.

Last year, we described the use of metagenomic sequencing to successfully diagnose a rare but treatable bacterial infection (neuroleptospirosis) in a critically ill 14-year old boy who had been sick without a diagnosis for over 4 months. For diseases such as acute tropical febrile illness that have a broad differential diagnosis (malaria, typhoid fever, dengue, Ebola, etc.), unbiased metagenomic sequencing is a very attractive diagnostic testing approach.

Our publication in Genome Medicine presents a ‘proof-of-concept’ study on leveraging MinION nanopore sequencing to metagenomically detect viruses in clinical samples. To demonstrate its utility for real-time detection of emerging viruses, we chose to focus on analyzing clinical samples collected from outbreak settings.

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