Ebola sequencing data released to global research community
A team of scientists that is part of an international, multi-organisational effort to curb further spread of deadly Ebola in Sierra Leone has released their first dataset of the virus’ genetic structure online. Professor Paul Kellam, Group Leader of Virus Genomics at the Wellcome Trust Sanger Institute, leads the team focused on mapping the genomic data.
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.
“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.
“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.”
Professor Paul Kellam Group Leader of Virus Genomics at the Wellcome Trust Sanger Institute
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, Dr Ian Goodfellow, 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.
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 over 11,000 lives with more the 27,000 people infected 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 specialised 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.
“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.”
Dr Ian Goodfellow Head of Virology at the University of Cambridge
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. The valuable sequencing data now being shared globally will be critical to help researchers stay ahead of the virus.”
Chris Linthwaite President, Genetic Sciences at Thermo Fisher Scientific
“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. 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.”
Dr Jeremy Farrar Director of the Wellcome Trust
The Ion AmpliSeq Ebola Panel, Ion PGM System and Ion Chef are For Research Use only. Not for use in diagnostic procedures
More information
Virological is a discussion forum for analysis and interpretation of virus molecular evolution and epidemiology.
Gene sequencing program
The gene sequencing program is based at the Makeni Ebola Treatment Centre (ETC) laboratory. The Makeni ETC is funded by the UK Department for International Development (DFID) and operated by International Medical Corps. The diagnostic laboratory is staffed by volunteers from Public Health England and the research laboratory is staffed by employees of the University of Cambridge. The equipment was provided by Thermo Fisher Scientific via funding obtained from the Wellcome Trust.
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International Medical Corps
International Medical Corps assists those in urgent need anywhere, anytime, no matter what the conditions, providing lifesaving health care and health care-related emergency services – often within hours. As conditions ease, we work with local leaders to rebuild stronger. In non-emergency settings, our focus is development. Through our training programs, we pass essential skills into local hands, preparing those in disaster-prone areas to better withstand adversity. Embedding these skills into the community lies at the heart of what we do: build self-reliance. It gives people hit by tragedy a sense of ownership over their own recovery and the ability to shape their own future as they rebuild. And wherever it occurs, it is an investment that benefits us all because it prepares local residents to be their own best First Responders should disaster strike.
University of Cambridge
The mission of the University of Cambridge is to contribute to society through the pursuit of education, learning and research at the highest international levels of excellence. To date, 90 affiliates of the University have won the Nobel Prize. Founded in 1209, the University comprises 31 autonomous Colleges, which admit undergraduates and provide small-group tuition, and 150 departments, faculties and institutions. Cambridge is a global university. Its 19,000 student body includes 3,700 international students from 120 countries. Cambridge researchers collaborate with colleagues worldwide, and the University has established larger-scale partnerships in Asia, Africa and America. The University sits at the heart of one of the world’s largest technology clusters. The ‘Cambridge Phenomenon’ has created 1,500 hi-tech companies, 12 of them valued at over US$1 billion and two at over US$10 billion. Cambridge promotes the interface between academia and business, and has a global reputation for innovation.
The Wellcome Trust Sanger Institute
The Wellcome Trust Sanger Institute is one of the world’s leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease.
The Wellcome Trust
The Wellcome Trust is a global charitable foundation dedicated to achieving extraordinary improvements in human and animal health. We support the brightest minds in biomedical research and the medical humanities. Our breadth of support includes public engagement, education and the application of research to improve health. We are independent of both political and commercial interests.
