SARS-CoV-2 Africa dashboard for real-time COVID-19 information

A hypothetical example of the application of this dashboard is shown in Fig. 2. The scenario is that Namibia’s Minister of Health wants to understand the spread of Omicron lineage to neighboring countries after reports of Omicron in South Africa and Botswana, to better understand how Namibia may be affected. Users would use filters to display the number of Omicron lineage genomes in each neighboring country. In fig. 2, on the left panel of the dashboard, there are filters to display data for specific countries, specific regions, or all countries. In this example, Namibia and its neighboring countries (South Africa, Botswana and Angola) have been selected. On the interactive map entitled “Genomes by country”, the metric “Genomes by variant” has been selected. In this case, the Omicron variant was selected. As seen in Fig. 2if the cursor hovers over a country on the map, the name of the country, the number of genomes produced by this country and the date are displayed.

The Case Study scenario screenshot shows how to investigate the spread of Omicron in Namibia and neighboring countries using the filters and graphs provided by the SARS-CoV dashboard interface -2 Africa. Logo courtesy of the GISAID Initiative.

By studying the numbers in the dashboard with these filters applied, it can be seen that the proportion of genomes deposited in GISAID at the end of October 2021 is dominated by the Delta lineage, with few Beta genomes remaining. During the first two weeks of November 2021, the Omicron BA.1 lineage rapidly grew to comprise 19% of all genomes. Watching the sliding scale animation for the Omicron lineages on the map shows the early detection of the lineage in South Africa, with a rapid progression from low (light pink) to high (dark purple) cumulative genome numbers. From these visualizations, the Minister would be aware of Omicron’s rapid spread and growth advantage over Delta, and could see that at this time Omicron had the potential to be the dominant variant in southern Africa. The Minister would be empowered to have the information necessary to enable consultation with local researchers, public health officials and clinicians to provide local and regional public health responses to mitigate the effects of Omicron on the population.