Periodic Reporting for period 1 - PANGenS (Pan-Africa network for genomic surveillance of poverty related diseases and emerging pathogens)
Période du rapport: 2023-07-01 au 2024-12-31
The relentless scourge of tuberculosis, malaria and emerging infectious diseases continues to threaten lives in Africa. The problem lies in the inadequate understanding of disease dynamics, limited capacity in genomics and fragmented data sharing. In this context, the EU-funded PANGenS project aims to transform Africa’s approach to disease control by leveraging genomic epidemiology. Its overall mission is to equip the continent with cutting-edge skills in genomics, data management and biobanking while promoting robust data sharing. With an arsenal of hypotheses, including improved surveillance, better responses to emerging pathogens and enhanced diagnostics, PANGenS aims to enhance disease surveillance, empower the next generation of African scientists and foster robust research collaborations within the continent. To establish infrastructure and expertise, we will conduct prove-of-concept projects applying genomic epidemiology to the two priority diseases in Africa: TB and Malaria. Institutions from the following countries are taking part in the study: Ghana, Mozambique, Tanzania, Namibia, Nigeria, Gabon, Benin, Togo, Liberia, South Africa, The Gambia, Switzerland, The Netherlands and Germany. The Noguchi Memorial Institute of Medical Research in Ghana and the German Research Center Borstel, Leibniz Lung Center are the coordinating institutes.
In the first phase of the PANGenS project, a management structure was set up to ensure smooth communication among all members. Regular meetings were organized within work packages, and a steering committee was formed with coordinators and team leaders from Ghana and Germany.
After a virtual kickoff meeting in September 2024, work began with an infrastructure assessment to create an effective work plan. Standard operating protocols were then developed and shared with all partners. Training programs were developed and the first workshops were held during the first annual conference, which took place in January 2024 at the Noguchi Memorial Institute for Medical Research, University of Ghana, in Ghana. Additional workshops throughout the year 2024 helped researchers learn next-generation sequencing and bioinformatics, essential for studying TB and malaria transmission and predicting drug-resistant TB strains. In 2024, some partner sites were equipped with the necessary software for bioinformatics analysis of sequencing data. A unique software for analyzing the core genome MLST called SeqSphere+ has been adapted to provide more understanding of drug resistance. Ethical approvals for the pilot studies are another key prerequisite for carrying out the proof-of-concept projects. Almost of these approvals were granted for the study in the first phase. This allowed the study centers to start taking samples in both studies: TB and malaria.
In order to store biological samples correctly and ensure that the material can be methodically analyzed later on, knowledge of biobanking and data management were shared during workshops. A database called REDCap for data management has been designed and its establishment in all participating sites has started.
After a virtual kickoff meeting in September 2024, work began with an infrastructure assessment to create an effective work plan. Standard operating protocols were then developed and shared with all partners. Training programs were developed and the first workshops were held during the first annual conference, which took place in January 2024 at the Noguchi Memorial Institute for Medical Research, University of Ghana, in Ghana. Additional workshops throughout the year 2024 helped researchers learn next-generation sequencing and bioinformatics, essential for studying TB and malaria transmission and predicting drug-resistant TB strains. In 2024, some partner sites were equipped with the necessary software for bioinformatics analysis of sequencing data. A unique software for analyzing the core genome MLST called SeqSphere+ has been adapted to provide more understanding of drug resistance. Ethical approvals for the pilot studies are another key prerequisite for carrying out the proof-of-concept projects. Almost of these approvals were granted for the study in the first phase. This allowed the study centers to start taking samples in both studies: TB and malaria.
In order to store biological samples correctly and ensure that the material can be methodically analyzed later on, knowledge of biobanking and data management were shared during workshops. A database called REDCap for data management has been designed and its establishment in all participating sites has started.
Although on the larger scale, specimen sampling and processing is still ongoing, efforts from the team has resulted in one publication in the journal, 'Nucleic Acids Research' on 23rd October 2024 with title, 'EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens'. The project looks very promising in the coming months with more sequencing and analyses. This will provide a better outlook of the epidemiology of TB and malaria on the African continent.