• Data disclaimer
  • Short epidemic update
  • Regional updates
    • North Africa
    • West Africa
    • Central Africa
    • East Africa
    • Southern Africa
  • South Africa
  • Sequencing and phylogenetics

Data disclaimer

The data report utilizes the 2019 Novel Coronavirus Visual Dashboard dataset that is operated by the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE). This dataset is updated daily and thus the numbers that are reported here may not reflect the latest case count in your country or region.

This report is intended for research purposes only. As is. The report is written and compiled by a group of virologist, epidemiologist and clinicians associated with the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) in collaboration with other scientist from the University of KwaZulu-Natal (UKZN CoV Big Data Consortium), the rest of South Africa and the African continent. This report is not intended for media publication, nor is it intended to serve as a source of information for the general public. It is strictly for educational, research and academic purposes. We urge members of the press and general public to heed the advise of the World Health Organization (WHO), the South African Department of Health (SA DoH) or the advise laid down by the African Centre for Disease Control and Prevention (Africa CDC).

This report will be updated regularly to keep track with the increasing numbers of cases. Please continue to visit the site to stay up to date with events as they unfold on the African continent.

Short epidemic update

COVID-19 originated in Wuhan, China in late 2019. Since January 2020, the virus has started to spread outside of China and as of the 25th of February 2020 new cases outside China exceeded new cases in mainland China. As of the writing of this report the global COVID-19 statistics is as follows:

DataType CaseCount
total cases 418678
new cases 40131
total deaths 18625
new deaths 2120

Africa has been relatively slow to report COVID-19 cases compared to other regions of the world. The first reported case on the continent was documented in Egypt on the 14th of February 2020. This case was linked to international travel of a Chinese national to Egypt 1. Algeria became the second country on the African continent to report a case of the virus on the 25th of February 2020. This case was also linked to international travel between Italy and Algeria 2.

However, the vast majority of cases on the continent have been reported since the start of the month of March 2020. As of the writing of this report the overall statistics for the African continent stands as follows:

DataType CaseCount
total cases 2077
new cases 404
total deaths 58
new deaths 6

Regional updates

The spread of the virus across the continent is not homogenous, with the bulk of infections concentrated in the North African region and in South Africa (excluding the rest of Southern African). Central, West and East Africa has reported relatively few infections to date.

North Africa

For the purpose of this report the North Africa region include the following countries and/or territories: Algeria, Egypt, Libya, Morocco, Sudan, Tunisia and Western Sahara.

The North African region has been the most severely effected in Africa with the bulk of cases reported in Egypt (n=256). The high number of cases reported in this region could primarily be attributed to its close proximity to other epidemic centers in Europe and the Middle East. To date, a total of 447 laboratory confirmed cases have been documented with 65 new cases being reported in the last 12 hours.

Index cases in most countries in this region were linked to international travel, but more and more community transmissions are being recorded (particularly in Egypt and Algeria).

West Africa

For the purpose of this report the West African region include the following countries and/or territories: Benin, Burkina Faso, Cabo Verde, Cote d’Ivoire, the Gambia, Ghana, Guinea, Guinea-Bissau, Liberia, Mali, Mauritania, Niger, Nigeria, Saint Helena, Senegal, Sierra Leone and Togo.

As of the time of this report, a total of 92 cases of COVID-19 have been reported in the West African region, with 21 new infections in the last 24 hours. The bulk of the infections in the region have been recorded in Senegal (n=31). To date, all cases are confirmed to be import cases with little to no evidence of community transmission in the region.

Central Africa

For the purpose of this report the Central African region include the following countries and/or territories: Angola, Cameroon, the Central African Republic (CAR), Chad, the Democratic Republic of the Congo (DRC annotated in the data as Congo Kinshasa), the Republic of the Congo (annotated in the data as Congo Brazzaville), Equatorial Guinea, Gabon and Sao Tome and Principe.

As of the writing of this report a total of 90 COVID-19 cases have been reported with 13 new infections in the last 24 hours. Only 1 death due to the virus have been reported till now.

