Pan-Africa network for genomic surveillance of poverty related diseases and emerging pathogens

The main aim of the proposed project is to use genomic epidemiology of tuberculosis, malaria and emerging and re-emerging pathogens in Africa as to better understand disease etiology, dynamics of disease transmission, and evolution of drug-resistant pathogens. The study also aims to increase Africa's capacity in bioinformatics, genomics, genomics data management, biobanking, and promote data sharing. Our goal is to improve the health of Africans with innovations in disease surveillance, equip the next generation of African scientists with cutting edge skills and strengthening south-south research collaborations. We propose the following hypotheses:

1. Increased capacity in genomic epidemiology will enable more effective disease surveillance in Africa.

2. Increased capacity in biobanking and genomics data management and analysis in Africa will enhance regional surveillance of infectious diseases and encourage timely and effective responses to emerging pathogens.

3. Regional whole genome sequence-based surveillance will improve the detection of DR-TB and inform the development of more sensitive and specific rapid diagnostics for the detection and surveillance of DR-TB in Africa and elsewhere.

4. Regional genomic surveillance of malaria parasites will inform a pre-emptive detection of emerging DR parasites and measure the impact of programmatic interventions for a data driven decision making by policy makers.

5. Implementation of harmonized genomic data analysis tools will allow the creation of continent-wide surveillance networks able to identify cross-border spread of DR variants and emerging pathogens.

To achieve this, PANGenS will develop genomic epidemiology capacity across Africa by establishing a collaborative framework that brings together all expertise to perform trainings and implementation in all relevant components ranging from wet lab to bioinformatics, and establish proof-of-concept studies for TB and malaria in in selected partner countries