To expedite the end-to-end integration of influenza and SARS-CoV-2 surveillance, the WHO Ethiopia Country Office and the WHO Regional Office for Africa organized a two-week on-site laboratory training course for staff of the National Influenza Centre, Ethiopia Public Health Institute, Addis Ababa, Ethiopia.
The course provided hands-on training and an in-depth understanding of next-generation sequencing (NGS), data analysis, and sharing of genetic data to public-access databases. The training also significantly increased the SARS-CoV-2 sample throughput with improvement in data quality, bioinformatic analysis and the processing of information.
Held at the Ethiopia Public Health Institute (EPHI) in Addis Ababa from 5-16 December 2022, the training was part of WHO Global Influenza Programme (GIP) support to national influenza laboratories in the WHO African Region.
Over the past two years, the GIP has leveraged the capacities of Global Influenza Surveillance and Response System (GISRS) laboratories to incorporate SARS CoV-2 testing into influenza sentinel surveillance testing. SARS CoV-2 surveillance, as part of influenza surveillance, allows for the global respiratory disease surveillance system to monitor organisms with pandemic potential. In 2021, GIP selected influenza laboratories in nine countries in the WHO African Region (Algeria, Cameroon, Cote d'Ivoire Ghana, Ethiopia, Sierra Leone, Kenya, Madagascar, and Mauritania) to participate in a project to expedite integration of SARS-CoV-2 into influenza surveillance.
A key aspect of this initiative is to support National Influenza Centres (NICs) to develop robust genomic surveillance capacities through sequencing influenza and SARS-CoV-2 isolates and sharing the information (genetic sequence data and metadata), to public-domain (Genbank) or public-access databases (GISAID). GISAID is a repository for sequence data which also provides analysis tools for genetic sequence and related clinical, epidemiological, geographical, and species-specific data.
In this context an expert from WHO Collaborating Centre (WHO CC) for Reference and Research on Influenza, Victorian Infectious Disease Reference Laboratory, Melbourne, Australia provided next-generation sequencing training to scientists from the National Influenza Centre at the Ethiopian Public Health Institute, Addis Ababa. NIC scientists were mentored to complete runs of next-generation sequencing and they successfully, obtained 37 whole genome sequences from SARS-CoV-2 positive samples. As mentioned, the course significantly improved their sample throughput and the quality of data was also improved with 100% genome coverage with no gaps. Based on the results obtained during the course, NIC scientists provided clade/lineage information of the most recent SARS-CoV-2 outbreak to the Ethiopian government.
To further establish their capacity, NIC Ethiopia staff were also supported by WHO to attend the International Influenza and SARS-CoV-2 Genetic Sequencing Course that was held in January 2023 in Ghana. This was organized by the WHO Regional Office for Africa and GIP in partnership with the United States Centers for Disease Control and Prevention, the Association of Public Health Laboratories and the Ghana NIC. WHO and the WHO Collaborating Centre in Melbourne will continue to provide training and mentoring support to the Ethiopia NIC. WHO will continue to strengthen respiratory disease surveillance across the African Region as part of pandemic preparedness and response efforts.
