In April 2015, Josh Quick, a bioinformatician and PhD student working at the Institute of Microbiology and Infection at the University of Birmingham travelled to the epicentre of the outbreak in Guinea. He took with him, for the first time, a portable genomic surveillance system carried in his hold luggage to read the genomes of Ebola virus samples taken from 14 patients in as little as 48 hours after the samples were collected.
Quick, who studies Ebola genomes along with Dr Nick Loman, describes this as the democratization of sequencing, in that it no longer has to rely on expensive infrastructure and costly equipment.
As of last year, the only way to practically sequence Ebola genomes was to export samples to specialist laboratories. Samples would be received in poor condition, and then the genome sequences could take weeks or months to generate. Our research has shown that this can be done in less than 48 hours from receipt of a patient sample.
A positive development during this outbreak has been the rapid development of vaccines and vaccine trials. Genomic surveillance is important in order to see whether the virus can evolve to evade such a vaccine, and in developing early treatments that directly interfere with the viral genome. Changes in those regions targeted by the treatment could result in resistance, therefore genome surveillance data is of great benefit to those involved in such efforts.
Whilst the ebola crisis may no longer be at the forefront of the headlines, dangers still remains and it is important that we are better prepared should this strain return in future – and it may be inevitable that Ebola strikes again in Africa.
Closer to home, genome sequencing is becoming mainstream: the Department of Health has announced a project to sequence 100,000 patient genomes with the West Midlands being one of 11 centres across the country that will lead the way in delivering the project. Armed with new technologies, it may soon be possible for individuals to sequence their own genomes and for infectious pathogens to be sequenced at home or in a GP surgery.
Find out more about the 100,000 Genomes project