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USAID, Broad Institute, Illumina partner in West Africa for Ebola

Wednesday, November 19, 2014

To help combat the Ebola epidemic in West Africa, the U.S. Agency for International Development (USAID), the Massachusetts-based Broad Institute of MIT and Harvard and San Diego, Calif.-based Illumina have entered into a public-private partnership.

The partnership will train local and outbreak-deployed personnel to sequence viral genomes from the outbreak and will extend surveillance operations. Genome sequencing of the virus is critical for genomic surveillance—tracking how the virus is moving and changing in real-time. This information may influence the development of diagnostics, vaccines and therapies.

The partnership will equip facilities in West Africa with state-of-the-art genome sequencing technology that will aid in Ebola response now and in clinical monitoring and pathogen surveillance in the future. Sequencing and patient monitoring facilities will be created first in Liberia, Nigeria, Senegal and Sierra Leone, and over the longer term in other West African countries. These centers will serve as hubs for the deployment of mobile laboratories to remote districts where large-scale capacity is not available.

“The U.S. is embracing a new model of development—one grounded in a focus on innovation, local leadership and public-private partnerships to accelerate progress in the most challenging places,” said Rajiv Shah, USAID administrator. “By partnering with experts from the Broad Institute and Illumina, we can give health workers the tools they need to win the fight against Ebola.”

A team of researchers led by Pardis Sabeti from the Broad Institute has been working with collaborators in Nigeria, Senegal and Sierra Leone for many years, training them to use state-of-the-art sequencing and diagnostic technology. Leveraging this experience, the team also will move to enable similar work in Liberia, the country hit hardest by the outbreak.

“We are thrilled to be working with USAID and Illumina,” said Sabeti, an associate professor at Harvard University and a senior associate member of the Broad Institute. “The generosity of our partners will enable our outstanding African collaborators to provide real-time information about the circulation and mutation of Ebola virus strains, which is critical for keeping diagnostics, vaccines and therapies up to date. And, importantly, this partnership will build long-term strength in Africa for genomic surveillance.”

“This is an urgent situation that needs our immediate attention,” said Rick Klausner, chief medical officer of Illumina. “Illumina’s MiSeq sequencing platform, with turnaround times of four to 24 hours, will provide high-throughput capacity for the analysis of heavy sample loads.”

The labs of professor Christian Happi of Redeemer’s University in Nigeria and professor Daouda Ndiaye of Université Cheikh Anta Diop in Senegal will be the first to receive the MiSeq desktop sequencers, ideal for targeted and small genome sequencing, with labs in Liberia and Sierra Leone subsequently receiving machines. Through support from the NIH and the World Bank, 11 researchers from Nigeria and Senegal completed an advanced training program in genomics at the Broad Institute this past summer, including in-depth work using Illumina technology. The lab of professor Happi, which played a key role in Ebola diagnosis, is set to sequence the 20 confirmed and suspected cases from the Nigerian outbreak that was declared over Oct. 20.

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