FEATURE GENOMICS DNA
ust a few weeks ago, in mid-February 2016, the journal Nature announced that it will make all papers relating to the Zika virus free to access until further notice. It also encouraged authors who have not already deposited their relevant sequence information in public archives to do so on submission, to help drive the shift towards fast data sharing during public-health emergencies.
In the same week, in the same journal, a large global group of researchers published a paper entitled ‘Real-time, portable genome sequencing for Ebola surveillance’.1
Genome sequencing in viral outbreaks needs to take place locally and happen quickly, in order for it to be useful in characterising the infectious agent and determining its evolutionary rate. While DNA analysis can be used to determine whether a patient has a certain virus, DNA
Unravelling J
Nadya Anscombe discusses the latest DNA sequencing methods, comparing optical with non-optical technologies
sequencing goes one step further and allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterisation of responses to vaccines and treatments. One of the reasons that the recent Ebola
outbreak in West Africa became the largest on record was that the virus mutated quickly. Genome sequencing can track the evolution of these mutations and be used to guide control measures, but only if the results are generated quickly enough to inform interventions. But performing DNA sequencing in Africa is challenging for many reasons – there is a lack of local sequencing capacity, transporting samples to remote facilities is a challenge and the ambient climate also creates problems. So a portable device that can reliably and quickly sequence DNA in the field has been a dream for researchers for many years. In their Nature paper, the 104 authors from 13
different countries describe how they transported the MinION by Oxford Nanopore in standard airline luggage to Guinea, and how they were able to generate results less than 24 hours after receiving an Ebola-positive sample, with the sequencing process taking as little as 15 to 60 minutes. They showed that real-time genomic
surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.
The MinION weighs less than 100g, is no bigger than an office stapler and plugs into a laptop using a USB cable.
It works by taking frequent electrical current
The MinION weighs less than 100g, is no bigger than an office stapler and plugs into a laptop using a USB cable
24 ELECTRO OPTICS l MARCH 2016
measurements as a single strand of DNA passes through a protein nanopore at 30 bases per second. DNA strands in the pore disrupts ionic flow, resulting in detectable changes in current that is dependent on the nucleotide sequence. Unlike the majority of the leading lab-based DNA sequencing technology, the MinION relies on electrical, rather than optical technology. As this article went to press, there were no optical-based mobile DNA sequencing devices on the market, and, according to Dr Matthias Schulze, marketing director for Coherent, this situation is not likely to change in the near future. ‘The big players are concentrating on increasing
the throughput of their products, and not on creating optical portable sequencing devices,’ said
@electrooptics |
www.electrooptics.com
Oxford Nanopore
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