Mars Bar-sized gadget could help combat outbreaks

It's called a MinION and, unlike the little yellow animated henchmen of the same name, could prove a handy helper for humans.

A team of Kiwi scientists known as the "virus hunters" have proven how the Mars Bar-sized gadget can speedily sequence entire influenza virus genomes, potentially making it a handy weapon in combatting global disease outbreaks.

The ESR scientists have been trialling the USB-operated device, which was developed by UK-based technology company Oxford Nanopore Technologies and has been provided to a select group of researchers around the world.

The hand-held gadget has made it possible to perform mitochondrial sequencing of the human genome - the individualised and genetic jigsaw puzzle that makes each of us up - in a much faster time than was previously possible, paving the way for GPs to prescribe us more specific antibiotics in the time it takes to perform a standard blood test today.

Scientists at the Malaghan Institute, who have been provided their own MinION, have been using it to run DNA tests over the past few months.

The device has been specifically used by the Wellington-based institute to sequence and compare different mitochondrial genomes, which are small compared with the full human genome sequence.

Sequencing mitochondrial genomes can be done much faster as scientists only have to work with around 16,300 "bases", or nucleotides that are measurable sub-units of the DNA.

The MinION works by reading off the genetic sequences from a DNA sample as it travels through about 500 tiny pores in the device, with the data fed into a laptop it is attached to via USB.

Naturally, these DNA bases will try to fly through at a rate of a million per second, but a specially-designed protein in the device slows this down to a rate of just 30 bases per second.

Now, researchers at ESR have used the MinION in a study to see how quickly influenza genomes could be decoded.

The ability to rapidly and accurately sequence influenza viruses to understand their DNA was critical when trying to determine the best way to treat and stop the spread of an outbreak.

Team leader Richard Hall says their study shows the potential for the device to be deployed in other outbreak scenarios such as bird flu and MERS-CoV.

"Existing methodology is reliable and robust and has served molecular biology well for over three decades, but it is labour-intensive, slow, and not easily adapted for processing large genomes or large numbers of samples," Dr Hall said.

"Using the MinION we were able to sequence all eight influenza genes from an influenza A virus and get a complete genome that was more than a 99 percent match with results obtained from traditional sequencing techniques.

"The ability to rapidly, and accurately, sequence influenza viruses is instrumental in the prevention and mitigation of influenza but applies equally to other viruses.

"With the way technology is moving it's not a stretch to imagine an outbreak scenario where first responders in the field are able to identify quickly and accurately exactly what they are dealing with without having to be science experts or needing to set up or access extensive lab facilities."

Their study, funded by the ESR Core Research Fund from the Ministry of Business Innovation and Employment, was the first article to report MinION sequencing of a major viral pathogen that affects humans and the findings were recently presented at an international conference.

ESR research assistant Nicole Moore, who attended the conference, said the work of the Virus Hunters team would add to the international body of evidence around the potential use of this technology in the field.

"The conference heard that the MinION has already proven its potential in outbreak situations like Salmonella and Ebola and that as well as initial analysis, it can be very valuable in contact tracing and identifying any mutations."