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News / 05.11.20

Scientific coalition developing surveillance system for detecting emerging pandemics in real-time

By David Cameron

The Sentinel system, which is first being applied in West Africa, will combine genomics with information technology to detect and contain known and new threats such as COVID-19

Researchers from the African Center of Excellence for Genomics of Infectious Diseases (ACEGID) and the Broad Institute of MIT and Harvard, together with their research and public health partners, are ramping up the Sentinel project, an early warning system that aims to combine genomics with new information technologies to detect and respond to emerging viral threats in real-time.

The Sentinel project is the first of eight new projects selected by the Audacious Project, a collaborative initiative housed at TED that supports projects offering “bold solutions to the world’s most urgent challenges.” The project, which was conceived long before COVID-19 emerged, is among three pandemic-related projects selected for funding this year. The remainder of the 2020 cohort will be announced in the coming weeks.

Elements of Sentinel are already in use to respond to COVID-19 in ACEGID partner sites in Nigeria, Senegal, Sierra Leone and Liberia. Last week the World Health Organization African Region reported a 43 percent increase in COVID-19 cases with a 38 percent increase in related deaths across the African continent. WHO officials have warned that Africa might become the next epicenter of the pandemic.

“We have seen communities of researchers and healthcare workers pull together in extraordinary ways to fight this pandemic,” said Christian Happi, director of the ACEGID and a professor of molecular biology and genomics, both at Redeemer’s University, Nigeria. “Sentinel is, and will continue to be, a powerful example of this.”

“This pandemic has shown us how unprepared we are everywhere in the world for a crisis of this magnitude,” said Pardis Sabeti, member of the Broad Institute, a professor of Organismic and Evolutionary Biology at Harvard University, and a professor in the Department of Immunology and Infectious Disease at Harvard Chan School of Public Health. “But while it’s clear that we are all very much behind the curve, this pandemic will hopefully prompt government leaders to take up new tools and technologies to combat COVID-19—and use them to prepare for future outbreaks.”

Sabeti and Happi, who have been studying infectious disease together for two decades, described the Sentinel project last week via a virtual TED Talk at "TED2020: The Prequel."

In addition to academic and clinical partners, the Sentinel team includes long-time partners Fathom Information Design, MASS Design Group, and Dimagi.

Three-pillared approach

Sabeti and Happi describe the project as a system comprising three pillars: detect, connect, and empower.

For the first pillar, detection, the researchers are leveraging ultra-sensitive genomic and CRISPR technologies to detect pathogens. One example is SHERLOCK, a platform that uses a simple paper strip to detect viruses and that may eventually be used in even the most remote areas with minimal equipment, possibly even none at all. Another diagnostic platform, CARMEN, harnesses microfluidics to massively scale up CRISPR diagnostics and can test for hundreds of known viruses simultaneously. CARMEN, which requires a lab to employ, was recently described in Nature. Funding made available through Audacious will allow the team to refine, validate, and deploy both of these research technologies.

For the second pillar, Sentinel will connect the public health community to data gleaned from these detection platforms, using mobile applications and cloud-based systems that enable healthcare workers and public health officials to share data, analyses, and insights in real time. The suite of tools includes Dimagi’s CommCare and Fathom’s connected mobile application Scout and data visualization dashboard. It also includes the Broad’s Terra platform to allow cloud-base analysis of genomic data.

And finally, it will empower the public health community by training thousands of healthcare professionals to use the Sentinel tools, deploying these diagnostic technologies for population-level testing. This is built on ACEGID and the Broad’s previous experiences training over 900 individuals from around the world.

By unifying these three pillars, the Sentinel team aims to detect and prevent pandemics before they start. Many aspects of Sentinel could be used to help manage the COVID-19 pandemic immediately.

Members of the Sentinel team have brought cutting edge genomics capacity to many Sentinel partner countries for over a decade, using these approaches to contain diseases such as monkeypox and yellow fever. Their teams were also at the forefront of the Ebola, Zika, and Lassa fever outbreaks.

Recently, Happi’s lab at Redeemer’s University sequenced the first COVID-19 genome on the African continent. “The entire international community now has access to this,” he said. “Sharing data is at the heart of Sentinel.”

The Sentinel team will leverage their existing collaborations to deploy the project first across West and Central Africa, eventually expanding to other countries and regions.

“The potential of Sentinel to transform infectious disease surveillance in Africa is boundless, and its mission complements our own: to strengthen surveillance, improve emergency response, and manage public health situations of regional and international consequence,” says John Nekengasong, director of the Africa CDC.

“The opportunity to use advanced genomics and the analytical infrastructure to support the diagnostic potential for patients and populations provides an exciting opportunity for the country and the region,” says Chikwe Ihekwuezu, director of the Nigeria Centre for Disease Control.

“The whole idea of Sentinel is that we can all stand guard and protect our communities,” said Sabeti. “Each one of us can be a sentinel by engaging with the health care system to uncover what is making us sick, and in the process we can warn our communities. That is what we profoundly want -- for each one of us to be empowered and support one another in the fight against deadly threats.”