Increasing Genomic Sequencing in Africa

COVID-19 has had a devastating effect on people’s lives and livelihoods. However, it has sparked important scientific research that has resulted in the world receiving a vaccine in record speed and has pushed genetic sequencing to the forefront of pandemic response. 

Thanks to genomic sequencing, the world quickly identified the virus that causes COVID-19 and created diagnostic tests and other response tools. Genomic sequencing is still critical in tracking COVID-19’s evolution and detecting variants of concern. 

The World Health Organization (WHO) is collaborating with African countries to increase pathogen surveillance by genome sequencing in order to detect and respond to COVID-19 variations effectively. WHO and the Africa Centre for Disease Control and Prevention developed a COVID-19 sequencing laboratory network in Africa in 2020, which has produced more than 43 000 sequencing data to date. 

In Cape Town, South Africa, the WHO Regional Office for Africa is currently partnering with the South African National Bioinformatics Institute (SANBI) to establish the Regional Centre of Excellence for Genomic Surveillance and Bioinformatics. In the first six months, WHO is providing technical assistance as well as approximately US$ 4.5 million for activities in the Southern African Development Community region. The center would first cover 14 southern countries, with monthly capacity increases of five-fold before expanding to serve more countries. 

WHO advises countries to send at least 5 % of their COVID-19 samples to a reference sequencing facility or to continue producing sequencing data if they have the capacity. Africa currently accounts for less than 1% of the more than 3,5 million COVID-19 sequences performed worldwide. 

Genomic sequencing activities in Southern Africa have doubled since the Regional Centre in South Africa began preliminary operations in July. Southern African countries sequenced 5510 samples in the first half of 2021, compared to over 24 000 today. This has aided countries in detecting the presence of and comprehending the impact of concern variants, particularly the Delta variant, which is the most contagious yet and is thought to be 30–60 % more transmissible. 

Since the start of the pandemic, African governments have been working to integrate routine genomic sequencing and surveillance into their national response. For example, in December 2020, South Africa found the highly transmissible Beta type of concern, allowing the country to alter public health precautions. 

The Delta variant, which fueled Africa’s now-disappearing third pandemic wave, has been found in 39 African countries, while the Alpha and Beta varieties have been found in 45 and 40 countries, respectively. The Alpha variation has been found in the majority of North, West, and Central African countries, while the Beta variant is more common in Southern Africa. 

Beyond COVID-19, genome sequencing has the ability to improve public health and transform responses to other important health risks. It has been utilized in Africa to enhance public health responses to HIV, polio, measles, hepatitis B and C, chikungunya, dengue, zika, and yellow fever over the last 20 years. It has the capacity to accomplish much more, according to experts.