Pathogen Genomics Surveillance Policy Framework

During the COVID-19 pandemic, African Union (AU) Member States have made significant progress in acquiring and deploying genomic sequencing tools for detecting SARS-CoV-2 and tracking its variants. Through these tools, the continent is endowed with knowledge, capacity and related infrastructure with immense potential for routine application of pathogen genomics for evidence-based public health decision-making. It is widely acknowledged that pathogen genomics provides a powerful approach towards the investigation, management, and surveillance of infectious diseases. With pathogen genomics capabilities having been scaled up in Africa to support the monitoring of SARS-CoV-2 variants of concern and interest, there is now a need to consolidate and expand pathogen genomics capacities, sustain the gains made, and expand them to contribute to sustainable, reliable, and relevant country-owned disease surveillance programs. While different Member States have different economic, technical, and pathogen genomics capabilities, ensuring that each develops a contextualized pathogen genomics strategy is considered a critical step towards sustainability.

The African pathogen genomic surveillance policy framework is intended to guide the African Union (AU) Member States in the development of national pathogen genomic surveillance strategies as part of national health plans. The framework presents a set of recommendations and actions to the attention of AU Member States so that they can formulate a pathogen genomic strategy suited to their context, with considerations for public health and clinical functions, cooperation among Member States, and sustainability. The framework sets out the vision and guiding principles, lays out considerations and proposes key specific actions for a set of priority areas relevant for the African context. The expected outcomes of the specific actions are enumerated along with a roadmap for implementing the specific actions over five years.

Africa CDC is committed to supporting AU Member States in developing and implementing national pathogen genomic strategies. Through the implementation of these strategies, the benefits of pathogen genomics in public health systems will be harnessed, capacities and capabilities built for early confirmation and characterization of disease outbreaks.  Africa CDC emphasizes that all AU Member States need to recognize the profound importance of integrating pathogen genomics into their public health systems. This approach will revolutionize our collective ability for surveillance and response to disease outbreaks, and significantly enhance our clinical care capacities.

The development of national policies guiding the integration of pathogen genomics into disease surveillance allows member states to define their priorities, requirements and context-specific approaches and ensure that pathogen genomics contributes to a resilient health system, adapt to new challenges and serve African citizens.  Africa CDC urges all AU Member States to consider the recommendations in this framework when developing their national pathogen genomics policies. Financial commitment is crucial in this endeavor. Africa CDC, therefore, advocates smart investment in this field to ensure the sustainability and growth of these interventions. Let us not see this as a cost but as an investment in a healthier future for our continent.