Webinar “Africa PGI Multi-pathogen data management & sharing platform”
Webinar “Africa PGI Multi-pathogen data management & sharing platform”
The second webinar organized under the AFROSCREEN project was held by Dr. Gerald Mboowa, who presented the project to create a database and real-time data sharing platform based in Africa.
In order to promote the exchange of experiences and stimulate reflection, a series of webinars is planned on topics of interest to the AFROSCREEN network. The second of these webinars was held by Dr Gerald Mboowa, Implementation Science Expert for Bioinformatics at Africa Pathogen Genomics Initiative (Africa PGI), Africa CDC.
Dr Mboowa talked about the creation of the Africa PGI data management and sharing platform to build capacity for pathogen genomic data access and analysis throughout the continent. Dr. Mboowa also stressed as Afrca PGI leverages on existing infrastructure: Specialized Genomics and Bioinformatics Centers (SGBC) and Regional COVID-19 Sequencing Laboratories, which roll out trainings and provide sequencing capacity for member countries. Since its creation, Africa PGI has distributed different next-generation sequencing platforms to at least 31 member countries, depending on laboratory capacities and needs. Compared to the previous shipping of disease outbreak samples abroad for sequencing, Africa PGI has reversed this practice. Currently, African-based sequencing laboratories have sequenced and shared more than 95% of all the available more than 100,000 SARS-CoV-2 genomes from Africa (https://bit.ly/3xOKQVL). Gradually, this has led to a reduction in turnaround time from sample collection to the sharing of the SARS-CoV-2 genomic data, and in a drastic increase of the number of African SARS-CoV-2 sequences shared with the international community.
Dr. Mboowa has underlined how the continent is underutilizing the pathogen genomic data that is being generating, mainly because of lack of expertise to mine the generated data for public health decision making, diagnostics innovations, drug as well as vaccine development. Indeed, “majority of of NCBI-SRA pathogen genomic data for different pathogens is coming from countries in Africa, but very few individuals on the continent can exhaustively analyze these data and make meaningful insights that can inform effectively investigation and disease control on the continent”. This observation, together with the high number of disease outbreaks detected annually in Africa (around 140), the importance that genome sequencing technology is acquiring in infectious disease investigation and control and the need to establish equitable terms for data access and sharing prompted Africa PGI to create a multi-pathogen data management and sharing platform.
The Africa PGI data platform will offer:
- Data management
- Analysis, visualisation & interpretation solutions for pathogen genomic sequences
- Data access and sharing
- Pathogen genomic data archive, including the raw data
PGI will capitalize on the efforts made on SARS-CoV-2 to respond to other pathogens. Indeed, the lessons learned thPGI will capitalize on the efforts made on SARS-CoV-2 to respond to other pathogens. Indeed, the lessons learned through SARS-CoV-2 genomic sequencing are the being used to respond to endemic outbreaks in the continent, as well as any other outbreaks that may come up. Technical working groups have been established to identify priority pathogens that will undergo routine pathogen genomics surveillance.
Dr. Mboowa has concluded acknowledging the Africa PGI founders and financing agencies and the collaborators throughout Africa and beyond, including the AFROSCREEN project, who are working closely with Africa CDC and PGI to make sure NGS and analytics capacities are brought to the continent.
To find out more:
- Dr Mboowa’s presentation
- Information on the Africa Pathogen Genomics Initiative : https://africacdc.org/news-item/us100-million-africa-pathogen-genomics-initiative-to-boost-disease-surveillance-and-emergency-response-capacity-in-africa/
In order to promote the exchange of experiences and stimulate reflection, a series of webinars is planned on topics of interest to the AFROSCREEN network. The second of these webinars was held by Dr Gerald Mboowa, Implementation Science Expert for Bioinformatics at Africa Pathogen Genomics Initiative (Africa PGI), Africa CDC.
Dr Mboowa talked about the creation of the Africa PGI data management and sharing platform to build capacity for pathogen genomic data access and analysis throughout the continent. Dr. Mboowa also stressed as Afrca PGI leverages on existing infrastructure: Specialized Genomics and Bioinformatics Centers (SGBC) and Regional COVID-19 Sequencing Laboratories, which roll out trainings and provide sequencing capacity for member countries. Since its creation, Africa PGI has distributed different next-generation sequencing platforms to at least 31 member countries, depending on laboratory capacities and needs. Compared to the previous shipping of disease outbreak samples abroad for sequencing, Africa PGI has reversed this practice. Currently, African-based sequencing laboratories have sequenced and shared more than 95% of all the available more than 100,000 SARS-CoV-2 genomes from Africa (https://bit.ly/3xOKQVL). Gradually, this has led to a reduction in turnaround time from sample collection to the sharing of the SARS-CoV-2 genomic data, and in a drastic increase of the number of African SARS-CoV-2 sequences shared with the international community.
Dr. Mboowa has underlined how the continent is underutilizing the pathogen genomic data that is being generating, mainly because of lack of expertise to mine the generated data for public health decision making, diagnostics innovations, drug as well as vaccine development. Indeed, “majority of of NCBI-SRA pathogen genomic data for different pathogens is coming from countries in Africa, but very few individuals on the continent can exhaustively analyze these data and make meaningful insights that can inform effectively investigation and disease control on the continent”. This observation, together with the high number of disease outbreaks detected annually in Africa (around 140), the importance that genome sequencing technology is acquiring in infectious disease investigation and control and the need to establish equitable terms for data access and sharing prompted Africa PGI to create a multi-pathogen data management and sharing platform.
The Africa PGI data platform will offer:
- Data management
- Analysis, visualisation & interpretation solutions for pathogen genomic sequences
- Data access and sharing
- Pathogen genomic data archive, including the raw data
PGI will capitalize on the efforts made on SARS-CoV-2 to respond to other pathogens. Indeed, the lessons learned thPGI will capitalize on the efforts made on SARS-CoV-2 to respond to other pathogens. Indeed, the lessons learned through SARS-CoV-2 genomic sequencing are the being used to respond to endemic outbreaks in the continent, as well as any other outbreaks that may come up. Technical working groups have been established to identify priority pathogens that will undergo routine pathogen genomics surveillance.
Dr. Mboowa has concluded acknowledging the Africa PGI founders and financing agencies and the collaborators throughout Africa and beyond, including the AFROSCREEN project, who are working closely with Africa CDC and PGI to make sure NGS and analytics capacities are brought to the continent.
To find out more:
- Dr Mboowa’s presentation
- Information on the Africa Pathogen Genomics Initiative : https://africacdc.org/news-item/us100-million-africa-pathogen-genomics-initiative-to-boost-disease-surveillance-and-emergency-response-capacity-in-africa/