East Africa

For the purpose of this report the East African region include the following countries and/or territories: Burundi, Comoros, Djibouti, Eritrea, Ethiopia, Kenya, Madagascar, Mauritius, Mayotte, Reunion, Rwanda, Seychelles, Somalia, South Sudan, Tanzania and Uganda.

As of the writing of this report, the East African region has been slow in reporting COVID-19 cases. To date, 169 cases have been reported with 25 new cases being reported in the last 24 hours. Early cases were all linked to recent international travel, but more community transmission are becoming more common. Till date, only 2 deaths due to COVID-19 have been reported in the East African region.

Southern Africa

For the purpuse of this report the Southern African region include the following countries and/or territories: Botwana, Eswatini (formally Swaziland), Lesotho, Malawi, Mozambique, Namibia, South Africa, Zambia and Zimbabwe.

South Africa was the first country in the region to report a positive case of COVID-19 on the 5th of March 2020. Eswatini and Namibia were the second and third countries to report COVID-19 cases in the region followed by Zambia, Zimbabwe and Mozambique. Currently, there are 570 confirmed cases in the region with 157 new cases being reported in the past 24 hours. Up untill recently, all of the cases have been linked to international travelers to epidemic centres. Imported cases have been linked to travelers returning from Europe, the United States, Brazil, Iran and South Korea. The first community transmission of the virus was reported in South Africa on the 15th of March 2020 and the number of community acquired infections are continuing to rise. The 23rd of March 2020 saw also the first reported death due to COVID-19, in Zimbabwe 3.

The numbers reported for Southern Africa above does not include the new cases reported on the 25th of March 2020.

South Africa

As of the 24th of March 2020, the National Institute for Communicable Diseases (NICD) has conducted 15529 tests for COVID-19. Currently, a total of 709 cases with 155 new cases in the last 24 hours have been reported in South Africa. The bulk of infections in South Africa are concentrated in the three economically most important provinces of Gauteng (n=336), the Western Cape (n=191), and KwaZulu-Natal (n=91). A full breakdown by province stands as follows:

Province CaseCount
GP 336
WC 191
KZN 91
FS 33
MP 9
NW 5
LP 4
EC 2
NC 2
Unknown 5
Total 709

The initial cases were all linked to returning nationals from foreign country but an increasing number of community-acquired cases are being reported in the past couple of days. For a breakdown of case numbers over time please refer to the plot below.

Sequencing and phylogenetics

Only three sequences from Africa have been generated and shared publicly for research use to date. The first sequence was generated from sampling of an Italy national in Nigeria and the second from a Congolese national that returned from France to the DRC. Phylogenetic analyses of these two sequences coupled with sequences from the rest of the world confirm the introduction of COVID-19 into these two countries from European sources. The final sequence was generated from the index patient in South Africa. This individual traveled in a tour group of 10 individuals to Italy and was the first patient to test positive for the virus in South Africa.

All of the African sequences belong to the A2a clade of COVID-19. This clade of COVID-19 is responsible for the majority of infections in Europe and South America with a small number of infections in the USA and on the African continent.

The current phylogenetic subclade for the A2a COVID-19 clade looks as follows:

Based on the above phylogeny and the sampling locations of the sampled sequences ancestral state reconstruction was performed to infer the most likely source of the internal nodes of the phylogeny above. These internal nodes character states can roughly be interpreted as the most probable ancestral location/country. This gives researchers insight into how pathogens, such as COVID-19, spread around the world. Ancestral state reconstruction and molecular clock analyses confirm Europe as the most like ancestral state for the two current African sequences. This support the hypothesis of transmission via travel between Europe and Nigeria and the DRC respectively. Similar to the Nigerian and DRC sequences, the ancestral state reconstruction for the South African sequence suggest a European ruite of introduction into South Africa.

The current global transmission inferred from the above phylogeny looks as follows:

For a full interactive browsing experience please visit the NextStrain build for COVID-19 at https://nextstrain.org/ncov.