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Fighting against the Covid-19 crisis

Sentinel: A Pandemic Preemption System

  • African Centre of Excellence for Genomics of Infectious Diseases
  • Afrique
  • 2021
  • Scale-up project

Project overview

Sentinel is an outbreak early warning program to detect viral threats in real-time and prepare the global community to stop diseases before they spread. To achieve this, it comprises a three-pronged strategy:
  1. DETECT (diagnostic and surveillance tools);
  2. CONNECT (datascience and actionable insights);
  3. EMPOWER (training andinfrastructure).
While conceptualized and initiated prior to the Covid-19 pandemic, Sentinel has been able to use its preemption tools to address immediate needs for robust diagnostic and sequencing capacity in Nigeria, Sierra Leone, and Senegal. Such activities are in close collaboration with the Africa CDC to support response across West and Central Africa, and engage with six clinical-laboratory satellite facilities in West Africa. While Sentinel is being piloted in West Africa, this framework is adaptable and may be deployed in other regions.

"Sentinel gives humanity the opportunity to play 'offense' against viral threats."

- Christian Happi, Director, ACEGID

Presentation of the organization

Sentinel is a global collaboration of clinicians, epidemiologists, geneticists, virologists, bioengineers, computer scientists, and public health policy makers. It is co-led by the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID) and the Broad Institute. For nearly a decade, the teams have collaborated to develop transformative diagnostic and sequencing technologies, invest in local response capacity in under-resourced areas, respond to public health emergencies, and train African researchers and scientists. The vision for Sentinel was conceived through their experience and expertise in the arena, receiving timely funding immediately prior to the Covid-19 pandemic.

How it works

Sentinel is built on three foundational pillars, each aiming at building health system resilience by addressing complex challenges for disease surveillance with cutting-edge tools and technologies.


Leveraging genomics-based diagnostic and surveillance tools to rapidly identify high-prority viruses:
  • Clinical Diagnostics: Develop and employ high-sensitivity, CRISPR-based diagnostic tools for point-of-need and hospital settings;
  • Disease Surveillance: Improve sequencing capabilities and capacity;
  • Process Improvement: Implement sample contamination and quality control measures, shortening pathogen assay design time.


  • Data Capture: Gather data from clinics, laboratories, and citizens for a holistic view;
  • Data Connectivity: Improve compatibility and seamless integration data across platforms;
  • Actionable Insights: Develop computational models and visualization tools for genomic data to inform public health response at all levels.


Building scientific capacity through hands-on training and improving infrastructure:
  • Training: Conduct premier, hands-on genomics training for academic researchers and public health professionals;
  • Infrastructure: Upgrade laboratory infrastructure and equipment;
  • Engagement: Build partnerships across the public health system, at all levels (e.g., Africa CDC, Nigeria, CDC, WHO Africa, ASLM)


During Sentinel’s first year, the outlined strategy was reoriented to respond to the Covid-19 pandemic in Western Africa and support efforts in other countries across the continent. As of December 2021, Sentinel has:
  • Conducted the first SARS-CoV-2 sequencing in Africa;
  • Trained researchers from 15 African countries on Next-Generation Sequencing;
  • Assembled 3,000+ whole SARS-CoV-2 genomes, including variants of concern;
  • Processed over 150,000 Covid-19 PCR tests for Nigeria.

2022 Outlook

In its second year, Sentinel will continue to build on Covid-19 response efforts, while using lessons learned to further inform its preemption capabilities. For DETECT, this includes a focus on moving CRISPR-based diagnostics toward regulatory approval and developing a deployment and manufacturing plan. For CONNECT, priorities include further piloting visualization tools to meet the needs of our sites and expanding current deployments. Through EMPOWER, Sentinel will initiate active sample collection for broad pathogen surveillance at our Sentinel sites across Nigeria, continue to deliver bioinformatics training to each of our partner sites, and expand sequencing capacity in Nigeria and across Africa.

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