Ebola Sequencing Data Released to Global Research Community Online
News Jun 03, 2015
The genetic analysis is now on virological.org and available for the global scientific community to monitor the pathogen’s evolution in real-time and conduct research that can lead to more effective strategies against further outbreaks.
The team of British scientists, funded by the Wellcome Trust, is using semi-conductor next-generation sequencing (NGS) technology to generate data in a lab facilitated by Public Health England and International Medical Corps.
Following two stints volunteering in a diagnostic laboratory attached to an Ebola Treatment Centre (ETC) in one of the worst affected parts of Sierra Leone, Ian Goodfellow, Ph.D., head of Virology at the University of Cambridge, returned a third time to study the virus at a molecular level using the advanced NGS platform. Paul Kellam, Ph.D., professor of the Virus Genomics laboratory at the Wellcome Trust Sanger Institute, leads the team focused on mapping the genomic data generated by Goodfellow and his colleagues.
“Sequencing the genome of a virus can tell us a lot about how it spreads and changes as it passes from person to person. While this information is invaluable to researchers, the rapid sharing of data does not always occur,” said Kellam. “It used to take months to process samples that had to be brought back to labs in the UK for analysis. Having sequencing capabilities on the ground helps generate data in a matter of days or at the longest weeks, which should have a profound impact on how the Ebola virus is researched and inevitably addressed on a global scale.”
Rapid sequencing enables epidemiologists to decipher the source of individual strains, and helps eliminate the need to rely upon Ebola patients to tell them how and where they contracted the virus, as different strains can be tracked as they are transmitted from person to person.
Since the first reported case in March 2014, the Ebola outbreak has claimed nearly 11,000 lives in West African countries. In response, Thermo Fisher Scientific has developed the new Ion AmpliSeq Ebola Panel for the Ion PGM and Ion Chef gene sequencing system. The entire system was selected for its ability to perform and adapt in atypical laboratory environments, including power supply availability, levels of dust in the air and the ability to maintain the equipment in the absence of access to service engineers, Goodfellow said.
“This proved to be a great opportunity to show how genome sequencing technology, typically used only in specialized laboratories, can be transported to and readily operated in more harsh environments in a real-world and real-time situation. Only by understanding the Ebola virus and other pathogens, which cause so much suffering in countries like Sierra Leone, can we take meaningful steps to protect communities from future outbreaks,” said Goodfellow. “My hope is that this technology will be used by the next generation of Sierra Leonean scientists and researchers to help provide a sustainable research and surveillance system in the future.”
The next-generation sequencing system was installed at the laboratory adjacent to an Ebola Treatment Centre in Makeni, which was funded by the United Kingdom’s Department for International Development and is run by Public Health England. The Ebola Treatment Centre is run by International Medical Corps.
In order to ensure a lasting benefit for the project beyond the current crisis, the next-generation sequencing system is expected to be installed at the University of Makeni, where it will be used by local scientists to study Ebola, and other pathogens that affect the region.
“This important and timely effort to better understand Ebola’s evolution at the molecular level would not have been possible without the active participation and support from each organization involved,” said Chris Linthwaite, president, Genetic Sciences at Thermo Fisher Scientific. “The valuable sequencing data now being shared globally will be critical to help researchers stay ahead of the virus.”
“We’ve learned many painful lessons from the Ebola outbreak, not least of which is that as a scientific community we must become less secretive with the data that is generated," added Dr. Jeremy Farrar, director of the Wellcome Trust. “The collective expertise of the world’s infectious disease experts is more powerful than any single lab, and the best way of tapping into this is to enhance the capacity to generate the data in the countries affected, rather than having to fly samples out to other countries and then to make the data openly and safely available, as soon as possible. The Wellcome Trust is delighted to support this crucial work with its centre of gravity in Sierra Leone.”
The Ion AmpliSeq Ebola Panel, Ion PGM System and Ion Chef are For Research Use only. Not for use in diagnostic procedures.