SEP 25, 2021 1:00 PM PDT

Mapping the Spread of COVID-19 in Africa Using Genomics

WRITTEN BY: Hannah Daniel

After a year-long study, researchers have assembled a detailed narrative about how the SARS-Cov-2 virus has spread on the continent of Africa.

When COVID-19 was first detected in Africa, many African countries began to do genomic testing on their infected citizens. This gave researchers a large set of genomes to study. 14,504 genomes were listed in the GISAID (Global Initiative for Sharing All Influenza Data) database encompassing 38 African countries and two overseas territories (Mayotte and Réunion). This sampling represents 1 case out of every 300, by their estimates.

Half of the sequences came from South Africa, which was hit the hardest by the pandemic, and corresponded to the percentage of cases reported in South Africa versus the rest of the continent. While genomic surveillance started early in many African countries, it is unknown whether this sampling was consistent. Therefore, many of the results focused on the introduction of COVID-19 into Africa and the spread of variants across the continent.

Researchers used the genomic similarities to determine where the viruses were imported from and then exported to— an incredible feat thanks to the diligent genomic surveillance of many African countries. They discovered that at least 757 of the imported cases occurred between the start of 2020 and February 2021— half of which appeared before June 2021 as the introduction of the virus began as importations from outside of Africa.

A narrative arose from the data: the first introductions of COVID-19 were predominantly carried by travelers returning from highly affected areas in Europe. The virus continued to spread, but as dynamics changed. During the later parts of the pandemic, the introductions started to come from other African countries and not from different continents. The leading importers seemed to be South Africa, Kenya, and Nigeria, but this may be because these countries also had the most significant number of genomic sequences in the database. However, it should be noted that South Africa was responsible for almost 80% of the introductions into other areas of the continent.

There was another caveat to this study, and it had to do with the sample size of the genome. Researchers describe their findings as the “tip of the iceberg” and suggest that more accurate conclusions could be drawn with increased sampling in Africa and globally.

Researchers also tracked the spread of variants across the continent. Specific tracking of one variant revealed that it spread rapidly at the end of 2020, implying that the current land and border controls are hindering the international spread of COVID-19.

The paper concludes with recommendations: researchers suggest that more effective testing at borders within African countries might curb the spread of the virus within and outside of the continent. They also urged more effective rollout of vaccines, warning that delayed rollout of the vaccines will create an excellent environment for new variants, with the provision that more trials are done so that the vaccines are also equipped to deal with new variants.

Sources: Science

About the Author
  • Hannah Daniel (she/they) is a recent graduate of Carnegie Mellon University, where she received a Bachelor of Science in Biology with an additional a minor in Creative Writing. She is currently located in the Washington D.C. area pursuing freelance writing opportunities and full-time science communications positions. In her free time, Hannah likes to watch science fiction movies and interrogate the truthfulness of their claims.
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