Most Covid-19 variants that resulted in travel bans against Africa originated in Europe: study

When SA identified new variants of Covid-19 during the height of the pandemic it faced discrimination, isolation and a tirade of travel bans from richer nations, with some labelling Africa as the main source of the variants.

But a new genomic surveillance study by Stellenbosch University, the KwaZulu-Natal Research Innovation and Sequencing Platform (Krisp) and other African scientists has found that even though Africa was “the most discriminated against and penalised continent in the world with travel bans”, Europe was the main source of some variants of concern.

Published in Science this week, in the study, titled “The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance”, researchers argue that despite limitations of low testing proportions on the continent, the latest data “sheds light on the distinct dispersal dynamics of variants of concern, particularly Alpha, Beta, Delta and Omicron, on the continent”.

According to the large consortium of African scientists and public health institutions that analysed genomic and epidemiological data in more than 50 countries, most of the introductions of variants in Africa were from abroad. The consortium found the initial waves of infections in Africa were primarily seeded by multiple introductions of viral lineages from abroad, mainly Europe.

The report shows how the rapid expansion of genomics surveillance in Africa allowed the continent’s scientific community to describe the introduction and spread of Covid-19 variants in African countries in real time during the pandemic.

They have described the latest research as “a feather in the cap of African science and the restoration of incorrect perceptions based on unscientific and inappropriate reactions in the international community”.

The Alpha variant that emerged in Europe at the end of 2020 was responsible for infections in 43 countries, with evidence of community transmission in Ghana, Nigeria, Kenya, Gabon and Angola.

For the Delta variant, the bulk of introductions were attributed to India, responsible for 72% of Beta infections. About 8% of Beta variants emerged in Europe, 5% in the UK and 2.5% the US.

Viral introductions of Delta also occurred between African countries in 7% of inferred introduction.

In the case of Omicron, the scientific results suggest 99% separate introduction or reintroduction of sublineages BA.2 into African countries are from Europe and 30% from Asia. Reintroduction of the Omicron variant into Africa originated more from Europe and North America than from other African countries.

SA was the first country to discover the Beta variant in 2020, and in 2021 it discovered the Omicron variant, which created immigration issues for South Africans after richer nations introduced blanket travel bans and the UK added SA to its travel red list.

In the paper scientists called for sustained investment for diagnostics and genomic surveillance in Africa as Covid-19 continues to evolve and other infectious diseases continue to emerge and threatening Africa’s healthcare system.

“These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century,” they said.

Dr Matshidiso Moeti, WHO regional director for Africa, described the enormous leap Africa made in genomic surveillance during the past two years as “the silver lining in the Covid-19 pandemic”.

“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.”

Lead researcher Houriiyah Tegally, bioinformatician at Krisp and Centre for Epidemic and Response and Innovation (CERI), described the latest research as an “inspiring experience”.

“We witnessed small countries with no previous genomics experience become empowered in sequencing and bioinformatics methods, and how they started to actively participate in regular pathogen genomic surveillance for SARS-CoV-2. I think it will be a real model of how scientists and public health officials across countries can form a unified front against infectious diseases in the future.”

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