Durban - The silver lining of the Covid-19 pandemic in Africa was the rapid expansion of genomic surveillance on the continent and how this allowed African scientists to describe the introduction and spread of variants in real-time.
A study published in Science this week highlighted the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most relevant being the detection of Beta and various Omicron subvariants. The findings also indicate that the majority of the covid variants in Africa were introduced from abroad.
The study was led by two labs that set up the network for genomic surveillance in South Africa - The KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP) at the University of KwaZulu-Natal and the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University, in close coordination with the Africa Centre for Disease Control, WHO Africa and 300 other institutions across the continent.
The initial waves of infections in Africa were primarily seeded by multiple introductions of viral lineages from abroad (mainly Europe). The Alpha variant that emerged in Europe at the end of 2020 caused infections in 43 countries with evidence of community transmission in Ghana, Nigeria, Kenya, Gabon and Angola.
For Delta, the bulk of introductions was attributed to India (72%), mainland Europe (8%), the UK (5%), and the US (2.5%). Viral introductions of Delta also occurred between African countries.
For Omicron, the scientific results show more reintroductions of the variant back into Africa, at least 69 from Europe and 102 from North America. This was amplified for Omicron BA.2; the results suggest 65% of which were from Europe and 30% from Asia.
“The ironic part of these results is that most of the introductions of variants in Africa were from abroad, but Africa was the most discriminated and penalised continent in the world with travel bans. Instead of unscientific and inappropriate reactions, we should be building on the infrastructure established in Africa so that the continent can rapidly pivot to other epidemics without the fear of being punished,” said Professor Tulio de Oliveira, director of the two institutes.
“The publication highlights that sustained investment for diagnostics and genomic surveillance in Africa was needed to not only combat Sars-CoV-2 on the continent but establish a platform to address the emerging, re-emerging, endemic infectious disease threats, such as Ebola, HIV/Aids, TB and Malaria. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century,” said Dr Yenew Kebede, Acting Head for Surveillance and Disease Intelligence at the Africa CDC.
“The enormous leap Africa made in genomic surveillance during the past two years is the silver lining in the Covid-19 pandemic,” said Dr Matshidiso Moeti, WHO Regional Director for Africa. “The continent is now better prepared to face down both old and emerging pathogens. This is a model of how when Africans are in the driving seat we can come up with lasting change and stay a step ahead of dangerous diseases,” he added.
The Independent on Saturday