Covid-19: towards improved sequencing of the virus in Africa

The Covid-19 pandemic has given a boost to the development of epidemiological and genomic surveillance capacities in Africa, which began in the 2000s to face the threat of an avian flu pandemic under the aegis of the World Health Organization (WHO), the Centers for Disease Control (CDC) in the United States, the Institut Pasteur and the Wellcome Trust. “At the start of the pandemic, there was no surveillance in Africa, although some laboratories could sequence SARS-CoV-2. At the end of 2020, WHO decided to build the first virus sequencing network, so that each region of Africa is represented, explains virologist Hieronyma Nelisiwe Gumede-Moeletsi from the WHO African office. We are only at the beginning of this network, but, as the emergency becomes clearer with the emergence of new variants, African countries realize that they must develop their own sequencing capacities ”, she specifies.

The quality of epidemiological surveillance networks is decisive for the early detection of variants

“There is an international will to develop sequencing with a very important role played by South Africa. The whole chain is important, from the collection of samples to their transport to specialized centers, which requires being able to detect positive cases across the whole of Africa, then to have an increase in analytical capacities and sequencing, adds virologist Sylvie Van der Werf, from the Institut Pasteur. This rise in power can only be gradual, she adds. South Africa has a long tradition of influenza surveillance, which certainly played a role in the identification of the Beta variant. Other countries, such as Nigeria, Senegal and Uganda, also have capacities that are lacking elsewhere, such as Mauritania or Burkina Faso. “

“Sequence five times more”

The quality of the epidemiological surveillance networks is decisive for the early detection of variants because it allows both the monitoring of the evolution of the epidemic and the detection of warning signals such as the existence of atypical chains of transmission of the virus. virus or an unexpected increase in the rate of hospitalization or death.

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This surveillance is failing at the scale of the African continent and, as of October 15, 2021, the WHO estimated that the 8.4 million officially detected cases represented only 1/7e the actual number of infections. Alone 70 million tests were carried out for a population of 1.3 billion inhabitants. Sequencing is also carried out in a limited number of reference centers, including those of the Genomic Surveillance Network for South Africa (NGS-SA), the Pasteur Institute in Dakar and the Kenya Medical Research Institute. Despite a homogeneous grid of the South African territory allowing a representative sampling of the territory, the capacities of the NGS-SA remain lower than those of the countries of the North. “We are sequencing samples taken from different regions and different districts because our sequencing capacity is only 600-700 samples per week compared to 10,000 in the UK. There is such a diversity of genomes here that we should be able to sequence five times more ”, testifies the bioinformatician Darren Martin, of the University of Cape Town.

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Covid-19: towards improved sequencing of the virus in Africa

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