Cross-AAPs acceleration of genomics for escalating infectious diseases

Throughout the COVID-19 pandemic, the Africa Asia Programmes (AAPs), AHRI, KWTRP, MLW, MORU and OUCRU, and CIDRI-Africa (Discovery Platform), played a crucial role supporting Ministries of Health with diagnostics, genomic surveillance and real-time data to guide decision-making. We propose to now apply these established capacities to pathogens with an escalating infection burden in Africa and Southeast Asia, driven by climate change or the emergence of drug resistance, and for which there is a dearth of genomics data across Africa and Southeast Asia limiting effective action. The selected pathogens are: 1) the vector-borne dengue and chikungunya viruses; 2) multidrug- resistant Klebsiella pneumoniae; and 3) Mycobacterium tuberculosis. The proposed project will harmonise resources for archived and prospective sample collection and surveillance, whole-genome and targeted next-generation sequencing, metagenomics, bioinformatics, and the interoperability of genomic data and metadata across sites via the HL7 Fast Healthcare Interoperability Resources data standard. We aim to determine the national and international spread of these infections to inform national policy strategies for arboviruses control and antibiotic stewardship. The project will be managed via shared governance and oversight, enabling active engagement of the multidisciplinary teams with policy stakeholders across eight countries to accelerate translation of our findings to practice.