Reflection on the implementation of genomic surveillance for COVID-19 and beyond in the African region

Since the first case was reported on February 14, 2020, the African region has experienced four separate waves of COVID-19. In all of these cases, WHO has continued to work with countries to Expanding genomic surveillance of pathogens to enable effective detection and response to SARS-CoV-2 variants, through sustainable investments in infrastructure and personnel.

To reflect on and advance this work, the WHO Regional Office for Africa (AFRO) convened a meeting of the COVID-19 epidemiology contact points of the health ministries of selected high-risk countries in Brazzaville, Republic of the Congo, between 10 and 13 August 2022. it was the goal Discuss initiatives to improve the quality and effectiveness of COVID-19 surveillance, including genomic surveillance. WHO AFRO regional virologist set the scene:

“Currently, 40 of the 47 Member States (85%) in the African region have in-country genome sequencing capabilities and 46 Member States (98%) share their genetic sequencing data through a publicly accessible database. The region has established a coordinated mechanism to maintain and strengthen these achievements and has established three centers of excellence in genome surveillance, developed standardized guides, offered capacity building for Ministry of Health staff, and established laboratory infrastructure for routine pathogen genomic surveillance, including wastewater monitoring.”

– dr Nicksy Gumede-Moeletsi, Regional Virologist, WHO/AFRO

Here are some highlights from stories shared by countries at the gathering.

Ethiopia

Genome sequencing capabilities have been established during the pandemic and the data generated continues to support public health decision-making for both COVID-19 and other priority disease areas, such as: B. Antimicrobial resistance using a one-health approach. However, despite promising progress, Ethiopia still has to overcome several challenges to improve sequencing capacity and quality, including: the small number of functioning laboratories, the lack of laboratory supplies, and the lack of sufficient bioinformatics capacity to analyze and interpret the 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 to guide the coordination and implementation of surveillance activities for SARS-CoV-2 and other pathogens between 2022 and 2026 is being developed.”

– Mr. Kebede Shitaye, Epidemiologist/Public Health Expert, WHO Country Office for Ethiopia

Democratic Republic of Congo

Leveraging genome sequencing capabilities built up during the Ebola outbreak in 2018, the Democratic Republic of Congo quickly initiated sequencing for SARS-CoV-2 after the first case was reported. Since then, the country’s regional reference laboratory has also been sequencing SARS-Cov-2 samples from four countries (Chad, Cameroon, the Central African Republic and the Republic of the Congo), with support from the WHO and other partners. This sequencing capacity is now being used for other national priority diseases 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 in the Global Initiative on Sharing Avian Influenza Data (GISAID). The first sequence was publicly released on March 25, 2020, two weeks after the first case was reported. We aim to strengthen existing sequencing capabilities and launch environmental genomic monitoring activities in the near future.”

– dr Justus Nsio, Epidemiologist, Ministry of Health, Democratic Republic of the Congo

Nigeria

Nigeria’s genome sequencing capacity has been built in various public and private sector institutions including the National Public Health Institute and academic and research centers to inform the response to COVID-19. Since the pandemic began, Nigeria has shared over 7,000 sequences in the Global Initiative on Sharing Avian Influenza Data (GISAID).

South Africa

South Africa has built world-class capacity for high-quality and timely genomic surveillance of SARS-CoV-2 and other pathogens with pandemic and epidemic potential, exemplified by the establishment of the Network for Genomic Surveillance in South Africa in May 2020, two months later Reporting of the first COVID-19 case. To maintain and strengthen the gains made, the country is committed to mobilizing domestic resources, strengthening the workforce and increasing access to pathogen sequencing tools in South Africa and other African countries.

The outcomes of the meeting and country reflections 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 integrate. In line with the recently launched Global Genomic Surveillance Strategy for Pathogens with Pandemic and Epidemic Potential 2022-2032, AFRO launched its flagship project, Transforming African Surveillance Systems, which aims to improve surveillance through increased genomic sequencing of pathogens, and will incorporate conclusions and lessons learned from the August meeting.