Laboratories at the Kenya Medical Research Institute will now sequence the genomes of Covid-19 viruses collected from neighbouring countries in East Africa.
The institute has joined a network of 12 specialised and regional reference laboratories that will provide sequencing, data analysis and other technical support services to countries that have no capacity.
In East Africa, only Kenya and Uganda have the capacity to sequence the virus genome.
The network was launched by the World Health Organization (WHO) and the Africa Centres for Disease Control and Prevention (Africa CDC).
“As we continue to tackle the Covid-19 pandemic in Africa, being able to not only track its evolution but also assess the possible mutation of the virus is crucial to mounting an effective response,” said Dr Matshidiso Moeti, WHO Regional Director for Africa.
“Through this new laboratory network dedicated to genome sequencing, we can better develop vaccines and treatment which are tailored to Africans and eventually bring Covid-19 under control.”
Ongoing sequencing is already providing crucial information for determining the type of SARS-CoV-2 lineage circulating in some countries.
It has shown that most of the SARS-CoV-2 genomes circulating in Africa are assigned to the B.1 lineage which emerged from the epidemic in Europe.
In Africa, 10 lineages have been identified and more than 80,000 sequences have been produced globally. Grouping viruses from different countries into the same lineage or sub-lineage has indicated a linkage or importation of viruses between countries.
“As the Covid-19 pandemic curve flattens in Africa, we must be prepared for a possible resurgence as already observed in some countries. With genomic sequencing we can have a better understanding of the pandemic through more precise identification of transmission clusters,” said Dr John Nkengasong, Director of Africa CDC.
A total of 2,016 sequences from 18 countries – Algeria, Benin Republic, Cameroon, DRC, Egypt, Gambia, Ghana, Kenya, Madagascar, Mali, Morocco, Nigeria, Senegal, Sierra Leone, South Africa, Tunisia, Uganda, and Zambia – have already been generated.
In Kenya, scientists reported early June they had successfully sequenced genomes of 122 samples.
They indicated there were at least nine separate importations of SARS-CoV-2 into the country prior to April 30 based on a proportion of sequenced cases.
The report showed that SARS-CoV-2 viruses circulating in the country do not differ from viruses circulating elsewhere in the world and provided evidence for local transmissions in Mombasa county, with clusters of infections showing local transmission following these introductions.