The ongoing Ebola outbreak in West Africa has claimed more than 11,000 victims, with 26,500 reported cases. It is by far the largest and most lethal Ebola outbreak ever seen.
This epidemic will leave scars – psychological, medical, social and economic – that will take many years to heal. Despite a coordinated international response to the outbreak, it has proved extremely difficult to control.
A recent advance in the control of outbreaks has been the development of genome surveillance.
Genome surveillance provides the ability to sequence the entire genetic code of a disease-causing microbe or pathogen. Such information provides an unprecedented view of how genomes evolve; their likely origins; and the genes that encode for proteins necessary for them to infect humans.
Until recently, genomic surveillance has been restricted to conventional academic settings, typically employing sequencing instruments costing hundreds of thousands of pounds and relying on well-equipped molecular laboratories.
At the University of Birmingham, we have been focusing on a new technique that holds promise for portable, real-time genomic surveillance. The aim is to improve our ability to react to outbreaks like Ebola and even novel pathogens.
Last month, Josh Quick, a bioinformatician and PhD student working in my group 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.
The system contained several MinIONs™: portable ‘USB stick’ sequencers developed by the British company Oxford Nanopore, as well as all the chemicals and pipettes and plastic tubes needed to generate sequences of the Ebola virus.
This equipment was set up in the European Mobile Laboratory; a mobile laboratory that provides diagnostic services to many Ebola-affected regions in Guinea and Sierra Leone. Within two weeks, Josh generated 14 Ebola genome sequences. The sequences were generated in as little as 48 hours from taking a patient’s blood sample.
The information generated is used by epidemiologists who are aiming to stop further spread of the virus.
By comparing samples from patients, it is possible to determine whether they are likely to be part of a chain of transmission or if there are unknown networks yet to be discovered. This works because the virus changes or mutates at a constant rate – about 20 differences per year. By comparing the number of differences between samples, it is possible to predict whether they form part of a recent transmission chain or network.
Josh left behind a fully functioning surveillance laboratory, which is now being run by the European Mobile Laboratory in Coyah to provide genome sequence information in real-time.
Genomic surveillance is increasingly important for detecting and managing outbreaks. We hope the ability to provide portable, real-time sequencing will improve our ability to respond in future.
As of last year, the only way to practically sequence Ebola genomes was to export samples to specialist laboratories, resulting in delays obtaining local permissions and significant challenges securing export permits and procuring expensive shipping to transport samples. Samples would be received in poor condition, and then the genome sequences could take weeks or months to generate.
We have now 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.
This week, the outbreak was declared over in Liberia. However, it is not yet over in Guinea or Sierra Leone, and recent reports have suggested that the virus can persist in bodily fluids even after recovery. 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.
Genomic surveillance can also be used to track foodborne pathogens.
In 2011, a German outbreak of Escherichia coli was one of the first to have genome data made available while it was taking place. We analysed genome data from this outbreak and showed that the strain causing disease was of a type previously unseen in such outbreaks, and tracked the likely source to a strain circulating in humans, rather than animals.
It may be that foodborne outbreaks can be detected back to source much more quickly with portable genome surveillance. In the future, food quality may be monitored by producers at source using genomics.
Even closer to home, genome sequencing is becoming mainstream: the Department of Health has announced a project to sequence 100,000 patient genomes. 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.
Dr Nick Loman
Institute of Microbiology and Infection, University of Birmingham
The University of Birmingham is currently running an appeal to help raise funds for the vital Ebola research being carried out by Dr Loman and his team.