To reflect and advance this project, the WHO Regional Office for Africa (AFRO) convened a meeting of the epidemiology focal points of COVID-19 from ministries of health of selected high-risk countries in Brazzaville (Republic of the Congo) held between 10 until August 13, 2022. The goal was to discuss initiatives aimed at improving the quality and effectiveness of COVID-19 surveillance, including genomic surveillance. The Regional Virologist at WHO AFRO set the scene: “Currently, 40 of the 47 Member States (85%) in the African region have in-country capabilities for genomic sequencing and 46 Member States (98%) share their genetic sequence data through a public database. The Region has established a coordinated mechanism to sustain and enhance these gains and has established three centers of excellence for genomic surveillance, developed standardized guidance documents, offered capacity building for staff in Ministries of Health, and established laboratory infrastructure for routine genomic surveillance of pathogens; including wastewater surveillance’. – Dr Nicksy Gumede-Moeletsi, Regional Virologist, WHO/AFRO Here are some highlights from stories shared by countries at the meeting.
Ethiopia
Genome sequencing capabilities were established during the pandemic and the data generated continue to support public health decision-making for both COVID-19 and other priority disease areas such as antimicrobial resistance using a One Health approach. However, despite promising gains, Ethiopia still needs to address several challenges to improve sequencing capacity and quality, including: a small number of operational laboratories, a lack of laboratory supplies, and a lack of adequate bioinformatics capabilities for analysis and the interpretation of sequencing data for timely action. “Genomic surveillance has played an important role in informing the response to COVID-19 in Ethiopia. A five-year national strategy is being developed to guide the coordination and implementation of surveillance activities for SARS-CoV-2 and other pathogens between 2022 and 2026 .” – Mr Kebede Shitaye, Epidemiologist/Public Health Specialist, WHO Office for Ethiopia
Democratic Republic of the Congo
Leveraging genomic sequencing capabilities built during the 2018 Ebola outbreak, the Democratic Republic of Congo quickly activated sequencing for SARS-CoV-2 after the first case was reported. Since then, the country’s Regional Reference Laboratory is also sequencing SARS-Cov-2 samples from four countries (Chad, Cameroon, Central African Republic and Republic of Congo), with support from WHO and other partners. This sequencing capability is now being used for other diseases of national priority such as monkeypox, polio, measles, malaria, cholera and yersinia pestis. “The Democratic Republic of the Congo was one of the first countries in the world to share sequences for SARS-CoV-2 with the Global Initiative for the Sharing of Avian Influenza Data (GISAID). The first sequence was published publicly on March 25, 2020, two weeks after the first case was reported. We are committed to enhancing existing sequencing capabilities and introducing genomic environmental monitoring activities in the near future.” – Dr. Justus Nsio, Epidemiologist, Ministry of Health, Democratic Republic of Congo
Nigeria
Nigeria’s genomic sequencing capabilities have been built in various public and private sector agencies, including the National Institute of Public Health and academic and research centers, to help inform the response to COVID-19. Since the start of the pandemic, Nigeria has shared more than 7,000 sequences with the Global Initiative for Sharing of Avian Influenza Data (GISAID). “The sequencing capacity created during the COVID-19 pandemic gives us an opportunity to enhance genomic surveillance of pathogens for other priority pathogens in the country. We are committed to strengthening coordination, human capacity and infrastructure for genomic surveillance.” – Dr Abubakar Jafiya, Epidemiologist, Nigeria Center for Disease Control, Nigeria
South Africa
South Africa has built world-class capabilities for quality and timely genomic surveillance of SARS-CoV-2 and other pathogens with pandemic and epidemic potential, as demonstrated by the establishment in May 2020 of the South African Genomic Surveillance Network, two months after the first case of COVID-19 was reported. To maintain and enhance the gains made, the country is committed to mobilizing domestic resources, strengthening the workforce and improving access to pathogen sequencing tools in South Africa and other African countries. “Through a strong collaborative mechanism, South Africa has followed and is sharing more than 44,700 SARS-CoV-2 samples representative of all regions and ages in a publicly accessible database. We have built significant pathogen surveillance capacity for SARS-CoV-2 and other pathogens and have integrated genomic surveillance into the broader public health surveillance system.” – Dr Patrick Devanand, National Professional Officer, Emergency Preparedness and Response, WHO Country Office for South Africa Outcomes from the meeting and reflections from countries on the role of genomic surveillance during the COVID-19 pandemic and other public health emergencies will enable the Region to effectively plan and integrate pathogen surveillance into the broader public health architecture. In line with the Global Genome Surveillance Strategy for Pathogens with Pandemic and Epidemic Potential 2022–2032, AFRO launched the Transforming African Surveillance Systems flagship project, which aims to strengthen surveillance through enhanced pathogen genome sequencing and will incorporate less inference. August meeting.
