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

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

 


A hypothetical example of an application for this dashboard is shown in Figure 1. 2The scenario is that Namibia’s Minister of Health should consider the spread of the Omicron lineage in neighboring countries following reports of Omicron in South Africa and Botswana in order to better understand how Namibia might be affected. I want to understand The user can use filters to display the number of Omicron phylogenetic genomes in neighboring countries.in the figure 2, the left panel of the dashboard has filters that allow you to view data for a specific country, a specific region, or all countries. In this example, Namibia and its neighboring countries (South Africa, Botswana, Angola) are selected. In the interactive map titled “Genomes by Country”, the metric “Genomes by Variant” is selected. In this case the Omicron variant was chosen. As seen in the figure. 2hover over a country on the map to see the country name, the number of genomes produced in that country, and the date.

Figure 2: Omicron spread case study.
Figure 2

A screenshot of a case study scenario shows how the filters and graphs provided by the SARS-CoV-2 Africa dashboard interface can be used to investigate the spread of Omicron in Namibia and neighboring countries. The logo is courtesy of the GISAID initiative.

Applying these filters and examining the dashboard numbers, we find that the percentage of genomes deposited in GISAID at the end of October 2021 is dominated by the delta lineage, with few remaining beta genomes. Within his first two weeks of November 2021, the Omicron BA.1 lineage proliferated rapidly and constituted his 19% of the total genome. A sliding scale animation of the Omicron lineages on the map shows early detection of lineages in South Africa and rapid progression from low (light pink) to high (dark purple) cumulative genome numbers. From these visualizations, Ministers can recognize Omicron’s rapid adoption and growth advantage over Delta, and confirm that Omicron could become the dominant subspecies in southern Africa at the time. The Minister will provide the necessary information to enable consultation with local researchers, public health officials, and clinicians to provide local and regional public health responses to reduce the impact of Omicron on the population. is authorized to obtain

Sources

1/ https://Google.com/

2/ https://www.nature.com/articles/s41564-022-01276-9

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