Africa’s scientists have had to pick testing over genome sequencing for a coronavirus vaccine

African scientists are working on genome sequencing but not in large enough numbers.
African scientists are working on genome sequencing but not in large enough numbers.
Image: REUTERS/Kenny Katombe
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Pools of genome sequences of SARS-CoV-2 from all over the world are currently being scrutinized by scientists for insight into the Covid-19 disease. If a vaccine is eventually discovered—based on the sequences pooled so far—Africa may end up with the ‘Rotaviruses Vaccine Problem’.

The Rotaviruses Vaccine Problem refers to the efficacy variation observed with vaccines developed for use against rotavirus infections, a leading cause of severe diarrhoea among young children worldwide. The vaccines happened to be effective in Europe and North America but less effective in Africa. The vaccines which were mainly based on rotavirus strains predominantly found in Europe and North America is believed to exhibit a lower efficacy in Africa due to the circulation of different strain in the continent.

Scientists in African countries have been working on genome sequencing for Covid-19 but have done just 90 out of the 7,679 done globally to date.

As early as two weeks after cases of a strange pneumonia-like sickness was reported in Wuhan, a city in China, scientists in the country did the first genome sequencing of the virus causing the sickness. Within a week, they had done five genome sequences of the virus identities as SARS-CoV-2—a new coronavirus. Since then over 7,700 genome sequences have been done as the virus which causes a highly infectious and deadly disease called Covid-19 spreads fast across the globe. These genome sequences which are being pooled into several databases are vital for tracking how the virus mutates over time as it spreads and for development of diagnostic tests and vaccines. One such pool is the GISAID’s SARS-CoV-2 genome sequence database.

Looking at the data from the database, Africa was observed to be a SARS-CoV-2 genomic data dark spot. So far Africa and South America each account for only about 1% of the total number of genome sequences in the global SARS-CoV-2 genomic database.

It is believed there should be more genomic data from Africa for vaccine development considering the peculiarities of the continent and the possibility of a major mutation of the virus.

“Vaccines are usually developed based on the available pools of sequence data. Therefore, little or no data for Africa amounts to poor or no representation at vaccine development,” says Dr Moses Olubusuyi Adewumi, a virologist at the College of Medicine, the University of Ibadan, Nigeria. “If Africans fail to generate essential data and make such available we’ll possibly suffer the same fate as with Rotavirus vaccine.”

The low representation of genome sequences from Africa is not the only problem observed. There is also a low distribution of the sources of the sequences within the continent. The number of countries with the virus in the continent increase to 51 as South Sudan announced its first Covid-19 case this week but of all these countries only five have sequenced the genome of the virus.

As of April 12,  the Democratic Republic of Congo , Senegal and Ghana account for over 85% of the genomic sequences from Africa.

DR Congo alone accounts for almost half of the total genome sequences from Africa. Dr Adewumi linked this to collaboration and funding from foreign organizations and support of the government of the country. He said the recent Ebola virus outbreaks in DR Congo had led to capacity development in some of the labs in the country. While Senegal is benefitting from the capacity of Institut Pasteur de Dakar, one of the most reputable research institution in Africa, Ghana is making good use of a World Bank-supported Centre of Excellence (CoE) research institution in the country.

Nigeria also has a similar World Bank-supported center where the first sequence of the SARS-CoV-2 virus was done in Africa.  However, the country has since put genome sequencing of the virus on hold. The country lacks labs with the capacity to run a Covid-19 test so the genomics labs that did the sequencing are now being used as test centers.

According to Dr Adewumi, who is currently working with one of the test labs at the University College Hospital, Ibadan, testing is currently the government’s priority and the country needs more labs to carry out tests.

To date only about 5,000 tests in Nigeria have been done compared with over 14,611 in Ghana and over 73,028 tests in South Africa.

The huge difference between the number of tests recorded for South Africa and other African countries is evidence of their superior lab capacity on the continent. The country also boasts of western and private research funding, yet only six genomes have been sequenced.

The pandemic has stretched the capacities and resources of institutions globally but these were already lacking in Africa. African countries are therefore being forced to choose between diagnosis and genome sequencing in other to cope.

They chose diagnosis.

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