Sequence data management and sharing

To rapidly alert the health authorities and international community should variants of interest emerge.


Number of sequences shared on GISAID since January 2022

The WHO has stressed the importance for all countries to set up a genome surveillance system for SARS-CoV-2 and to rapidly share information in public databases in order to understand and eradicate the virus globally. In Africa at present, sequences have been obtained and uploaded to the GISAID public database for less than 1% of reported Covid-19 cases.

The AFROSCREEN project reinforces the genome surveillance system of each country in which it is in place, and supports its development where it does not yet exist.

The implementation of routine genome surveillance of variants in the laboratories is accompanied by very rapid provision of results to the national health authorities and international community, for example through the public platform GISAID. This enables phylogenetic analysis of the sequenced strains. In addition to highlighting variants of concern (VOCs), this also makes it possible to conduct molecular epidemiology studies on the circulation of SARS-CoV-2 strains in Africa and to estimate the date and place of their emergence using phylogeography and molecular clock analyses.

The final objective of the project is to make sequencing and epidemiological data available to help decision-makers define public health priorities and preventive measures to control and limit the circulation of variants.


The open-access platform GISAID facilitates the rapid sharing of data on all flu viruses and the coronavirus responsible for Covid-19.

This includes the genetic sequences and the clinical and epidemiological data associated with the viruses (sex, age, date and place the sample was taken, vaccine status, etc.), to help researchers understand how the viruses evolve and spread during epidemics and pandemics.

VOIs and VOCs

The World Health Organisation (WHO) classifies the variants of interest (VOIs) and variants of concern (VOCs) according to their potential risks to public health: increased transmissibility, diagnostic failure, reduced efficacy of natural and vaccine-induced immunity, and reduced sensitivity to treatment.

Molecular epidemiology

Molecular epidemiology is a branch of epidemiology that uses molecular markers to describe or analyse pathological phenomena. It makes it possible to link, epidemiologically, clusters of an infectious disease by tracing the strains of the pathogenic agent and to identify chains of transmission.